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Li SY, Zhang N, Zhang H, Wang N, Du YY, Li HN, Huang CS, Li XR. Deciphering the TCF19/miR-199a-5p/SP1/LOXL2 pathway: Implications for breast cancer metastasis and epithelial-mesenchymal transition. Cancer Lett 2024; 597:216995. [PMID: 38851313 DOI: 10.1016/j.canlet.2024.216995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/11/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024]
Abstract
Globally, breast cancer (BC) is the predominant malignancy with a significant death rate due to metastasis. The epithelial-mesenchymal transition (EMT) is a fundamental initiator for metastatic progression. Through advanced computational strategies, TCF19 was identified as a critical EMT-associated gene with diagnostic and prognostic significance in BC, based on a novel EMT score. Molecular details and the pro-EMT impact of the TCF19/miR-199a-5p/SP1/LOXL2 axis were explored in BC cell lines through in vitro validations, and the oncogenic and metastatic potential of TCF19 and LOXL2 were investigated using subcutaneous and tail-vein models. Additionally, BC-specific enrichment of TCF19 and LOXL2 was measured using a distribution landscape driven by diverse genomic analysis techniques. Molecular pathways revealed that TCF19-induced LOXL2 amplification facilitated migratory, invasive, and EMT activities of BC cells in vitro, and promoted the growth and metastatic establishment of xenografts in vivo. TCF19 decreases the expression of miR-199a-5p and alters the nuclear dynamics of SP1, modulating SP1's affinity for the LOXL2 promoter, leading to increased LOXL2 expression and more malignant characteristics in BC cells. These findings unveil a novel EMT-inducing pathway, the TCF19/miR-199a-5P/SP1/LOXL2 axis, highlighting the pivotal role of TCF19 and suggesting potential for novel therapeutic approaches for more focused BC interventions.
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Affiliation(s)
- Shu-Yu Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Nan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, PR China
| | - Ning Wang
- Huzhou Central Hospital, Affiliated Hospital of Zhejiang University, Huzhou, PR China
| | - Ya-Ying Du
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Han-Ning Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China.
| | - Chen-Shen Huang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, PR China.
| | - Xing-Rui Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China.
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Urnikyte A, Masiulyte A, Pranckeniene L, Kučinskas V. Disentangling archaic introgression and genomic signatures of selection at human immunity genes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105528. [PMID: 37977419 DOI: 10.1016/j.meegid.2023.105528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/04/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Pathogens and infectious diseases have imposed exceptionally strong selective pressure on ancient and modern human genomes and contributed to the current variation in many genes. There is evidence that modern humans acquired immune variants through interbreeding with ancient hominins, but the impact of such variants on human traits is not fully understood. The main objectives of this research were to infer the genetic signatures of positive selection that may be involved in adaptation to infectious diseases and to investigate the function of Neanderthal alleles identified within a set of 50 Lithuanian genomes. Introgressed regions were identified using the machine learning tool ArchIE. Recent positive selection signatures were analysed using iHS. We detected high-scoring signals of positive selection at innate immunity genes (EMB, PARP8, HLAC, and CDSN) and evaluated their interactions with the structural proteins of pathogens. Interactions with human immunodeficiency virus (HIV) 1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. Overall, genomic regions introgressed from Neanderthals were shown to be enriched in genes related to immunity, keratinocyte differentiation, and sensory perception.
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Affiliation(s)
- Alina Urnikyte
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
| | - Abigaile Masiulyte
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania
| | - Laura Pranckeniene
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
| | - Vaidutis Kučinskas
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
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Ma X, Wang Q, Sun C, Agarwal I, Wu H, Chen J, Zhao C, Qi G, Teng Q, Yuan C, Yan S, Peng J, Li R, Song K, Zhang Q, Kong B. Targeting TCF19 sensitizes MSI endometrial cancer to anti-PD-1 therapy by alleviating CD8 + T cell exhaustion via TRIM14-IFN-β axis. Cell Rep 2023; 42:112944. [PMID: 37566545 DOI: 10.1016/j.celrep.2023.112944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/25/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Immune checkpoint blockade (ICB) therapies display clinical efficacy in microsatellite instable (MSI) endometrial cancer (EC) treatment, the key mechanism of which is reversing T cell exhaustion and restoration of anti-tumor immunity. Here, we demonstrate that transcription factor 19 (TCF19), one of the most significantly differentially expressed genes between MSI and microsatellite stable (MSS) patients in The Cancer Genome Atlas (TCGA)-EC cohort, is associated with poor prognosis and immune exhaustion signature. Specifically, TCF19 is significantly elevated in MSI EC, which in turn promotes tripartite motif-containing 14 (TRIM14) transcription and correlates with hyperactive signaling of the TANK-binding kinase 1 (TBK1)-interferon regulatory factor 3 (IRF3)-interferon β (IFN-β) pathway. The TCF19-TRIM14 axis promotes tumorigenicity under non-immunological background, and the enhanced downstream secretion of IFN-β facilitates CD8+ T cell exhaustion through cell differentiation reprogramming. Finally, using humanized models, we show that a combination of TCF19 inhibition and ICB therapy demonstrates more effective anti-tumor responses. Together, our study indicates that targeting TCF19 is a potent strategy for alleviating CD8+ T cell exhaustion and synergizing with ICB in tumor treatment.
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Affiliation(s)
- Xinyue Ma
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Qiuman Wang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Chenggong Sun
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Indu Agarwal
- Department of Pathology, Northwestern University, Chicago, IL 60208, USA
| | - Huan Wu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Jingying Chen
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Chen Zhao
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Gonghua Qi
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Qiuli Teng
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Cunzhong Yuan
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Shi Yan
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Jiali Peng
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Rongrong Li
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Qing Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China.
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China; Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China.
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Keller MP, Hudkins KL, Shalev A, Bhatnagar S, Kebede MA, Merrins MJ, Davis DB, Alpers CE, Kimple ME, Attie AD. What the BTBR/J mouse has taught us about diabetes and diabetic complications. iScience 2023; 26:107036. [PMID: 37360692 PMCID: PMC10285641 DOI: 10.1016/j.isci.2023.107036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Human and mouse genetics have delivered numerous diabetogenic loci, but it is mainly through the use of animal models that the pathophysiological basis for their contribution to diabetes has been investigated. More than 20 years ago, we serendipidously identified a mouse strain that could serve as a model of obesity-prone type 2 diabetes, the BTBR (Black and Tan Brachyury) mouse (BTBR T+ Itpr3tf/J, 2018) carrying the Lepob mutation. We went on to discover that the BTBR-Lepob mouse is an excellent model of diabetic nephropathy and is now widely used by nephrologists in academia and the pharmaceutical industry. In this review, we describe the motivation for developing this animal model, the many genes identified and the insights about diabetes and diabetes complications derived from >100 studies conducted in this remarkable animal model.
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Affiliation(s)
- Mark P. Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kelly L. Hudkins
- Department of Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Anath Shalev
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, UK
| | - Sushant Bhatnagar
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, UK
| | - Melkam A. Kebede
- School of Medical Sciences, Faculty of Medicine and Health, Charles Perkins Centre, University of Sydney, Camperdown, Sydney, NSW 2006, Australia
| | - Matthew J. Merrins
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Dawn Belt Davis
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Charles E. Alpers
- Department of Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Michelle E. Kimple
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Immunotherapeutic Value of Transcription Factor 19 (TCF19) Associated with Renal Clear Cell Carcinoma: A Comprehensive Analysis of 33 Human Cancer Cases. JOURNAL OF ONCOLOGY 2022; 2022:1488165. [PMID: 36111242 PMCID: PMC9470357 DOI: 10.1155/2022/1488165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 12/04/2022]
Abstract
Background We aimed to study the relationship between transcription factor 19 (TCF19) and cancer immunotherapy in the 33 types of human cancers. Methods The Cancer Genome Atlas database was analyzed to obtain the gene expression data and clinical characteristics for the cases of 33 types of cancers. GSE67501, GSE78220, and IMvigor 210 were included in the immunotherapy cohorts. Relevant data were obtained by analyzing the gene expression database. The prognostic value of TCF19 was determined by analyzing various clinical parameters, such as survival duration, age, the stage of the tumor, and sex of the patients. The single-sample gene set enrichment analysis method was used to determine the activity of TCF19 and the method was also used to assess the differences between the TCF19 transcriptome and protein levels. The correlation between TCF19 and various immune processes and elements such as immunosuppressants, stimulants, and major histocompatibility complexes were analyzed to gain insights into the role of TCF19. The coherent paths associated with the process of TCF19 signal transduction and the influence of TCF19 on immunotherapy biomarkers have also been discussed herein. Finally, three independent immunotherapy methods were used to understand the relationship between TCF19 and immunotherapy response. Results It was observed that TCF19 was not significantly influenced by the age (5/33), sex (3/33), or tumor stage (3/21) of cancer patients. But the results revealed that TCF19 exhibited a potential prognostic value and could predict the survival rate of the patients. In some cases of this study, the activity and expression of TCF19 were taken at the same level (7/33). Conclusion TCF19 is strongly related to immune cell infiltration, immunomodulators, and immunotherapy markers. Our study demonstrated that high expression levels of TCF19 are strongly linked with the immune-related pathways. Nevertheless, it is noteworthy that TCF19 is not significantly associated with immunotherapy response.
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Zajec A, Trebušak Podkrajšek K, Tesovnik T, Šket R, Čugalj Kern B, Jenko Bizjan B, Šmigoc Schweiger D, Battelino T, Kovač J. Pathogenesis of Type 1 Diabetes: Established Facts and New Insights. Genes (Basel) 2022; 13:genes13040706. [PMID: 35456512 PMCID: PMC9032728 DOI: 10.3390/genes13040706] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 01/08/2023] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease characterized by the T-cell-mediated destruction of insulin-producing β-cells in pancreatic islets. It generally occurs in genetically susceptible individuals, and genetics plays a major role in the development of islet autoimmunity. Furthermore, these processes are heterogeneous among individuals; hence, different endotypes have been proposed. In this review, we highlight the interplay between genetic predisposition and other non-genetic factors, such as viral infections, diet, and gut biome, which all potentially contribute to the aetiology of T1D. We also discuss a possible active role for β-cells in initiating the pathological processes. Another component in T1D predisposition is epigenetic influences, which represent a link between genetic susceptibility and environmental factors and may account for some of the disease heterogeneity. Accordingly, a shift towards personalized therapies may improve the treatment results and, therefore, result in better outcomes for individuals in the long-run. There is also a clear need for a better understanding of the preclinical phases of T1D and finding new predictive biomarkers for earlier diagnosis and therapy, with the final goal of reverting or even preventing the development of the disease.
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Affiliation(s)
- Ana Zajec
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Katarina Trebušak Podkrajšek
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tine Tesovnik
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
| | - Robert Šket
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
| | - Barbara Čugalj Kern
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Darja Šmigoc Schweiger
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadej Battelino
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jernej Kovač
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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D'Antonio M, Nguyen JP, Arthur TD, Matsui H, D'Antonio-Chronowska A, Frazer KA. SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues. Cell Rep 2021; 37:110020. [PMID: 34762851 PMCID: PMC8563343 DOI: 10.1016/j.celrep.2021.110020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/06/2021] [Accepted: 10/28/2021] [Indexed: 01/08/2023] Open
Abstract
Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types.
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Affiliation(s)
- Matteo D'Antonio
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Jennifer P Nguyen
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Timothy D Arthur
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | | | | | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.
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