142 results on '"Andreas, Gnirke"'
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2. Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis.
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Marco A Coelho, Márcia David-Palma, Terrance Shea, Katharine Bowers, Sage McGinley-Smith, Arman W Mohammad, Andreas Gnirke, Andrey M Yurkov, Minou Nowrousian, Sheng Sun, Christina A Cuomo, and Joseph Heitman
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Biology (General) ,QH301-705.5 - Abstract
In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
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- 2024
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3. A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing.
- Author
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Per A Adastra, Neva C Durand, Namita Mitra, Saul Godinez Pulido, Ragini Mahajan, Alyssa Blackburn, Zane L Colaric, Joshua W M Theisen, David Weisz, Olga Dudchenko, Andreas Gnirke, Suhas S P Rao, Parwinder Kaur, Erez Lieberman Aiden, and Aviva Presser Aiden
- Subjects
Medicine ,Science - Abstract
Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). The vast majority of diagnostic methods meeting our analytical criteria that are currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations of the virus to achieve this degree of sensitivity and specificity. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy given sufficient viral load. The genotypic data in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of positive and negative clinical nasal mid-turbinate swab samples 100% match those obtained in a clinical diagnostic lab using the Center for Disease Control's 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8-hour experiment at the cost of ~$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity using this approach.
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- 2023
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4. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
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Alessandro Pastore, Federico Gaiti, Sydney X. Lu, Ryan M. Brand, Scott Kulm, Ronan Chaligne, Hongcang Gu, Kevin Y. Huang, Elena K. Stamenova, Wendy Béguelin, Yanwen Jiang, Rafael C. Schulman, Kyu-Tae Kim, Alicia Alonso, John N. Allan, Richard R. Furman, Andreas Gnirke, Catherine J. Wu, Ari M. Melnick, Alexander Meissner, Bradley E. Bernstein, Omar Abdel-Wahab, and Dan A. Landau
- Subjects
Science - Abstract
In chronic lymphocytic leukemia (CLL), evolution is driven by transcriptional and epigenetic heterogeneity. Here, the authors integrate epigenomic analyses to show how intra-tumoral epigenetic diversity results in divergent chromatin states in CLL cells, increasing cell-to-cell transcriptional heterogeneity.
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- 2019
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5. Genome-wide tracking of dCas9-methyltransferase footprints
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Christina Galonska, Jocelyn Charlton, Alexandra L. Mattei, Julie Donaghey, Kendell Clement, Hongcang Gu, Arman W. Mohammad, Elena K. Stamenova, Davide Cacchiarelli, Sven Klages, Bernd Timmermann, Tobias Cantz, Hans R. Schöler, Andreas Gnirke, Michael J. Ziller, and Alexander Meissner
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Science - Abstract
Catalytically inactive Cas9 fused to a methyltransferase has emerged as a promising epigenome modifying tool. Here the authors generate a methylation depleted but maintenance competent mouse ES cell line and find ubiquitous off-target activity.
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- 2018
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6. Virus genomes reveal factors that spread and sustained the Ebola epidemic.
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Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno R. Faria, Daniel J. Park, Jason T. Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L. Caddy, Matthew Cotten, Jonathan D'Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Michael J. Elmore, Lawrence S. Fakoli, Ousmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart L. Haagmans, Julian A. Hiscox, Umaru Jah, Jeffrey R. Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke W. Meredith, James Qu, Joshua Quick, Suzan D. Pas, My V. T. Phan, Georgios Pollakis, Chantal B. Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. G. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete Alice Tobin, Mohamed A. Vandi, Simon J. Watson 0002, Kendra West, Shannon Whitmer, Michael R. Wiley, Sarah M. Winnicki, Shirlee Wohl, Roman Wölfel, Nathan L. Yozwiak, Kristian G. Andersen, Sylvia O. Blyden, Fatorma Bolay, Miles W. Carroll, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian T. Happi, Edward C. Holmes, Brima Kargbo, Sakoba Keïta, Paul Kellam, Marion Koopmans, Jens H. Kuhn, Nicholas J. Loman, N'Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo F. Palacios, Oliver G. Pybus, Pardis C. Sabeti, Amadou Sall, Ute Ströher, Isatta Wurie, Marc A. Suchard, Philippe Lemey, and Andrew Rambaut
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- 2017
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7. Figure S5 from Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy
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Alexander Meissner, Catherine J. Wu, Andreas Gnirke, Elias Campo, Thomas J. Kipps, Bernd Timmermann, Sven Klages, Donna S. Neuberg, Kenneth J. Livak, Shuqiang Li, Lili Wang, Jennifer R. Brown, Stacey M. Fernandes, Neil E. Kay, Tait D. Shanafelt, Esteban Braggio, Susan L. Slager, Connie Lesnick, Arman W. Mohammad, Laura Rassenti, Hongcang Gu, Michaela Gruber, Kendell Clement, Camilla K. Lemvigh, Noelia Purroy, Anat Biran, and Helene Kretzmer
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Non-uniform dynamics of single CpGs among CLL progression
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- 2023
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8. Table S3 from Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy
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Alexander Meissner, Catherine J. Wu, Andreas Gnirke, Elias Campo, Thomas J. Kipps, Bernd Timmermann, Sven Klages, Donna S. Neuberg, Kenneth J. Livak, Shuqiang Li, Lili Wang, Jennifer R. Brown, Stacey M. Fernandes, Neil E. Kay, Tait D. Shanafelt, Esteban Braggio, Susan L. Slager, Connie Lesnick, Arman W. Mohammad, Laura Rassenti, Hongcang Gu, Michaela Gruber, Kendell Clement, Camilla K. Lemvigh, Noelia Purroy, Anat Biran, and Helene Kretzmer
- Abstract
Table of correlation between time points within one sample and number of hyper- or hypomethylated CpGs for all CLL (top) and naïve and memory B cell samples (bottom)
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- 2023
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9. Supplementary Figures and Legends from Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy
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Alexander Meissner, Catherine J. Wu, Andreas Gnirke, Elias Campo, Thomas J. Kipps, Bernd Timmermann, Sven Klages, Donna S. Neuberg, Kenneth J. Livak, Shuqiang Li, Lili Wang, Jennifer R. Brown, Stacey M. Fernandes, Neil E. Kay, Tait D. Shanafelt, Esteban Braggio, Susan L. Slager, Connie Lesnick, Arman W. Mohammad, Laura Rassenti, Hongcang Gu, Michaela Gruber, Kendell Clement, Camilla K. Lemvigh, Noelia Purroy, Anat Biran, and Helene Kretzmer
- Abstract
Supplementary Figures 1-7 and matching legends
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- 2023
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10. Data from Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy
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Alexander Meissner, Catherine J. Wu, Andreas Gnirke, Elias Campo, Thomas J. Kipps, Bernd Timmermann, Sven Klages, Donna S. Neuberg, Kenneth J. Livak, Shuqiang Li, Lili Wang, Jennifer R. Brown, Stacey M. Fernandes, Neil E. Kay, Tait D. Shanafelt, Esteban Braggio, Susan L. Slager, Connie Lesnick, Arman W. Mohammad, Laura Rassenti, Hongcang Gu, Michaela Gruber, Kendell Clement, Camilla K. Lemvigh, Noelia Purroy, Anat Biran, and Helene Kretzmer
- Abstract
Most human cancers converge to a deregulated methylome with reduced global levels and elevated methylation at select CpG islands. To investigate the emergence and dynamics of the cancer methylome, we characterized genome-wide DNA methylation in preneoplastic monoclonal B-cell lymphocytosis (MBL) and chronic lymphocytic leukemia (CLL), including serial samples collected across disease course. We detected the aberrant tumor-associated methylation landscape at CLL diagnosis and found no significant differentially methylated regions in the high-count MBL-to-CLL transition. Patient methylomes showed remarkable stability with natural disease and posttherapy progression. Single CLL cells were consistently aberrantly methylated, indicating a homogeneous transition to the altered epigenetic state and a distinct expression profile together with MBL cells compared with normal B cells. Our longitudinal analysis reveals the cancer methylome to emerge early, which may provide a platform for subsequent genetically driven growth dynamics, and, together with its persistent presence, suggests a central role in disease onset.Significance:DNA methylation data from a large cohort of patients with MBL and CLL show that epigenetic transformation emerges early and persists throughout disease stages with limited subsequent changes. Our results indicate an early role for this aberrant landscape in the normal-to-preneoplastic transition that may reflect a pan-cancer mechanism.See related commentary by Rossi, p. 6.This article is highlighted in the In This Issue feature, p. 1
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- 2023
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11. Data from Discovery of Candidate DNA Methylation Cancer Driver Genes
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Dan A. Landau, Olivier Elemento, Catherine J. Wu, Stephan Stilgenbauer, Alexander Meissner, Michael Hallek, Jérôme Moreaux, Marcin Imielinski, Andreas Gnirke, Doron Betel, Chao Zhang, Kirsten Fischer, Anna Maria Fink, Daniel Mertens, Eugen Tausch, Johannes Bloehdorn, Ronan Chaligne, Loïc Renaud, and Heng Pan
- Abstract
Epigenetic alterations, such as promoter hypermethylation, may drive cancer through tumor suppressor gene inactivation. However, we have limited ability to differentiate driver DNA methylation (DNAme) changes from passenger events. We developed DNAme driver inference–MethSig–accounting for the varying stochastic hypermethylation rate across the genome and between samples. We applied MethSig to bisulfite sequencing data of chronic lymphocytic leukemia (CLL), multiple myeloma, ductal carcinoma in situ, glioblastoma, and to methylation array data across 18 tumor types in TCGA. MethSig resulted in well-calibrated quantile–quantile plots and reproducible inference of likely DNAme drivers with increased sensitivity/specificity compared with benchmarked methods. CRISPR/Cas9 knockout of selected candidate CLL DNAme drivers provided a fitness advantage with and without therapeutic intervention. Notably, DNAme driver risk score was closely associated with adverse outcome in independent CLL cohorts. Collectively, MethSig represents a novel inference framework for DNAme driver discovery to chart the role of aberrant DNAme in cancer.Significance:MethSig provides a novel statistical framework for the analysis of DNA methylation changes in cancer, to specifically identify candidate DNA methylation driver genes of cancer progression and relapse, empowering the discovery of epigenetic mechanisms that enhance cancer cell fitness.This article is highlighted in the In This Issue feature, p. 2113
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- 2023
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12. Supplementary Table S4 from Discovery of Candidate DNA Methylation Cancer Driver Genes
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Dan A. Landau, Olivier Elemento, Catherine J. Wu, Stephan Stilgenbauer, Alexander Meissner, Michael Hallek, Jérôme Moreaux, Marcin Imielinski, Andreas Gnirke, Doron Betel, Chao Zhang, Kirsten Fischer, Anna Maria Fink, Daniel Mertens, Eugen Tausch, Johannes Bloehdorn, Ronan Chaligne, Loïc Renaud, and Heng Pan
- Abstract
Copy number changes in MethSig CLL DNAme drivers.
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- 2023
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13. Supplementary Data from Discovery of Candidate DNA Methylation Cancer Driver Genes
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Dan A. Landau, Olivier Elemento, Catherine J. Wu, Stephan Stilgenbauer, Alexander Meissner, Michael Hallek, Jérôme Moreaux, Marcin Imielinski, Andreas Gnirke, Doron Betel, Chao Zhang, Kirsten Fischer, Anna Maria Fink, Daniel Mertens, Eugen Tausch, Johannes Bloehdorn, Ronan Chaligne, Loïc Renaud, and Heng Pan
- Abstract
Supplementary Figure S1 to S7 and Supplementary Notes.
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- 2023
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14. Data from Activation of Notch and Myc Signaling via B-cell–Restricted Depletion of Dnmt3a Generates a Consistent Murine Model of Chronic Lymphocytic Leukemia
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Catherine J. Wu, Alexander Meissner, Ruben D. Carrasco, Lili Wang, Anthony Letai, Donna S. Neuberg, Andreas Gnirke, John C. Aster, Thomas J. Kipps, Jennifer R. Brown, Stephan Stilgenbauer, Clare Sun, Eugen Tausch, Stacey M. Fernandes, Elizabeth Witten, Mei Zheng, Kristen Stevenson, Gabriela Brunsting Hoffmann, Arman Mohammad, Laura Z. Rassenti, Fara Faye Regis, Leah Billington, Nathan Dangle, Catherine Gutierrez, Mohamed Uduman, Fabienne Lucas, Salma Parvin, Elisa ten Hacken, Helene Kretzmer, Shanye Yin, and Anat Biran
- Abstract
Chronic lymphocytic leukemia (CLL) is characterized by disordered DNA methylation, suggesting these epigenetic changes might play a critical role in disease onset and progression. The methyltransferase DNMT3A is a key regulator of DNA methylation. Although DNMT3A somatic mutations in CLL are rare, we found that low DNMT3A expression is associated with more aggressive disease. A conditional knockout mouse model showed that homozygous depletion of Dnmt3a from B cells results in the development of CLL with 100% penetrance at a median age of onset of 5.3 months, and heterozygous Dnmt3a depletion yields a disease penetrance of 89% with a median onset at 18.5 months, confirming its role as a haploinsufficient tumor suppressor. B1a cells were confirmed as the cell of origin of disease in this model, and Dnmt3a depletion resulted in focal hypomethylation and activation of Notch and Myc signaling. Amplification of chromosome 15 containing the Myc gene was detected in all CLL mice tested, and infiltration of high-Myc–expressing CLL cells in the spleen was observed. Notably, hyperactivation of Notch and Myc signaling was exclusively observed in the Dnmt3a CLL mice, but not in three other CLL mouse models tested (Sf3b1-Atm, Ikzf3, and MDR), and Dnmt3a-depleted CLL were sensitive to pharmacologic inhibition of Notch signaling in vitro and in vivo. Consistent with these findings, human CLL samples with lower DNMT3A expression were more sensitive to Notch inhibition than those with higher DNMT3A expression. Altogether, these results suggest that Dnmt3a depletion induces CLL that is highly dependent on activation of Notch and Myc signaling.Significance:Loss of DNMT3A expression is a driving event in CLL and is associated with aggressive disease, activation of Notch and Myc signaling, and enhanced sensitivity to Notch inhibition.
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- 2023
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15. Targets and genomic constraints of ectopic Dnmt3b expression
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Yingying Zhang, Jocelyn Charlton, Rahul Karnik, Isabel Beerman, Zachary D Smith, Hongcang Gu, Patrick Boyle, Xiaoli Mi, Kendell Clement, Ramona Pop, Andreas Gnirke, Derrick J Rossi, and Alexander Meissner
- Subjects
liver ,stem cells ,blood ,MEFs ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
DNA methylation plays an essential role in mammalian genomes and expression of the responsible enzymes is tightly controlled. Deregulation of the de novo DNA methyltransferase DNMT3B is frequently observed across cancer types, yet little is known about its ectopic genomic targets. Here, we used an inducible transgenic mouse model to delineate rules for abnormal DNMT3B targeting, as well as the constraints of its activity across different cell types. Our results explain the preferential susceptibility of certain CpG islands to aberrant methylation and point to transcriptional state and the associated chromatin landscape as the strongest predictors. Although DNA methylation and H3K27me3 are usually non-overlapping at CpG islands, H3K27me3 can transiently co-occur with DNMT3B-induced DNA methylation. Our genome-wide data combined with ultra-deep locus-specific bisulfite sequencing suggest a distributive activity of ectopically expressed Dnmt3b that leads to discordant CpG island hypermethylation and provides new insights for interpreting the cancer methylome.
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- 2018
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16. Discovery of Candidate DNA Methylation Cancer Driver Genes
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Marcin Imielinski, Anna-Maria Fink, Eugen Tausch, Ronan Chaligne, Michael Hallek, Heng Pan, Catherine J. Wu, Kirsten Fischer, Johannes Bloehdorn, Alexander Meissner, Daniel Mertens, Jérôme Moreaux, Loïc Renaud, Stephan Stilgenbauer, Chao Zhang, Dan A. Landau, Andreas Gnirke, Doron Betel, Olivier Elemento, Institut de génétique humaine (IGH), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[SDV]Life Sciences [q-bio] ,Bisulfite sequencing ,Computational biology ,Biology ,Article ,Epigenesis, Genetic ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,CRISPR ,Epigenetics ,Gene ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,0303 health sciences ,Cas9 ,Cancer ,Methylation ,DNA Methylation ,medicine.disease ,Leukemia, Lymphocytic, Chronic, B-Cell ,3. Good health ,Oncology ,030220 oncology & carcinogenesis ,DNA methylation - Abstract
Epigenetic alterations, such as promoter hypermethylation, may drive cancer through tumor suppressor gene inactivation. However, we have limited ability to differentiate driver DNA methylation (DNAme) changes from passenger events. We developed DNAme driver inference–MethSig–accounting for the varying stochastic hypermethylation rate across the genome and between samples. We applied MethSig to bisulfite sequencing data of chronic lymphocytic leukemia (CLL), multiple myeloma, ductal carcinoma in situ, glioblastoma, and to methylation array data across 18 tumor types in TCGA. MethSig resulted in well-calibrated quantile–quantile plots and reproducible inference of likely DNAme drivers with increased sensitivity/specificity compared with benchmarked methods. CRISPR/Cas9 knockout of selected candidate CLL DNAme drivers provided a fitness advantage with and without therapeutic intervention. Notably, DNAme driver risk score was closely associated with adverse outcome in independent CLL cohorts. Collectively, MethSig represents a novel inference framework for DNAme driver discovery to chart the role of aberrant DNAme in cancer. Significance: MethSig provides a novel statistical framework for the analysis of DNA methylation changes in cancer, to specifically identify candidate DNA methylation driver genes of cancer progression and relapse, empowering the discovery of epigenetic mechanisms that enhance cancer cell fitness. This article is highlighted in the In This Issue feature, p. 2113
- Published
- 2021
- Full Text
- View/download PDF
17. Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis
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Magali Soumillon, Anamaria Necsulea, Manuela Weier, David Brawand, Xiaolan Zhang, Hongcang Gu, Pauline Barthès, Maria Kokkinaki, Serge Nef, Andreas Gnirke, Martin Dym, Bernard de Massy, Tarjei S. Mikkelsen, and Henrik Kaessmann
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexity in major mammalian organs have been scarce. Here, using extensive RNA-seq data, we show that transcription of the genome is substantially more widespread in the testis than in other organs across representative mammals. Furthermore, we reveal that meiotic spermatocytes and especially postmeiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding and long noncoding RNA genes but also poorly conserves intergenic sequences, suggesting that it may not be of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data suggest that this prevalent transcription, which most likely promoted the birth of new genes during evolution, is facilitated by an overall permissive chromatin in these germ cells that results from extensive chromatin remodeling.
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- 2013
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18. Activation of Notch and Myc signaling via B cell-restricted depletion of Dnmt3a generates a consistent murine model of chronic lymphocytic leukemia
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Laura Z. Rassenti, Elisa Ten Hacken, Arman W. Mohammad, Eugen Tausch, Lili Wang, Mohamed Uduman, Jennifer R. Brown, Ruben D. Carrasco, Andreas Gnirke, Stacey M. Fernandes, Shanye Yin, Elizabeth Witten, Clare Sun, Catherine J. Wu, Alexander Meissner, Nathan J Dangle, Catherine Gutierrez, Fara Faye Regis, Gabriela Brunsting Hoffmann, Fabienne Lucas, Thomas J. Kipps, Kristen E. Stevenson, Donna Neuberg, Anthony Letai, Jon C. Aster, Anat Biran, Stephan Stilgenbauer, Salma Parvin, Mei Zheng, Helene Kretzmer, and Leah Billington
- Subjects
Male ,Cancer Research ,Methyltransferase ,Lymphoma ,Somatic cell ,Chronic lymphocytic leukemia ,Drug Resistance ,Apoptosis ,Mice, SCID ,DNA Methyltransferase 3A ,Mice ,immune system diseases ,Mice, Inbred NOD ,hemic and lymphatic diseases ,Conditional gene knockout ,Receptors ,Tumor Cells, Cultured ,2.1 Biological and endogenous factors ,RNA-Seq ,Chronic ,Aetiology ,Cancer ,Mice, Knockout ,Cultured ,Leukemia ,Tumor ,Receptors, Notch ,Hematology ,Prognosis ,Lymphocytic ,Tumor Cells ,Anti-Bacterial Agents ,Gene Expression Regulation, Neoplastic ,Survival Rate ,medicine.anatomical_structure ,Oncology ,DNA methylation ,embryonic structures ,Female ,Notch ,Knockout ,Oncology and Carcinogenesis ,Notch signaling pathway ,Biology ,SCID ,Article ,Proto-Oncogene Proteins c-myc ,Rare Diseases ,Daptomycin ,medicine ,Genetics ,Biomarkers, Tumor ,Animals ,Humans ,Epigenetics ,Oncology & Carcinogenesis ,B cell ,Cell Proliferation ,Neoplastic ,Animal ,B-Cell ,medicine.disease ,Leukemia, Lymphocytic, Chronic, B-Cell ,Xenograft Model Antitumor Assays ,Disease Models, Animal ,Gene Expression Regulation ,Drug Resistance, Neoplasm ,Disease Models ,Cancer research ,Inbred NOD ,Neoplasm ,Biomarkers - Abstract
Chronic lymphocytic leukemia (CLL) is characterized by disordered DNA methylation, suggesting these epigenetic changes might play a critical role in disease onset and progression. The methyltransferase DNMT3A is a key regulator of DNA methylation. Although DNMT3A somatic mutations in CLL are rare, we found that low DNMT3A expression is associated with more aggressive disease. A conditional knockout mouse model showed that homozygous depletion of Dnmt3a from B cells results in the development of CLL with 100% penetrance at a median age of onset of 5.3 months, and heterozygous Dnmt3a depletion yields a disease penetrance of 89% with a median onset at 18.5 months, confirming its role as a haploinsufficient tumor suppressor. B1a cells were confirmed as the cell of origin of disease in this model, and Dnmt3a depletion resulted in focal hypomethylation and activation of Notch and Myc signaling. Amplification of chromosome 15 containing the Myc gene was detected in all CLL mice tested, and infiltration of high-Myc–expressing CLL cells in the spleen was observed. Notably, hyperactivation of Notch and Myc signaling was exclusively observed in the Dnmt3a CLL mice, but not in three other CLL mouse models tested (Sf3b1-Atm, Ikzf3, and MDR), and Dnmt3a-depleted CLL were sensitive to pharmacologic inhibition of Notch signaling in vitro and in vivo. Consistent with these findings, human CLL samples with lower DNMT3A expression were more sensitive to Notch inhibition than those with higher DNMT3A expression. Altogether, these results suggest that Dnmt3a depletion induces CLL that is highly dependent on activation of Notch and Myc signaling. Significance: Loss of DNMT3A expression is a driving event in CLL and is associated with aggressive disease, activation of Notch and Myc signaling, and enhanced sensitivity to Notch inhibition.
- Published
- 2021
19. Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia
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Alicia Alonso, Alessandro Pastore, Caroline Sheridan, Rafael C. Schulman, Joshua Felsenfeld, Ronan Chaligne, Kyu-Tae Kim, Kendell Clement, Evan Biederstedt, Federico Gaiti, Hongcang Gu, Dan A. Landau, Alexander Meissner, Lili Wang, Davide Risso, Erica B. Bhavsar, Catherine J. Wu, Andreas Gnirke, Ryan M. Brand, Martin J. Aryee, Richard R. Furman, John N. Allan, Kirill Grigorev, Kevin Y. Huang, Nathaniel D. Omans, and Steven Kothen-Hill
- Subjects
Epigenomics ,0301 basic medicine ,Mutation rate ,Transcription, Genetic ,Bisulfite sequencing ,Biology ,Article ,somatic evolution ,Time ,Epigenesis, Genetic ,Evolution, Molecular ,Epigenome ,03 medical and health sciences ,0302 clinical medicine ,Mutation Rate ,Biological Clocks ,medicine ,cancer ,Humans ,Cell Lineage ,Epigenetics ,B cell ,Genetics ,Multidisciplinary ,epigenetics ,Base Sequence ,Sequence Analysis, RNA ,Human evolutionary genetics ,leukemia ,DNA Methylation ,Leukemia, Lymphocytic, Chronic, B-Cell ,Chromatin ,single cell ,3. Good health ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,DNA methylation ,Single-Cell Analysis - Abstract
Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer1. Chronic lymphocytic leukaemia (CLL) is a highly informative model for cancer evolution as it undergoes substantial genetic diversification and evolution after therapy2,3. The CLL epigenome is also an important disease-defining feature4,5, and growing populations of cells in CLL diversify by stochastic changes in DNA methylation known as epimutations6. However, previous studies using bulk sequencing methods to analyse the patterns of DNA methylation were unable to determine whether epimutations affect CLL populations homogeneously. Here, to measure the epimutation rate at single-cell resolution, we applied multiplexed single-cell reduced-representation bisulfite sequencing to B cells from healthy donors and patients with CLL. We observed that the common clonal origin of CLL results in a consistently increased epimutation rate, with low variability in the cell-to-cell epimutation rate. By contrast, variable epimutation rates across healthy B cells reflect diverse evolutionary ages across the trajectory of B cell differentiation, consistent with epimutations serving as a molecular clock. Heritable epimutation information allowed us to reconstruct lineages at high-resolution with single-cell data, and to apply this directly to patient samples. The CLL lineage tree shape revealed earlier branching and longer branch lengths than in normal B cells, reflecting rapid drift after the initial malignant transformation and a greater proliferative history. Integration of single-cell bisulfite sequencing analysis with single-cell transcriptomes and genotyping confirmed that genetic subclones mapped to distinct clades, as inferred solely on the basis of epimutation information. Finally, to examine potential lineage biases during therapy, we profiled serial samples during ibrutinib-associated lymphocytosis, and identified clades of cells that were preferentially expelled from the lymph node after treatment, marked by distinct transcriptional profiles. The single-cell integration of genetic, epigenetic and transcriptional information thus charts the lineage history of CLL and its evolution with therapy. A single-cell approach is used to follow the heritable stochastic changes to DNA methylation that occur in primary chronic lymphocytic leukaemia and healthy B cells, allowing the tracing of cell lineage histories and evolution during treatment with ibrutinib.
- Published
- 2019
- Full Text
- View/download PDF
20. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design
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Sharon Isern, Onikepe A. Folarin, Philomena Eromon, Thiago Moreno L. Souza, Yasmine Rangel Vieira, Kimberly García, Christian B. Matranga, Douglas S. Kwon, Etienne Simon-Loriere, Shirlee Wohl, Ivette Lorenzana, Hayden C. Metsky, Patrick Brehio, Katherine J. Siddle, David K Yang, Scott F. Michael, Giselle Barbosa-Lima, Adrianne Gladden-Young, Leda Parham, Lauren M. Paul, Augustine Goba, Bjӧrn Corleis, Todd M. Allen, Andreas Gnirke, Pardis C. Sabeti, Scott Hennigan, Eva Harris, Jonathan A. Runstadler, Andrew Goldfarb, Lee Gehrke, Sandra Smole, Christian T. Happi, Amanda L Tan, Angel Balmaseda, Damien C. Tully, Anne Piantadosi, Fernando A. Bozza, Aaron E. Lin, Gregory D. Ebel, Daniel J. Park, Amber Carter, James Qu, Donald S. Grant, Ikponmwonsa Odia, Irene Bosch, Lisa E. Hensley, and Kayla G. Barnes
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Sequence analysis ,Computer science ,Oligonucleotides ,Biomedical Engineering ,Nigeria ,Genomics ,Bioengineering ,Genome, Viral ,Computational biology ,Full coverage ,Genome ,Applied Microbiology and Biotechnology ,Article ,Disease Outbreaks ,03 medical and health sciences ,Lassa Fever ,0302 clinical medicine ,Animals ,Humans ,Genomic library ,Gene Library ,030304 developmental biology ,Sequence (medicine) ,0303 health sciences ,Computational Biology ,Genetic Variation ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Culicidae ,Virus Diseases ,Metagenomics ,Scalability ,Metagenome ,Molecular Medicine ,Oligonucleotide Probes ,030217 neurology & neurosurgery ,Biotechnology - Abstract
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.
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- 2019
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21. Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy
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Kendell Clement, Camilla K. Lemvigh, Michaela Gruber, Andreas Gnirke, Laura Z. Rassenti, Anat Biran, Arman W. Mohammad, Donna Neuberg, Kenneth J. Livak, Catherine J. Wu, Neil E. Kay, Jennifer R. Brown, Thomas J. Kipps, Connie Lesnick, Helene Kretzmer, Shuqiang Li, Lili Wang, Bernd Timmermann, Stacey M. Fernandes, Noelia Purroy, Sven Klages, Susan L. Slager, Esteban Braggio, Tait D. Shanafelt, Elias Campo, Hongcang Gu, and Alexander Meissner
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Lymphocytosis ,Lymphoma ,Chronic lymphocytic leukemia ,Oncology and Carcinogenesis ,Biology ,Article ,Epigenome ,Rare Diseases ,medicine ,Genetics ,Humans ,2.1 Biological and endogenous factors ,Epigenetics ,Chronic ,Aetiology ,Cancer ,Leukemia ,Human Genome ,B-Cell ,General Medicine ,Methylation ,Hematology ,DNA Methylation ,medicine.disease ,Leukemia, Lymphocytic, Chronic, B-Cell ,Lymphocytic ,Differentially methylated regions ,CpG site ,DNA methylation ,Cancer research ,Disease Progression ,CpG Islands ,Generic health relevance ,medicine.symptom - Abstract
Most human cancers converge to a deregulated methylome with reduced global levels and elevated methylation at select CpG islands. To investigate the emergence and dynamics of the cancer methylome, we characterized genome-wide DNA methylation in preneoplastic monoclonal B-cell lymphocytosis (MBL) and chronic lymphocytic leukemia (CLL), including serial samples collected across disease course. We detected the aberrant tumor-associated methylation landscape at CLL diagnosis and found no significant differentially methylated regions in the high-count MBL-to-CLL transition. Patient methylomes showed remarkable stability with natural disease and posttherapy progression. Single CLL cells were consistently aberrantly methylated, indicating a homogeneous transition to the altered epigenetic state and a distinct expression profile together with MBL cells compared with normal B cells. Our longitudinal analysis reveals the cancer methylome to emerge early, which may provide a platform for subsequent genetically driven growth dynamics, and, together with its persistent presence, suggests a central role in disease onset. Significance: DNA methylation data from a large cohort of patients with MBL and CLL show that epigenetic transformation emerges early and persists throughout disease stages with limited subsequent changes. Our results indicate an early role for this aberrant landscape in the normal-to-preneoplastic transition that may reflect a pan-cancer mechanism. See related commentary by Rossi, p. 6. This article is highlighted in the In This Issue feature, p. 1
- Published
- 2021
22. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
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David C. Hooper, Anthony A. Philippakis, Jessie M. Gaeta, Sinéad B. Chapman, Christopher Tomkins-Tinch, Caroline N. Cusick, Matthew R. Bauer, John A. Branda, Steven K. Reilly, Lawrence C. Madoff, Kim A. Lagerborg, Stephen F. Schaffner, Molly Kemball, Timelia Fink, Bronwyn MacInnis, Melissa Rudy, Damien Slater, Jeremy Luban, Daniel J. Park, Jacob E. Lemieux, Edward T. Ryan, William P. Hanage, Melis N. Anahtar, Andreas Gnirke, Sushma Chaluvadi, Felecia Cerrato, Adrianne Gladden-Young, Katelyn Flowers, James J. O’Connell, Anna Neumann, Tami D. Lieberman, Eric S. Rosenberg, Catherine M. Brown, Cameron Myhrvold, Bennett M. Shaw, Erica Normandin, Katherine C. DeRuff, Katherine J. Siddle, Jason B. Harris, Sarah E Turbett, Glen R. Gallagher, Travis P. Baggett, Christine Loreth, Pardis C. Sabeti, Virginia M. Pierce, Lydia A. Krasilnikova, Sandra Smole, Amber Carter, Maha R. Farhat, Regina C. LaRocque, Meagan Burns, Aaron E. Lin, and Gordon Adams
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0301 basic medicine ,2019-20 coronavirus outbreak ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Genome, Viral ,law.invention ,Disease Outbreaks ,03 medical and health sciences ,0302 clinical medicine ,law ,Vulnerable population ,Humans ,030212 general & internal medicine ,Phylogeny ,Multidisciplinary ,Phylogenetic tree ,Extramural ,SARS-CoV-2 ,COVID-19 ,030104 developmental biology ,Transmission (mechanics) ,Geography ,Evolutionary biology ,Epidemiological Monitoring ,Skilled Nursing Facility ,Boston - Abstract
Phylogenetics of superspreading One important characteristic of coronavirus epidemiology is the occurrence of superspreading events. These are marked by a disproportionate number of cases originating from often-times asymptomatic individuals. Using a rich sequence dataset from the early stages of the Boston outbreak, Lemieux et al. identified superspreading events in specific settings and analyzed them phylogenetically (see the Perspective by Alizon). Using ancestral trait inference, the authors identified several importation events, further investigated the context and contribution of particular superspreading events to the establishment of local and wider SARS-CoV-2 transmission, and used viral phylogenies to describe sustained transmission. Science , this issue p. eabe3261 ; see also p. 574
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- 2020
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23. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect
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Pavan Bachireddy, Nathan Mathewson, Samuel S. Freeman, Arman W. Mohammad, Nikolaos Barkas, Donna Neuberg, Gad Getz, Natalie Bavli, Kendell Clement, Juliet Forman, Jennifer R. Brown, Thomas J. Kipps, Liudmila Elagina, Christina Ennis, Vincent T. Ho, Sachet A. Shukla, Edwin P. Alyea, Jerome Ritz, Robert J. Soiffer, Ignaty Leshchiner, Laura Z. Rassenti, Catherine J. Wu, Vinhkhang N Nguyen, Derin B. Keskin, Peter V. Kharchenko, Andreas Gnirke, and Satyen H. Gohil
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Homologous ,Lymphoma ,medicine.medical_treatment ,Chronic lymphocytic leukemia ,Cell ,Graft vs Host Disease ,Graft vs Leukemia Effect ,Hematopoietic stem cell transplantation ,Human leukocyte antigen ,Medical and Health Sciences ,Article ,Transcriptome ,Rare Diseases ,HLA Antigens ,Stem Cell Research - Nonembryonic - Human ,immune system diseases ,hemic and lymphatic diseases ,Genetics ,medicine ,Transplantation, Homologous ,Humans ,Epigenetics ,Chronic ,Cancer ,Transplantation ,Chemotherapy ,Leukemia ,business.industry ,Hematopoietic Stem Cell Transplantation ,B-Cell ,Hematology ,General Medicine ,Biological Sciences ,Stem Cell Research ,medicine.disease ,Leukemia, Lymphocytic, Chronic, B-Cell ,Lymphocytic ,surgical procedures, operative ,medicine.anatomical_structure ,Cancer research ,Stem Cell Research - Nonembryonic - Non-Human ,Stem cell ,business - Abstract
Leukemic relapse remains a major barrier to successful allogeneic hematopoietic stem cell transplantation (allo-HSCT) for aggressive hematologic malignancies. The basis for relapse of advanced lymphoid malignancies remains incompletely understood and may involve escape from the graft-versus-leukemia (GvL) effect. We hypothesized that for patients with chronic lymphocytic leukemia (CLL) treated with allo-HSCT, leukemic cell-intrinsic features influence transplant outcomes by directing the evolutionary trajectories of CLL cells. Integrated genetic, transcriptomic, and epigenetic analyses of CLL cells from 10 patients revealed that the clinical kinetics of post-HSCT relapse are shaped by distinct molecular dynamics. Early relapses after allo-HSCT exhibited notable genetic stability; single CLL cell transcriptional analysis demonstrated a cellular heterogeneity that was static over time. In contrast, CLL cells relapsing late after allo-HSCT displayed notable genetic evolution and evidence of neoantigen depletion, consistent with marked single-cell transcriptional shifts that were unique to each patient. We observed a greater rate of epigenetic change for late relapses not seen in early relapses or relapses after chemotherapy alone, suggesting that the selection pressures of the GvL bottleneck are unlike those imposed by chemotherapy. No selective advantage for human leukocyte antigen (HLA) loss was observed, even when present in pretransplant subpopulations. Gain of stem cell modules was a common signature associated with leukemia relapse regardless of posttransplant relapse kinetics. These data elucidate the biological pathways that underlie GvL resistance and posttransplant relapse.
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- 2020
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24. Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events
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Jacob E. Lemieux, Katherine J. Siddle, Bennett M. Shaw, Christine Loreth, Stephen F. Schaffner, Adrianne Gladden-Young, Gordon Adams, Timelia Fink, Christopher H. Tomkins-Tinch, Lydia A. Krasilnikova, Katherine C. DeRuff, Melissa Rudy, Matthew R. Bauer, Kim A. Lagerborg, Erica Normandin, Sinead B. Chapman, Steven K. Reilly, Melis N. Anahtar, Aaron E. Lin, Amber Carter, Cameron Myhrvold, Molly E. Kemball, Sushma Chaluvadi, Caroline Cusick, Katelyn Flowers, Anna Neumann, Felecia Cerrato, Maha Farhat, Damien Slater, Jason B. Harris, John Branda, David Hooper, Jessie M. Gaeta, Travis P. Baggett, James O’Connell, Andreas Gnirke, Tami D. Lieberman, Anthony Philippakis, Meagan Burns, Catherine M. Brown, Jeremy Luban, Edward T. Ryan, Sarah E. Turbett, Regina C. LaRocque, William P. Hanage, Glen R. Gallagher, Lawrence C. Madoff, Sandra Smole, Virginia M. Pierce, Eric Rosenberg, Pardis C. Sabeti, Daniel J. Park, and Bronwyn L. Maclnnis
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medicine.medical_specialty ,Geography ,Coronavirus disease 2019 (COVID-19) ,Phylogenetic tree ,Homeless shelter ,Transmission (medicine) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Epidemiology ,medicine ,Outbreak ,Article ,Contact tracing ,Demography - Abstract
SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.
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- 2020
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25. A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing
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Saul Godinez Pulido, Suhas S.P. Rao, Andreas Gnirke, Zane Colaric, Joshua W. M. Theisen, Alyssa Blackburn, Erez Lieberman Aiden, Parwinder Kaur, David Weisz, Aviva Presser Aiden, Brian Glenn St Hilaire, Neva C. Durand, Namita Mitra, Ragini Mahajan, and Olga Dudchenko
- Subjects
Whole genome sequencing ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,medicine ,Sequence assembly ,Symptom onset ,Computational biology ,Biology ,medicine.disease_cause ,Genome ,DNA sequencing ,Highly sensitive ,Coronavirus - Abstract
Early detection of infection with SARS-CoV-2 is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing andde novogenome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). Almost all diagnostic methods currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require larger concentrations of the virus to achieve this degree of accuracy. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy. The genotypic data contained in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of both positive and negative clinical nasopharyngeal swab samples 100% match the diagnoses obtained in a clinical diagnostic lab using the Center for Disease Control’s 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8- hour experiment at the cost of ∼$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity in this approach.
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- 2020
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26. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to graft-versus-leukemia
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Jennifer R. Brown, Robert J. Soiffer, Christina Ennis, Gad Getz, Kendell Clement, Liudmila Elagina, Andreas Gnirke, Jerome Ritz, Peter V. Kharchenko, Edwin P. Alyea, Nikolas Barkas, Sachet A. Shukla, Samuel S. Freeman, Juliet Forman, Arman W. Mohammad, Laura Z. Rassenti, Satyen H. Gohil, Ignaty Leshchiner, Donna Neuberg, Thomas J. Kipps, Vincent T. Ho, Pavan Bachireddy, Vinhkhang N Nguyen, Catherine J. Wu, and Natalie Bavli
- Subjects
0303 health sciences ,Chemotherapy ,medicine.medical_treatment ,Chronic lymphocytic leukemia ,Human leukocyte antigen ,Hematopoietic stem cell transplantation ,Biology ,medicine.disease ,3. Good health ,Transcriptome ,03 medical and health sciences ,Leukemia ,surgical procedures, operative ,0302 clinical medicine ,immune system diseases ,hemic and lymphatic diseases ,030220 oncology & carcinogenesis ,medicine ,Cancer research ,Epigenetics ,Stem cell ,030304 developmental biology - Abstract
Resistance to the graft-versus-leukemia (GvL) effect remains the major barrier to successful allogeneic hematopoietic stem cell transplantation (allo-HSCT) for aggressive hematologic malignancies. The basis of GvL resistance for advanced lymphoid malignancies remains incompletely understood. We hypothesized that for patients with chronic lymphocytic leukemia (CLL) treated with allo-HSCT, leukemic cell-intrinsic features shape GvL outcomes by directing the evolutionary trajectories of CLL cells. Integrated genetic, transcriptomic and epigenetic analyses of CLL cells from 10 patients revealed that the clinical kinetics of post- HSCT relapse are shaped by distinct molecular dynamics and suggest that the selection pressures of the GvL bottleneck are unlike those imposed by chemotherapy. No selective advantage for HLA loss was observed, even when present in pre-transplant subpopulations. Regardless of post-transplant relapse kinetics, gain of stem cell modules was a common signature associated with leukemia relapse. These data elucidate the biological pathways that underlie GvL resistance and post-transplant relapse.One Sentence SummaryWe find that the clinical kinetics of chronic lymphocytic leukemia relapse after stem cell transplant are underwritten by distinct genetic and epigenetic evolutionary trajectories and suggest that the selection pressures of the post-transplant, immunologic bottleneck are unlike those imposed by chemotherapy.
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- 2020
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27. DNA methylation is a key mechanism for maintaining monoallelic expression on autosomes
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Asia Mendelevich, Luca Pinello, Sunil Gupta, Sébastien Vigneau, S.V. Vinogradova, Alexander Gusev, Henry W. Long, Andreas Gnirke, Kyomi J. Igarashi, Lafontaine Dl, Alves-Pereira Cf, Alexander A. Gimelbrant, Anwesha Nag, Andrew Bortvin, and Kendell Clement
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Genetics ,Regulation of gene expression ,0303 health sciences ,Autosome ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Allelic Imbalance ,DNA methylation ,Epigenetics ,Imprinting (psychology) ,Allele ,Gene ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
In diploid cells, maternal and paternal copies of genes usually have similar transcriptional activity. Mammalian allele-specific epigenetic mechanisms such as X-chromosome inactivation (XCI) and imprinting were historically viewed as rare exceptions to this rule. The discovery of mitotically stable monoallelic autosomal expression (MAE) a decade ago revealed an additional allele-specific mode regulating thousands of mammalian genes. However, despite its prevalence, the mechanistic basis of MAE remains unknown. To uncover the mechanism of MAE maintenance, we devised a small-molecule screen for reactivation of silenced alleles across multiple loci using targeted RNA sequencing. Contrary to previous reports, we identified DNA methylation as a key mechanism of MAE mitotic maintenance. In contrast with the binary choice of the active allele in XCI, stringent transcriptome-wide analysis revealed MAE as a regulatory mode with tunable control of allele-specific expression, dependent on the extent of DNA methylation. In a subset of MAE genes, allelic imbalance was insensitive to changes in DNA methylation, implicating additional mechanisms in MAE maintenance in these loci. Our findings identify a key mechanism of MAE maintenance, reveal tunability of this mode of gene regulation, and provide the essential platform for probing the biological role of MAE in development and disease.
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- 2020
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28. Genome-wide tracking of dCas9-methyltransferase footprints
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Kendell Clement, Hans R. Schöler, Alexandra L. Mattei, Elena K. Stamenova, Julie Donaghey, Andreas Gnirke, Hongcang Gu, Alexander Meissner, Bernd Timmermann, Christina Galonska, Arman W. Mohammad, Jocelyn Charlton, Tobias Cantz, Sven Klages, Michael J. Ziller, Davide Cacchiarelli, Galonska, Christina, Charlton, Jocelyn, Mattei, Alexandra L, Donaghey, Julie, Clement, Kendell, Gu, Hongcang, Mohammad, Arman W, Stamenova, Elena K, Cacchiarelli, Davide, Klages, Sven, Timmermann, Bernd, Cantz, Tobia, Schöler, Hans R, Gnirke, Andrea, Ziller, Michael J, and Meissner, Alexander
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0301 basic medicine ,Methyltransferase ,Science ,General Physics and Astronomy ,Computational biology ,Biology ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Article ,Cell Line ,03 medical and health sciences ,Mice ,Genome editing ,Bacterial Proteins ,CRISPR-Associated Protein 9 ,Animals ,Humans ,Epigenetics ,DNA (Cytosine-5-)-Methyltransferases ,lcsh:Science ,Embryonic Stem Cells ,Gene Editing ,Multidisciplinary ,Cas9 ,General Chemistry ,Methylation ,Epigenome ,Endonucleases ,030104 developmental biology ,DNA methylation ,lcsh:Q - Abstract
In normal mammalian development cytosine methylation is essential and is directed to specific regions of the genome. Despite notable advances through mapping its genome-wide distribution, studying the direct contribution of DNA methylation to gene and genome regulation has been limited by the lack of tools for its precise manipulation. Thus, combining the targeting capability of the CRISPR–Cas9 system with an epigenetic modifier has attracted interest in the scientific community. In contrast to profiling the genome-wide cleavage of a nuclease competent Cas9, tracing the global activity of a dead Cas9 (dCas9) methyltransferase fusion protein is challenging within a highly methylated genome. Here, we report the generation and use of an engineered, methylation depleted but maintenance competent mouse ES cell line and find surprisingly ubiquitous nuclear activity of dCas9-methyltransferases. Subsequent experiments in human somatic cells refine these observations and point to an important difference between genetic and epigenetic editing tools that require unique experimental considerations., Catalytically inactive Cas9 fused to a methyltransferase has emerged as a promising epigenome modifying tool. Here the authors generate a methylation depleted but maintenance competent mouse ES cell line and find ubiquitous off-target activity.
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- 2018
29. Genetic determinants and epigenetic effects of pioneer-factor occupancy
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Julie Donaghey, Kendell Clement, Jennifer S. Chen, Andreas Gnirke, Casey A. Gifford, John L. Rinn, Michael J. Ziller, Ramona Pop, Rahul Karnik, Elena K. Stamenova, Jocelyn Charlton, David R. Kelley, Sudhir Thakurela, Hongcang Gu, Alexander Meissner, Zachary D. Smith, Davide Cacchiarelli, Donaghey, Julie, Thakurela, Sudhir, Charlton, Jocelyn, Chen, Jennifer S., Smith, Zachary D., Gu, Hongcang, Pop, Ramona, Clement, Kendell, Stamenova, Elena K., Karnik, Rahul, Kelley, David R., Gifford, Casey A., Cacchiarelli, Davide, Rinn, John L., Gnirke, Andrea, Ziller, Michael J., and Meissner, Alexander
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0301 basic medicine ,Computational biology ,Biology ,Epigenesis, Genetic ,03 medical and health sciences ,chemistry.chemical_compound ,Genetics ,Humans ,Cell Lineage ,Gene Regulatory Networks ,Epigenetics ,Gene ,Transcription factor ,Cells, Cultured ,reproductive and urinary physiology ,Regulation of gene expression ,Binding Sites ,Pioneer factor ,DNA replication ,Computational Biology ,Epistasis, Genetic ,DNA ,Hep G2 Cells ,respiratory system ,GATA4 Transcription Factor ,HEK293 Cells ,030104 developmental biology ,Gene Expression Regulation ,chemistry ,A549 Cells ,embryonic structures ,DNA methylation ,Hepatocyte Nuclear Factor 3-beta ,Octamer Transcription Factor-3 ,Genes, Switch ,Protein Binding ,Transcription Factors - Abstract
Transcription factors (TFs) direct developmental transitions by binding to target DNA sequences, influencing gene expression and establishing complex gene-regultory networks. To systematically determine the molecular components that enable or constrain TF activity, we investigated the genomic occupancy of FOXA2, GATA4 and OCT4 in several cell types. Despite their classification as pioneer factors, all three TFs exhibit cell-type-specific binding, even when supraphysiologically and ectopically expressed. However, FOXA2 and GATA4 can be distinguished by low enrichment at loci that are highly occupied by these factors in alternative cell types. We find that expression of additional cofactors increases enrichment at a subset of these sites. Finally, FOXA2 occupancy and changes to DNA accessibility can occur in G1-arrested cells, but subsequent loss of DNA methylation requires DNA replication.
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- 2018
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30. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.
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Michael J Ziller, Fabian Müller, Jing Liao, Yingying Zhang, Hongcang Gu, Christoph Bock, Patrick Boyle, Charles B Epstein, Bradley E Bernstein, Thomas Lengauer, Andreas Gnirke, and Alexander Meissner
- Subjects
Genetics ,QH426-470 - Abstract
DNA methylation plays an important role in development and disease. The primary sites of DNA methylation in vertebrates are cytosines in the CpG dinucleotide context, which account for roughly three quarters of the total DNA methylation content in human and mouse cells. While the genomic distribution, inter-individual stability, and functional role of CpG methylation are reasonably well understood, little is known about DNA methylation targeting CpA, CpT, and CpC (non-CpG) dinucleotides. Here we report a comprehensive analysis of non-CpG methylation in 76 genome-scale DNA methylation maps across pluripotent and differentiated human cell types. We confirm non-CpG methylation to be predominantly present in pluripotent cell types and observe a decrease upon differentiation and near complete absence in various somatic cell types. Although no function has been assigned to it in pluripotency, our data highlight that non-CpG methylation patterns reappear upon iPS cell reprogramming. Intriguingly, the patterns are highly variable and show little conservation between different pluripotent cell lines. We find a strong correlation of non-CpG methylation and DNMT3 expression levels while showing statistical independence of non-CpG methylation from pluripotency associated gene expression. In line with these findings, we show that knockdown of DNMTA and DNMT3B in hESCs results in a global reduction of non-CpG methylation. Finally, non-CpG methylation appears to be spatially correlated with CpG methylation. In summary these results contribute further to our understanding of cytosine methylation patterns in human cells using a large representative sample set.
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- 2011
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31. ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.
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Ellen Markljung, Lin Jiang, Jacob D Jaffe, Tarjei S Mikkelsen, Ola Wallerman, Martin Larhammar, Xiaolan Zhang, Li Wang, Veronica Saenz-Vash, Andreas Gnirke, Anders M Lindroth, Romain Barrés, Jie Yan, Sara Strömberg, Sachinandan De, Fredrik Pontén, Eric S Lander, Steven A Carr, Juleen R Zierath, Klas Kullander, Claes Wadelius, Kerstin Lindblad-Toh, Göran Andersson, Göran Hjälm, and Leif Andersson
- Subjects
Biology (General) ,QH301-705.5 - Abstract
A single nucleotide substitution in intron 3 of IGF2 in pigs abrogates a binding site for a repressor and leads to a 3-fold up-regulation of IGF2 in skeletal muscle. The mutation has major effects on muscle growth, size of the heart, and fat deposition. Here, we have identified the repressor and find that the protein, named ZBED6, is previously unknown, specific for placental mammals, and derived from an exapted DNA transposon. Silencing of Zbed6 in mouse C2C12 myoblasts affected Igf2 expression, cell proliferation, wound healing, and myotube formation. Chromatin immunoprecipitation (ChIP) sequencing using C2C12 cells identified about 2,500 ZBED6 binding sites in the genome, and the deduced consensus motif gave a perfect match with the established binding site in Igf2. Genes associated with ZBED6 binding sites showed a highly significant enrichment for certain Gene Ontology classifications, including development and transcriptional regulation. The phenotypic effects in mutant pigs and ZBED6-silenced C2C12 myoblasts, the extreme sequence conservation, its nucleolar localization, the broad tissue distribution, and the many target genes with essential biological functions suggest that ZBED6 is an important transcription factor in placental mammals, affecting development, cell proliferation, and growth.
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- 2009
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32. Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells
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Arman W. Mohammad, Konrad Hochedlinger, Jiho Choi, Bruno Di Stefano, Steven P. Gygi, Sang Yong Kim, Ruslan I. Sadreyev, Kaixuan Lin, Ryan M. Walsh, Haruhiko Koseki, Andrew Xiao, Kendell Clement, Andrej J. Savol, Junko Odajima, Justin Brumbaugh, Toshihiro Shioda, Jean Charron, Hongcang Gu, Alexander Meissner, Christopher M. Rose, Aaron J. Huebner, Andreas Gnirke, and Jafar Sharif
- Subjects
0301 basic medicine ,Genetics ,Multidisciplinary ,Methyltransferase ,urogenital system ,Wnt signaling pathway ,Biology ,Embryonic stem cell ,Article ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,Downregulation and upregulation ,embryonic structures ,DNA methylation ,Inner cell mass ,Epigenetics ,biological phenomena, cell phenomena, and immunity ,Genomic imprinting ,reproductive and urinary physiology - Abstract
Concomitant activation of the Wnt pathway and suppression of Mapk signalling by two small molecule inhibitors (2i) in the presence of leukaemia inhibitory factor (LIF) (hereafter termed 2i/L) induces a naive state in mouse embryonic stem (ES) cells that resembles the inner cell mass (ICM) of the pre-implantation embryo. Since the ICM exists only transiently in vivo, it remains unclear how sustained propagation of naive ES cells in vitro affects their stability and functionality. Here we show that prolonged culture of male mouse ES cells in 2i/L results in irreversible epigenetic and genomic changes that impair their developmental potential. Furthermore, we find that female ES cells cultured in conventional serum plus LIF medium phenocopy male ES cells cultured in 2i/L. Mechanistically, we demonstrate that the inhibition of Mek1/2 is predominantly responsible for these effects, in part through the downregulation of DNA methyltransferases and their cofactors. Finally, we show that replacement of the Mek1/2 inhibitor with a Src inhibitor preserves the epigenetic and genomic integrity as well as the developmental potential of ES cells. Taken together, our data suggest that, although short-term suppression of Mek1/2 in ES cells helps to maintain an ICM-like epigenetic state, prolonged suppression results in irreversible changes that compromise their developmental potential.
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- 2017
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33. Robust Discovery of Candidate DNA Methylation Cancer Drivers
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Catherine J. Wu, Kirsten Fischer, Andreas Gnirke, Johannes Bloehdorn, Stephan Stilgenbauer, Doron Betel, Olivier Elemento, Daniel Mertens, Michael Hallek, Eugen Tausch, Jérôme Moreaux, Ronan Chaligne, Alexander Meissner, Marcin Imielinski, Anna-Maria Fink, Heng Pan, Dan A. Landau, Loïc Renaud, and Chao Zhang
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medicine.medical_specialty ,Positive selection ,Immunology ,Disease progression ,Cancer ,Cell Biology ,Hematology ,Tp53 mutation ,medicine.disease ,Biochemistry ,Clinical trial ,Family medicine ,medicine ,Dose effect ,Cancer gene ,Psychology ,Bristol-Myers - Abstract
The field of cancer genomics has been empowered by increasingly sophisticated inference tools to distinguish driver mutations from the vastly greater number of passenger mutations. Epigenetic alterations such as promoter DNA hypermethylation have been shown to drive cancer through inactivation of tumor suppressor genes (TSGs), but growing malignant populations also accrue pervasive stochastic epigenetic changes in DNA methylation (DNAme), most of which likely carry little functional impact. Unlike with somatic mutations, we have limited ability to robustly differentiate driver DNAme changes (DNAme drivers) from stochastic, passenger DNAme changes. To address this challenge, we developed MethSig, a statistical inference framework that accounts for the varying stochastic hypermethylation rates across the genome and between samples. MethSig estimates expected background DNAme changes, thereby allowing the identification of epigenetically disrupted loci, where observed hypermethylation significantly exceeds expectation, potentially reflecting positive selection (Fig. 1a). We applied MethSig to reduced representation bisulfite sequencing (RRBS) data of chronic lymphocytic leukemia (CLL) cohorts, which include 304 CLLs collected in a prospective clinical trial (CLL8) and 103 CLLs in a previously published study (CLL-DFCI, Landau et al., 2014), as well as other malignancies where RRBS data is available, including ductal carcinoma in situ (Abba et al., 2015) and multiple myeloma. Area under the receiver operating characteristic curve (AUROC) was used to evaluate sensitivity and specificity of methods in the inference of likely DNAme drivers. We identified two key features that are likely to be strongly associated with true candidate DNAme drivers: gene silencing in relation to promoter hypermethylation and association with clinical outcome. MethSig qualitatively improved ROC across those clinical and biological read outs (0.955 of MethSig, 95% confidence interval [CI] 0.945 - 0.965, versus 0.703 of benchmarked methods, 95% CI 0.669 - 0.737, Fig. 1b used CLL8 as an example). We identified 189 candidate DNAme drivers in CLL, which include known TSGs, and are enriched in genes hypermethylated or inactivated across cancer types. To further validate MethSig's inferences, selected CLL candidate DNAme drivers (DUSP22, RPRM) underwent CRISPR/Cas9 knockout (KO) in CLL cells and stable KO clones were generated through single-cell cloning to eliminate genetic heterogeneity effect. The RPRM and DUSP22 KO clones showed faster growth without treatment (Fig. 1c) and superior fitness in ibrutinib/fludarabine treatment compared with controls (Fig. 1d). Notably, we observed a gene dose effect in the RPRM KO clones (Fig. 1c-d, greater growth of the bi-allelic compared to mono-allelic KO). Elastic net regression with a Cox proportional hazards model was used to evaluate DNAme drivers' contribution to the prediction of failure-free survival after treatment (FFS; failure defined as retreatment or death) and a rigorous training (CLL8) and validation (an independent cohort CLL-DFCI) cohort study design was implemented to safeguard from overfitting and poor generalizability. DNAme drivers were found to be associated with shorter FFS in independent CLL cohorts (Fig. 1e-f). A regression model including established CLL risk indicators (IGHV unmutated status, del[17p] or TP53 mutation) showed an adjusted hazard ratio of 2.3 (95% CI 1.6 - 3.3, P = 2 × 10-6) in CLL8 cohort and 3.2 (95% CI 1.2 - 8.8, P = 0.02) in CLL-DFCI cohort for patients with high risk. Application of MethSig to CLL relapsed after chemoimmunotherapy further identified relapse-specific DNAme drivers, enriched in TP53 targets as well as DNA damage pathway, which indicates that CLL relapse after chemotherapy may follow an alternative path compared to CLL progression in the absence of therapy, offering novel insights for therapeutic strategies to address drug-resistant or relapsed cancer. Collectively, our data support a novel framework for the analysis of DNAme changes in cancer to specifically identify DNAme drivers of disease progression and relapse, empowering the discovery of epigenetic mechanisms that enhance cancer cell fitness. This work addressed a central gap between cancer epigenetics and cancer genetics, where such tools have had a transformative impact in precision oncology and cancer gene discovery. Disclosures Tausch: Janssen-Cilag: Consultancy, Honoraria, Research Funding; Roche: Consultancy, Honoraria, Research Funding; AbbVie: Consultancy, Honoraria, Research Funding. Fink:AbbVie: Other: travel grants; Janssen: Honoraria; Celgene: Research Funding. Fischer:AbbVie: Honoraria; F. Hoffmann-La Roche: Honoraria, Other: travel grants. Gnirke:FL67 Inc.: Consultancy. Moreaux:Diag2Tec: Consultancy. Hallek:Celgene: Consultancy, Research Funding; Pharmacyclics: Consultancy, Research Funding; AbbVie: Consultancy, Research Funding; Gilead: Consultancy, Research Funding; Mundipharma: Consultancy, Research Funding; Janssen: Consultancy, Research Funding; Roche: Consultancy, Research Funding. Stilgenbauer:Janssen-Cilag: Consultancy, Honoraria, Other: travel support, Research Funding; Genentech: Consultancy, Honoraria, Other: travel support, Research Funding; Gilead: Consultancy, Honoraria, Other: travel support, Research Funding; Genzyme: Consultancy, Honoraria, Other: travel support, Research Funding; Pharmacyclics: Consultancy, Honoraria, Other, Research Funding; F. Hoffmann-LaRoche: Consultancy, Honoraria, Other: travel support, Research Funding; Celgene: Consultancy, Honoraria, Other: travel support, Research Funding; Boehringer-Ingelheim: Consultancy, Honoraria, Other: travel support, Research Funding; Amgen: Consultancy, Honoraria, Other: travel support, Research Funding; AbbVie: Consultancy, Honoraria, Other: travel support, Research Funding; GlaxoSmithKline: Consultancy, Honoraria, Other: travel support, Research Funding; Novartis: Consultancy, Honoraria, Other, Research Funding; Mundipharma: Consultancy, Honoraria, Other, Research Funding. Wu:BionTech: Current equity holder in publicly-traded company; Pharmacyclics: Research Funding. Elemento:Acuamark: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; OneThree Biotech: Current equity holder in private company, Other: Cofounder; Owkin: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Sanofi: Research Funding; Eli Lilly: Research Funding; Volastra Therapeutics: Current equity holder in private company, Other: Cofounder; Freenome: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Genetic Intelligence: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Janssen: Research Funding. Landau:Bristol Myers Squibb: Research Funding; Illumina: Research Funding.
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- 2020
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34. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
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Ronan Chaligne, Alicia Alonso, Wendy Béguelin, Rafael C. Schulman, Hongcang Gu, Alexander Meissner, Sydney X. Lu, Ari Melnick, Kyu-Tae Kim, Ryan M. Brand, Federico Gaiti, Catherine J. Wu, Bradley E. Bernstein, Yanwen Jiang, Kevin Y. Huang, Elena K. Stamenova, Dan A. Landau, Scott Kulm, Omar Abdel-Wahab, John N. Allan, Alessandro Pastore, Andreas Gnirke, and Richard R. Furman
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Epigenomics ,0301 basic medicine ,Chronic lymphocytic leukaemia ,Science ,General Physics and Astronomy ,Computational biology ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Cancer epigenetics ,immune system diseases ,hemic and lymphatic diseases ,Epigenetics ,lcsh:Science ,Regulation of gene expression ,Multidisciplinary ,General Chemistry ,Epigenome ,Gene regulation ,Chromatin ,030104 developmental biology ,Histone ,030220 oncology & carcinogenesis ,DNA methylation ,biology.protein ,lcsh:Q - Abstract
Cancer evolution is fueled by epigenetic as well as genetic diversity. In chronic lymphocytic leukemia (CLL), intra-tumoral DNA methylation (DNAme) heterogeneity empowers evolution. Here, to comprehensively study the epigenetic dimension of cancer evolution, we integrate DNAme analysis with histone modification mapping and single cell analyses of RNA expression and DNAme in 22 primary CLL and 13 healthy donor B lymphocyte samples. Our data reveal corrupted coherence across different layers of the CLL epigenome. This manifests in decreased mutual information across epigenetic modifications and gene expression attributed to cell-to-cell heterogeneity. Disrupted epigenetic-transcriptional coordination in CLL is also reflected in the dysregulation of the transcriptional output as a function of the combinatorial chromatin states, including incomplete Polycomb-mediated gene silencing. Notably, we observe unexpected co-mapping of typically mutually exclusive activating and repressing histone modifications, suggestive of intra-tumoral epigenetic diversity. Thus, CLL epigenetic diversification leads to decreased coordination across layers of epigenetic information, likely reflecting an admixture of cells with diverging cellular identities., In chronic lymphocytic leukemia (CLL), evolution is driven by transcriptional and epigenetic heterogeneity. Here, the authors integrate epigenomic analyses to show how intra-tumoral epigenetic diversity results in divergent chromatin states in CLL cells, increasing cell-to-cell transcriptional heterogeneity.
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- 2019
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35. TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers
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Nina Bailly, Andreas Gnirke, Alexander Meissner, Elena K. Stamenova, Eric J. Martin, Franz-Josef Müller, Jocelyn Charlton, Björn Brändl, Zachary D. Smith, Alexandra L. Mattei, Evangelos Kiskinis, Jing Liao, Pay Giesselmann, and Eunmi J. Jung
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Pluripotent Stem Cells ,Somatic cell ,Biology ,Article ,Cell Line ,DNA Methyltransferase 3A ,Epigenesis, Genetic ,Mixed Function Oxygenases ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Proto-Oncogene Proteins ,Genetics ,Animals ,Humans ,DNA (Cytosine-5-)-Methyltransferases ,Enhancer ,Embryonic Stem Cells ,030304 developmental biology ,Regulation of gene expression ,Mice, Knockout ,0303 health sciences ,Gene Expression Regulation, Developmental ,Cell Differentiation ,Methylation ,DNA Methylation ,Embryonic stem cell ,Cell biology ,Enhancer Elements, Genetic ,Epiblast ,DNA methylation ,embryonic structures ,Stem cell ,030217 neurology & neurosurgery ,Germ Layers - Abstract
Mammalian cells stably maintain high levels of DNA methylation despite expressing both positive (DNMT3A/B) and negative (TET1–3) regulators. Here, we used wildtype and TET triple knockout human embryonic stem cells (ESCs), generated DNMT3-null as well as TET and DNMT3-null pentuple knockouts, and compared methylation patterns using whole genome bisulfite sequencing (WGBS). The greatest impact on global methylation levels was observed in DNMT3-deficient cells, including reproducible focal demethylation at thousands of normally methylated loci. This demethylation depends upon TET expression and only occurs when both DNMT3s are absent. Dynamic loci are enriched for hydroxymethylcytosine and overlap with subsets of putative somatic enhancers that are methylated in ESCs and can be activated upon differentiation. We observe similar dynamics in mouse ESCs that were less frequenct in epiblast stem cells (EpiSCs) and scarce in somatic tissues, suggesting a conserved pluripotency-linked mechanism. Taken together, our data reveal tightly regulated competition between DNMT3s and TETs at thousands of somatic regulatory sequences within pluripotent cells.
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- 2019
36. Development and Validation of a Mass Spectrometry–Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease
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Todd A. Carter, Matthew DeFelice, Heidi L. Rehm, Stanislav Kmoch, Lucienne Ronco, Brendan Blumenstiel, Niall J. Lennon, Stacey Gabriel, Kendrah Kidd, Andreas Gnirke, Ozge Birsoy, Eric S. Lander, Anthony J. Bleyer, Massachusetts Institute of Technology. Department of Biology, and Lander, Eric Steven
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0301 basic medicine ,Pathology ,medicine.medical_specialty ,Genotype ,030232 urology & nephrology ,Disease ,Biology ,medicine.disease_cause ,Medullary cystic kidney disease ,Sensitivity and Specificity ,Mass Spectrometry ,Workflow ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,MUC1 ,Genetics ,Mutation ,Mucin-1 ,Mucin ,Reproducibility of Results ,Polycystic Kidney, Autosomal Dominant ,medicine.disease ,Variable number tandem repeat ,030104 developmental biology ,Molecular Diagnostic Techniques ,Molecular Medicine ,Kidney disease - Abstract
Mucin-1 kidney disease, previously described as medullary cystic kidney disease type 1 (MCKD1, OMIM 174000), is an autosomal dominant tubulointerstitial kidney disease recently shown to be caused by a single-base insertion within the variable number tandem repeat region of the MUC1 gene. Because of variable age of disease onset and often subtle signs and symptoms, clinical diagnosis of mucin-1 kidney disease and differentiation from other forms of hereditary kidney disease have been difficult. The causal insertion resides in a variable number tandem repeat region with high GC content, which has made detection by standard next-generation sequencing impossible to date. The inherently difficult nature of this mutation required an alternative method for routine detection and clinical diagnosis of the disease. We therefore developed and validated a mass spectrometry–based probe extension assay with a series of internal controls to detect the insertion event using 24 previously characterized positive samples from patients with mucin-1 kidney disease and 24 control samples known to be wild type for the variant. Validation results indicate an accurate and reliable test for clinically establishing the molecular diagnosis of mucin-1 kidney disease with 100% sensitivity and specificity across 275 tests called., Carlos Slim Foundation. Slim Initiative for Genomic Medicine
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- 2016
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37. The Hi-Culfite assay reveals relationships between chromatin contacts and DNA methylation state
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Yiqun Jiang, Eric S. Lander, Elena Stamenova, Suhas S.P. Rao, Muhammad S. Shamim, Ivan D. Bochkov, Erez Lieberman Aiden, Andreas Gnirke, Olga Dudchenko, Su-Chen Huang, and Neva C. Durand
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Genetics ,0303 health sciences ,03 medical and health sciences ,0302 clinical medicine ,Chemistry ,Bisulfite sequencing ,DNA methylation ,Methylation ,030217 neurology & neurosurgery ,030304 developmental biology ,3. Good health ,Chromatin - Abstract
Hi-Culfite, a protocol combining Hi-C and whole-genome bisulfite sequencing (WGBS), determines chromatin contacts and DNA methylation simultaneously. Hi-Culfite also reveals relationships that cannot be seen when the two assays are performed separately. For instance, we show that loci associated with open chromatin exhibit context-sensitive methylation: when their spatial neighbors lie in closed chromatin, they are much more likely to be methylated.
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- 2018
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38. Targets and genomic constraints of ectopic Dnmt3b expression
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Jocelyn Charlton, Ramona Pop, Rahul Karnik, Derrick J. Rossi, Hongcang Gu, Alexander Meissner, Isabel Beerman, Xiaoli Mi, Zachary D. Smith, Patrick Boyle, Yingying Zhang, Andreas Gnirke, and Kendell Clement
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0301 basic medicine ,Mouse ,QH301-705.5 ,Science ,DNMT3B ,Bisulfite sequencing ,Gene Expression ,Mice, Transgenic ,Genomics ,Biology ,liver ,Genome ,DNA methyltransferase ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,stem cells ,blood ,Neoplasms ,Animals ,Humans ,DNA (Cytosine-5-)-Methyltransferases ,Biology (General) ,Embryonic Stem Cells ,Cancer Biology ,Genetics ,General Immunology and Microbiology ,General Neuroscience ,Genetics and Genomics ,General Medicine ,DNA Methylation ,Recombinant Proteins ,Chromatin ,030104 developmental biology ,Gene Expression Regulation ,CpG site ,DNA methylation ,MEFs ,Medicine ,CpG Islands ,Research Article ,Human - Abstract
DNA methylation plays an essential role in mammalian genomes and expression of the responsible enzymes is tightly controlled. Deregulation of the de novo DNA methyltransferase DNMT3B is frequently observed across cancer types, yet little is known about its ectopic genomic targets. Here, we used an inducible transgenic mouse model to delineate rules for abnormal DNMT3B targeting, as well as the constraints of its activity across different cell types. Our results explain the preferential susceptibility of certain CpG islands to aberrant methylation and point to transcriptional state and the associated chromatin landscape as the strongest predictors. Although DNA methylation and H3K27me3 are usually non-overlapping at CpG islands, H3K27me3 can transiently co-occur with DNMT3B-induced DNA methylation. Our genome-wide data combined with ultra-deep locus-specific bisulfite sequencing suggest a distributive activity of ectopically expressed Dnmt3b that leads to discordant CpG island hypermethylation and provides new insights for interpreting the cancer methylome.
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- 2018
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39. Comparative genomic analysis of embryonic, lineage-converted and stem cell-derived motor neurons
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Nicholas Atwater, Hongcang Gu, Alexander Meissner, Kevin Eggan, Kendell Clement, Kate E. Galloway, Justin K. Ichida, Andreas Gnirke, Kimberly N. Babos, Kim A. Staats, Yingxiao Shi, Evangelos Kiskinis, Esther Y. Son, and Brandi N. Davis-Dusenbery
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Pluripotent Stem Cells ,0301 basic medicine ,Cell type ,Transcription, Genetic ,Biology ,Epigenesis, Genetic ,Transcriptome ,03 medical and health sciences ,Directed differentiation ,medicine ,Animals ,Cell Lineage ,Induced pluripotent stem cell ,Molecular Biology ,Motor Neurons ,Genomics ,Motor neuron ,Embryo, Mammalian ,Stem Cells and Regeneration ,Embryonic stem cell ,Cell biology ,Mice, Inbred C57BL ,030104 developmental biology ,medicine.anatomical_structure ,Stem cell ,Reprogramming ,Developmental Biology - Abstract
Advances in stem cell science allow the production of different cell types in vitro either through the recapitulation of developmental processes, often termed “directed differentiation,” or the forced expression of lineage-specific transcription factors. Although cells produced by both approaches are increasingly used in translational applications, their quantitative similarity to their primary counterparts remains largely unresolved. To investigate the similarity between in vitro-derived and primary cell types, we harvested and purified mouse spinal motor neurons and compared them to motor neurons produced by transcription factor-mediated lineage conversion of fibroblasts or directed differentiation of pluripotent stem cells. To enable unbiased analysis of these motor neuron types and their cells of origin, we then subjected them to whole transcriptome and DNA methylome analysis by RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS). Despite major differences in methodology, lineage conversion and directed differentiation both produce cells that closely approximate the primary motor neuron state. However, we identify differences in Fas signaling, the Hox code, and synaptic gene expression between lineage-converted and directed differentiation motor neurons that affect their utility in translational studies.
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- 2018
40. Author response: Targets and genomic constraints of ectopic Dnmt3b expression
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Ramona Pop, Hongcang Gu, Alexander Meissner, Kendell Clement, Jocelyn Charlton, Xiaoli Mi, Patrick Boyle, Rahul Karnik, Isabel Beerman, Zachary D. Smith, Andreas Gnirke, Derrick J. Rossi, and Yingying Zhang
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Expression (architecture) ,DNMT3B ,Biology ,Cell biology - Published
- 2018
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41. Global delay in nascent strand DNA methylation
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Jocelyn Charlton, Kendell Clement, Zachary D. Smith, Ramona Pop, Alexander M. Tsankov, Bernd Timmermann, David Santos, Sven Klages, Michael J. Ziller, Veronika Akopian, Timothy L. Downing, Evangelos Kiskinis, Hongcang Gu, Alexander Meissner, and Andreas Gnirke
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0301 basic medicine ,DNA Replication ,Male ,Bisulfite sequencing ,Mitosis ,Biology ,Methylation ,Article ,DNA Methyltransferase 3A ,Epigenesis, Genetic ,03 medical and health sciences ,chemistry.chemical_compound ,Cytosine ,Structural Biology ,Neoplasms ,Humans ,Epigenetics ,DNA (Cytosine-5-)-Methyltransferases ,Molecular Biology ,Embryonic Stem Cells ,Cell Proliferation ,Regulation of gene expression ,Motor Neurons ,Genome, Human ,Sequence Analysis, RNA ,Cell Cycle ,DNA replication ,DNA ,DNA Methylation ,HCT116 Cells ,Cell biology ,030104 developmental biology ,CpG site ,chemistry ,Gene Expression Regulation ,DNA methylation ,CpG Islands ,Transcription Factors - Abstract
Cytosine methylation is widespread among organisms and essential for mammalian development. In line with early postulations of an epigenetic role in gene regulation, symmetric CpG methylation can be mitotically propagated over many generations with extraordinarily high fidelity. Here, we combine BrdU labeling and immunoprecipitation with genome-wide bisulfite sequencing to explore the inheritance of cytosine methylation onto newly replicated DNA in human cells. Globally, we observe a pronounced lag between the copying of genetic and epigenetic information in embryonic stem cells that is reconsolidated within hours to accomplish faithful mitotic transmission. Populations of arrested cells show a global reduction of lag-induced intermediate CpG methylation when compared to proliferating cells, whereas sites of transcription factor engagement appear cell-cycle invariant. Alternatively, the cancer cell line HCT116 preserves global epigenetic heterogeneity independently of cell-cycle arrest. Taken together, our data suggest that heterogeneous methylation largely reflects asynchronous proliferation, but is intrinsic to actively engaged cis-regulatory elements and cancer.
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- 2018
42. Capturing diverse microbial sequence with comprehensive and scalable probe design
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James Qu, Ikponmwonsa Odia, Douglas S. Kwon, Yasmine Rangel Vieira, Etienne Simon-Loriere, Hayden C. Metsky, Patrick Brehio, Leda Parham, Giselle Barbosa-Lima, Scott F. Michael, Scott Hennigan, David K Yang, Andreas Gnirke, Gregory D. Ebel, Augustine Goba, Eva Harris, Shirlee Wohl, Adrianne Gladden-Young, Fernando A. Bozza, Kayla G. Barnes, Amber Carter, Katherine J. Siddle, Lauren M. Paul, Aaron E. Lin, Souza Tml, Sandra Smole, Jonathan A. Runstadler, Pardis C. Sabeti, Damien C. Tully, Anne Piantadosi, Daniel J. Park, Christian T. Happi, Sharon Isern, Ivette Lorenzana, Andrew Goldfarb, Lee Gehrke, Bjӧrn Corleis, Todd M. Allen, Amanda L Tan, Angel Balmaseda, Philomena Eromon, Kimberly García, Irene Bosch, Donald S. Grant, Lisa E. Hensley, Onikepe A. Folarin, and Christian B. Matranga
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0303 health sciences ,03 medical and health sciences ,030306 microbiology ,Computer science ,Viral genomes ,Metagenomics ,Scalability ,Genomics ,Computational biology ,Full coverage ,Genome ,030304 developmental biology ,Sequence (medicine) - Abstract
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. We developed CATCH (Compact Aggregation of Targets for Comprehensive Hybridization), a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs compact probe sets that achieve full coverage of known sequence diversity and that scale well with this diversity. To illustrate applications of CATCH, we focused on capturing viral genomes. We designed, synthesized, and validated multiple probe sets, including one that targets whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriched unique viral content on average 18× and allowed us to assemble genomes that we could not otherwise recover, while accurately preserving within-sample diversity. We used this approach to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of viral infections in samples with unknown content. Together, this work demonstrates a path toward more sensitive, cost-effective metagenomic sequencing.
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- 2018
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43. Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade
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Andreas Gnirke, Bastian Schilling, Qian Zhan, Dirk Schadendorf, Alexander Meissner, Taha Merghoub, Levi A. Garraway, George F. Murphy, Patrick Ryan Potts, Nir Hacohen, Ying Huang, Patrick C. Lee, Diana Miao, Clyde Bango, Arman W. Mohammad, Christine G. Lian, Catherine J. Wu, Jedd D. Wolchok, Daniel Gusenleitner, Eliezer M. Van Allen, Derin B. Keskin, Donna Neuberg, Pavan Bachireddy, Rupert Langer, Christina Galonska, Kendell Clement, Zachary J. Cartun, Jeffrey S. Weber, Alexandra Snyder, Mehrtash Babadi, F. Stephen Hodi, and Sachet A. Shukla
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0301 basic medicine ,Male ,Skin Neoplasms ,medicine.medical_treatment ,Medizin ,chemical and pharmacologic phenomena ,Mice, Transgenic ,General Biochemistry, Genetics and Molecular Biology ,Article ,Epigenesis, Genetic ,03 medical and health sciences ,Mice ,Antigens, Neoplasm ,Cell Line, Tumor ,Neoplasms ,medicine ,Autophagy ,Animals ,Humans ,CTLA-4 Antigen ,610 Medicine & health ,Melanoma ,Germ-Line Mutation ,biology ,Gene Expression Profiling ,Antibodies, Monoclonal ,hemic and immune systems ,Immunotherapy ,DNA Methylation ,medicine.disease ,Ipilimumab ,Immune checkpoint ,Ubiquitin ligase ,Blockade ,Gene expression profiling ,030104 developmental biology ,CTLA-4 ,biology.protein ,Cancer research ,570 Life sciences ,Female ,Melanoma-Specific Antigens - Abstract
CTLA-4 immune checkpoint blockade is clinically effective in a subset of patients with metastatic melanoma. We identify a subcluster of MAGE-A cancer-germline antigens, located within a narrow 75 kb region of chromosome Xq28, that predicts resistance uniquely to blockade of CTLA-4, but not PD-1. We validate this gene expression signature in an independent anti-CTLA-4-treated cohort and show its specificity to the CTLA-4 pathway with two independent anti-PD-1-treated cohorts. Autophagy, a process critical for optimal anti-cancer immunity, has previously been shown to be suppressed by the MAGE-TRIM28 ubiquitin ligase in vitro. We now show that the expression of the key autophagosome component LC3B and other activators of autophagy are negatively associated with MAGE-A protein levels in human melanomas, including samples from patients with resistance to CTLA-4 blockade. Our findings implicate autophagy suppression in resistance to CTLA-4 blockade in melanoma, suggesting exploitation of autophagy induction for potential therapeutic synergy with CTLA-4 inhibitors.
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- 2018
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44. The African coelacanth genome provides insights into tetrapod evolution
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Mariko Forconi, Tereza Manousaki, Peter F. Stadler, Anna Maria Fausto, Simon D. M. White, Shigehiro Kuraku, Sumir Panji, Marcia Lara, Andreas Gnirke, Hervé Philippe, Shaohua Fan, Axel Meyer, Jean Nicolas Volff, Tsutomu Miyake, Sante Gnerre, Thorsten Burmester, Anne Nitsche, Igor Schneider, John J. Stegeman, Alison P. Lee, Kerstin Lindblad-Toh, Peter van Heusden, Chris T. Amemiya, Michael S. Campbell, Ettore Olmo, Vydianathan Ravi, Jason Turner-Maier, Denis Baurain, Gary W. Litman, Federica Di Palma, Nicolas Rohner, Manfred Schartl, Giuseppe Scapigliati, Oleg Simakov, Aaron M. Berlin, Barbara Picone, Ingo Braasch, Byrappa Venkatesh, David R. Nelson, Wilfried Haerty, Diana Tabbaa, M. Gail Mueller, Francesco Buonocore, Eric S. Lander, Gianluca De Moro, Uljana Hesse, Chris P. Ponting, Nathalie Feiner, Junaid Gamieldien, Clifford J. Tabin, Gregory L. Blatch, Tatsuya Ota, Steve Hoffmann, Maria Assunta Biscotti, John H. Postlethwait, Chris L. Organ, Jessica Alföldi, Lin Fan, Mark Robinson, Stephen M. J. Searle, Louise Williams, Mark E. Hahn, Sonja J. Prohaska, Jared V. Goldstone, Dariusz Przybylski, Iain MacCallum, Rosemary A. Dorrington, Joshua Z. Levin, Tatjana Sauka-Spengler, Kenta Sumiyama, Nil Ratan Saha, Henner Brinkmann, Jeremy Johnson, John P. Cannon, Filipe J. Ribeiro, Marco Gerdol, David B. Jaffe, Adriana Canapa, Hakim Tafer, Marco Barucca, Mark Yandell, Evan Mauceli, Alan Christoffels, Sibel I. Karchner, Adrienne L. Edkins, J. Joshua Smith, Bronwen Aken, Neil H. Shubin, Ted Sharpe, Domitille Chalopin, Alberto Pallavicini, Molecular Genetics Program, Benaroya Research Institute, Department of Biology, Northern Arizona University [Flagstaff], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Partenaires INRAE, Université de Montréal (UdeM), Institute of Neuroscience, University of Oregon [Eugene], University of Konstanz, Instituto de Ciências Biológicas, Federal University of Para - Universidade Federal do Para [Belem - Brésil], Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), Utah State University (USU), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Rhodes University, Grahamstown, Department of Life Sciences, Università degli studi di Trieste, Wellcome Trust Sanger Institute, Università Politecnica delle Marche [Ancona] (UNIVPM), Université de Liège, Victoria University [Melbourne], Department for Innovation in Biological, Agro-Food and Forest Systems, Tuscia University, University of Hamburg, Eccles Institute of Human Genetics, University of Utah, University of South Florida [Tampa] (USF), South African National Bioinformatics Institute (SANBI), University of the Western Cape, International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft-University of Konstanz, Biology Department (WHOI), Woods Hole Oceanographic Institution (WHOI), University of Oxford [Oxford], Leipzig University, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA, Keio University, All Children’s Hospital, University of Tennessee, Bioinformatics Group, Department of Computer Science, Universität Leipzig [Leipzig], Graduate University for Advanced Studies, Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore, European Molecular Biology Laboratory (EMBL), National Institute of Genetics (NIG), University of Chicago, Department Physiological Chemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), South African National Department of Science and Technology, National Human Genome Research Institute (NHGRI), European Science Foundation, Amemiya, Chris T., Alföldi, Jessica, Meyer, Axel, Lindblad-Toh, Kerstin, Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Trieste = University of Trieste, Università degli studi della Tuscia [Viterbo], University of the Western Cape (UWC), University of Oxford, Universität Leipzig, Julius-Maximilians-Universität Würzburg (JMU), Chris T., Amemiya, Jessica, Alföldi, Alison P., Lee, Shaohua, Fan, Hervé, Philippe, Iain, Maccallum, Ingo, Braasch, Tereza, Manousaki, Igor, Schneider, Nicolas, Rohner, Chris, Organ, Domitille, Chalopin, Jeramiah J., Smith, Mark, Robinson, Rosemary A., Dorrington, Gerdol, Marco, Bronwen, Aken, Maria Assunta, Biscotti, Marco, Barucca, Denis, Baurain, Aaron M., Berlin, Gregory L., Blatch, Francesco, Buonocore, Thorsten, Burmester, Michael S., Campbell, Adriana, Canapa, John P., Cannon, Alan, Christoffel, DE MORO, Gianluca, Adrienne L., Edkin, Lin, Fan, Anna Maria, Fausto, Nathalie, Feiner, Mariko, Forconi, Junaid, Gamieldien, Sante, Gnerre, Andreas, Gnirke, Jared V., Goldstone, Wilfried, Haerty, Mark E., Hahn, Uljana, Hesse, Steve, Hoffmann, Jeremy, Johnson, Sibel I., Karchner, Shigehiro, Kuraku, Marcia, Lara, Joshua Z., Levin, Gary W., Litman, Evan, Mauceli, Tsutomu, Miyake, M., Gail Mueller, David R., Nelson, Anne, Nitsche, Ettore, Olmo, Tatsuya, Ota, Pallavicini, Alberto, Sumir, Panji, Barbara, Picone, Chris P., Ponting, Sonja J., Prohaska, Dariusz, Przybylski, Nil Ratan, Saha, Vydianathan, Ravi, Filipe J., Ribeiro, Tatjana Sauka, Spengler, Giuseppe, Scapigliati, Stephen M. J., Searle, Ted, Sharpe, Oleg, Simakov, Peter F., Stadler, John J., Stegeman, Kenta, Sumiyama, Diana, Tabbaa, Hakim, Tafer, Jason Turner, Maier, Peter van, Heusden, Simon, White, Louise, William, Mark, Yandell, Henner, Brinkmann, Jean Nicolas, Volff, Clifford J., Tabin, Neil, Shubin, Manfred, Schartl, David B., Jaffe, John H., Postlethwait, Byrappa, Venkatesh, Federica Di, Palma, Eric S., Lander, Axel, Meyer, and Kerstin Lindblad, Toh
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0106 biological sciences ,terrestrial environment ,adaptation, ancestry, brain, excretion, finfish, gene expression, genome, immunity, olfaction, phylogenetics, protein, terrestrial environment, tetrapod ,[SDV]Life Sciences [q-bio] ,LATIMERIA-MENADOENSIS ,adaptation ,Chick Embryo ,MITOCHONDRIAL GENOME ,LIVING FOSSIL ,SEQUENCE ,GENES ,MODEL ,TRANSCRIPTION ,CHROMOSOMES ,RETENTION ,CHALUMNAE ,01 natural sciences ,Genome ,Animals, Genetically Modified ,Mice ,poisson ,Coelacanth ,Conserved Sequence ,Phylogeny ,Lungfish ,0303 health sciences ,Multidisciplinary ,biology ,Latimeria ,Fishes ,Genes, Homeobox ,Vertebrate ,Genomics ,Biological Evolution ,phylogenetics ,Enhancer Elements, Genetic ,évolution du génome ,Vertebrates ,excretion ,Comperative genomics ,Living fossil ,olfaction ,Genome evolution ,finfish ,brain ,Molecular Sequence Data ,tetrapod ,010603 evolutionary biology ,Article ,Evolution, Molecular ,03 medical and health sciences ,ddc:570 ,biology.animal ,Animals ,[INFO]Computer Science [cs] ,14. Life underwater ,030304 developmental biology ,Comparative genomics ,ancestry ,génome ,Extremities ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,biology.organism_classification ,immunity ,body regions ,Immunoglobulin M ,Evolutionary biology ,gene expression ,protein ,Sequence Alignment - Abstract
Acquisition and storage of Latimeria chalumnae samples was supported by grants from the African Coelacanth Ecosystem Programme of the South African National Department of Science and Technology. Generation of the Latimeria chalumnae and Protopterus annectens sequences by the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University was supported by grants from the National Human Genome Research Institute (NHGRI). K.L.T. is the recipient of a EURYI award from the European Science Foundation. We would also like to thank the Genomics Sequencing Platform of the Broad Institute for sequencing the L. chalumnae genome and L. chalumnae and P. annectens transcriptomes, S. Ahamada, R. Stobbs and the Association pour le Protection de Gombesa (APG) for their help in obtaining coelacanth samples, Y. Zhao for the use of data from Rana chensinensis, and L. Gaffney, C. Hamilton and J. Westlund for assistance with figure preparation. 10; International audience; The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
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- 2013
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45. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells
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Kendell Clement, Andreas Gnirke, Alexander M. Tsankov, J. Keith Joung, Christina Galonska, Casey A. Gifford, Julie Donaghey, Rahul Karnik, Shengdar Q. Tsai, William Mallard, Veronika Akopian, John L. Rinn, Ramona Pop, Jing Liao, Michael J. Ziller, Hongcang Gu, Alexander Meissner, and Deepak Reyon
- Subjects
DNA (Cytosine-5-)-Methyltransferase 1 ,Methyltransferase ,Cell Survival ,Cellular differentiation ,Bisulfite sequencing ,Gene Expression ,Apoptosis ,Biology ,DNA Methyltransferase 3A ,Epigenesis, Genetic ,Gene Knockout Techniques ,Mice ,Catalytic Domain ,Genetics ,Animals ,Humans ,DNA (Cytosine-5-)-Methyltransferases ,Epigenetics ,Induced pluripotent stem cell ,Cells, Cultured ,Embryonic Stem Cells ,Cell Proliferation ,Epigenomics ,Base Sequence ,urogenital system ,Cell Differentiation ,DNA Methylation ,Embryonic stem cell ,Molecular biology ,Coculture Techniques ,embryonic structures ,DNA methylation ,CpG Islands - Abstract
DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Here we inactivated all three catalytically active DNA methyltransferases (DNMTs) in human embryonic stem cells (ESCs) using CRISPR/Cas9 genome editing to further investigate the roles and genomic targets of these enzymes. Disruption of DNMT3A or DNMT3B individually as well as of both enzymes in tandem results in viable, pluripotent cell lines with distinct effects on the DNA methylation landscape, as assessed by whole-genome bisulfite sequencing. Surprisingly, in contrast to findings in mouse, deletion of DNMT1 resulted in rapid cell death in human ESCs. To overcome this immediate lethality, we generated a doxycycline-responsive tTA-DNMT1* rescue line and readily obtained homozygous DNMT1-mutant lines. However, doxycycline-mediated repression of exogenous DNMT1* initiates rapid, global loss of DNA methylation, followed by extensive cell death. Our data provide a comprehensive characterization of DNMT-mutant ESCs, including single-base genome-wide maps of the targets of these enzymes.
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- 2015
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46. Notch-mediated expansion of cord blood progenitors: maintenance of transcriptional and epigenetic fidelity
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Colleen Delaney, Irwin D. Bernstein, Alexander Meissner, Raphael Gottardo, Patrick Boyle, Bradley E. Bernstein, Andreas Gnirke, Christoph Bock, Sangsoon Woo, and Ann Dahlberg
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Regulation of gene expression ,Genetics ,Cancer Research ,Receptors, Notch ,Transcription, Genetic ,media_common.quotation_subject ,Fidelity ,Hematology ,Biology ,Fetal Blood ,Hematopoietic Stem Cells ,Article ,Epigenesis, Genetic ,Cell biology ,Mice ,Gene Expression Regulation ,Oncology ,Cord blood ,Animals ,Humans ,Epigenetics ,Progenitor cell ,media_common - Abstract
Notch-mediated expansion of cord blood progenitors: maintenance of transcriptional and epigenetic fidelity
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- 2015
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47. Transcription factor binding dynamics during human ESC differentiation
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Hongcang Gu, Alexander Meissner, Alexander M. Tsankov, Veronika Akopian, Andreas Gnirke, Michael J. Ziller, Julie Donaghey, and Ido Amit
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Epigenomics ,Transcription, Genetic ,Cellular differentiation ,Biology ,Article ,Epigenesis, Genetic ,Histones ,Humans ,Cell Lineage ,Induced pluripotent stem cell ,Transcription factor ,Embryonic Stem Cells ,Genetics ,Multidisciplinary ,Genome, Human ,Cell Differentiation ,Epigenome ,DNA Methylation ,Chromatin Assembly and Disassembly ,Embryonic stem cell ,Chromatin ,Cell biology ,Enhancer Elements, Genetic ,DNA methylation ,Germ Layers ,Protein Binding ,Signal Transduction ,Transcription Factors - Abstract
Summary Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage specific behavior of selected factors. In addition to the orchestrated remodeling of the chromatin landscape, we find that the binding of several transcription factors is strongly associated with specific loss of DNA methylation in one germ layer and in many cases a reciprocal gain in the other layers. Taken together, our work shows context-dependent rewiring of transcription factor binding, downstream signaling effectors, and the epigenome during human embryonic stem cell differentiation.
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- 2015
48. Virus genomes reveal factors that spread and sustained the Ebola epidemic
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Kilian Stoecker, Chantal B.E.M. Reusken, Stephen F. Schaffner, Marion Koopmans, Sarah M. Winnicki, Augustine Goba, My V. T. Phan, Lucy Thorne, Michael R. Wiley, Simon Dellicour, Andrew Rambaut, James Qu, Fatorma K. Bolay, Christian T. Happi, Stephen K. Gire, Oliver G. Pybus, Jeffrey R. Kugelman, Bernice Dahn, Pardis C. Sabeti, Marc A. Suchard, Gytis Dudas, Kristian G. Andersen, Gustavo Palacios, Mohamed A. Vandi, Simon J. Watson, Saskia L. Smits, Amadou A. Sall, Isatta Wurie, Miles W. Carroll, Andrew J. Tatem, David A. Matthews, Georgios Pollakis, Sahr M. Gevao, George F. Gao, Philippe Lemey, Filip Bielejec, Shannon L.M. Whitmer, Roman Wölfel, Nuno R. Faria, Jonathan D'ambrozio, Jason T. Ladner, Christine M. Malboeuf, Danny Asogun, Christian B. Matranga, Christophe Fraser, N’Faly Magassouba, Guy Baele, Luke W. Meredith, Robert F. Garry, Ekaete Alice Tobin, Etienne Simon-Loriere, Pierre Formenty, Sophie Duraffour, Jens H. Kuhn, Edward C. Holmes, Paul Kellam, Ousmane Faye, Brima Kargbo, Kendra West, Sarah L Caddy, Dhamari Naidoo, Stuart T. Nichol, Rachel Sealfon, Joshua Quick, Shirlee Wohl, Andreas Gnirke, Matthew Cotten, Mariano Sanchez-Lockhart, Donald S. Grant, Nicholas J. Loman, Trevor Bedford, Antonino Di Caro, Daniel J. Park, Julian A. Hiscox, Sylvia O. Blyden, Stephan Günther, Lawrence Fakoli, Susan D. Pas, Suzanne Mate, Armando Arias, Ian Goodfellow, Bart L. Haagmans, Adrianne Gladden-Young, Joseph W. Diclaro, Nathan L. Yozwiak, Merle L. Gilbert, Umaru Jah, Sakoba Keita, Michael J. Elmore, Jia Lu, John S. Schieffelin, Ute Ströher, Tolbert Nyenswah, Luiz Max Carvalho, Boubacar Diallo, Di Liu, Department of Virology, Virology, Wang, Sarah [0000-0002-9790-7420], Lu, Jia [0000-0003-3995-324X], Meredith, Luke [0000-0002-3802-8290], Goodfellow, Ian [0000-0002-9483-510X], and Apollo - University of Cambridge Repository
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0301 basic medicine ,DYNAMICS ,Internationality ,OUTBREAK ,Climate ,viruses ,medicine.disease_cause ,Genome ,DISEASE ,law.invention ,Disease Outbreaks ,law ,Viral ,Phylogeny ,Molecular Epidemiology ,Travel ,Multidisciplinary ,Geography ,Research Support, Non-U.S. Gov't ,Ebolavirus ,Multidisciplinary Sciences ,Infectious Diseases ,Transmission (mechanics) ,Ebola ,Science & Technology - Other Topics ,Infection ,TRANSMISSION ,HYPERMUTATION ,General Science & Technology ,Genome, Viral ,Biology ,MEASLES ,Virus ,Article ,Sierra leone ,Vaccine Related ,03 medical and health sciences ,SDG 3 - Good Health and Well-being ,Research Support, N.I.H., Extramural ,Biodefense ,SURVEILLANCE ,medicine ,Journal Article ,Humans ,Ebola virus ,Science & Technology ,Prevention ,REAL-TIME ,Outbreak ,Hemorrhagic Fever, Ebola ,Virology ,EVOLUTION ,Emerging Infectious Diseases ,Good Health and Well Being ,030104 developmental biology ,GUINEA ,Linear Models ,Hemorrhagic Fever ,Biological dispersal ,Research Support, U.S. Gov't, Non-P.H.S ,Demography - Abstract
The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics. ispartof: Nature vol:544 issue:7650 pages:309- ispartof: location:England status: published
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- 2017
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49. Multiple introductions of Zika virus into the United States revealed through genomic epidemiology
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Nathan D Grubaugh, Jason T Ladner, Moritz UG Kraemer, Gytis Dudas, Amanda L Tan, Karthik Gangavarapu, Michael R Wiley, Stephen White, Julien Thézé, Diogo M Magnani, Karla Prieto, Daniel Reyes, Andrea Bingham, Lauren M Paul, Refugio Robles-Sikisaka, Glenn Oliveira, Darryl Pronty, Hayden C Metsky, Mary Lynn Baniecki, Kayla G Barnes, Bridget Chak, Catherine A Freije, Adrianne Gladden-Young, Andreas Gnirke, Cynthia Luo, Bronwyn MacInnis, Christian B Matranga, Daniel J Park, James Qu, Stephen F Schaffner, Christopher Tomkins-Tinch, Kendra L West, Sarah M Winnicki, Shirlee Wohl, Nathan L Yozwiak, Joshua Quick, Joseph R Fauver, Kamran Khan, Shannon E Brent, Robert C Reiner, Paola N Lichtenberger, Michael Ricciardi, Varian K Bailey, David I Watkins, Marshall R Cone, Edgar W Kopp, Kelly N Hogan, Andrew C Cannons, Reynald Jean, Robert F Garry, Nicholas J Loman, Nuno R Faria, Mario C Porcelli, Chalmers Vasquez, Elyse R Nagle, Derek AT Cummings, Danielle Stanek, Andrew Rambaut, Mariano Sanchez-Lockhart, Pardis C Sabeti, Leah D Gillis, Scott F Michael, Trevor Bedford, Oliver G Pybus, Sharon Isern, Gustavo Palacios, and Kristian G Andersen
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0303 health sciences ,medicine.medical_specialty ,Direct sequencing ,030231 tropical medicine ,Genetic data ,Zoology ,Outbreak ,Biology ,biology.organism_classification ,Virology ,3. Good health ,law.invention ,Zika virus ,03 medical and health sciences ,0302 clinical medicine ,Transmission (mechanics) ,law ,Epidemiology ,Pandemic ,medicine ,High incidence ,030304 developmental biology - Abstract
Zika virus (ZIKV) is currently causing an unprecedented pandemic linked to severe congenital syndromes1,2. In July 2016, mosquito-borne ZIKV transmission was first reported in the continental United States and since then, hundreds of locally acquired infections have been described3. To gain insights into the timing, source, and likely route(s) of introduction into the United States, we tracked the virus from its first detection in Miami, Florida by direct sequencing of ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We detected at least four distinct ZIKV introductions and estimate that 11-52 introductions contributed to the outbreak in Florida. Furthermore, our data suggests that ZIKV transmission likely started in the spring of 2016 - several months before initial detection. By analyzing epidemiological, surveillance, and genetic data, we discovered that several spatially distinct ZIKV transmission zones were likely portions of the same outbreak, rather than isolated events. Our analyses show that most introductions are linked to the Caribbean, which is supported by the high incidence rates and traffic, especially via cruises, from the region into Miami. By comparing mosquito abundance and travel capacity across the United States, we find that southern Florida is especially vulnerable to ZIKV introductions and at risk of repeat occurrences. By tracking the virus from its initial introduction into the United States, we provide a deeper understanding of how ZIKV initiates and sustains transmission in new regions.
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- 2017
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50. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer
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Andreas Gnirke, Kendell Clement, Hongcang Gu, Alexander Meissner, Davide Cacchiarelli, Franziska Michor, Julie Donaghey, Zachary D. Smith, Jiantao Shi, Smith, Zachary D, Shi, Jiantao, Gu, Hongcang, Donaghey, Julie, Clement, Kendell, Cacchiarelli, Davide, Gnirke, Andrea, Michor, Franziska, and Meissner, Alexander
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0301 basic medicine ,Male ,Placenta ,Biology ,Epigenesis, Genetic ,03 medical and health sciences ,Mice ,Pregnancy ,Neoplasms ,Ectoderm ,Animals ,Humans ,Cell Lineage ,Cancer epigenetics ,Epigenetics ,Promoter Regions, Genetic ,Genetics ,Regulation of gene expression ,Multidisciplinary ,Gene Expression Regulation, Developmental ,Methylation ,Epigenome ,DNA Methylation ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,Blastocyst ,CpG site ,Epiblast ,DNA methylation ,CpG Islands ,Female ,Germ Layers - Abstract
In mammals, the canonical somatic DNA methylation landscape is established upon specification of the embryo proper and subsequently disrupted within many cancer types1–4. However, the underlying mechanisms that direct this genome-scale transformation remain elusive, with no clear model for its systematic acquisition or potential developmental utility5,6. Here, we analysed global remethylation from the mouse preimplantation embryo into the early epiblast and extraembryonic ectoderm. We show that these two states acquire highly divergent genomic distributions with substantial disruption of bimodal, CpG density-dependent methylation in the placental progenitor7,8. The extraembryonic epigenome includes specific de novo methylation at hundreds of embryonically protected CpG island promoters, particularly those that are associated with key developmental regulators and are orthologously methylated across most human cancer types9. Our data suggest that the evolutionary innovation of extraembryonic tissues may have required co-option of DNA methylation-based suppression as an alternative to regulation by Polycomb-group proteins, which coordinate embryonic germ-layer formation in response to extraembryonic cues10. Moreover, we establish that this decision is made deterministically, downstream of promiscuously used—and frequently oncogenic—signalling pathways, via a novel combination of epigenetic cofactors. Methylation of developmental gene promoters during tumorigenesis may therefore reflect the misappropriation of an innate trajectory and the spontaneous reacquisition of a latent, developmentally encoded epigenetic landscape.
- Published
- 2017
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