1
|
De Lillo A, Pathak GA, Low A, De Angelis F, Abou Alaiwi S, Miller EJ, Fuciarelli M, Polimanti R. Clinical spectrum of Transthyretin amyloidogenic mutations among diverse population origins. Hum Genomics 2024; 18:31. [PMID: 38523305 PMCID: PMC10962184 DOI: 10.1186/s40246-024-00596-7] [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: 12/06/2023] [Accepted: 03/08/2024] [Indexed: 03/26/2024] Open
Abstract
PURPOSE Coding mutations in the Transthyretin (TTR) gene cause a hereditary form of amyloidosis characterized by a complex genotype-phenotype correlation with limited information regarding differences among worldwide populations. METHODS We compared 676 diverse individuals carrying TTR amyloidogenic mutations (rs138065384, Phe44Leu; rs730881165, Ala81Thr; rs121918074, His90Asn; rs76992529, Val122Ile) to 12,430 non-carriers matched by age, sex, and genetically-inferred ancestry to assess their clinical presentations across 1,693 outcomes derived from electronic health records in UK biobank. RESULTS In individuals of African descent (AFR), Val122Ile mutation was linked to multiple outcomes related to the circulatory system (fold-enrichment = 2.96, p = 0.002) with the strongest associations being cardiac congenital anomalies (phecode 747.1, p = 0.003), endocarditis (phecode 420.3, p = 0.006), and cardiomyopathy (phecode 425, p = 0.007). In individuals of Central-South Asian descent (CSA), His90Asn mutation was associated with dermatologic outcomes (fold-enrichment = 28, p = 0.001). The same TTR mutation was linked to neoplasms in European-descent individuals (EUR, fold-enrichment = 3.09, p = 0.003). In EUR, Ala81Thr showed multiple associations with respiratory outcomes related (fold-enrichment = 3.61, p = 0.002), but the strongest association was with atrioventricular block (phecode 426.2, p = 2.81 × 10- 4). Additionally, the same mutation in East Asians (EAS) showed associations with endocrine-metabolic traits (fold-enrichment = 4.47, p = 0.003). In the cross-ancestry meta-analysis, Val122Ile mutation was associated with peripheral nerve disorders (phecode 351, p = 0.004) in addition to cardiac congenital anomalies (fold-enrichment = 6.94, p = 0.003). CONCLUSIONS Overall, these findings highlight that TTR amyloidogenic mutations present ancestry-specific and ancestry-convergent associations related to a range of health domains. This supports the need to increase awareness regarding the range of outcomes associated with TTR mutations across worldwide populations to reduce misdiagnosis and delayed diagnosis of TTR-related amyloidosis.
Collapse
Affiliation(s)
- Antonella De Lillo
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, 06510, USA
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, 06510, USA
- VA CT Healthcare Center, West Haven, CT, USA
| | - Aislinn Low
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, 06510, USA
- VA CT Healthcare Center, West Haven, CT, USA
| | - Flavio De Angelis
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, 06510, USA
- Department of Physical and Mental Health, and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Sarah Abou Alaiwi
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Edward J Miller
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Maria Fuciarelli
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, 06510, USA.
- VA CT Healthcare Center, West Haven, CT, USA.
- Wu Tsai Institute, Yale University, New Haven, CT, USA.
| |
Collapse
|
2
|
De Lillo A, Wendt FR, Pathak GA, Polimanti R. Characterizing the polygenic architecture of complex traits in populations of East Asian and European descent. Hum Genomics 2023; 17:67. [PMID: 37475089 PMCID: PMC10360343 DOI: 10.1186/s40246-023-00514-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/13/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023] Open
Abstract
To investigate the polygenicity of complex traits in populations of East Asian (EAS) and European (EUR) descents, we leveraged genome-wide data from Biobank Japan, UK Biobank, and FinnGen cohorts. Specifically, we analyzed up to 215 outcomes related to 18 health domains, assessing their polygenic architecture via descriptive statistics, such as the proportion of susceptibility SNPs per trait (πc). While we did not observe EAS-EUR differences in the overall distribution of polygenicity parameters across the phenotypes investigated, there were ancestry-specific patterns in the polygenicity differences between health domains. In EAS, pairwise comparisons across health domains showed enrichment for πc differences related to hematological and metabolic traits (hematological fold-enrichment = 4.45, p = 2.15 × 10-7; metabolic fold-enrichment = 4.05, p = 4.01 × 10-6). For both categories, the proportion of susceptibility SNPs was lower than that observed for several other health domains (EAS-hematological median πc = 0.15%, EAS-metabolic median πc = 0.18%) with the strongest πc difference with respect to respiratory traits (EAS-respiratory median πc = 0.50%; hematological-p = 2.26 × 10-3; metabolic-p = 3.48 × 10-3). In EUR, pairwise comparisons showed multiple πc differences related to the endocrine category (fold-enrichment = 5.83, p = 4.76 × 10-6), where these traits showed a low proportion of susceptibility SNPs (EUR-endocrine median πc = 0.01%) with the strongest difference with respect to psychiatric phenotypes (EUR-psychiatric median πc = 0.50%; p = 1.19 × 10-4). Simulating sample sizes of 1,000,000 and 5,000,000 individuals, we also showed that ancestry-specific polygenicity patterns translate into differences across health domains in the genetic variance explained by susceptibility SNPs projected to be genome-wide significant (e.g., EAS hematological-neoplasm p = 2.18 × 10-4; EUR endocrine-gastrointestinal p = 6.80 × 10-4). These findings highlight that traits related to the same health domains may present ancestry-specific variability in their polygenicity.
Collapse
Affiliation(s)
- Antonella De Lillo
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, 06510, USA
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Frank R Wendt
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, 06510, USA
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, 06510, USA
- VA CT Healthcare Center, West Haven, CT, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, 06510, USA.
- VA CT Healthcare Center, West Haven, CT, USA.
- Wu Tsai Institute, Yale University, New Haven, CT, USA.
| |
Collapse
|
3
|
De Lillo A, Wendt FR, Pathak GA, Polimanti R. Characterizing the polygenic architecture of complex traits in populations of East Asian and European descent. medRxiv 2023:2023.05.25.23290542. [PMID: 37398225 PMCID: PMC10312887 DOI: 10.1101/2023.05.25.23290542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
To investigate the polygenicity of complex traits in populations of East Asian (EAS) and European (EUR) descents, we leveraged genome-wide data from Biobank Japan, UK Biobank, and FinnGen cohorts. Specifically, we analyzed up to 215 outcomes related to 18 health domains, assessing their polygenic architecture via descriptive statistics, such as the proportion of susceptibility SNPs per trait (π c ). While we did not observe EAS-EUR differences in the overall distribution of polygenicity parameters across the phenotypes investigated, there were ancestry-specific patterns in the polygenicity differences between health domains. In EAS, pairwise comparisons across health domains showed enrichment for π c differences related to hematological and metabolic traits (hematological fold-enrichment=4.45, p=2.15×10 -7 ; metabolic fold-enrichment=4.05, p=4.01×10 -6 ). For both categories, the proportion of susceptibility SNPs was lower than that observed for several other health domains (EAS-hematological median π c =0.15%, EAS-metabolic median π c =0.18%) with the strongest π c difference with respect to respiratory traits (EAS-respiratory median π c =0.50%; Hematological-p=2.26×10 -3 ; Metabolic-p=3.48×10 -3 ). In EUR, pairwise comparisons showed multiple π c differences related to the endocrine category (fold-enrichment=5.83, p=4.76×10 -6 ), where these traits showed a low proportion of susceptibility SNPs (EUR-endocrine median π c =0.01%) with the strongest difference with respect to psychiatric phenotypes (EUR-psychiatric median π c =0.50%; p=1.19×10 -4 ). Simulating sample sizes of 1,000,000 and 5,000,000 individuals, we also showed that ancestry-specific polygenicity patterns translate into differences across health domains in the genetic variance explained by susceptibility SNPs projected to be genome-wide significant (e.g., EAS hematological-neoplasm p=2.18×10 -4 ; EUR endocrine-gastrointestinal p=6.80×10 -4 ). These findings highlight that traits related to the same health domains may present ancestry-specific variability in their polygenicity.
Collapse
|
4
|
Wendt FR, Pathak GA, Vahey J, Qin X, Koller D, Cabrera-Mendoza B, Haeny A, Harrington KM, Rajeevan N, Duong LM, Levey DF, De Angelis F, De Lillo A, Bigdeli TB, Pyarajan S, Gaziano JM, Gelernter J, Aslan M, Provenzale D, Helmer DA, Hauser ER, Polimanti R. Modeling the longitudinal changes of ancestry diversity in the Million Veteran Program. Hum Genomics 2023; 17:46. [PMID: 37268996 PMCID: PMC10239111 DOI: 10.1186/s40246-023-00487-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/06/2022] [Accepted: 05/05/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND The Million Veteran Program (MVP) participants represent 100 years of US history, including significant social and demographic changes over time. Our study assessed two aspects of the MVP: (i) longitudinal changes in population diversity and (ii) how these changes can be accounted for in genome-wide association studies (GWAS). To investigate these aspects, we divided MVP participants into five birth cohorts (N-range = 123,888 [born from 1943 to 1947] to 136,699 [born from 1948 to 1953]). RESULTS Ancestry groups were defined by (i) HARE (harmonized ancestry and race/ethnicity) and (ii) a random-forest clustering approach using the 1000 Genomes Project and the Human Genome Diversity Project (1kGP + HGDP) reference panels (77 world populations representing six continental groups). In these groups, we performed GWASs of height, a trait potentially affected by population stratification. Birth cohorts demonstrate important trends in ancestry diversity over time. More recent HARE-assigned Europeans, Africans, and Hispanics had lower European ancestry proportions than older birth cohorts (0.010 < Cohen's d < 0.259, p < 7.80 × 10-4). Conversely, HARE-assigned East Asians showed an increase in European ancestry proportion over time. In GWAS of height using HARE assignments, genomic inflation due to population stratification was prevalent across all birth cohorts (linkage disequilibrium score regression intercept = 1.08 ± 0.042). The 1kGP + HGDP-based ancestry assignment significantly reduced the population stratification (mean intercept reduction = 0.045 ± 0.007, p < 0.05) confounding in the GWAS statistics. CONCLUSIONS This study provides a characterization of ancestry diversity of the MVP cohort over time and compares two strategies to infer genetically defined ancestry groups by assessing differences in controlling population stratification in genome-wide association studies.
Collapse
Affiliation(s)
- Frank R Wendt
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Jacqueline Vahey
- Durham VA Medical Center, Durham, NC, USA
- Duke University, Carmichael Building, 300 N Duke St, Durham, NC, 27701, USA
| | - Xuejun Qin
- Durham VA Medical Center, Durham, NC, USA
- Duke University, Carmichael Building, 300 N Duke St, Durham, NC, 27701, USA
| | - Dora Koller
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Brenda Cabrera-Mendoza
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Angela Haeny
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Kelly M Harrington
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Nallakkandi Rajeevan
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
- Yale Center for Medical Informatics, Yale School of Medicine, New Haven, CT, USA
| | - Linh M Duong
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Daniel F Levey
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Flavio De Angelis
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | | | - Tim B Bigdeli
- SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- VA New York Harbor Healthcare System, Brooklyn, NY, USA
| | - Saiju Pyarajan
- Massachusetts Area Veterans Epidemiology, Research, and Information Center (MAVERIC), Jamaica Plain, MA, USA
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard School of Medicine, Boston, MA, USA
| | - John Michael Gaziano
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard School of Medicine, Boston, MA, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, VA CT Healthcare System, West Haven, CT, USA
| | - Mihaela Aslan
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Dawn Provenzale
- Durham VA Medical Center, Durham, NC, USA
- Duke University, Carmichael Building, 300 N Duke St, Durham, NC, 27701, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Drew A Helmer
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth R Hauser
- Durham VA Medical Center, Durham, NC, USA.
- Duke University, Carmichael Building, 300 N Duke St, Durham, NC, 27701, USA.
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA.
| |
Collapse
|
5
|
De Angelis F, Zeleznik OA, Wendt FR, Pathak GA, Tylee DS, De Lillo A, Koller D, Cabrera-Mendoza B, Clifford RE, Maihofer AX, Nievergelt CM, Curhan GC, Curhan SG, Polimanti R. Sex differences in the polygenic architecture of hearing problems in adults. Genome Med 2023; 15:36. [PMID: 37165447 PMCID: PMC10173489 DOI: 10.1186/s13073-023-01186-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 12/23/2022] [Accepted: 04/28/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Hearing problems (HP) in adults are common and are associated with several comorbid conditions. Its prevalence increases with age, reflecting the cumulative effect of environmental factors and genetic predisposition. Although several risk loci have been already identified, HP biology and epidemiology are still insufficiently investigated by large-scale genetic studies. METHODS Leveraging the UK Biobank, the Nurses' Health Studies (I and II), the Health Professionals Follow-up Study, and the Million Veteran Program, we conducted a comprehensive genome-wide investigation of HP in 748,668 adult participants (discovery N = 501,825; replication N = 226,043; cross-ancestry replication N = 20,800). We leveraged the GWAS findings to characterize HP polygenic architecture, exploring sex differences, polygenic risk across ancestries, tissue-specific transcriptomic regulation, cause-effect relationships with genetically correlated traits, and gene interactions with HP environmental risk factors. RESULTS We identified 54 risk loci and demonstrated that HP polygenic risk is shared across ancestry groups. Our transcriptomic regulation analysis highlighted the potential role of the central nervous system in HP pathogenesis. The sex-stratified analyses showed several additional associations related to peripheral hormonally regulated tissues reflecting a potential role of estrogen in hearing function. This evidence was supported by the multivariate interaction analysis that showed how genes involved in brain development interact with sex, noise pollution, and tobacco smoking in relation to their HP associations. Additionally, the genetically informed causal inference analysis showed that HP is linked to many physical and mental health outcomes. CONCLUSIONS The results provide many novel insights into the biology and epidemiology of HP in adults. Our sex-specific analyses and transcriptomic associations highlighted molecular pathways that may be targeted for drug development or repurposing. Additionally, the potential causal relationships identified may support novel preventive screening programs to identify individuals at risk.
Collapse
Affiliation(s)
- Flavio De Angelis
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Oana A Zeleznik
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Frank R Wendt
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Daniel S Tylee
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Antonella De Lillo
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Dora Koller
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Brenda Cabrera-Mendoza
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Royce E Clifford
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, La Jolla, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Adam X Maihofer
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Caroline M Nievergelt
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Gary C Curhan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sharon G Curhan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA.
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA.
| |
Collapse
|
6
|
Koller D, Wendt FR, Pathak GA, De Lillo A, De Angelis F, Cabrera-Mendoza B, Tucci S, Polimanti R. Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations. BMC Biol 2022; 20:249. [PMID: 36344982 PMCID: PMC9641937 DOI: 10.1186/s12915-022-01449-2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Introgression from extinct Neanderthal and Denisovan human species has been shown to contribute to the genetic pool of modern human populations and their phenotypic spectrum. Evidence of how Neanderthal introgression shaped the genetics of human traits and diseases has been extensively studied in populations of European descent, with signatures of admixture reported for instance in genes associated with pigmentation, immunity, and metabolic traits. However, limited information is currently available about the impact of archaic introgression on other ancestry groups. Additionally, to date, no study has been conducted with respect to the impact of Denisovan introgression on the health and disease of modern populations. Here, we compare the way evolutionary pressures shaped the genetics of complex traits in East Asian and European populations, and provide evidence of the impact of Denisovan introgression on the health of East Asian and Central/South Asian populations. RESULTS Leveraging genome-wide association statistics from the Biobank Japan and UK Biobank, we assessed whether Denisovan and Neanderthal introgression together with other evolutionary genomic signatures were enriched for the heritability of physiological and pathological conditions in populations of East Asian and European descent. In EAS, Denisovan-introgressed loci were enriched for coronary artery disease heritability (1.69-fold enrichment, p=0.003). No enrichment for archaic introgression was observed in EUR. We also performed a phenome-wide association study of Denisovan and Neanderthal alleles in six ancestry groups available in the UK Biobank. In EAS, the Denisovan-introgressed SNP rs62391664 in the major histocompatibility complex region was associated with albumin/globulin ratio (beta=-0.17, p=3.57×10-7). Neanderthal-introgressed alleles were associated with psychiatric and cognitive traits in EAS (e.g., "No Bipolar or Depression"-rs79043717 beta=-1.5, p=1.1×10-7), and with blood biomarkers (e.g., alkaline phosphatase-rs11244089 beta=0.1, p=3.69×10-116) and red hair color (rs60733936 beta=-0.86, p=4.49×10-165) in EUR. In the other ancestry groups, Neanderthal alleles were associated with several traits, also including the use of certain medications (e.g., Central/South East Asia: indapamide - rs732632 beta=-2.38, p=5.22×10-7). CONCLUSIONS Our study provides novel evidence regarding the impact of archaic introgression on the genetics of complex traits in worldwide populations, highlighting the specific contribution of Denisovan introgression in EAS populations.
Collapse
Affiliation(s)
- Dora Koller
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, 08028, Spain
| | - Frank R Wendt
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
| | - Antonella De Lillo
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- Department of Biology, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Flavio De Angelis
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
- Department of Biology, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Brenda Cabrera-Mendoza
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, 06511, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA.
- VA CT Healthcare Center, West Haven, CT, 06516, USA.
| |
Collapse
|
7
|
Cabrera-Mendoza B, Wendt FR, Pathak GA, De Angelis F, De Lillo A, Koller D, Polimanti R. The association of obesity-related traits on COVID-19 severity and hospitalization is affected by socio-economic status: a multivariable Mendelian randomization study. Int J Epidemiol 2022; 51:1371-1383. [PMID: 35751636 PMCID: PMC9278255 DOI: 10.1093/ije/dyac129] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/18/2021] [Accepted: 05/30/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Due to its large impact on human health, socio-economic status (SES) could at least partially influence the established association between obesity and coronavirus disease 2019 (COVID-19) severity. To estimate the independent effect of body size and SES on the clinical manifestations of COVID-19, we conducted a Mendelian randomization (MR) study. METHODS Applying two-sample MR approaches, we evaluated the effects of body mass index (BMI, n = 322 154), waist circumference (WC, n = 234 069), hip circumference (n = 213 019) and waist-hip ratio (n = 210 088) with respect to three COVID-19 outcomes: severe respiratory COVID-19 (cases = 8779, controls = 1 000 875), hospitalized COVID-19 (cases = 17 992, controls = 1 810 493) and COVID-19 infection (cases = 87 870, controls = 2 210 804). Applying a multivariable MR (MVMR) approach, we estimated the effect of these anthropometric traits on COVID-19 outcomes accounting for the effect of SES assessed as household income (n = 286 301). RESULTS BMI and WC were associated with severe respiratory COVID-19 [BMI: odds ratio (OR) = 1.51, CI = 1.24-1.84, P = 3.01e-05; WC: OR = 1.48, 95% CI = 1.15-1.91, P = 0.0019] and hospitalized COVID-19 (BMI: OR = 1.50, 95% CI = 1.32-1.72, P = 8.83e-10; WC: OR = 1.41, 95% CI = 1.20-1.67, P = 3.72e-05). Conversely, income was associated with lower odds of severe respiratory (OR = 0.70, 95% CI = 0.53-0.93, P = 0.015) and hospitalized COVID-19 (OR = 0.78, 95% CI = 0.66-0.92, P = 0.003). MVMR analyses showed that the effect of these obesity-related traits on increasing the odds of COVID-19 negative outcomes becomes null when accounting for income. Conversely, the association of income with lower odds of COVID-19 negative outcomes is not affected when including the anthropometric traits in the multivariable model. CONCLUSION Our findings indicate that SES contributes to the effect of obesity-related traits on COVID-19 severity and hospitalization.
Collapse
Affiliation(s)
- Brenda Cabrera-Mendoza
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA CT Healthcare System, West Haven, CT, USA
| | - Frank R Wendt
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA CT Healthcare System, West Haven, CT, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA CT Healthcare System, West Haven, CT, USA
| | - Flavio De Angelis
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA CT Healthcare System, West Haven, CT, USA
| | | | - Dora Koller
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA CT Healthcare System, West Haven, CT, USA
| | - Renato Polimanti
- Corresponding author. Department of Psychiatry, Yale University School of Medicine, VA CT 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA. E-mail:
| |
Collapse
|
8
|
Pathak GA, De Lillo A, Wendt FR, De Angelis F, Koller D, Mendoza BC, Jacoby D, Miller EJ, Buxbaum JN, Polimanti R. The integration of genetically-regulated transcriptomics and electronic health records highlights a pattern of medical outcomes related to increased hepatic transthyretin expression. Amyloid 2022; 29:110-119. [PMID: 34935565 PMCID: PMC9213571 DOI: 10.1080/13506129.2021.2018678] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Transthyretin (TTR) is the precursor of the fibrils that compromise organ function in hereditary and sporadic systemic amyloidoses (ATTR). RNA-interference and anti-sense therapeutics targeting TTR hepatic transcription have been shown to reduce TTR amyloid formation. In the present study, we leveraged genetic and phenotypic information from the UK Biobank and transcriptomic profiles from the Genotype-Tissue Expression project to test the association of genetically regulated TTR gene expression with 7149 traits assessed in 420,531 individuals. We conducted a multi-tissue analysis of TTR transcription and identified an association with a operational procedure related to bone fracture (p = 5.46×10-6). Using tissue-specific TTR expression information, we demonstrated that the association is driven by the genetic regulation of TTR hepatic expression (odds ratio [OR] = 3.46, p = 9.51×10-5). Using the UK Biobank electronic health records (EHRs), we investigated the comorbidities affecting individuals undergoing this surgical procedure. Excluding bone fracture EHRs, we identified a pattern of health outcomes previously associated with ATTR manifestations. These included osteoarthritis (OR = 3.18, p = 9.18×10-8), carpal tunnel syndrome (OR = 2.15, p = .002), and a history of gastrointestinal diseases (OR = 2.01, p = 8.07×10-4). In conclusion, our study supports that TTR hepatic expression can affect health outcomes linked to physiological and pathological processes presumably related to the encoded protein.
Collapse
Affiliation(s)
- Gita A. Pathak
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Antonella De Lillo
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Frank R. Wendt
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Flavio De Angelis
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Dora Koller
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Brenda Cabrera Mendoza
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Daniel Jacoby
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Edward J. Miller
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
- Corresponding author: Renato Polimanti, Ph.D., Yale University School of Medicine, Department of Psychiatry. VA CT 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA. Phone: +1 (203) 932-5711 x5745. Fax: +1 (203) 937-3897.
| |
Collapse
|
9
|
Wendt FR, De Lillo A, Pathak GA, De Angelis F, Polimanti R. Host Genetic Liability for Severe COVID-19 Associates with Alcohol Drinking Behavior and Diabetic Outcomes in Participants of European Descent. Front Genet 2021; 12:765247. [PMID: 34966408 PMCID: PMC8711039 DOI: 10.3389/fgene.2021.765247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/08/2021] [Indexed: 12/16/2022] Open
Abstract
Risk factors and long-term consequences of COVID-19 infection are unclear but can be investigated with large-scale genomic data. To distinguish correlation from causation, we performed in-silico analyses of three COVID-19 outcomes (N > 1,000,000). We show genetic correlation and putative causality with depressive symptoms, metformin use (genetic causality proportion (gĉp) with severe respiratory COVID-19 = 0.576, p = 1.07 × 10−5 and hospitalized COVID-19 = 0.713, p = 0.003), and alcohol drinking status (gĉp with severe respiratory COVID-19 = 0.633, p = 7.04 × 10−5 and hospitalized COVID-19 = 0.848, p = 4.13 × 10−13). COVID-19 risk loci associated with several hematologic biomarkers. Comprehensive findings inform genetic contributions to COVID-19 epidemiology, molecular mechanisms, and risk factors and potential long-term health effects of severe response to infection.
Collapse
Affiliation(s)
- Frank R Wendt
- Division of Human Genetics in Psychiatry, Yale School of Medicine, New Haven, CT, United States.,VA CT Healthcare System, West Haven, CT, United States
| | - Antonella De Lillo
- Division of Human Genetics in Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Gita A Pathak
- Division of Human Genetics in Psychiatry, Yale School of Medicine, New Haven, CT, United States.,VA CT Healthcare System, West Haven, CT, United States
| | - Flavio De Angelis
- Division of Human Genetics in Psychiatry, Yale School of Medicine, New Haven, CT, United States.,VA CT Healthcare System, West Haven, CT, United States
| | | | - Renato Polimanti
- Division of Human Genetics in Psychiatry, Yale School of Medicine, New Haven, CT, United States.,VA CT Healthcare System, West Haven, CT, United States
| |
Collapse
|
10
|
De Lillo A, D'Antona S, Pathak GA, Wendt FR, De Angelis F, Fuciarelli M, Polimanti R. Cross-ancestry genome-wide association studies identified heterogeneous loci associated with differences of allele frequency and regulome tagging between participants of European descent and other ancestry groups from the UK Biobank. Hum Mol Genet 2021; 30:1457-1467. [PMID: 33890984 PMCID: PMC8283210 DOI: 10.1093/hmg/ddab114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/09/2021] [Revised: 04/14/2021] [Accepted: 01/09/2021] [Indexed: 01/28/2023] Open
Abstract
To investigate cross-ancestry genetics of complex traits, we conducted a phenome-wide analysis of loci with heterogeneous effects across African, Admixed-American, Central/South Asian, East Asian, European and Middle Eastern participants of the UK Biobank (N = 441 331). Testing 843 phenotypes, we identified 82 independent genomic regions mapping variants showing genome-wide significant (GWS) associations (P < 5 × 10-8) in the trans-ancestry meta-analysis and GWS heterogeneity among the ancestry-specific effects. These included (i) loci with GWS association in one ancestry and concordant but heterogeneous effects among the other ancestries and (ii) loci with a GWS association in one ancestry group and an experiment-wide significant discordant effect (P < 6.1 × 10-4) in at least another ancestry. Since the trans-ancestry GWS associations were mostly driven by the European ancestry sample size, we investigated the differences of the allele frequency (ΔAF) and linkage disequilibrium regulome tagging (ΔLD) between European populations and the other ancestries. Within loci with concordant effects, the degree of heterogeneity was associated with European-Middle Eastern ΔAF (P = 9.04 × 10-6) and ΔLD of European populations with respect to African, Admixed-American and Central/South Asian groups (P = 8.21 × 10-4, P = 7.17 × 10-4 and P = 2.16 × 10-3, respectively). Within loci with discordant effects, ΔAF and ΔLD of European populations with respect to African and Central/South Asian ancestries were associated with the degree of heterogeneity (ΔAF: P = 7.69 × 10-3 and P = 5.31 × 10-3, ΔLD: P = 0.016 and P = 2.65 × 10-4, respectively). Considering the traits associated with cross-ancestry heterogeneous loci, we observed enrichments for blood biomarkers (P = 5.7 × 10-35) and physical appearance (P = 1.38 × 10-4). This suggests that these specific phenotypic classes may present considerable cross-ancestry heterogeneity owing to large allele frequency and LD variation among worldwide populations.
Collapse
Affiliation(s)
- Antonella De Lillo
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT 06516, USA
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Salvatore D'Antona
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Frank R Wendt
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Flavio De Angelis
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT 06516, USA
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Maria Fuciarelli
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| |
Collapse
|
11
|
Goswami A, Wendt FR, Pathak GA, Tylee DS, De Angelis F, De Lillo A, Polimanti R. Role of microbes in the pathogenesis of neuropsychiatric disorders. Front Neuroendocrinol 2021; 62:100917. [PMID: 33957173 PMCID: PMC8364482 DOI: 10.1016/j.yfrne.2021.100917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/25/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023]
Abstract
Microbes inhabit different anatomical sites of the human body including oral cavity, gut, and skin. A growing literature highlights how microbiome variation is associated with human health and disease. There is strong evidence of bidirectional communication between gut and brain mediated by neurotransmitters and microbial metabolites. Here, we review the potential involvement of microbes residing in the gut and in other body sites in the pathogenesis of eight neuropsychiatric disorders, discussing findings from animal and human studies. The data reported provide a comprehensive overview of the current state of the microbiome research in neuropsychiatry, including hypotheses about the mechanisms underlying the associations reported and the translational potential of probiotics and prebiotics.
Collapse
Affiliation(s)
- Aranyak Goswami
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Frank R Wendt
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Daniel S Tylee
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Flavio De Angelis
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Antonella De Lillo
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA.
| |
Collapse
|
12
|
Pathak GA, Wendt FR, De Lillo A, Nunez YZ, Goswami A, De Angelis F, Fuciarelli M, Kranzler HR, Gelernter J, Polimanti R. Epigenomic Profiles of African-American Transthyretin Val122Ile Carriers Reveals Putatively Dysregulated Amyloid Mechanisms. Circ Genom Precis Med 2021; 14:e003011. [PMID: 33428857 DOI: 10.1161/circgen.120.003011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The Val122Ile mutation in Transthyretin (TTR) gene causes a rare, difficult to diagnose hereditary form of cardiac amyloidosis. This mutation is most common in the United States and mainly present in people of African descent. The carriers have an increased risk of congestive heart failure, peripheral edema, and several other noncardiac phenotypes such as carpal tunnel syndrome, and arthroplasty which are top reasons for ambulatory/outpatient surgeries (OSs) in the country. METHODS We conducted first-ever epigenome-wide association study using the Illumina's EPIC array, in Val122Ile carriers of African descent for heart disease and multiple OSs-an early disease indicator. Differential methylation across genome wide cytosine-phosphate guanine (CpG) sites was tested between carriers with and without heart disease and OS. Significant CpG sites were investigated for cis-mQTLs loci, followed by gene ontology and protein-protein interaction network. We also investigated the significant CpG sites in a secondary cohort of carriers for replication. RESULTS Five differentially methylated sites (P≤2.1×10-8) in genes-FAM129B, SKI, WDR27, GLS, and an intergenic site near RP11-550A5.2, and one differentially methylated region containing KCNA6 and GALNT3 (P=1.1×10-12) were associated with heart disease. For OS, we observe 4 sites-2 sites in UBE2E3 and SEC14L5, and other 2 in intergenic regions (P≤1.8×10-7) and 3 regions overlapping SH3D21, EVA1B, LTB4R2, and CIDEB (P≤3.9×10-7). Functional protein-interaction module analysis identified ABCA1 (P=0.001) for heart disease. Six cis-mQTLs were associated with one of the significant CpG sites (FAM129B; P=4.1×10-24). We replicated 2 CpG sites (cg18546846 and cg06641417; P<0.05) in an external cohort of biopsy-confirmed cases of TTR (transthyretin) amyloidosis. The genes identified are involved in transport and clearance of amyloid deposits (GLS, ABCA1, FAM129B); cardiac fibrosis (SKI); and muscle tissue regulation (SKI, FAM129B). CONCLUSIONS These findings highlight the link between a complex amyloid circuit and diverse symptoms of Val122Ile.
Collapse
Affiliation(s)
- Gita A Pathak
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.).,Veteran Affairs Connecticut Healthcare System, West Haven, CT (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.)
| | - Frank R Wendt
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.).,Veteran Affairs Connecticut Healthcare System, West Haven, CT (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.)
| | - Antonella De Lillo
- Department of Biology, University of Rome Tor Vergata, Italy (A.D.L., F.D.A., M.F.)
| | - Yaira Z Nunez
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.).,Veteran Affairs Connecticut Healthcare System, West Haven, CT (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.)
| | - Aranyak Goswami
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.).,Veteran Affairs Connecticut Healthcare System, West Haven, CT (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.)
| | - Flavio De Angelis
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.).,Veteran Affairs Connecticut Healthcare System, West Haven, CT (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.).,Department of Biology, University of Rome Tor Vergata, Italy (A.D.L., F.D.A., M.F.)
| | - Maria Fuciarelli
- Department of Biology, University of Rome Tor Vergata, Italy (A.D.L., F.D.A., M.F.)
| | - Henry R Kranzler
- University of Pennsylvania Perelman School of Medicine and VISN 4 MIRECC, Crescenz VAMC, Philadelphia (H.R.K.)
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.).,Veteran Affairs Connecticut Healthcare System, West Haven, CT (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.)
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.).,Veteran Affairs Connecticut Healthcare System, West Haven, CT (G.A.P., F.R.W., Y.Z.N., A.G., F.D.A., J.G., R.P.)
| |
Collapse
|
13
|
Wendt FR, De Lillo A, Pathak GA, De Angelis F, Polimanti R. Host genetic liability for severe COVID-19 overlaps with alcohol drinking behavior and diabetic outcomes in over 1 million participants. medRxiv 2020:2020.11.08.20227884. [PMID: 33200138 PMCID: PMC7668748 DOI: 10.1101/2020.11.08.20227884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
To distinguish correlation from causation, we performed in-silico analyses of three COVID-19 outcomes (N>1,000,000). We show genetic correlation and putative causality with depressive symptoms, metformin use, and alcohol use. COVID-19 risk loci associated with several hematologic biomarkers. Comprehensive findings inform genetic contributions to COVID-19 epidemiology, molecular mechanisms, and risk factors.
Collapse
|
14
|
De Lillo A, Pathak GA, De Angelis F, Di Girolamo M, Luigetti M, Sabatelli M, Perfetto F, Frusconi S, Manfellotto D, Fuciarelli M, Polimanti R. Epigenetic profiling of Italian patients identified methylation sites associated with hereditary transthyretin amyloidosis. Clin Epigenetics 2020; 12:176. [PMID: 33203445 PMCID: PMC7672937 DOI: 10.1186/s13148-020-00967-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/07/2020] [Accepted: 11/03/2020] [Indexed: 11/10/2022] Open
Abstract
Hereditary transthyretin (TTR) amyloidosis (hATTR) is a rare life-threatening disorder caused by amyloidogenic coding mutations located in TTR gene. To understand the high phenotypic variability observed among carriers of TTR disease-causing mutations, we conducted an epigenome-wide association study (EWAS) assessing more than 700,000 methylation sites and testing epigenetic difference of TTR coding mutation carriers vs. non-carriers. We observed a significant methylation change at cg09097335 site located in Beta-secretase 2 (BACE2) gene (standardized regression coefficient = -0.60, p = 6.26 × 10-8). This gene is involved in a protein interaction network enriched for biological processes and molecular pathways related to amyloid-beta metabolism (Gene Ontology: 0050435, q = 0.007), amyloid fiber formation (Reactome HSA-977225, q = 0.008), and Alzheimer's disease (KEGG hsa05010, q = 2.2 × 10-4). Additionally, TTR and BACE2 share APP (amyloid-beta precursor protein) as a validated protein interactor. Within TTR gene region, we observed that Val30Met disrupts a methylation site, cg13139646, causing a drastic hypomethylation in carriers of this amyloidogenic mutation (standardized regression coefficient = -2.18, p = 3.34 × 10-11). Cg13139646 showed co-methylation with cg19203115 (Pearson's r2 = 0.32), which showed significant epigenetic differences between symptomatic and asymptomatic carriers of amyloidogenic mutations (standardized regression coefficient = -0.56, p = 8.6 × 10-4). In conclusion, we provide novel insights related to the molecular mechanisms involved in the complex heterogeneity of hATTR, highlighting the role of epigenetic regulation in this rare disorder.
Collapse
Affiliation(s)
| | - Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, VA CT Healthcare Center, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, USA
- VA CT Healthcare Center, West Haven, CT, USA
| | - Flavio De Angelis
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Department of Psychiatry, Yale University School of Medicine, VA CT Healthcare Center, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, USA
- VA CT Healthcare Center, West Haven, CT, USA
| | - Marco Di Girolamo
- Clinical Pathophysiology Center, Fatebenefratelli Foundation -'San Giovanni Calibita' Fatebenefratelli Hospital, Rome, Italy
| | - Marco Luigetti
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Neurologia, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Mario Sabatelli
- Università Cattolica del Sacro Cuore, Rome, Italy
- Centro Clinico NEMO Adulti, Rome, Italy
| | - Federico Perfetto
- Regional Amyloid Centre, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Sabrina Frusconi
- Genetic Diagnostics Unit, Laboratory Department, Careggi University Hospital, Florence, Italy
| | - Dario Manfellotto
- Clinical Pathophysiology Center, Fatebenefratelli Foundation -'San Giovanni Calibita' Fatebenefratelli Hospital, Rome, Italy
| | - Maria Fuciarelli
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, VA CT Healthcare Center, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, USA.
- VA CT Healthcare Center, West Haven, CT, USA.
| |
Collapse
|
15
|
Pathak G, Wendt F, De Lillo A, Nunez Y, Goswami A, De Angelis F, Fuciarelli M, Kranzler H, Gelernter J, Polimanti R. Abstract 357: DNA Methylation Profiles of African American Val122Ile-Transthyretin Mutation Carriers Reveals Genes Involved in Amyloidosis Regulation. Circ Res 2020. [DOI: 10.1161/res.127.suppl_1.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The
Transthyretin
(
TTR
) Val122Ile mutation causes a rare life-threatening disorder attributable to amyloid deposition. This mutation is mainly present in people of African descent; carriers have an increased risk of congestive heart failure and several other non-cardiac phenotypes such as carpal tunnel syndrome, peripheral edema, and arthroplasty. Cardiac disease in Val122Ile carriers may not depend solely on this mutation and other uninvestigated factors could contribute to clinical heterogeneity. One possible mechanism is through DNA methylation, the addition of a methyl group on CG-dinucleotides, which can result in altered gene expression. We investigated methylation changes contributing to heart disease in Val122Ile carriers to identify non-TTR regulatory mechanisms. We investigated 96 Val122Ile carriers of genetically-confirmed African descent using the Illumina EPIC array, which covers 850,000 methylation sites across the genome. We found changes in five methylated sites associated with heart disease. These map to
FAM129B, SKI, WDR27, GLS
, and an intergenic site near RP11-550A5.2 (p=1.6 to 4.6e-8), and a methylated region containing
KCNA6
and
GALNT3
(p=1.1e-12). Weighted methylated sites mapped to PPI network analysis identified
ABCA1
gene (p=0.001). We also found six cis-mQTLs associated with the
FAM129B
CpG site (p=4.1e-24 to 2.8e-14). We replicated two of the aforementioned CpG sites near RP11-550A5.2 (p=0.021) and in
FAM129B
(p=0.016) at nominal significance in a case-control analysis of confirmed cases of TTR amyloidosis.
GLS
encodes glutaminase, which catalyzes the conversion of glutamine to glutamate. Its expression is increased in amyloid-beta neurons and neurofibrillary tangles.
ABCA1
regulates cholesterol transport and interacts with
APOA1
and
APP
; its dysregulation increases amyloid deposition. Increasing
FAM129B
expression improves the clearance of amyloid deposits and rescues hippocampal neurons from apoptosis. The
SKI
expression modulates
TGF-beta
, resulting in cardiac fibrosis. Of note,
SKI
and
FAM129B
together are involved in the regularion of various muscle tissues. Collectively, these findings suggest that a complex amyloid-related gene circuit could explain diverse symptoms in Val122Ile carriers.
Collapse
|
16
|
De Lillo A, De Angelis F, Di Girolamo M, Luigetti M, Frusconi S, Manfellotto D, Fuciarelli M, Polimanti R. Phenome-wide association study of TTR and RBP4 genes in 361,194 individuals reveals novel insights in the genetics of hereditary and wildtype transthyretin amyloidoses. Hum Genet 2019; 138:1331-1340. [DOI: 10.1007/s00439-019-02078-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/22/2019] [Indexed: 12/30/2022]
|
17
|
Iorio A, De Lillo A, De Angelis F, Di Girolamo M, Luigetti M, Sabatelli M, Pradotto L, Mauro A, Mazzeo A, Stancanelli C, Perfetto F, Frusconi S, My F, Manfellotto D, Fuciarelli M, Polimanti R. Non-coding variants contribute to the clinical heterogeneity of TTR amyloidosis. Eur J Hum Genet 2017. [PMID: 28635949 DOI: 10.1038/ejhg.2017.95] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Coding mutations in TTR gene cause a rare hereditary form of systemic amyloidosis, which has a complex genotype-phenotype correlation. We investigated the role of non-coding variants in regulating TTR gene expression and consequently amyloidosis symptoms. We evaluated the genotype-phenotype correlation considering the clinical information of 129 Italian patients with TTR amyloidosis. Then, we conducted a re-sequencing of TTR gene to investigate how non-coding variants affect TTR expression and, consequently, phenotypic presentation in carriers of amyloidogenic mutations. Polygenic scores for genetically determined TTR expression were constructed using data from our re-sequencing analysis and the GTEx (Genotype-Tissue Expression) project. We confirmed a strong phenotypic heterogeneity across coding mutations causing TTR amyloidosis. Considering the effects of non-coding variants on TTR expression, we identified three patient clusters with specific expression patterns associated with certain phenotypic presentations, including late onset, autonomic neurological involvement, and gastrointestinal symptoms. This study provides novel data regarding the role of non-coding variation and the gene expression profiles in patients affected by TTR amyloidosis, also putting forth an approach that could be used to investigate the mechanisms at the basis of the genotype-phenotype correlation of the disease.
Collapse
Affiliation(s)
- Andrea Iorio
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | | | - Marco Di Girolamo
- Clinical Pathophysiology Center, AFaR Foundation - 'San Giovanni Calibita' Fatebenefratelli Hospital, Rome, Italy
| | - Marco Luigetti
- Department of Geriatrics, Institute of Neurology, Catholic University of the Sacred Heart, Fondazione Policlinico Universitario A. Gemelli, Rome, Italy.,Department of Neurosciences, Institute of Neurology, Catholic University of the Sacred Heart, Fondazione Policlinico Universitario A. Gemelli, Rome, Italy.,Department of Orthopedics, Institute of Neurology, Catholic University of the Sacred Heart, Fondazione Policlinico Universitario A. Gemelli, Rome, Italy
| | | | - Luca Pradotto
- Division of Neurology and Neurorehabilitation, San Giuseppe Hospital, IRCCS-Istituto Auxologico Italiano, Piancavallo (VB), Italy
| | - Alessandro Mauro
- Division of Neurology and Neurorehabilitation, San Giuseppe Hospital, IRCCS-Istituto Auxologico Italiano, Piancavallo (VB), Italy.,Department of Neuroscience, University of Turin, Turin, Italy
| | - Anna Mazzeo
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Claudia Stancanelli
- Unit of Neurology, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Federico Perfetto
- Regional Amyloid Centre, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Sabrina Frusconi
- Genetic Diagnostics Unit, Laboratory Department, Careggi University Hospital, Florence, Italy
| | - Filomena My
- Division of Neurology, 'Vito Fazzi Hospital', Lecce, Italy
| | - Dario Manfellotto
- Clinical Pathophysiology Center, AFaR Foundation - 'San Giovanni Calibita' Fatebenefratelli Hospital, Rome, Italy
| | - Maria Fuciarelli
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA.,VA CT Healthcare Center, West Haven, CT, USA
| |
Collapse
|