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Strober BJ, Tayeb K, Popp J, Qi G, Gordon MG, Perez R, Ye CJ, Battle A. SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models. Genome Biol 2024; 25:28. [PMID: 38254214 PMCID: PMC10801966 DOI: 10.1186/s13059-023-03152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-specific expression quantitative trait loci (eQTLs) from single-cell transcriptomic data. This allows discovery of the contexts or cell types modulating genetic regulation without prior knowledge. Applied to peripheral blood single-cell eQTL data, SURGE contexts capture continuous representations of distinct cell types and groupings of biologically related cell types. We demonstrate the disease-relevance of SURGE context-specific eQTLs using colocalization analysis and stratified LD-score regression.
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Affiliation(s)
- Benjamin J Strober
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Joshua Popp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guanghao Qi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - M Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Richard Perez
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. Genome Biol 2023; 24:236. [PMID: 37858253 PMCID: PMC10588049 DOI: 10.1186/s13059-023-03067-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.
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Affiliation(s)
- Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Research Computing Center, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Vesalius Therapeutics, Cambridge, MA, USA
| | - Anthony Hung
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Department of Statistics, University of Chicago, Chicago, IL, USA.
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Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. bioRxiv 2023:2023.03.03.531029. [PMID: 36945441 PMCID: PMC10028846 DOI: 10.1101/2023.03.03.531029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.
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Affiliation(s)
- Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Research Computing Center, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Vesalius Therapeutics, Cambridge, MA, USA
| | - Anthony Hung
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Department of Statistics, University of Chicago, Chicago, IL, USA
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Arvanitis M, Tayeb K, Strober BJ, Battle A. Redefining tissue specificity of genetic regulation of gene expression in the presence of allelic heterogeneity. Am J Hum Genet 2022; 109:223-239. [PMID: 35085493 PMCID: PMC8874223 DOI: 10.1016/j.ajhg.2022.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 01/05/2022] [Indexed: 01/03/2023] Open
Abstract
Uncovering the functional impact of genetic variation on gene expression is important in understanding tissue biology and the pathogenesis of complex traits. Despite large efforts to map expression quantitative trait loci (eQTLs) across many human tissues, our ability to translate those findings to understanding human disease has been incomplete, and the majority of disease loci are not explained by association with expression of a target gene. Cell-type specificity and the presence of multiple independent causal variants for many eQTLs are potential confounders contributing to the apparent discrepancy with disease loci. In this study, we investigate the tissue specificity of genetic effects on gene expression and the overlap with disease loci while considering the presence of multiple causal variants within and across tissues. We find evidence of pervasive tissue specificity of eQTLs, often masked by linkage disequilibrium that misleads traditional meta-analytic approaches. We propose CAFEH (colocalization and fine-mapping in the presence of allelic heterogeneity), a Bayesian method that integrates genetic association data across multiple traits, incorporating linkage disequilibrium to identify causal variants. CAFEH outperforms previous approaches in colocalization and fine-mapping. Using CAFEH, we show that genes with highly tissue-specific genetic effects are under greater selection, enriched in differentiation and developmental processes, and more likely to be involved in human disease. Last, we demonstrate that CAFEH can efficiently leverage the widespread allelic heterogeneity in genetic regulation of gene expression to prioritize the target tissue in genome-wide association complex trait loci, thereby improving our ability to interpret complex trait genetics.
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Affiliation(s)
- Marios Arvanitis
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21211, USA; Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karl Tayeb
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Benjamin J Strober
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21211, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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Tabesh M, Magliano DJ, Tanamas SK, Surmont F, Bahendeka S, Chiang C, Elgart JF, Gagliardino JJ, Kalra S, Krishnamoorthy S, Luk A, Maegawa H, Motala AA, Pirie F, Ramachandran A, Tayeb K, Vikulova O, Wong J, Shaw JE. Cardiovascular disease management in people with diabetes outside North America and Western Europe in 2006 and 2015. Diabet Med 2019; 36:878-887. [PMID: 30402961 PMCID: PMC6618273 DOI: 10.1111/dme.13858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/02/2018] [Indexed: 01/07/2023]
Abstract
AIM Optimal treatment of cardiovascular disease is essential to decrease mortality among people with diabetes, but information is limited on how actual treatment relates to guidelines. We analysed changes in therapeutic approaches to anti-hypertensive and lipid-lowering medications in people with Type 2 diabetes from 2006 and 2015. METHODS Summary data from clinical services in seven countries outside North America and Western Europe were collected for 39 684 people. Each site summarized individual-level data from outpatient medical records for 2006 and 2015. Data included: demographic information, blood pressure (BP), total cholesterol levels and percentage of people taking statins, anti-hypertensive medication (angiotensin-converting enzyme inhibitors, calcium channel blockers, angiotensin II receptor blockers, thiazide diuretics) and antiplatelet drugs. RESULTS From 2006 to 2015, mean cholesterol levels decreased in six of eight sites (range: -0.5 to -0.2), whereas the proportion with BP levels > 140/90 mmHg increased in seven of eight sites. Decreases in cholesterol paralleled increases in statin use (range: 3.1 to 47.0 percentage points). Overall, utilization of anti-hypertensive medication did not change. However, there was an increase in the use of angiotensin II receptor blockers and a decrease in angiotensin-converting enzyme inhibitors. The percentage of individuals receiving calcium channel blockers and aspirin remained unchanged. CONCLUSIONS Our findings indicate that control of cholesterol levels improved and coincided with increased use of statins. The percentage of people with BP > 140/90 mmHg was higher in 2015 than in 2006. Hypertension treatment shifted from using angiotensin-converting enzyme inhibitors to angiotensin II receptor blockers. Despite the potentially greater tolerability of angiotensin II receptor blockers, there was no associated improvement in BP levels.
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Affiliation(s)
- M. Tabesh
- Baker Heart and Diabetes InstituteMelbourneAustralia
- Department of Epidemiology and Preventive MedicineSchool of Public Health and Preventive MedicineMonash UniversityMelbourneAustralia
| | - D. J. Magliano
- Baker Heart and Diabetes InstituteMelbourneAustralia
- Department of Epidemiology and Preventive MedicineSchool of Public Health and Preventive MedicineMonash UniversityMelbourneAustralia
| | - S. K. Tanamas
- Baker Heart and Diabetes InstituteMelbourneAustralia
| | | | - S. Bahendeka
- MKPGMS‐Uganda Martyrs University & St. Francis Hospital NsambyaKampalaUganda
| | - C.‐E. Chiang
- General Clinical Research CenterTaipei Veterans General HospitalTaipeiTaiwan
| | - J. F. Elgart
- CENEXA. Centro de Endocrinología Experimental y Aplicada (UNLP‐CONICET)La PlataArgentina
| | - J. J. Gagliardino
- CENEXA. Centro de Endocrinología Experimental y Aplicada (UNLP‐CONICET)La PlataArgentina
| | - S. Kalra
- Bharti Research Institute of Diabetes & EndocrinologyBharti HospitalKarnalHaryanaIndia
| | | | - A. Luk
- Department of Medicine and TherapeuticsPrince of Wales HospitalHong Kong SARChina
| | - H. Maegawa
- Shiga University of Medical ScienceShigaJapan
| | - A. A. Motala
- Department of Diabetes and EndocrinologyUniversity of KwaZulu NatalDurbanSouth Africa
| | - F. Pirie
- Department of Diabetes and EndocrinologyUniversity of KwaZulu NatalDurbanSouth Africa
| | | | - K. Tayeb
- Diabetes Center at AlNoor Specialist HospitalMakkahSaudi Arabia
| | - O. Vikulova
- FGBU ‘Endocrinology Research Center’Ministry of HealthMoscowRussia
| | - J. Wong
- Royal Prince Alfred Hospital Diabetes Centre and the University of SydneySydneyAustralia
| | - J. E. Shaw
- Baker Heart and Diabetes InstituteMelbourneAustralia
- Department of Epidemiology and Preventive MedicineSchool of Public Health and Preventive MedicineMonash UniversityMelbourneAustralia
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Strober BJ, Elorbany R, Rhodes K, Krishnan N, Tayeb K, Battle A, Gilad Y. Dynamic genetic regulation of gene expression during cellular differentiation. Science 2019; 364:1287-1290. [PMID: 31249060 PMCID: PMC6623972 DOI: 10.1126/science.aaw0040] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 06/04/2019] [Indexed: 12/12/2022]
Abstract
Genetic regulation of gene expression is dynamic, as transcription can change during cell differentiation and across cell types. We mapped expression quantitative trait loci (eQTLs) throughout differentiation to elucidate the dynamics of genetic effects on cell type-specific gene expression. We generated time-series RNA sequencing data, capturing 16 time points during the differentiation of induced pluripotent stem cells to cardiomyocytes, in 19 human cell lines. We identified hundreds of dynamic eQTLs that change over time, with enrichment in enhancers of relevant cell types. We also found nonlinear dynamic eQTLs, which affect only intermediate stages of differentiation and cannot be found by using data from mature tissues. These fleeting genetic associations with gene regulation may explain some of the components of complex traits and disease. We highlight one example of a nonlinear eQTL that is associated with body mass index.
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Affiliation(s)
- B J Strober
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - R Elorbany
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL 60637, USA
| | - K Rhodes
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - N Krishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - K Tayeb
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - A Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Y Gilad
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
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Tayeb K, Saâdi I, Kharmash M, Hadadi K, El Omari-Alaoui H, El Ghazi E, Mansouri A, Errihani H, Benjaafar N, El Gueddari BK. [Primary squamous cell carcinoma of the breast. Report of three cases]. Cancer Radiother 2002; 6:366-8. [PMID: 12504775 DOI: 10.1016/s1278-3218(02)00258-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Primary squamous cell carcinoma of the breast is a rare neoplasma included in metaplastic breast cancer. The histogenesis remains unknown. Clinical and radiological appearances are not specific. Nodal involvement is rare and hormones receptors are negative. The treatment is based on surgery associated to radiation therapy and chemotherapy. Prognosis seems to be similar to others breast carcinoma. We report three cases of primary squamous cell carcinoma of the breast recruited at National Institute of Oncology with review of the literature.
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Affiliation(s)
- K Tayeb
- Service de radiothérapie, institut national d'oncologie, BP 6213 RI, Rabat, Maroc
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