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2. Differential Peripheral Blood Glycoprotein Profiles in Symptomatic and Asymptomatic COVID-19

Author

Pickering, Chad, Zhou, Bo, Xu, Gege, Rice, Rachel, Ramachandran, Prasanna, Huang, Hector, Pham, Tho D, Schapiro, Jeffrey M, Cong, Xin, Chakraborty, Saborni, Edwards, Karlie, Reddy, Srinivasa T, Guirgis, Faheem, Wang, Taia T, Serie, Daniel, and Lindpaintner, Klaus

Subjects
Microbiology, Biological Sciences, Sepsis, Hematology, Infectious Diseases, Aetiology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Artificial Intelligence, COVID-19, Chromatography, Liquid, Glycopeptides, Glycoproteins, Humans, SARS-CoV-2, glycoproteomics, biomarkers, glycosylation
Abstract

Glycosylation is the most common form of post-translational modification of proteins, critically affecting their structure and function. Using liquid chromatography and mass spectrometry for high-resolution site-specific quantification of glycopeptides coupled with high-throughput artificial intelligence-powered data processing, we analyzed differential protein glycoisoform distributions of 597 abundant serum glycopeptides and nonglycosylated peptides in 50 individuals who had been seriously ill with COVID-19 and in 22 individuals who had recovered after an asymptomatic course of COVID-19. As additional comparison reference phenotypes, we included 12 individuals with a history of infection with a common cold coronavirus, 16 patients with bacterial sepsis, and 15 healthy subjects without history of coronavirus exposure. We found statistically significant differences, at FDR < 0.05, for normalized abundances of 374 of the 597 peptides and glycopeptides interrogated between symptomatic and asymptomatic COVID-19 patients. Similar statistically significant differences were seen when comparing symptomatic COVID-19 patients to healthy controls (350 differentially abundant peptides and glycopeptides) and common cold coronavirus seropositive subjects (353 differentially abundant peptides and glycopeptides). Among healthy controls and sepsis patients, 326 peptides and glycopeptides were found to be differentially abundant, of which 277 overlapped with biomarkers that showed differential expression between symptomatic COVID-19 cases and healthy controls. Among symptomatic COVID-19 cases and sepsis patients, 101 glycopeptide and peptide biomarkers were found to be statistically significantly abundant. Using both supervised and unsupervised machine learning techniques, we found specific glycoprotein profiles to be strongly predictive of symptomatic COVID-19 infection. LASSO-regularized multivariable logistic regression and K-means clustering yielded accuracies of 100% in an independent test set and of 96% overall, respectively. Our findings are consistent with the interpretation that a majority of glycoprotein modifications observed which are shared among symptomatic COVID-19 and sepsis patients likely represent a generic consequence of a severe systemic immune and inflammatory state. However, there are glycoisoform changes that are specific and particular to severe COVID-19 infection. These may be representative of either COVID-19-specific consequences or susceptibility to or predisposition for a severe course of the disease. Our findings support the potential value of glycoproteomic biomarkers in the biomedical understanding and, potentially, the clinical management of serious acute infectious conditions.

Published
2022

3. Early Detection of Advanced Adenomas and Colorectal Carcinoma by Serum Glycoproteome Profiling

Author

Ding, Nik Sheng, Rice, Rachel, Cong, Xin, Schwarz, Flavio, Serie, Daniel, Wallace, Michael B., Aguilar, Humberto, Brown, Colin C., Clark, Larry E., Jr., Dang, Long, Hellstern, Paul A., Jr., Kimberly, James R., Lankarani, Ali, Misra, Bharat K., Nguyen, Hoa, Pineau, Benoit C., Siegel, Jonathan D., Trawick, Eric P., Desai, Khushbu, Gupta, Samir, May, Folasade P., Xu, Gege, Shaukat, Aasma, and Hommes, Daniel W.

Published
2024
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4. Adaptive immune signature in HER2-positive breast cancer in NCCTG (Alliance) N9831 and NeoALTTO trials

Author

Chumsri, Saranya, Li, Zhuo, Serie, Daniel J., Norton, Nadine, Mashadi-Hossein, Afshin, Tenner, Kathleen, Brauer, Heather Ann, Warren, Sarah, Danaher, Patrick, Colon-Otero, Gerardo, Partridge, Ann H., Carey, Lisa A., Hilbers, Florentine, Van Dooren, Veerle, Holmes, Eileen, Di Cosimo, Serena, Werner, Olena, Huober, Jens Bodo, Dueck, Amylou C., Sotiriou, Christos, Saura, Cristina, Moreno-Aspitia, Alvaro, Knutson, Keith L., Perez, Edith A., and Thompson, E. Aubrey

Published
2022
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5. Potential genetic modifiers of disease risk and age at onset in patients with frontotemporal lobar degeneration and GRN mutations: a genome-wide association study

Author

Pottier, Cyril, Zhou, Xiaolai, Perkerson, Ralph B, Baker, Matt, Jenkins, Gregory D, Serie, Daniel J, Ghidoni, Roberta, Benussi, Luisa, Binetti, Giuliano, de Munain, Adolfo López, Zulaica, Miren, Moreno, Fermin, Le Ber, Isabelle, Pasquier, Florence, Hannequin, Didier, Sánchez-Valle, Raquel, Antonell, Anna, Lladó, Albert, Parsons, Tammee M, Finch, NiCole A, Finger, Elizabeth C, Lippa, Carol F, Huey, Edward D, Neumann, Manuela, Heutink, Peter, Synofzik, Matthis, Wilke, Carlo, Rissman, Robert A, Slawek, Jaroslaw, Sitek, Emilia, Johannsen, Peter, Nielsen, Jørgen E, Ren, Yingxue, van Blitterswijk, Marka, DeJesus-Hernandez, Mariely, Christopher, Elizabeth, Murray, Melissa E, Bieniek, Kevin F, Evers, Bret M, Ferrari, Camilla, Rollinson, Sara, Richardson, Anna, Scarpini, Elio, Fumagalli, Giorgio G, Padovani, Alessandro, Hardy, John, Momeni, Parastoo, Ferrari, Raffaele, Frangipane, Francesca, Maletta, Raffaele, Anfossi, Maria, Gallo, Maura, Petrucelli, Leonard, Suh, EunRan, Lopez, Oscar L, Wong, Tsz H, van Rooij, Jeroen GJ, Seelaar, Harro, Mead, Simon, Caselli, Richard J, Reiman, Eric M, Sabbagh, Marwan Noel, Kjolby, Mads, Nykjaer, Anders, Karydas, Anna M, Boxer, Adam L, Grinberg, Lea T, Grafman, Jordan, Spina, Salvatore, Oblak, Adrian, Mesulam, M-Marsel, Weintraub, Sandra, Geula, Changiz, Hodges, John R, Piguet, Olivier, Brooks, William S, Irwin, David J, Trojanowski, John Q, Lee, Edward B, Josephs, Keith A, Parisi, Joseph E, Ertekin-Taner, Nilüfer, Knopman, David S, Nacmias, Benedetta, Piaceri, Irene, Bagnoli, Silvia, Sorbi, Sandro, Gearing, Marla, Glass, Jonathan, Beach, Thomas G, Black, Sandra E, Masellis, Mario, Rogaeva, Ekaterina, Vonsattel, Jean-Paul, Honig, Lawrence S, Kofler, Julia, Bruni, Amalia C, Snowden, Julie, Mann, David, and Pickering-Brown, Stuart

Subjects
Biomedical and Clinical Sciences, Neurosciences, Clinical Sciences, Frontotemporal Dementia (FTD), Neurodegenerative, Dementia, Genetics, Aging, Prevention, Brain Disorders, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Human Genome, Alzheimer's Disease Related Dementias (ADRD), Acquired Cognitive Impairment, 2.1 Biological and endogenous factors, Aetiology, Neurological, Age of Onset, Aged, Case-Control Studies, Cerebellum, Female, Frontotemporal Lobar Degeneration, Genetic Predisposition to Disease, Genome-Wide Association Study, Glial Cell Line-Derived Neurotrophic Factor Receptors, Humans, Male, Middle Aged, Mutation, Progranulins, RNA, Messenger, Neurology & Neurosurgery, Clinical sciences
Abstract

BackgroundLoss-of-function mutations in GRN cause frontotemporal lobar degeneration (FTLD). Patients with GRN mutations present with a uniform subtype of TAR DNA-binding protein 43 (TDP-43) pathology at autopsy (FTLD-TDP type A); however, age at onset and clinical presentation are variable, even within families. We aimed to identify potential genetic modifiers of disease onset and disease risk in GRN mutation carriers.MethodsThe study was done in three stages: a discovery stage, a replication stage, and a meta-analysis of the discovery and replication data. In the discovery stage, genome-wide logistic and linear regression analyses were done to test the association of genetic variants with disease risk (case or control status) and age at onset in patients with a GRN mutation and controls free of neurodegenerative disorders. Suggestive loci (p

Published
2018

6. Conserved brain myelination networks are altered in Alzheimer's and other neurodegenerative diseases

Author

Allen, Mariet, Wang, Xue, Burgess, Jeremy D, Watzlawik, Jens, Serie, Daniel J, Younkin, Curtis S, Nguyen, Thuy, Malphrus, Kimberly G, Lincoln, Sarah, Carrasquillo, Minerva M, Ho, Charlotte, Chakrabarty, Paramita, Strickland, Samantha, Murray, Melissa E, Swarup, Vivek, Geschwind, Daniel H, Seyfried, Nicholas T, Dammer, Eric B, Lah, James J, Levey, Allan I, Golde, Todd E, Funk, Cory, Li, Hongdong, Price, Nathan D, Petersen, Ronald C, Graff‐Radford, Neill R, Younkin, Steven G, Dickson, Dennis W, Crook, Julia R, Asmann, Yan W, and Ertekin‐Taner, Nilüfer

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Aging, Acquired Cognitive Impairment, Dementia, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Brain Disorders, Neurodegenerative, Alzheimer's Disease, 2.1 Biological and endogenous factors, Aetiology, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Alzheimer Disease, Brain, Cohort Studies, Computational Biology, Female, Gene Expression Regulation, Genetic Predisposition to Disease, Humans, Male, Myelin Sheath, Neurons, Supranuclear Palsy, Progressive, Transcriptome, Proteinopathies, Alzheimer's disease, Progressive supranuclear palsy, Myelination, Coexpression networks, Temporal cortex, Cerebellum, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionComparative transcriptome analyses in Alzheimer's disease (AD) and other neurodegenerative proteinopathies can uncover both shared and distinct disease pathways.MethodsWe analyzed 940 brain transcriptomes including patients with AD, progressive supranuclear palsy (PSP; a primary tauopathy), and control subjects.ResultsWe identified transcriptional coexpression networks implicated in myelination, which were lower in PSP temporal cortex (TCX) compared with AD. Some of these associations were retained even after adjustments for brain cell population changes. These TCX myelination network structures were preserved in cerebellum but they were not differentially expressed in cerebellum between AD and PSP. Myelination networks were downregulated in both AD and PSP, when compared with control TCX samples.DiscussionDownregulation of myelination networks may underlie both PSP and AD pathophysiology, but may be more pronounced in PSP. These data also highlight conservation of transcriptional networks across brain regions and the influence of cell type changes on these networks.

Published
2018

7. Latent trait modeling of tau neuropathology in progressive supranuclear palsy

Author

Kouri, Naomi, Murray, Melissa E., Reddy, Joseph S., Serie, Daniel J., Soto-Beasley, Alexandra, Allen, Mariet, Carrasquillo, Minerva M., Wang, Xue, Castanedes, Monica Casey, Baker, Matthew C., Rademakers, Rosa, Uitti, Ryan J., Graff-Radford, Neill R., Wszolek, Zbigniew K., Schellenberg, Gerard D., Crook, Julia E., Ertekin-Taner, Nilüfer, Ross, Owen A., and Dickson, Dennis W.

Published
2021
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8. A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci

Author

Rand, Kristin A, Song, Chi, Dean, Eric, Serie, Daniel J, Curtin, Karen, Sheng, Xin, Hu, Donglei, Huff, Carol Ann, Bernal-Mizrachi, Leon, Tomasson, Michael H, Ailawadhi, Sikander, Singhal, Seema, Pawlish, Karen, Peters, Edward S, Bock, Cathryn H, Stram, Alex, Van Den Berg, David J, Edlund, Christopher K, Conti, David V, Zimmerman, Todd, Hwang, Amie E, Huntsman, Scott, Graff, John, Nooka, Ajay, Kong, Yinfei, Pregja, Silvana L, Berndt, Sonja I, Blot, William J, Carpten, John, Casey, Graham, Chu, Lisa, Diver, W Ryan, Stevens, Victoria L, Lieber, Michael R, Goodman, Phyllis J, Hennis, Anselm JM, Hsing, Ann W, Mehta, Jayesh, Kittles, Rick A, Kolb, Suzanne, Klein, Eric A, Leske, Cristina, Murphy, Adam B, Nemesure, Barbara, Neslund-Dudas, Christine, Strom, Sara S, Vij, Ravi, Rybicki, Benjamin A, Stanford, Janet L, Signorello, Lisa B, Witte, John S, Ambrosone, Christine B, Bhatti, Parveen, John, Esther M, Bernstein, Leslie, Zheng, Wei, Olshan, Andrew F, Hu, Jennifer J, Ziegler, Regina G, Nyante, Sarah J, Bandera, Elisa V, Birmann, Brenda M, Ingles, Sue A, Press, Michael F, Atanackovic, Djordje, Glenn, Martha J, Cannon-Albright, Lisa A, Jones, Brandt, Tricot, Guido, Martin, Thomas G, Kumar, Shaji K, Wolf, Jeffrey L, Deming Halverson, Sandra L, Rothman, Nathaniel, Brooks-Wilson, Angela R, Rajkumar, S Vincent, Kolonel, Laurence N, Chanock, Stephen J, Slager, Susan L, Severson, Richard K, Janakiraman, Nalini, Terebelo, Howard R, Brown, Elizabeth E, De Roos, Anneclaire J, Mohrbacher, Ann F, Colditz, Graham A, Giles, Graham G, Spinelli, John J, Chiu, Brian C, Munshi, Nikhil C, Anderson, Kenneth C, Levy, Joan, Zonder, Jeffrey A, Orlowski, Robert Z, Lonial, Sagar, Camp, Nicola J, Vachon, Celine M, Ziv, Elad, Stram, Daniel O, and Hazelett, Dennis J

Subjects
Biomedical and Clinical Sciences, Cancer, Clinical Research, Genetics, Rare Diseases, Hematology, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Adult, Aged, Black People, Female, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Middle Aged, Multiple Myeloma, Polycomb Repressive Complex 1, Polymorphism, Single Nucleotide, Protein Serine-Threonine Kinases, Repressor Proteins, Transmembrane Activator and CAML Interactor Protein, White People, Medical and Health Sciences, Epidemiology, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundGenome-wide association studies (GWAS) in European populations have identified genetic risk variants associated with multiple myeloma.MethodsWe performed association testing of common variation in eight regions in 1,318 patients with multiple myeloma and 1,480 controls of European ancestry and 1,305 patients with multiple myeloma and 7,078 controls of African ancestry and conducted a meta-analysis to localize the signals, with epigenetic annotation used to predict functionality.ResultsWe found that variants in 7p15.3, 17p11.2, 22q13.1 were statistically significantly (P < 0.05) associated with multiple myeloma risk in persons of African ancestry and persons of European ancestry, and the variant in 3p22.1 was associated in European ancestry only. In a combined African ancestry-European ancestry meta-analysis, variation in five regions (2p23.3, 3p22.1, 7p15.3, 17p11.2, 22q13.1) was statistically significantly associated with multiple myeloma risk. In 3p22.1, the correlated variants clustered within the gene body of ULK4 Correlated variants in 7p15.3 clustered around an enhancer at the 3' end of the CDCA7L transcription termination site. A missense variant at 17p11.2 (rs34562254, Pro251Leu, OR, 1.32; P = 2.93 × 10-7) in TNFRSF13B encodes a lymphocyte-specific protein in the TNF receptor family that interacts with the NF-κB pathway. SNPs correlated with the index signal in 22q13.1 cluster around the promoter and enhancer regions of CBX7 CONCLUSIONS: We found that reported multiple myeloma susceptibility regions contain risk variants important across populations, supporting the use of multiple racial/ethnic groups with different underlying genetic architecture to enhance the localization and identification of putatively functional alleles.ImpactA subset of reported risk loci for multiple myeloma has consistent effects across populations and is likely to be functional. Cancer Epidemiol Biomarkers Prev; 25(12); 1609-18. ©2016 AACR.

Published
2016

11. 43 Harnessing the power of glycoproteomics: a cutting-edge approach for predicting treatment efficacy in metastatic melanoma with immune checkpoint inhibitors

Author

Najjar, Yana G, primary, Pickering, Chad, additional, Aiyetan, Paul, additional, Xu, Gege, additional, Rice, Rachel, additional, Mitchell, Alan, additional, Bhadra, Ranjan, additional, Dhar, Chirag, additional, Ebert, Lisa M, additional, Brown, Michael P, additional, Tapia-Rico, Gonzalo, additional, Frederick, Dennie, additional, Cong, Xin, additional, Serie, Daniel, additional, Lindpaintner, Klaus, additional, Schwarz, Flavio, additional, Boland, Genevieve M, additional, and Markowitz, Joseph, additional

Published
2023
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12. Transcriptomic analysis to identify genes associated with selective hippocampal vulnerability in Alzheimer’s disease

Author

Crist, Angela M., Hinkle, Kelly M., Wang, Xue, Moloney, Christina M., Matchett, Billie J., Labuzan, Sydney A., Frankenhauser, Isabelle, Azu, Nkem O., Liesinger, Amanda M., Lesser, Elizabeth R., Serie, Daniel J., Quicksall, Zachary S., Patel, Tulsi A., Carnwath, Troy P., DeTure, Michael, Tang, Xiaojia, Petersen, Ronald C., Duara, Ranjan, Graff-Radford, Neill R., Allen, Mariet, Carrasquillo, Minerva M., Li, Hu, Ross, Owen A., Ertekin-Taner, Nilüfer, Dickson, Dennis W., Asmann, Yan W., Carter, Rickey E., and Murray, Melissa E.

Published
2021
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13. Genome-wide association study identifies variants at 16p13 associated with survival in multiple myeloma patients.

Author

Dean, Eric, Hu, Donglei, Martino, Alessandro, Serie, Daniel, Curtin, Karen, Campa, Daniele, Aftab, Blake, Bracci, Paige, Buda, Gabriele, Zhao, Yi, Caswell-Jin, Jennifer, Diasio, Robert, Dumontet, Charles, Dudziński, Marek, Greenberg, Alexandra, Huntsman, Scott, Jamroziak, Krzysztof, Jurczyszyn, Artur, Kumar, Shaji, Atanackovic, Djordje, Glenn, Martha, Cannon-Albright, Lisa, Jones, Brandt, Lee, Adam, Marques, Herlander, Martin, Thomas, Martinez-Lopez, Joaquin, Rajkumar, Vincent, Sainz, Juan, Vangsted, Annette, Wątek, Marzena, Wolf, Jeffrey, Slager, Susan, Camp, Nicola, Canzian, Federico, Vachon, Celine, Ziv, Elad, and Fejerman, Laura

Subjects
Chromosomes, Human, Pair 16, Genome-Wide Association Study, Humans, Kaplan-Meier Estimate, Multiple Myeloma, Polymorphism, Single Nucleotide
Abstract

Here we perform the first genome-wide association study (GWAS) of multiple myeloma (MM) survival. In a meta-analysis of 306 MM patients treated at UCSF and 239 patients treated at the Mayo clinic, we find a significant association between SNPs near the gene FOPNL on chromosome 16p13 and survival (rs72773978; P=6 × 10(-10)). Patients with the minor allele are at increased risk for mortality (HR: 2.65; 95% CI: 1.94-3.58) relative to patients homozygous for the major allele. We replicate the association in the IMMEnSE cohort including 772 patients, and a University of Utah cohort including 318 patients (rs72773978 P=0.044). Using publicly available data, we find that the minor allele was associated with increased expression of FOPNL and increased expression of FOPNL was associated with higher expression of centrosomal genes and with shorter survival. Polymorphisms at the FOPNL locus are associated with survival among MM patients.

Published
2015

14. Genome-wide association study of corticobasal degeneration identifies risk variants shared with progressive supranuclear palsy.

Author

Kouri, Naomi, Ross, Owen A, Dombroski, Beth, Younkin, Curtis S, Serie, Daniel J, Soto-Ortolaza, Alexandra, Baker, Matthew, Finch, Ni Cole A, Yoon, Hyejin, Kim, Jungsu, Fujioka, Shinsuke, McLean, Catriona A, Ghetti, Bernardino, Spina, Salvatore, Cantwell, Laura B, Farlow, Martin R, Grafman, Jordan, Huey, Edward D, Ryung Han, Mi, Beecher, Sherry, Geller, Evan T, Kretzschmar, Hans A, Roeber, Sigrun, Gearing, Marla, Juncos, Jorge L, Vonsattel, Jean Paul G, Van Deerlin, Vivianna M, Grossman, Murray, Hurtig, Howard I, Gross, Rachel G, Arnold, Steven E, Trojanowski, John Q, Lee, Virginia M, Wenning, Gregor K, White, Charles L, Höglinger, Günter U, Müller, Ulrich, Devlin, Bernie, Golbe, Lawrence I, Crook, Julia, Parisi, Joseph E, Boeve, Bradley F, Josephs, Keith A, Wszolek, Zbigniew K, Uitti, Ryan J, Graff-Radford, Neill R, Litvan, Irene, Younkin, Steven G, Wang, Li-San, Ertekin-Taner, Nilüfer, Rademakers, Rosa, Hakonarsen, Hakon, Schellenberg, Gerard D, and Dickson, Dennis W

Subjects
Cerebral Cortex, Humans, Basal Ganglia Diseases, Supranuclear Palsy, Progressive, Neurodegenerative Diseases, Kinesin, SOS1 Protein, tau Proteins, Myelin Proteins, Case-Control Studies, Polymorphism, Single Nucleotide, Adult, Aged, Aged, 80 and over, Middle Aged, Female, Male, Genome-Wide Association Study, Young Adult, RNA, Long Noncoding, and over, Polymorphism, Single Nucleotide, RNA, Long Noncoding, Supranuclear Palsy, Progressive
Abstract

Corticobasal degeneration (CBD) is a neurodegenerative disorder affecting movement and cognition, definitively diagnosed only at autopsy. Here, we conduct a genome-wide association study (GWAS) in CBD cases (n=152) and 3,311 controls, and 67 CBD cases and 439 controls in a replication stage. Associations with meta-analysis were 17q21 at MAPT (P=1.42 × 10(-12)), 8p12 at lnc-KIF13B-1, a long non-coding RNA (rs643472; P=3.41 × 10(-8)), and 2p22 at SOS1 (rs963731; P=1.76 × 10(-7)). Testing for association of CBD with top progressive supranuclear palsy (PSP) GWAS single-nucleotide polymorphisms (SNPs) identified associations at MOBP (3p22; rs1768208; P=2.07 × 10(-7)) and MAPT H1c (17q21; rs242557; P=7.91 × 10(-6)). We previously reported SNP/transcript level associations with rs8070723/MAPT, rs242557/MAPT, and rs1768208/MOBP and herein identified association with rs963731/SOS1. We identify new CBD susceptibility loci and show that CBD and PSP share a genetic risk factor other than MAPT at 3p22 MOBP (myelin-associated oligodendrocyte basic protein).

Published
2015

17. S355 Targeting the Sugar Code: Serum Glycoproteome Profiling for Early Detection of Advanced Adenoma and Colorectal Cancer

Author

Liu, Julia J., primary, Gupta, Samir, additional, Shaukat, Aasma, additional, Ding, Nik Sheng, additional, Pohl, Heiko, additional, Desai, Khushbu, additional, Chandrasekar, Dharini, additional, Guerrier, Christina, additional, Ramachandran, Prasanna, additional, Islas-Rios, Karina, additional, Shipman, Richard D., additional, Čaval, Tomislav, additional, Campbell, Matthew P., additional, Dhar, Chirag, additional, Xu, Gege, additional, Schwarz, Flavio, additional, Serie, Daniel, additional, Dekker, Evelien, additional, Wallace, Michael B., additional, Hommes, Daniel, additional, and May, Folasade P., additional

Published
2023
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18. Inherited variants in regulatory T cell genes and outcome of ovarian cancer.

Author

Goode, Ellen L, DeRycke, Melissa, Kalli, Kimberly R, Oberg, Ann L, Cunningham, Julie M, Maurer, Matthew J, Fridley, Brooke L, Armasu, Sebastian M, Serie, Daniel J, Ramar, Priya, Goergen, Krista, Vierkant, Robert A, Rider, David N, Sicotte, Hugues, Wang, Chen, Winterhoff, Boris, Phelan, Catherine M, Schildkraut, Joellen M, Weber, Rachel P, Iversen, Ed, Berchuck, Andrew, Sutphen, Rebecca, Birrer, Michael J, Hampras, Shalaka, Preus, Leah, Gayther, Simon A, Ramus, Susan J, Wentzensen, Nicolas, Yang, Hannah P, Garcia-Closas, Montserrat, Song, Honglin, Tyrer, Jonathan, Pharoah, Paul PD, Konecny, Gottfried, Sellers, Thomas A, Ness, Roberta B, Sucheston, Lara E, Odunsi, Kunle, Hartmann, Lynn C, Moysich, Kirsten B, and Knutson, Keith L

Subjects
Humans, Ovarian Neoplasms, Genetic Predisposition to Disease, Antigens, CD80, Follow-Up Studies, Gene Expression Regulation, Neoplastic, Polymorphism, Single Nucleotide, Alleles, Quantitative Trait Loci, Aged, Middle Aged, Female, T-Lymphocytes, Regulatory, Genome-Wide Association Study, B7-1 Antigen, Gene Expression Regulation, Neoplastic, Polymorphism, Single Nucleotide, T-Lymphocytes, Regulatory, General Science & Technology
Abstract

Although ovarian cancer is the most lethal of gynecologic malignancies, wide variation in outcome following conventional therapy continues to exist. The presence of tumor-infiltrating regulatory T cells (Tregs) has a role in outcome of this disease, and a growing body of data supports the existence of inherited prognostic factors. However, the role of inherited variants in genes encoding Treg-related immune molecules has not been fully explored. We analyzed expression quantitative trait loci (eQTL) and sequence-based tagging single nucleotide polymorphisms (tagSNPs) for 54 genes associated with Tregs in 3,662 invasive ovarian cancer cases. With adjustment for known prognostic factors, suggestive results were observed among rarer histological subtypes; poorer survival was associated with minor alleles at SNPs in RGS1 (clear cell, rs10921202, p=2.7×10(-5)), LRRC32 and TNFRSF18/TNFRSF4 (mucinous, rs3781699, p=4.5×10(-4), and rs3753348, p=9.0×10(-4), respectively), and CD80 (endometrioid, rs13071247, p=8.0×10(-4)). Fo0r the latter, correlative data support a CD80 rs13071247 genotype association with CD80 tumor RNA expression (p=0.006). An additional eQTL SNP in CD80 was associated with shorter survival (rs7804190, p=8.1×10(-4)) among all cases combined. As the products of these genes are known to affect induction, trafficking, or immunosuppressive function of Tregs, these results suggest the need for follow-up phenotypic studies.

Published
2013

19. Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy

Author

Allen, Mariet, Wang, Xue, Serie, Daniel J., Strickland, Samantha L., Burgess, Jeremy D., Koga, Shunsuke, Younkin, Curtis S., Nguyen, Thuy T., Malphrus, Kimberly G., Lincoln, Sarah J., Alamprese, Melissa, Zhu, Kuixi, Chang, Rui, Carrasquillo, Minerva M., Kouri, Naomi, Murray, Melissa E., Reddy, Joseph S., Funk, Cory, Price, Nathan D., Golde, Todd E., Younkin, Steven G., Asmann, Yan W., Crook, Julia E., Dickson, Dennis W., and Ertekin-Taner, Nilüfer

Published
2018
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20. Coffee consumption and risk of renal cell carcinoma

Author

Antwi, Samuel O., Eckel-Passow, Jeanette E., Diehl, Nancy D., Serie, Daniel J., Custer, Kaitlynn M., Arnold, Michelle L., Wu, Kevin J., Cheville, John C., Thiel, David D., Leibovich, Bradley C., and Parker, Alexander S.

Published
2017

21. Systems biology approach to late-onset Alzheimer's disease genome-wide association study identifies novel candidate genes validated using brain expression data and Caenorhabditis elegans experiments

Author

Mukherjee, Shubhabrata, Russell, Joshua C., Carr, Daniel T., Burgess, Jeremy D., Allen, Mariet, Serie, Daniel J., Boehme, Kevin L., Kauwe, John S.K., Naj, Adam C., Fardo, David W., Dickson, Dennis W., Montine, Thomas J., Ertekin-Taner, Nilufer, Kaeberlein, Matt R., and Crane, Paul K.

Published
2017
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22. A candidate regulatory variant at the TREM gene cluster associates with decreased Alzheimer's disease risk and increased TREML1 and TREM2 brain gene expression

Author

Carrasquillo, Minerva M., Allen, Mariet, Burgess, Jeremy D., Wang, Xue, Strickland, Samantha L., Aryal, Shivani, Siuda, Joanna, Kachadoorian, Michaela L., Medway, Christopher, Younkin, Curtis S., Nair, Asha, Wang, Chen, Chanana, Pritha, Serie, Daniel, Nguyen, Thuy, Lincoln, Sarah, Malphrus, Kimberly G., Morgan, Kevin, Golde, Todd E., Price, Nathan D., White, Charles C., De Jager, Philip L., Bennett, David A., Asmann, Yan W., Crook, Julia E., Petersen, Ronald C., Graff-Radford, Neill R., Dickson, Dennis W., Younkin, Steven G., and Ertekin-Taner, Nilüfer

Published
2017
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26. Supplemental Table 2 from Effects of Age and Immune Landscape on Outcome in HER2-Positive Breast Cancer in the NCCTG N9831 (Alliance) and NSABP B-31 (NRG) Trials

Author

Chumsri, Saranya, primary, Serie, Daniel J., primary, Li, Zhuo, primary, Pogue-Geile, Katherine L., primary, Soyano-Muller, Aixa E., primary, Mashadi-Hossein, Afshin, primary, Warren, Sarah, primary, Lou, Yanyan, primary, Colon-Otero, Gerardo, primary, Knutson, Keith L., primary, Perez, Edith A., primary, Moreno-Aspitia, Alvaro, primary, and Thompson, E. Aubrey, primary

Published
2023
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27. Supplemental Figure 1 from Effects of Age and Immune Landscape on Outcome in HER2-Positive Breast Cancer in the NCCTG N9831 (Alliance) and NSABP B-31 (NRG) Trials

Author

Chumsri, Saranya, primary, Serie, Daniel J., primary, Li, Zhuo, primary, Pogue-Geile, Katherine L., primary, Soyano-Muller, Aixa E., primary, Mashadi-Hossein, Afshin, primary, Warren, Sarah, primary, Lou, Yanyan, primary, Colon-Otero, Gerardo, primary, Knutson, Keith L., primary, Perez, Edith A., primary, Moreno-Aspitia, Alvaro, primary, and Thompson, E. Aubrey, primary

Published
2023
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28. Supplementary Tables from Identification of Novel Variants in Colorectal Cancer Families by High-Throughput Exome Sequencing

Author

DeRycke, Melissa S., primary, Gunawardena, Shanaka R., primary, Middha, Sumit, primary, Asmann, Yan W., primary, Schaid, Daniel J., primary, McDonnell, Shannon K., primary, Riska, Shaun M., primary, Eckloff, Bruce W., primary, Cunningham, Julie M., primary, Fridley, Brooke L., primary, Serie, Daniel J., primary, Bamlet, William R., primary, Cicek, Mine S., primary, Jenkins, Mark A., primary, Duggan, David J., primary, Buchanan, Daniel, primary, Clendenning, Mark, primary, Haile, Robert W., primary, Woods, Michael O., primary, Gallinger, Steven N., primary, Casey, Graham, primary, Potter, John D., primary, Newcomb, Polly A., primary, Le Marchand, Loïc, primary, Lindor, Noralane M., primary, Thibodeau, Stephen N., primary, and Goode, Ellen L., primary

Published
2023
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29. Supplementary Figure 1 from Identification of Novel Variants in Colorectal Cancer Families by High-Throughput Exome Sequencing

Author

DeRycke, Melissa S., primary, Gunawardena, Shanaka R., primary, Middha, Sumit, primary, Asmann, Yan W., primary, Schaid, Daniel J., primary, McDonnell, Shannon K., primary, Riska, Shaun M., primary, Eckloff, Bruce W., primary, Cunningham, Julie M., primary, Fridley, Brooke L., primary, Serie, Daniel J., primary, Bamlet, William R., primary, Cicek, Mine S., primary, Jenkins, Mark A., primary, Duggan, David J., primary, Buchanan, Daniel, primary, Clendenning, Mark, primary, Haile, Robert W., primary, Woods, Michael O., primary, Gallinger, Steven N., primary, Casey, Graham, primary, Potter, John D., primary, Newcomb, Polly A., primary, Le Marchand, Loïc, primary, Lindor, Noralane M., primary, Thibodeau, Stephen N., primary, and Goode, Ellen L., primary

Published
2023
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30. Supplemental Table 3 from Effects of Age and Immune Landscape on Outcome in HER2-Positive Breast Cancer in the NCCTG N9831 (Alliance) and NSABP B-31 (NRG) Trials

Author

Chumsri, Saranya, primary, Serie, Daniel J., primary, Li, Zhuo, primary, Pogue-Geile, Katherine L., primary, Soyano-Muller, Aixa E., primary, Mashadi-Hossein, Afshin, primary, Warren, Sarah, primary, Lou, Yanyan, primary, Colon-Otero, Gerardo, primary, Knutson, Keith L., primary, Perez, Edith A., primary, Moreno-Aspitia, Alvaro, primary, and Thompson, E. Aubrey, primary

Published
2023
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31. Supplementary Figure 2 from Identification of Novel Variants in Colorectal Cancer Families by High-Throughput Exome Sequencing

Author

DeRycke, Melissa S., primary, Gunawardena, Shanaka R., primary, Middha, Sumit, primary, Asmann, Yan W., primary, Schaid, Daniel J., primary, McDonnell, Shannon K., primary, Riska, Shaun M., primary, Eckloff, Bruce W., primary, Cunningham, Julie M., primary, Fridley, Brooke L., primary, Serie, Daniel J., primary, Bamlet, William R., primary, Cicek, Mine S., primary, Jenkins, Mark A., primary, Duggan, David J., primary, Buchanan, Daniel, primary, Clendenning, Mark, primary, Haile, Robert W., primary, Woods, Michael O., primary, Gallinger, Steven N., primary, Casey, Graham, primary, Potter, John D., primary, Newcomb, Polly A., primary, Le Marchand, Loïc, primary, Lindor, Noralane M., primary, Thibodeau, Stephen N., primary, and Goode, Ellen L., primary

Published
2023
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32. Description of supplementary files from Identification of Novel Variants in Colorectal Cancer Families by High-Throughput Exome Sequencing

Author

DeRycke, Melissa S., primary, Gunawardena, Shanaka R., primary, Middha, Sumit, primary, Asmann, Yan W., primary, Schaid, Daniel J., primary, McDonnell, Shannon K., primary, Riska, Shaun M., primary, Eckloff, Bruce W., primary, Cunningham, Julie M., primary, Fridley, Brooke L., primary, Serie, Daniel J., primary, Bamlet, William R., primary, Cicek, Mine S., primary, Jenkins, Mark A., primary, Duggan, David J., primary, Buchanan, Daniel, primary, Clendenning, Mark, primary, Haile, Robert W., primary, Woods, Michael O., primary, Gallinger, Steven N., primary, Casey, Graham, primary, Potter, John D., primary, Newcomb, Polly A., primary, Le Marchand, Loïc, primary, Lindor, Noralane M., primary, Thibodeau, Stephen N., primary, and Goode, Ellen L., primary

Published
2023
Full Text
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33. Supplemental Table 1 from Effects of Age and Immune Landscape on Outcome in HER2-Positive Breast Cancer in the NCCTG N9831 (Alliance) and NSABP B-31 (NRG) Trials

Author

Chumsri, Saranya, primary, Serie, Daniel J., primary, Li, Zhuo, primary, Pogue-Geile, Katherine L., primary, Soyano-Muller, Aixa E., primary, Mashadi-Hossein, Afshin, primary, Warren, Sarah, primary, Lou, Yanyan, primary, Colon-Otero, Gerardo, primary, Knutson, Keith L., primary, Perez, Edith A., primary, Moreno-Aspitia, Alvaro, primary, and Thompson, E. Aubrey, primary

Published
2023
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34. Diagnosing and staging epithelial ovarian cancer by serum glycoproteomic profiling

Author

Dhar, Chirag, primary, Ramachandran, Prasanna, additional, Xu, Gege, additional, Pickering, Chad, additional, Caval, Tomislav, additional, Rice, Rachel, additional, Zhou, Bo, additional, Srinivasan, Apoorva, additional, Hundal, Itati, additional, Cheng, Robert, additional, Aiyetan, Paul, additional, Chu, Chih-Wei, additional, Herzog, Thomas J., additional, Olawaiye, Alexander Babatunde, additional, Czerwieniec, Gregg, additional, Jacob, Francis, additional, Serie, Daniel, additional, Lindpaintner, Klaus, additional, and Schwarz, Flavio, additional

Published
2023
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39. Evaluation of memory endophenotypes for association with CLU, CR1, and PICALM variants in black and white subjects

Author

Pedraza, Otto, Allen, Mariet, Jennette, Kyle, Carrasquillo, Minerva, Crook, Julia, Serie, Daniel, Pankratz, V. Shane, Palusak, Ryan, Nguyen, Thuy, Malphrus, Kimberly, Ma, Li, Bisceglio, Gina, Roberts, Rosebud O., Lucas, John A., Ivnik, Robert J., Smith, Glenn E., Graff-Radford, Neill R., Petersen, Ronald C., Younkin, Steven G., and Ertekin-Taner, Nilüfer

Published
2014
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41. Plasma glycoproteomic biomarkers identify metastatic melanoma patients with reduced clinical benefit from immune checkpoint inhibitor therapy.

Author

Pickering, Chad, Aiyetan, Paul, Gege Xu, Mitchell, Alan, Rice, Rachel, Najjar, Yana G., Markowitz, Joseph, Ebert, Lisa M., Brown, Michael P., Tapia-Rico, Gonzalo, Frederick, Dennie, Xin Cong, Serie, Daniel, Lindpaintner, Klaus, Schwarz, Flavio, and Boland, Genevieve M.

Subjects
IMMUNE checkpoint inhibitors, IPILIMUMAB, ARTIFICIAL intelligence, MELANOMA, BIOMARKERS, METASTASIS, TURNAROUND time
Abstract

The clinical success of immune-checkpoint inhibitors (ICI) in both resected and metastatic melanoma has confirmed the validity of therapeutic strategies that boost the immune system to counteract cancer. However, half of patients with metastatic disease treated with even the most aggressive regimen do not derive durable clinical benefit. Thus, there is a critical need for predictive biomarkers that can identify individuals who are unlikely to benefit with high accuracy so that these patients may be spared the toxicity of treatment without the likely benefit of response. Ideally, such an assay would have a fast turnaround time and minimal invasiveness. Here, we utilize a novel platform that combines mass spectrometry with an artificial intelligence-based data processing engine to interrogate the blood glycoproteome in melanoma patients before receiving ICI therapy. We identify 143 biomarkers that demonstrate a difference in expression between the patients who died within six months of starting ICI treatment and those who remained progression-free for three years. We then develop a glycoproteomic classifier that predicts benefit of immunotherapy (HR=2.7; p=0.026) and achieves a significant separation of patients in an independent cohort (HR=5.6; p=0.027). To understand how circulating glycoproteins may affect efficacy of treatment, we analyze the differences in glycosylation structure and discover a fucosylation signature in patients with shorter overall survival (OS). We then develop a fucosylation-based model that effectively stratifies patients (HR=3.5; p=0.0066). Together, our data demonstrate the utility of plasma glycoproteomics for biomarker discovery and prediction of ICI benefit in patients with metastatic melanoma and suggest that protein fucosylation may be a determinant of anti-tumor immunity. [ABSTRACT FROM AUTHOR]

Published
2023
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42. Replication of progressive supranuclear palsy genome-wide association study identifies SLCO1A2 and DUSP10 as new susceptibility loci

Author

Sanchez-Contreras, Monica Y., Kouri, Naomi, Cook, Casey N., Serie, Daniel J., Heckman, Michael G., Finch, NiCole A., Caselli, Richard J., Uitti, Ryan J., Wszolek, Zbigniew K., Graff-Radford, Neill, Petrucelli, Leonard, Wang, Li-San, Schellenberg, Gerard D., Dickson, Dennis W., Rademakers, Rosa, and Ross, Owen A.

Published
2018
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43. Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci

Author

Allen, Mariet, Burgess, Jeremy D., Ballard, Travis, Serie, Daniel, Wang, Xue, Younkin, Curtis S., Sun, Zhifu, Kouri, Naomi, Baheti, Saurabh, Wang, Chen, Carrasquillo, Minerva M., Nguyen, Thuy, Lincoln, Sarah, Malphrus, Kimberly, Murray, Melissa, Golde, Todd E., Price, Nathan D., Younkin, Steven G., Schellenberg, Gerard D., Asmann, Yan, Ordog, Tamas, Crook, Julia, Dickson, Dennis, and Ertekin-Taner, Nilüfer

Published
2016
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44. Abstract 2799: Peripheral blood glycoproteomic biomarkers as a powerful new tool for the detection of nasopharyngeal carcinoma

Author

Lindpaintner, Klaus, primary, Aye, Thi Thin, additional, Xu, Gege, additional, Rice, Rachel, additional, Mtchell, Alan, additional, Serie, Daniel, additional, Malek, A, additional, Low, LH, additional, Tan, Lp, additional, Low, Ct, additional, Wong, Cy, additional, Sawali, H, additional, Yapp, Yy, additional, and Khoo, As, additional

Published
2022
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46. Novel plasma glycoprotein biomarkers predict progression-free survival in surgically resected clear cell renal cell carcinoma

Author

Serie, Daniel J., primary, Myers, Amanda A., additional, Haehn, Daniela A., additional, Parker, Alexander S., additional, Bajalia, Essa M., additional, Gonzalez, Giovanni A., additional, Li, Qiongyu, additional, Wong, Maurice Yu, additional, Moser, Kaitlynn C., additional, Zhou, Bo, additional, and Thiel, David D., additional

Published
2022
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48. NOVEL PLASMA GLYCOPROTEIN BIOMARKERS PREDICT PROGRESSION-FREE SURVIVAL IN SURGICALLY RESECTED CLEAR CELL RENAL CELL CARCINOMA

Author

Serie, Daniel, primary, Myers, Amanda A, additional, Haehn, Daniela A, additional, Parker, Alexander, additional, Bajalia, Essa, additional, Gonzalez, Giovanni, additional, Li, Qiongyu, additional, Lindpaintner, Klaus, additional, Wong, Maurice Y, additional, Moser, Kaitlynn, additional, Zhou, Bo, additional, and Thiel, David D, additional

Published
2022
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49. Differential Peripheral Blood Glycoprotein Profiles in Symptomatic and Asymptomatic COVID-19

Author

Pickering, Chad, primary, Zhou, Bo, additional, Xu, Gege, additional, Rice, Rachel, additional, Huang, Hector, additional, Pham, Tho, additional, Shapiro, Jeffrey, additional, Cong, Xin, additional, Chakraborty, Saborni, additional, Edwards, Karlie, additional, Reddy, Srinavasa, additional, Giurgis, Faheem, additional, Wang, Taia T., additional, Serie, Daniel, additional, and Lindpaintner, Klaus, additional

Published
2022
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50. 30 Blood-based glycoprotein signatures in advanced non-small-cell lung carcinoma (NSCLC) receiving first-line immune checkpoint blockade

Author

Lindpaintner, Klaus, primary, Cheng, Michael, additional, Prendergast, Jillian, additional, Normington, Karl, additional, Wong, Maurice, additional, Xu, Gege, additional, Cong, Xini, additional, Rice, Rachel, additional, Lawrence, Marissa, additional, Michael, Kesi, additional, and Serie, Daniel, additional

Published
2021
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