30 results on '"Sole Gatto"'
Search Results
2. Comprehensive RNA-Sequencing Analysis in Serum and Muscle Reveals Novel Small RNA Signatures with Biomarker Potential for DMD
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Anna M.L. Coenen-Stass, Helena Sork, Sole Gatto, Caroline Godfrey, Amarjit Bhomra, Kaarel Krjutškov, Jonathan R. Hart, Jakub O. Westholm, Liz O’Donovan, Andreas Roos, Hanns Lochmüller, Pier Lorenzo Puri, Samir EL Andaloussi, Matthew J.A. Wood, and Thomas C. Roberts
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Therapeutics. Pharmacology ,RM1-950 - Abstract
Extracellular small RNAs (sRNAs), including microRNAs (miRNAs), are promising biomarkers for diseases such as Duchenne muscular dystrophy (DMD), although their biological relevance is largely unknown. To investigate the relationship between intracellular and extracellular sRNA levels on a global scale, we performed sRNA sequencing in four muscle types and serum from wild-type, dystrophic mdx, and mdx mice in which dystrophin protein expression was restored by exon skipping. Differentially abundant sRNAs were identified in serum (mapping to miRNA, small nuclear RNA [snRNA], and PIWI-interacting RNA [piRNA] loci). One novel candidate biomarker, miR-483, was increased in both mdx serum and muscle, and also elevated in DMD patient sera. Dystrophin restoration induced global shifts in miRNA (including miR-483) and snRNA-fragment abundance toward wild-type levels. Specific serum piRNA-like sRNAs also responded to exon skipping therapy. Absolute miRNA expression in muscle was positively correlated with abundance in the circulation, although multiple highly expressed miRNAs in muscle were not elevated in mdx serum, suggesting that both passive and selective release mechanisms contribute to serum miRNA levels. In conclusion, this study has revealed new insights into the sRNA biology of dystrophin deficiency and identified novel DMD biomarkers. Keywords: small RNA sequencing, microRNA, piRNA, Duchenne muscular dystrophy, extracellular miRNA
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- 2018
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3. Dynamics of cellular states of fibro-adipogenic progenitors during myogenesis and muscular dystrophy
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Barbora Malecova, Sole Gatto, Usue Etxaniz, Magda Passafaro, Amy Cortez, Chiara Nicoletti, Lorenzo Giordani, Alessio Torcinaro, Marco De Bardi, Silvio Bicciato, Francesca De Santa, Luca Madaro, and Pier Lorenzo Puri
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Science - Abstract
Fibro-adipogenic progenitors (FAPs) resident in skeletal muscle are involved in both regeneration and maladaptive processes. Here, the authors identify subpopulations of FAPs with biological activities implicated in physiological muscle repair that are altered in pathological conditions such as muscular dystrophies.
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- 2018
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4. Muscle-relevant genes marked by stable H3K4me2/3 profiles and enriched MyoD binding during myogenic differentiation.
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Huanhuan Cui, Vikas Bansal, Marcel Grunert, Barbora Malecova, Alessandra Dall'Agnese, Lucia Latella, Sole Gatto, Tammy Ryan, Kerstin Schulz, Wei Chen, Cornelia Dorn, Pier Lorenzo Puri, and Silke R Sperling
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Medicine ,Science - Abstract
Post-translational modifications of histones play a key role in the regulation of gene expression during development and differentiation. Numerous studies have shown the dynamics of combinatorial regulation by transcription factors and histone modifications, in the sense that different combinations lead to distinct expression outcomes. Here, we investigated gene regulation by stable enrichment patterns of histone marks H3K4me2 and H3K4me3 in combination with the chromatin binding of the muscle tissue-specific transcription factor MyoD during myogenic differentiation of C2C12 cells. Using k-means clustering, we found that specific combinations of H3K4me2/3 profiles over and towards the gene body impact on gene expression and marks a subset of genes important for muscle development and differentiation. By further analysis, we found that the muscle key regulator MyoD was significantly enriched on this subset of genes and played a repressive role during myogenic differentiation. Among these genes, we identified the pluripotency gene Patz1, which is repressed during myogenic differentiation through direct binding of MyoD to promoter elements. These results point to the importance of integrating histone modifications and MyoD chromatin binding for coordinated gene activation and repression during myogenic differentiation.
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- 2017
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5. TBP/TFIID-dependent activation of MyoD target genes in skeletal muscle cells
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Barbora Malecova, Alessandra Dall'Agnese, Luca Madaro, Sole Gatto, Paula Coutinho Toto, Sonia Albini, Tammy Ryan, Làszlò Tora, and Pier Lorenzo Puri
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muscle differentiation ,muscle regeneration ,transcription ,myoD ,TBP ,TFIID ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Change in the identity of the components of the transcription pre-initiation complex is proposed to control cell type-specific gene expression. Replacement of the canonical TFIID-TBP complex with TRF3/TBP2 was reported to be required for activation of muscle-gene expression. The lack of a developmental phenotype in TBP2 null mice prompted further analysis to determine whether TBP2 deficiency can compromise adult myogenesis. We show here that TBP2 null mice have an intact regeneration potential upon injury and that TBP2 is not expressed in established C2C12 muscle cell or in primary mouse MuSCs. While TFIID subunits and TBP are downregulated during myoblast differentiation, reduced amounts of these proteins form a complex that is detectable on promoters of muscle genes and is essential for their expression. This evidence demonstrates that TBP2 does not replace TBP during muscle differentiation, as previously proposed, with limiting amounts of TFIID-TBP being required to promote muscle-specific gene expression.
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- 2016
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6. Supplementary Material from The KRASG12C Inhibitor MRTX849 Reconditions the Tumor Immune Microenvironment and Sensitizes Tumors to Checkpoint Inhibitor Therapy
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Peter Olson, James G. Christensen, Kwok-Kin Wong, Adam Pavlicek, Julio Fernandez-Banet, Sole Gatto, Jill Hallin, Lars D. Engstrom, Jiehui Deng, David H. Peng, Lauren Hargis, Ruth Aranda, Niranjan Sudhakar, Andrew Calinisan, Shuai Li, and David M. Briere
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Supplementary Material
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- 2023
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7. Supplementary Data from The KRASG12C Inhibitor MRTX849 Provides Insight toward Therapeutic Susceptibility of KRAS-Mutant Cancers in Mouse Models and Patients
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James G. Christensen, Peter Olson, Pasi A. Jänne, Kyriakos P. Papadopoulos, Piro Lito, Sai-Hong Ignatius Ou, Melissa L. Johnson, Igor I. Rybkin, Matthew A. Marx, Douglas P. Cassidy, Emanuel F. Patricoin, Elisa Baldelli, Mariaelena Pierobon, Jeremy Barton, Richard C. Chao, Karen Velastagui, Adam Pavlicek, Julio Fernandez-Banet, Sole Gatto, Yaohua Xue, Guy P. Vigers, John P. Fischer, Jay B. Fell, Michael R. Burkard, Joshua A. Ballard, Brian R. Baer, Vickie Bowcut, Niranjan Sudhakar, David M. Briere, Ruth Aranda, Andrew Calinisan, Lauren Hargis, Lars D. Engstrom, and Jill Hallin
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Supplementary Composite Figure File
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- 2023
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8. Data from The KRASG12C Inhibitor MRTX849 Reconditions the Tumor Immune Microenvironment and Sensitizes Tumors to Checkpoint Inhibitor Therapy
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Peter Olson, James G. Christensen, Kwok-Kin Wong, Adam Pavlicek, Julio Fernandez-Banet, Sole Gatto, Jill Hallin, Lars D. Engstrom, Jiehui Deng, David H. Peng, Lauren Hargis, Ruth Aranda, Niranjan Sudhakar, Andrew Calinisan, Shuai Li, and David M. Briere
- Abstract
KRASG12C inhibitors, including MRTX849, are promising treatment options for KRAS-mutant non–small cell lung cancer (NSCLC). PD-1 inhibitors are approved in NSCLC; however, strategies to enhance checkpoint inhibitor therapy (CIT) are needed. KRASG12C mutations are smoking-associated transversion mutations associated with high tumor mutation burden, PD-L1 positivity, and an immunosuppressive tumor microenvironment. To evaluate the potential of MRTX849 to augment CIT, its impact on immune signaling and response to CIT was evaluated. In human tumor xenograft models, MRTX849 increased MHC class I protein expression and decreased RNA and/or plasma protein levels of immunosuppressive factors. In a KrasG12C-mutant CT26 syngeneic mouse model, MRTX849 decreased intratumoral myeloid-derived suppressor cells and increased M1-polarized macrophages, dendritic cells, CD4+, and CD8+ T cells. Similar results were observed in lung KrasG12C-mutant syngeneic and a genetically engineered mouse (GEM) model. In the CT26 KrasG12C model, MRTX849 demonstrated marked tumor regression when tumors were established in immune-competent BALB/c mice; however, the effect was diminished when tumors were grown in T-cell–deficient nu/nu mice. Tumors progressed following anti–PD-1 or MRTX849 single-agent treatment in immune-competent mice; however, combination treatment demonstrated durable, complete responses (CRs). Tumors did not reestablish in the same mice that exhibited durable CRs when rechallenged with tumor cell inoculum, demonstrating these mice developed adaptive antitumor immunity. In a GEM model, treatment with MRTX849 plus anti–PD-1 led to increased progression-free survival compared with either single agent alone. These data demonstrate KRAS inhibition reverses an immunosuppressive tumor microenvironment and sensitizes tumors to CIT through multiple mechanisms.
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- 2023
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9. Figures S1-S7 from The KRASG12C Inhibitor MRTX849 Reconditions the Tumor Immune Microenvironment and Sensitizes Tumors to Checkpoint Inhibitor Therapy
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Peter Olson, James G. Christensen, Kwok-Kin Wong, Adam Pavlicek, Julio Fernandez-Banet, Sole Gatto, Jill Hallin, Lars D. Engstrom, Jiehui Deng, David H. Peng, Lauren Hargis, Ruth Aranda, Niranjan Sudhakar, Andrew Calinisan, Shuai Li, and David M. Briere
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Figures S1-S7
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- 2023
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10. Data from The KRASG12C Inhibitor MRTX849 Provides Insight toward Therapeutic Susceptibility of KRAS-Mutant Cancers in Mouse Models and Patients
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James G. Christensen, Peter Olson, Pasi A. Jänne, Kyriakos P. Papadopoulos, Piro Lito, Sai-Hong Ignatius Ou, Melissa L. Johnson, Igor I. Rybkin, Matthew A. Marx, Douglas P. Cassidy, Emanuel F. Patricoin, Elisa Baldelli, Mariaelena Pierobon, Jeremy Barton, Richard C. Chao, Karen Velastagui, Adam Pavlicek, Julio Fernandez-Banet, Sole Gatto, Yaohua Xue, Guy P. Vigers, John P. Fischer, Jay B. Fell, Michael R. Burkard, Joshua A. Ballard, Brian R. Baer, Vickie Bowcut, Niranjan Sudhakar, David M. Briere, Ruth Aranda, Andrew Calinisan, Lauren Hargis, Lars D. Engstrom, and Jill Hallin
- Abstract
Despite decades of research, efforts to directly target KRAS have been challenging. MRTX849 was identified as a potent, selective, and covalent KRASG12C inhibitor that exhibits favorable drug-like properties, selectively modifies mutant cysteine 12 in GDP-bound KRASG12C, and inhibits KRAS-dependent signaling. MRTX849 demonstrated pronounced tumor regression in 17 of 26 (65%) KRASG12C-positive cell line– and patient-derived xenograft models from multiple tumor types, and objective responses have been observed in patients with KRASG12C-positive lung and colon adenocarcinomas. Comprehensive pharmacodynamic and pharmacogenomic profiling in sensitive and partially resistant nonclinical models identified mechanisms implicated in limiting antitumor activity including KRAS nucleotide cycling and pathways that induce feedback reactivation and/or bypass KRAS dependence. These factors included activation of receptor tyrosine kinases (RTK), bypass of KRAS dependence, and genetic dysregulation of cell cycle. Combinations of MRTX849 with agents that target RTKs, mTOR, or cell cycle demonstrated enhanced response and marked tumor regression in several tumor models, including MRTX849-refractory models.Significance:The discovery of MRTX849 provides a long-awaited opportunity to selectively target KRASG12C in patients. The in-depth characterization of MRTX849 activity, elucidation of response and resistance mechanisms, and identification of effective combinations provide new insight toward KRAS dependence and the rational development of this class of agents.See related commentary by Klempner and Hata, p. 20.This article is highlighted in the In This Issue feature, p. 1
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- 2023
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11. Discovery and preclinical evaluation of anti-miR-17 oligonucleotide RGLS4326 for the treatment of polycystic kidney disease
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Michael Kim, Mandeep Takhar, S. Neben, John R. Androsavich, Tania Valencia, Vishal Patel, Philip Bentley, Kara Kersjes, Scott Davis, Edmund C. Lee, Tiffany Chu, Randy Soriano, Jian Li, Sole Gatto, Kai Liu, Salma Sarwary, Andrea Flaten, Adam Pavlicek, Steven Lockton, Matanel Yheskel, Charles R. Allerson, Wright Timothy, Julia Kaplan, Graham Jang, Tate Owen, and Annelie Schairer
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0301 basic medicine ,Male ,Oligonucleotides ,General Physics and Astronomy ,Disease ,urologic and male genital diseases ,0302 clinical medicine ,Polycystic kidney disease ,Medicine ,Cyst ,Gene Regulatory Networks ,Tissue Distribution ,lcsh:Science ,Kidney ,Polycystic Kidney Diseases ,Multidisciplinary ,Pharmaceutics ,female genital diseases and pregnancy complications ,3. Good health ,medicine.anatomical_structure ,Kidney Tubules ,030220 oncology & carcinogenesis ,miRNAs ,Science ,Autosomal dominant polycystic kidney disease ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Polysome ,Animals ,Humans ,RNA, Messenger ,Gene ,Cell Proliferation ,PKD1 ,Base Sequence ,business.industry ,urogenital system ,General Chemistry ,medicine.disease ,Hematopoiesis ,Mice, Inbred C57BL ,Disease Models, Animal ,Macaca fascicularis ,MicroRNAs ,030104 developmental biology ,Cancer research ,lcsh:Q ,business ,HeLa Cells - Abstract
Autosomal dominant polycystic kidney disease (ADPKD), caused by mutations in either PKD1 or PKD2 genes, is one of the most common human monogenetic disorders and the leading genetic cause of end-stage renal disease. Unfortunately, treatment options for ADPKD are limited. Here we report the discovery and characterization of RGLS4326, a first-in-class, short oligonucleotide inhibitor of microRNA-17 (miR-17), as a potential treatment for ADPKD. RGLS4326 is discovered by screening a chemically diverse and rationally designed library of anti-miR-17 oligonucleotides for optimal pharmaceutical properties. RGLS4326 preferentially distributes to kidney and collecting duct-derived cysts, displaces miR-17 from translationally active polysomes, and de-represses multiple miR-17 mRNA targets including Pkd1 and Pkd2. Importantly, RGLS4326 demonstrates a favorable preclinical safety profile and attenuates cyst growth in human in vitro ADPKD models and multiple PKD mouse models after subcutaneous administration. The preclinical characteristics of RGLS4326 support its clinical development as a disease-modifying treatment for ADPKD., Autosomal dominant polycystic kidney disease (ADPKD) is a leading genetic cause of end-stage renal disease with limited treatment options. Here the authors discover and characterize a microRNA inhibitor as a potential treatment for ADPKD.
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- 2019
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12. The KRAS(G12C) Inhibitor MRTX849 Reconditions the Tumor Immune Microenvironment and Sensitizes Tumors to Checkpoint Inhibitor Therapy
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Jill Hallin, Shuai Li, Sole Gatto, Julio Fernandez-Banet, Adam Pavlicek, Lars D. Engstrom, Ruth Aranda, David H. Peng, James G. Christensen, Niranjan Sudhakar, Peter Olson, Andrew Calinisan, Kwok-Kin Wong, Jiehui Deng, Lauren Hargis, and David Briere
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0301 basic medicine ,Cancer Research ,Acetonitriles ,Mutant ,Antineoplastic Agents ,medicine.disease_cause ,Article ,Piperazines ,law.invention ,Proto-Oncogene Proteins p21(ras) ,03 medical and health sciences ,Mice ,0302 clinical medicine ,law ,Cell Line, Tumor ,medicine ,Tumor Microenvironment ,Animals ,Humans ,Immune Checkpoint Inhibitors ,Cell Proliferation ,Mutation ,Tumor microenvironment ,Lung ,business.industry ,Blood proteins ,Disease Models, Animal ,030104 developmental biology ,medicine.anatomical_structure ,Pyrimidines ,Oncology ,030220 oncology & carcinogenesis ,Cancer research ,Suppressor ,KRAS ,business ,CD8 - Abstract
KRASG12C inhibitors, including MRTX849, are promising treatment options for KRAS-mutant non–small cell lung cancer (NSCLC). PD-1 inhibitors are approved in NSCLC; however, strategies to enhance checkpoint inhibitor therapy (CIT) are needed. KRASG12C mutations are smoking-associated transversion mutations associated with high tumor mutation burden, PD-L1 positivity, and an immunosuppressive tumor microenvironment. To evaluate the potential of MRTX849 to augment CIT, its impact on immune signaling and response to CIT was evaluated. In human tumor xenograft models, MRTX849 increased MHC class I protein expression and decreased RNA and/or plasma protein levels of immunosuppressive factors. In a KrasG12C-mutant CT26 syngeneic mouse model, MRTX849 decreased intratumoral myeloid-derived suppressor cells and increased M1-polarized macrophages, dendritic cells, CD4+, and CD8+ T cells. Similar results were observed in lung KrasG12C-mutant syngeneic and a genetically engineered mouse (GEM) model. In the CT26 KrasG12C model, MRTX849 demonstrated marked tumor regression when tumors were established in immune-competent BALB/c mice; however, the effect was diminished when tumors were grown in T-cell–deficient nu/nu mice. Tumors progressed following anti–PD-1 or MRTX849 single-agent treatment in immune-competent mice; however, combination treatment demonstrated durable, complete responses (CRs). Tumors did not reestablish in the same mice that exhibited durable CRs when rechallenged with tumor cell inoculum, demonstrating these mice developed adaptive antitumor immunity. In a GEM model, treatment with MRTX849 plus anti–PD-1 led to increased progression-free survival compared with either single agent alone. These data demonstrate KRAS inhibition reverses an immunosuppressive tumor microenvironment and sensitizes tumors to CIT through multiple mechanisms.
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- 2021
13. The KRAS
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Jill, Hallin, Lars D, Engstrom, Lauren, Hargis, Andrew, Calinisan, Ruth, Aranda, David M, Briere, Niranjan, Sudhakar, Vickie, Bowcut, Brian R, Baer, Joshua A, Ballard, Michael R, Burkard, Jay B, Fell, John P, Fischer, Guy P, Vigers, Yaohua, Xue, Sole, Gatto, Julio, Fernandez-Banet, Adam, Pavlicek, Karen, Velastagui, Richard C, Chao, Jeremy, Barton, Mariaelena, Pierobon, Elisa, Baldelli, Emanuel F, Patricoin, Douglas P, Cassidy, Matthew A, Marx, Igor I, Rybkin, Melissa L, Johnson, Sai-Hong Ignatius, Ou, Piro, Lito, Kyriakos P, Papadopoulos, Pasi A, Jänne, Peter, Olson, and James G, Christensen
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Acetonitriles ,Lung Neoplasms ,Pyrrolidines ,Mice, Nude ,Adenocarcinoma of Lung ,Antineoplastic Agents ,Apoptosis ,Mice, SCID ,Piperazines ,Proto-Oncogene Proteins p21(ras) ,Mice ,Mice, Inbred NOD ,Tumor Cells, Cultured ,Animals ,Humans ,Cell Proliferation ,Mice, Inbred BALB C ,Clinical Trials, Phase I as Topic ,Middle Aged ,Prognosis ,Xenograft Model Antitumor Assays ,Disease Models, Animal ,Pyrimidines ,Mutation ,Female ,Signal Transduction - Abstract
Despite decades of research, efforts to directly target KRAS have been challenging. MRTX849 was identified as a potent, selective, and covalent KRAS
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- 2019
14. Abstract 5684: Drug-anchored in vitro and in vivo CRISPR screens to identify targetable vulnerabilities and modifiers of response to MRTX849 in KRASG12C-mutant models
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Peter D. Olson, Adam Pavlicek, Ruth Aranda, Lars D. Engstrom, Laura Waters, James G. Christensen, Julio Fernandez-Banet, and Sole Gatto
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Neuroblastoma RAS viral oncogene homolog ,Cancer Research ,Mutation ,biology ,medicine.medical_treatment ,Context (language use) ,medicine.disease_cause ,Targeted therapy ,Oncology ,SPRY2 ,Cancer research ,medicine ,biology.protein ,PTEN ,KRAS ,PI3K/AKT/mTOR pathway - Abstract
MRTX849 is a recently described covalent KRASG12C inhibitor in active clinical development in non-small cell lung cancer (NSCLC) and other cancers harboring this mutation. Additional genetic alterations in hallmark pathways are co-incident with KRASG12C mutations in NSCLC and several of these alterations have been shown to contribute to the oncogenic phenotype. The impact of co-occurring genetic alterations on KRAS dependency or response to KRAS targeted therapy is unknown. Evaluation of MRTX849 across a panel of cell and patient-derived xenograft models demonstrated strong single agent activity in the majority of models tested, however, a subset of models were less responsive. A focused sgRNA library targeting ~1,000 genes was tested in MRTX849-anchored CRISPR/Cas9 screens in vitro and in vivo in multiple KRASG12C-mutant cell lines. Several genes that act either upstream or downstream of KRAS were depleted with MRTX849 treatment which illuminated specific targetable vulnerabilities in the context of KRASG12C inhibition. These data provided a catalogue of putative combination targets. sgRNAs targeting EGFR, PTPN11 (SHP2), SOS1, mTOR, CDK1/2/4/6 were all depleted in MRTX849-treated (or vehicle-treated) cell lines or xenograft models. Furthermore, treatment with small molecules targeting selected vulnerabilities confirmed these genetic data. Finally, targeting FGFR1 exhibited context-dependent dropout that may conditionally address receptor tyrosine kinase reactivation following MRTX849 treatment. This observation was further confirmed utilizing the FGFR family inhibitor BGJ398. Further evaluation of dependencies utilizing an integrated analysis of RNAseq data also revealed KRAS regulates and is critically dependent on specific pro-survival genes BCL2L1, MCL1 and BIRC5 (Survivin) for cancer cell viability. On the other hand, loss of tumor suppressors including KEAP1, NF1, CBL, RB1 and PTEN conferred a growth advantage and partial resistance to MRTX849 treatment in selected models. sgRNAs targeting the RAS pathway genes SPRY2 and NRAS were also enriched providing additional insight into the wiring of KRAS mutant tumors and adaptive response to KRASG12C inhibition. These data provide key insight into the genes that mediate the mechanism of action of, as well as confer partial resistance to, MRTX849, and identify combination targets that augment the anti-tumor effect of MRTX849. Citation Format: Lars D. Engstrom, Laura Waters, Sole Gatto, Julio Fernandez-Banet, Ruth Aranda, Adam Pavlicek, James G. Christensen, Peter Olson. Drug-anchored in vitro and in vivo CRISPR screens to identify targetable vulnerabilities and modifiers of response to MRTX849 in KRASG12C-mutant models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5684.
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- 2020
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15. CD6-ALCAM signaling regulates multiple effector/memory T cell functions
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Jeanette Ampudia, William W. Young-Greenwald, Jana Badrani, Sole Gatto, Adam Pavlicek, Taylor Doherty, Stephen Connelly, and Cherie T Ng
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Immunology ,Immunology and Allergy - Abstract
CD6 is a T-cell costimulatory receptor that has been implicated in the pathogenesis of multiple autoimmune and inflammatory diseases. Primarily expressed on CD4 T cells, CD6 promotes immune synapse formation, T-cell activation and T-cell migration via interaction with its ligand activated leukocyte cell adhesion molecule (ALCAM). While the contribution of CD6 to T cell activation has been well described, less is known regarding the role of CD6 on effector and memory T cells (Teff). Thus, to better characterize this, we examined phosphorylation signaling patterns during CD6 co-stimulation together with the impact of CD6 on differentiated Teff functions. Profiling of ~100 phosphorylation targets associated with T-cell receptor signaling revealed that CD6 co-stimulation on T cells activates factors in pathways involved in actin polymerization, motility, integrin activation and T-cell activation. Comparison of Tnaive cells vs. Teff demonstrated differing levels of phosphorylation in response to CD6 stimulation. Furthermore, CD6 signaling on Teff sustained phosphorylation of these pathways at later timepoints compared to CD28 stimulation. Blockade of the CD6 pathway, using the clinically tested anti-CD6 mAb itolizumab during re-stimulation of CD4 Teff cells in the presence of ALCAM, inhibited multiple effector functions including proliferation and changes in blast size. This effect was observed exclusively in the presence of ALCAM, indicating that the effect was specific to blockade of the CD6-ALCAM pathway. These findings demonstrate that the CD6-ALCAM pathway is a key regulator of effector T-cell functions and further support targeting this pathway to directly inhibit both naïve and effector T cell populations.
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- 2020
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16. 767 ACTIVATION OF FXR SUPPRESSES TNFA AND IL-6 SIGNALING PATHWAYS AND IMPROVES COLITIS IN TWO CHRONIC MOUSE MODELS OF IBD
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Karensa L. Douglas, Alison M. Bendele, Alvaro Ortiz, Brandee Wagner, Xueqing Liu, Ken Song, Connor Ohlsen, Nicholas R. Smith, Sole Gatto, Melissa Walker, Nhin Lu, Adam Pavlicek, Robert O'Connell, Jing Qian, Steve Govek, Kyoung-Jin Lee, Pauline Chai, Douglas Zook, Johnny Y. Nagasawa, and Angelica Milik
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Hepatology ,business.industry ,Gastroenterology ,Cancer research ,medicine ,Tumor necrosis factor alpha ,Colitis ,medicine.disease ,business ,Il 6 signaling - Published
- 2020
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17. Denervation-activated STAT3-IL-6 signalling in fibro-adipogenic progenitors promotes myofibres atrophy and fibrosis
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Usue Etxaniz, Sole Gatto, Vittoria Pagliarini, Ricardo Rojas-García, Maria Vittoria Alfonsi, David Sala, Sara Marinelli, Francesca Lugarini, Daisy Proietti, Alessandra Sacco, Lorenzo Giordani, Luca Madaro, Claudio Sette, Pier Lorenzo Puri, Chiara Nicoletti, Magda Passafaro, Marco De Bardi, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Fondazione Santa Lucia [IRCCS], Clinical and Behavioral Neurology [IRCCS Santa Lucia], CIBER de Enfermedades Raras (CIBERER), Centre de recherche en Myologie – U974 SU-INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Department of Biomedicine and Prevention, Università degli Studi di Roma Tor Vergata [Roma], and Sanford Burnham Prebys Medical Discovery Institute
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0301 basic medicine ,Male ,Cancer Research ,Pathology ,[SDV]Life Sciences [q-bio] ,Quadriceps Muscle ,Superoxide Dismutase-1 ,Fibrosis ,Myocyte ,atrophy and fibrosis ,Amyotrophic lateral sclerosis ,Spinal cord injury ,Denervation ,Adipogenesis ,Sciatic Nerve ,Muscle atrophy ,Cell biology ,Muscular Atrophy ,Oncology ,Neuromuscular Agents ,cell biology ,STAT3-IL-6 ,medicine.symptom ,Cell cycle ,Cell death ,Drug resistance ,Gemcitabine ,Nab-paclitaxel ,Pancreatic adenocarcinoma ,Signal Transduction ,STAT3 Transcription Factor ,congenital, hereditary, and neonatal diseases and abnormalities ,medicine.medical_specialty ,Myoblasts, Skeletal ,Mice, Transgenic ,Cardiotoxins ,Cell Line ,Muscular Atrophy, Spinal ,03 medical and health sciences ,Atrophy ,medicine ,Animals ,Humans ,neoplasms ,Spinal Cord Injuries ,Settore BIO/16 - ANATOMIA UMANA ,business.industry ,Interleukin-6 ,Amyotrophic Lateral Sclerosis ,Cell Biology ,Spinal muscular atrophy ,medicine.disease ,digestive system diseases ,Coculture Techniques ,Mice, Inbred C57BL ,Disease Models, Animal ,030104 developmental biology ,Mutation ,business - Abstract
Fibro-adipogenic progenitors (FAPs) are typically activated in response to muscle injury, and establish functional interactions with inflammatory and muscle stem cells (MuSCs) to promote muscle repair. We found that denervation causes progressive accumulation of FAPs, without concomitant infiltration of macrophages and MuSC-mediated regeneration. Denervation-activated FAPs exhibited persistent STAT3 activation and secreted elevated levels of IL-6, which promoted muscle atrophy and fibrosis. FAPs with aberrant activation of STAT3-IL-6 signalling were also found in mouse models of spinal cord injury, spinal muscular atrophy, amyotrophic lateral sclerosis (ALS) and in muscles of ALS patients. Inactivation of STAT3-IL-6 signalling in FAPs effectively countered muscle atrophy and fibrosis in mouse models of acute denervation and ALS (SODG93A mice). Activation of pathogenic FAPs following loss of integrity of neuromuscular junctions further illustrates the functional versatility of FAPs in response to homeostatic perturbations and suggests their potential contribution to the pathogenesis of neuromuscular diseases.
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- 2018
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18. Dynamics of cellular states of fibro-adipogenic progenitors during myogenesis and muscular dystrophy
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Amy Cortez, Chiara Nicoletti, Silvio Bicciato, Lorenzo Giordani, Usue Etxaniz, Luca Madaro, Marco De Bardi, Pier Lorenzo Puri, Barbora Malecova, Alessio Torcinaro, Magda Passafaro, Sole Gatto, and Francesca De Santa
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Male ,0301 basic medicine ,Genetics and Molecular Biology (all) ,physics and astronomy (all) ,Duchenne muscular dystrophy ,Cellular differentiation ,General Physics and Astronomy ,Muscle Development ,Biochemistry ,Mice ,chemistry (all) ,biochemistry ,genetics and molecular biology (all) ,Muscular dystrophy ,lcsh:Science ,Mice, Inbred ICR ,Adipogenesis ,Multidisciplinary ,Myogenesis ,Stem Cells ,Chemistry (all) ,Cell Differentiation ,Flow Cytometry ,Receptor, TIE-2 ,Cell biology ,medicine.anatomical_structure ,medicine.symptom ,congenital, hereditary, and neonatal diseases and abnormalities ,Science ,Vascular Cell Adhesion Molecule-1 ,Inflammation ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Physics and Astronomy (all) ,medicine ,Animals ,Regeneration ,Muscle, Skeletal ,neoplasms ,Sequence Analysis, RNA ,Gene Expression Profiling ,Macrophages ,Regeneration (biology) ,Skeletal muscle ,General Chemistry ,medicine.disease ,digestive system diseases ,Mice, Inbred C57BL ,Muscular Dystrophy, Duchenne ,Gene expression profiling ,030104 developmental biology ,Mice, Inbred mdx ,lcsh:Q ,Biochemistry, Genetics and Molecular Biology (all) - Abstract
Fibro-adipogenic progenitors (FAPs) are currently defined by their anatomical position, expression of non-specific membrane-associated proteins, and ability to adopt multiple lineages in vitro. Gene expression analysis at single-cell level reveals that FAPs undergo dynamic transitions through a spectrum of cell states that can be identified by differential expression levels of Tie2 and Vcam1. Different patterns of Vcam1-negative Tie2high or Tie2low and Tie2low/Vcam1-expressing FAPs are detected during neonatal myogenesis, response to acute injury and Duchenne Muscular Dystrophy (DMD). RNA sequencing analysis identified cell state-specific transcriptional profiles that predict functional interactions with satellite and inflammatory cells. In particular, Vcam1-expressing FAPs, which exhibit a pro-fibrotic expression profile, are transiently activated by acute injury in concomitance with the inflammatory response. Aberrant persistence of Vcam1-expressing FAPs is detected in DMD muscles or upon macrophage depletion, and is associated with muscle fibrosis, thereby revealing how disruption of inflammation-regulated FAPs dynamics leads to a pathogenic outcome., Fibro-adipogenic progenitors (FAPs) resident in skeletal muscle are involved in both regeneration and maladaptive processes. Here, the authors identify subpopulations of FAPs with biological activities implicated in physiological muscle repair that are altered in pathological conditions such as muscular dystrophies.
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- 2018
19. Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells
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Sole, Gatto, Pier Lorenzo, Puri, and Barbora, Malecova
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Quality Control ,Gene Expression Profiling ,Statistics as Topic ,Cell Culture Techniques ,Computational Biology ,Gene Expression ,Cell Separation ,Web Browser ,Flow Cytometry ,Muscle Development ,Real-Time Polymerase Chain Reaction ,Immunophenotyping ,Mice ,Animals ,Cluster Analysis ,Single-Cell Analysis ,Muscle, Skeletal ,Transcriptome ,Biomarkers ,Software - Abstract
Single cell gene expression profiling is a fundamental tool for studying the heterogeneity of a cell population by addressing the phenotypic and functional characteristics of each cell. Technological advances that have coupled microfluidic technologies with high-throughput quantitative RT-PCR analyses have enabled detailed analyses of single cells in various biological contexts. In this chapter, we describe the procedure for isolating the skeletal muscle interstitial cells termed Fibro-Adipogenic Progenitors (FAPs ) and their gene expression profiling at the single cell level. Moreover, we accompany our bench protocol with bioinformatics analysis designed to process raw data as well as to visualize single cell gene expression data. Single cell gene expression profiling is therefore a useful tool in the investigation of FAPs heterogeneity and their contribution to muscle homeostasis.
- Published
- 2017
20. Muscle-relevant genes marked by stable H3K4me2/3 profiles and enriched MyoD binding during myogenic differentiation
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Tammy Ryan, Barbora Malecova, Alessandra Dall’Agnese, Lucia Latella, Marcel Grunert, Wei Chen, Vikas Bansal, Sole Gatto, Pier Lorenzo Puri, Kerstin Schulz, Huanhuan Cui, Cornelia Dorn, and Silke Sperling
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0301 basic medicine ,Cancer Research ,Cellular differentiation ,Organogenesis ,Gene Expression ,lcsh:Medicine ,MyoD ,Muscle Development ,Biochemistry ,Histones ,Myoblasts ,Mice ,Animal Cells ,Morphogenesis ,Medicine and Health Sciences ,Cluster Analysis ,lcsh:Science ,Cells, Cultured ,Connective Tissue Cells ,Genetics ,Regulation of gene expression ,Multidisciplinary ,biology ,PITX2 ,Reverse Transcriptase Polymerase Chain Reaction ,Chromatin binding ,Cell Differentiation ,Muscle Differentiation ,Neoplasm Proteins ,Histone ,Connective Tissue ,Technology Platforms ,Cellular Types ,Anatomy ,Research Article ,Protein Binding ,DNA transcription ,Methylation ,Cell Line ,03 medical and health sciences ,DNA-binding proteins ,Animals ,Humans ,Gene Regulation ,Transcription factor ,MyoD Protein ,Gene Expression Profiling ,Lysine ,lcsh:R ,Biology and Life Sciences ,Proteins ,Cell Biology ,Fibroblasts ,Repressor Proteins ,030104 developmental biology ,Biological Tissue ,Gene Ontology ,HEK293 Cells ,Cardiovascular and Metabolic Diseases ,biology.protein ,H3K4me3 ,lcsh:Q ,Organism Development ,Developmental Biology - Abstract
Post-translational modifications of histones play a key role in the regulation of gene expression during development and differentiation. Numerous studies have shown the dynamics of combinatorial regulation by transcription factors and histone modifications, in the sense that different combinations lead to distinct expression outcomes. Here, we investigated gene regulation by stable enrichment patterns of histone marks H3K4me2 and H3K4me3 in combination with the chromatin binding of the muscle tissue-specific transcription factor MyoD during myogenic differentiation of C2C12 cells. Using k-means clustering, we found that specific combinations of H3K4me2/3 profiles over and towards the gene body impact on gene expression and marks a subset of genes important for muscle development and differentiation. By further analysis, we found that the muscle key regulator MyoD was significantly enriched on this subset of genes and played a repressive role during myogenic differentiation. Among these genes, we identified the pluripotency gene Patz1, which is repressed during myogenic differentiation through direct binding of MyoD to promoter elements. These results point to the importance of integrating histone modifications and MyoD chromatin binding for coordinated gene activation and repression during myogenic differentiation.
- Published
- 2017
21. Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells
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Pier Lorenzo Puri, Barbora Malecova, and Sole Gatto
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0301 basic medicine ,education.field_of_study ,medicine.diagnostic_test ,Population ,Cell ,Skeletal muscle ,Computational biology ,Biology ,Phenotype ,Flow cytometry ,Gene expression profiling ,03 medical and health sciences ,030104 developmental biology ,medicine.anatomical_structure ,Gene expression ,medicine ,Progenitor cell ,education - Abstract
Single cell gene expression profiling is a fundamental tool for studying the heterogeneity of a cell population by addressing the phenotypic and functional characteristics of each cell. Technological advances that have coupled microfluidic technologies with high-throughput quantitative RT-PCR analyses have enabled detailed analyses of single cells in various biological contexts. In this chapter, we describe the procedure for isolating the skeletal muscle interstitial cells termed Fibro-Adipogenic Progenitors (FAPs ) and their gene expression profiling at the single cell level. Moreover, we accompany our bench protocol with bioinformatics analysis designed to process raw data as well as to visualize single cell gene expression data. Single cell gene expression profiling is therefore a useful tool in the investigation of FAPs heterogeneity and their contribution to muscle homeostasis.
- Published
- 2017
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22. Abstract LB-C09: The KRASG12C inhibitor MRTX849 reconditions the tumor immune microenvironment and leads to durable complete responses in combination with anti-PD-1 therapy in a syngeneic mouse model
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James G. Christensen, David Briere, Jill Hallin, Adam Pavlicek, Lauren Hargis, Julio Fernandez-Banet, Peter D. Olson, Ruth Aranda, Lars D. Engstrom, Niranjan Sudhakar, Andrew Calinisan, and Sole Gatto
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0301 basic medicine ,Cancer Research ,Tumor microenvironment ,biology ,business.industry ,T cell ,Antigen presentation ,Cancer ,Pembrolizumab ,medicine.disease ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,Oncology ,030220 oncology & carcinogenesis ,Cancer research ,biology.protein ,Medicine ,Adenocarcinoma ,Antibody ,business ,CD8 - Abstract
After decades of research, covalent inhibitors targeting KRASG12C are entering clinical trials. KRASG12C mutations are found in 14% of non-small cell lung cancer (NSCLC) adenocarcinoma as well as several other cancer types at lower frequencies. KRASG12C mutations are smoking-associated transversion mutations that are associated with a relatively high total mutation burden (TMB) and PD-L1 positivity. Although pembrolizumab is clinically active in KRAS-mutant NSCLC, response rates remain modest and strategies to augment the clinical activity of checkpoint inhibitor (CPI) therapy is an area of major clinical investigation. MRTX849 was identified as a potent, selective, and covalent KRASG12C inhibitor presently in clinical development. To evaluate the potential of MRTX849 to augment CPI therapy, the impact of MRTX849 on immune signaling molecules and response to anti-PD-1 therapy was evaluated. In a panel of human xenograft models, MRTX849 increased MHC Class I protein expression and decreased RNA and circulating protein expression of signaling molecules including VEGFA, CXCL1 and CXCL8, demonstrating MRTX849 modulates factors that are implicated in antigen presentation or an immunosuppressive tumor microenvironment through a tumor cell-mediated mechanism. In a CT26 syngeneic mouse model engineered to express KRASG12C, MRTX849 decreased intratumoral immunosuppressive myeloid-derived suppressor cell (MDSC) populations and increased immune-enhancing M1-polarized macrophages, dendritic cells, CD4+ and CD8+ T cell populations when administered as a single agent. These effects were also observed in tumors from MRTX849 plus anti-PD-1 treated mice. In efficacy studies, MRTX849 plus anti-PD-1 antibody treatment resulted in durable, complete responses in six out of ten animals whereas all but one of the tumors eventually progressed in the anti-PD-1 or MRTX849 single agent treatment groups. To further interrogate the mechanism of response to the combination, the six mice with complete responses were re-implanted with CT26KRASG12C cell inoculum and tumors failed to form, demonstrating combination-treated mice developed durable anti-tumor immunity. In summary, these data demonstrate MRTX849 in combination with anti-PD-1 therapy leads to durable complete regressions through an immune-mediated anti-tumor response. Citation Format: David M Briere, Andrew Calinisan, Ruth Aranda, Niranjan Sudhakar, Lauren Hargis, Sole Gatto, Julio Fernandez-Banet, Adam Pavlicek, Lars D Engstrom, Jill Hallin, James G Christensen, Peter Olson. The KRASG12C inhibitor MRTX849 reconditions the tumor immune microenvironment and leads to durable complete responses in combination with anti-PD-1 therapy in a syngeneic mouse model [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr LB-C09. doi:10.1158/1535-7163.TARG-19-LB-C09
- Published
- 2019
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23. Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation
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Anthony D. Schmitt, Julia di Iulio, Amalio Telenti, Ranjan J. Perera, Bing Ren, Zhen Ye, Yarui Diao, Luca Caputo, Sole Gatto, Pier Lorenzo Puri, Chiara Nicoletti, Mattia Forcato, Alessandra Dall’Agnese, and Silvio Bicciato
- Subjects
Transcription, Genetic ,Myoblasts, Skeletal ,trans-differentiation ,Biology ,Muscle Development ,MyoD ,Article ,Cell Line ,Mice ,Structure-Activity Relationship ,03 medical and health sciences ,0302 clinical medicine ,Gene expression ,Animals ,Humans ,cell identity ,chromatin organization ,insulated neighborhoods ,looping interactions ,MYOD ,Enhancer ,Molecular Biology ,Transcription factor ,Gene ,MyoD Protein ,030304 developmental biology ,0303 health sciences ,Binding Sites ,Gene Expression Regulation, Developmental ,Promoter ,Cell Biology ,Fibroblasts ,Cellular Reprogramming ,Chromatin Assembly and Disassembly ,Chromatin ,Cell biology ,Phenotype ,CTCF ,Cell Transdifferentiation ,Nucleic Acid Conformation ,Female ,030217 neurology & neurosurgery ,Protein Binding - Abstract
MYOD-directed fibroblast trans-differentiation into skeletal muscle provides a unique model to investigate how one transcription factor (TF) reconfigures the three-dimensional chromatin architecture to control gene expression, which is otherwise achieved by the combinatorial activities of multiple TFs. Integrative analysis of genome-wide high-resolution chromatin interactions, MYOD and CTCF DNA-binding profile, and gene expression, revealed that MYOD directs extensive re-wiring of interactions involving cis-regulatory and structural genomic elements, including promoters, enhancers and insulated neighborhoods (INs). Re-configured INs were hot-spots of differential interactions, whereby MYOD binding to highly constrained sequences at IN boundaries and/or inside INs leads to alterations of promoter-enhancer interactions to repress cell-of-origin genes and to activate muscle-specific genes. Functional evidence shows that MYOD-directed re-configuration of chromatin interactions temporally preceded the effect on gene expression and was mediated by direct MYOD-DNA binding. These data illustrate a model whereby a single TF alters multi-loop hubs to drive somatic cell trans-differentiation.
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- 2019
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24. Author response: TBP/TFIID-dependent activation of MyoD target genes in skeletal muscle cells
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Sole Gatto, Sonia Albini, Pier Lorenzo Puri, Barbora Malecova, Laszlo Tora, Alessandra Dall’Agnese, Luca Madaro, Paula Coutinho Toto, and Tammy Ryan
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medicine.anatomical_structure ,Chemistry ,medicine ,Skeletal muscle ,Transcription factor II D ,MyoD ,Gene ,Cell biology - Published
- 2016
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25. Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient
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Maria R. Matarazzo, Juan Sandoval, Dori Huertas, Sebastian Moran, Joaquín Dopazo, Laia Simó-Riudalbas, Sergi Sayols, Karolina Szczesna, Sole Gatto, Manel Esteller, Ignacio Medina, Holger Heyn, Jose V. Sanchez-Mut, and Enrique Vidal
- Subjects
Cancer Research ,transposon ,Primary Immunodeficiency Diseases ,Bisulfite sequencing ,DNMT3B ,DNA methyltransferase ,histone ,Biology ,Epigenesis, Genetic ,X chromosome ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Sulfites ,DNA (Cytosine-5-)-Methyltransferases ,Epigenetics ,Molecular Biology ,RNA-Directed DNA Methylation ,Cell Line, Transformed ,030304 developmental biology ,Genetics ,B-Lymphocytes ,0303 health sciences ,DNA methylation ,Genome, Human ,Immunologic Deficiency Syndromes ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Molecular biology ,whole genome bisulfite sequencing ,Child, Preschool ,Face ,030220 oncology & carcinogenesis ,Mutation ,CpG island ,Illumina Methylation Assay ,Female ,Human genome ,immunodeficiency ,Research Paper - Abstract
The immunodeficiency, centromere instability and facial anomalies (ICF) syndrome is associated to mutations of the DNA methyl-transferase DNMT3B, resulting in a reduction of enzyme activity. Aberrant expression of immune system genes and hypomethylation of pericentromeric regions accompanied by chromosomal instability were determined as alterations driving the disease phenotype. However, so far only technologies capable to analyze single loci were applied to determine epigenetic alterations in ICF patients. In the current study, we performed whole-genome bisulphite sequencing to assess alteration in DNA methylation at base pair resolution. Genome-wide we detected a decrease of methylation level of 42%, with the most profound changes occurring in inactive heterochromatic regions, satellite repeats and transposons. Interestingly, transcriptional active loci and ribosomal RNA repeats escaped global hypomethylation. Despite a genome-wide loss of DNA methylation the epigenetic landscape and crucial regulatory structures were conserved. Remarkably, we revealed a mislocated activity of mutant DNMT3B to H3K4me1 loci resulting in hypermethylation of active promoters. Functionally, we could associate alterations in promoter methylation with the ICF syndrome immunodeficient phenotype by detecting changes in genes related to the B-cell receptor mediated maturation pathway.
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- 2012
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26. Genome-Wide DNA Methylation Analysis Identifies Novel Hypomethylated Non-Pericentromeric Genes with Potential Clinical Implications in ICF Syndrome
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Juan Sandoval, Maria R. Matarazzo, Manel Esteller, Ana B. Crujeiras, Angel Diaz-Lagares, Sole Gatto, Miriam Gagliardi, Laia Simó-Riudalbas, and Universitat de Barcelona
- Subjects
Male ,DNMT3B ,ADN ,Centromere ,lcsh:Medicine ,Biology ,medicine.disease_cause ,Cell Line ,medicine ,Chromosomes, Human ,Humans ,DNA (Cytosine-5-)-Methyltransferases ,lcsh:Science ,Promoter Regions, Genetic ,Gene ,Genetics ,Mutation ,Multidisciplinary ,Genome, Human ,lcsh:R ,Mutació (Biologia) ,Immunologic Deficiency Syndromes ,Genetic Variation ,Reproducibility of Results ,Methylation ,DNA ,Sequence Analysis, DNA ,Fibroblasts ,Mutation (Biology) ,DNA Methylation ,Molecular biology ,Genome-Wide DNA methylation ,Expressió gènica ,CpG site ,Gene Expression Regulation ,Case-Control Studies ,DNA methylation ,Human genome ,lcsh:Q ,CpG Islands ,Female ,Gene expression ,human activities ,DNA hypomethylation ,Research Article - Abstract
Introduction and Results Immunodeficiency, centromeric instability and facial anomalies syndrome (ICF) is a rare autosomal recessive disease, characterized by severe hypomethylation in pericentromeric regions of chromosomes (1, 16 and 9), marked immunodeficiency and facial anomalies. The majority of ICF patients present mutations in the DNMT3B gene, affecting the DNA methyltransferase activity of the protein. In the present study, we have used the Infinium 450K DNA methylation array to evaluate the methylation level of 450,000 CpGs in lymphoblastoid cell lines and untrasformed fibroblasts derived from ICF patients and healthy donors. Our results demonstrate that ICF-specific DNMT3B variants A603T/STP807ins and V699G/R54X cause global DNA hypomethylation compared to wild-type protein. We identified 181 novel differentially methylated positions (DMPs) including subtelomeric and intrachromosomic regions, outside the classical ICF-related pericentromeric hypomethylated positions. Interestingly, these sites were mainly located in intergenic regions and inside the CpG islands. Among the identified hypomethylated CpG-island associated genes, we confirmed the overexpression of three selected genes, BOLL, SYCP2 and NCRNA00221, in ICF compared to healthy controls, which are supposed to be expressed in germ line and silenced in somatic tissues. Conclusions In conclusion, this study contributes in clarifying the direct relationship between DNA methylation defect and gene expression impairment in ICF syndrome, identifying novel direct target genes of DNMT3B. A high percentage of the DMPs are located in the subtelomeric regions, indicating a specific role of DNMT3B in methylating these chromosomal sites. Therefore, we provide further evidence that hypomethylation in specific non-pericentromeric regions of chromosomes might be involved in the molecular pathogenesis of ICF syndrome. The detection of DNA hypomethylation at BOLL, SYCP2 and NCRNA00221 may pave the way for the development of specific clinical biomarkers with the aim to facilitate the identification of ICF patients.
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- 2014
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27. The Role of DNMT3B Mutations in the Pathogenesis of ICF Syndrome
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Sole Gatto, Maurizio D'Esposito, and Maria R. Matarazzo
- Subjects
Regulation of gene expression ,Methyltransferase ,Histone methyltransferase ,DNMT3B ,DNA methylation ,Epigenetics ,Computational biology ,Biology ,DNA methyltransferase ,Chromatin - Abstract
DNA methylation plays an important role in epigenetic signaling, having an impact on gene regulation, chromatin structure, development, and disease. The human genetic disease, called immunodeficiency, centromere instability, facial abnormalities (ICF) syndrome, is one example of the consequence of the impaired setting and maintenance of proper DNA methylation patterns. Here, we review the key properties of the mammalian de novo DNA methyltransferase DNMT3B, whose dysfunction is responsible for the ICF molecular phenotype, and take a closer look at the effects of the reported mutations on its methyltransferase activity. Moreover, we focus on the central role of DNMT3B in the epigenetic signaling network and the key questions still unsolved in the field, such as how this enzyme is targeted to specific genomic regions, leaving some others unmethylated, and how the DNA methylation pattern is modified during development and in response to environmental cues. The emerging models are multifaceted, involving both the intrinsic properties of DNMT3B and the influence of its interaction partners. In this regard, the ICF mutations provide us with a valuable model to understand the molecular properties of this DNA methyltransferase. The current knowledge and the proposed hypothesis about these topics will be summarized.
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- 2012
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28. Variegated silencing throughepigenetic modifications of a large Xq region in a case of balanced X;2translocation with Incontinentia Pigmenti-like phenotype
- Author
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Maria R. Matarazzo, Valentina Ronga, Lucio Nitsch, Ambra Lanzo, Daniela Melis, Generoso Andria, Gerarda Cappuccio, Anna Conti, Antonella Izzo, Maurizio D'Esposito, Rita Genesio, Sole Gatto, Genesio, R, Melis, Daniela, Gatto, S, Izzo, Antonella, Ronga, V, Cappuccio, Gerarda, Lanzo, A, Andria, Generoso, D'Esposito, M, Matarazzo, Mr, Conti, Anna, and Nitsch, Lucio
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Genetics ,Chromosomes, Human, X ,Cancer Research ,Heterochromatin ,Chromosomal translocation ,Incontinentia pigmenti ,DNA Methylation ,Biology ,medicine.disease ,Translocation, Genetic ,Epigenesis, Genetic ,I-kappa B Kinase ,Chromatin ,Histones ,X,autosome translocation, epigenetic silencing, incontinentia pigmenti, IKBKG, PEV-like heterochromatization ,Phenotype ,IKBKG ,DNA methylation ,medicine ,Humans ,Gene silencing ,Gene Silencing ,Incontinentia Pigmenti ,Epigenetics ,Molecular Biology - Abstract
Molecular mechanisms underlying aberrant phenotypes in balanced X;autosome translocations are scarcely understood. We report the case of a de novo reciprocal balanced translocation X;2(q23;q33) presenting phenotypic alterations highly suggestive of Incontinentia Pigmenti (IP) syndrome, a genodermatosis with abnormal skin pigmentation and neurological failure, segregating as X-linked dominant disorder. Through molecular studies, we demonstrated that the altered phenotype could not be ascribed to chromosome microdeletions or to XIST-mediated inactivation of Xq24-qter. Interestingly, we found that the Xq24-qter region, which translocated downstream of the heterochromatic band 2q34, undergoes epigenetic silencing mediated by DNA methylation and histone alterations. Among the downregulated genes, we found the inhibitor of kappa light polypeptide gene enhancer in B cells, kinase gamma (IKBKG/NEMO), the causative gene of IP. We hypothesize that a mosaic functional nullisomy of the translocated genes, through a Position Effect Variegation-like heterochromatization, might be responsible for the proband's phenotypic anomalies. Partial silencing of IKBKG may be responsible for the skin anomalies observed, thereby mimicking the IP pathological condition. In addition to its clinical relevance, this paper addresses fundamental issues related to the chromatin status and nuclear localization of a human euchromatic region translocated proximally to heterochromatin. In conclusion, the study provides new insight into long-range gene silencing mechanisms and their direct impact in human disease.
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- 2011
29. Epigenetic alteration of microRNAs in DNMT3B-mutated patients of ICF syndrome
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Sole Gatto, Maria R. Matarazzo, Maria Strazzullo, Floriana Della Ragione, Margherita Mutarelli, Maurizio D'Esposito, Amelia Cimmino, Muller Fabbri, Alessandro Weisz, and Lorenzo Ferraro
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Cancer Research ,Primary Immunodeficiency Diseases ,DNMT3B ,Biology ,medicine.disease_cause ,Epigenesis, Genetic ,Histones ,Chromosomal Instability ,microRNA ,medicine ,Humans ,Histone code ,Abnormalities, Multiple ,DNA (Cytosine-5-)-Methyltransferases ,Epigenetics ,Molecular Biology ,Genetics ,Mutation ,DNA methylation ,histone marks ,Immunologic Deficiency Syndromes ,Up-Regulation ,Chromatin ,MicroRNAs ,Histone ,ICF syndrome ,Face ,Cancer research ,biology.protein ,CpG Islands - Abstract
Immunodeficiency, Centromeric region instability, Facial anomalies (ICF; OMIM #242860) syndrome, due to mutations in the DNMT3B gene, is characterized by inheritance of aberrant patterns of DNA methylation and heterochromatin defects. Patients show variable agammaglobulinemia and a reduced number of T cells, making them prone to infections and death before adulthood. Other variable symptoms include facial dysmorphism, growth and mental retardation. Despite the recent advances in identifying the dysregulated genes, the molecular mechanisms, which underlie the altered gene expression causing ICF phenotype complexity, are not well understood. Held the recently-shown tight correlation between epigenetics and microRNAs (miRNAs), we searched for miRNAs regulated by DNMT3B activity, comparing cell lines from ICF patients with those from healthy individuals. We observe that eighty-nine miRNAs, some of which involved in immune function, development and neurogenesis, are dysregulated in ICF (LCLs) compared to wild-type cells. Significant DNA hypomethylation of miRNA CpG islands was not observed in cases of miRNA up-regulation in ICF cells, suggesting a more subtle effect of DNMT3B deficiency on their regulation; however, a modification of histone marks, especially H3K27 and H3K4 trimethylation, and H4 acetylation, was observed concomitantly with changes in microRNA expression. Functional correlation between miRNA and mRNA expression of their targets allow us to suppose a regulation either at mRNA level or at protein level. These results provide a better understanding of how DNA methylation and histone code interact to regulate the class of microRNA genes and enable us to predict molecular events possibly contributing to ICF condition.
- Published
- 2010
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30. Epigenomic and transcriptional effects of Dnmt3b mutations in human ICF syndrome-derived B cell lines
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Sole Gatto, Maria R. Matarazzo, Valentina Proserpio, Maurizio D'Esposito, Sarah A. Teichmann, Sylwia Leppert, and Claudia Angelini
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Genetics ,Histone ,biology ,DNMT3B ,Global DNA Methylation Profile ,DNA methylation ,biology.protein ,Epigenetics ,Epigenome ,Methylation ,Epigenomics - Abstract
Immunodeficiency, Centromeric region instability, Facial anomalies (ICF) syndrome (OMIM 242860), is a human autosomic recessive disease due to mutations in the Dnmt3b gene, characterized by in -heritance of aberrant patterns of DNA methylation and heterochromatin defects (1). How mutations in Dnmt3B and the resulting deficiency in DNA methyltransferase activity result mainly in immunode -ficiency has not been clarified yet. Patients show variable agammaglobulinemia and a reduced number of T cells, making them prone to infections and death before adulthood. It is already known that the expression of several genes and microRNAs is deregulated in ICF lymphoblastoid cell lines (LCLs), being both up- and down-regulated (2,3). Surprisingly, subtle but significant reduction of pro-moter methylation was seen in only few analyzed upregulated genes and approximately half of them were marked with loss of repressive histone modifications, particularly H3K27 trimethylation, and gain in transcriptionally active H3K9 acetylation and H3K4 trimethylation marks, while an exten -sive change of histone modifications of upregulated miRNAs was always observed.It is clear that Dnmt3B mutations affect not only DNA methylation, but also several other expres-sion regulators. In order to assess to what extent these mutations affect the epigenetic landscape of the whole genome we examined the global DNA methylation profile using the Infinium assay from Illumina, the genome-wide mapping of 3meK4H3, 3meK27H3 and RNA Polymerase II (Pol II) by chro -matin immunoprecipitation-sequencing (ChIP-seq) and correlated those to mRNA transcriptome (obtained by RNA-seq) and to microRNA expression (by previous microarray results) in ICF and control LCLs. We found a positive correlation between active genes, binding of Pol II and 3meK4H3 binding and an opposite correlation with 3meK27H3 binding and DNA methylation as expected. Moreover, we identified several regions of interest, which are differentially enriched between the patient and the controls. The complete results will be shown in the poster.Beyond its relevance to ICF syndrome, by addressing the impaired DNMT3B functions in abnor-mal epigenome cases and how these reflect to the transcriptomes of the affected cells, these data will provide new insights in the field, unravelling the physiological contribution of DNMT3B to the epigenetic network.
- Published
- 2012
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