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Zhong Y, Tubbs JD, Leung PBM, Zhan N, Hui TCK, Ho KKY, Hung KSY, Cheung EFC, So HC, Lui SSY, Sham PC. Whole-exome sequencing in a Chinese sample provides preliminary evidence for the link between rare/low-frequency immune-related variants and early-onset schizophrenia. Asian J Psychiatr 2024; 96:104046. [PMID: 38663229 DOI: 10.1016/j.ajp.2024.104046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/06/2024] [Indexed: 06/01/2024]
Abstract
Rare and low-frequency variants contribute to schizophrenia (SCZ), and may influence its age-at-onset (AAO). We examined the association of rare or low-frequency deleterious coding variants in Chinese patients with SCZ. We collected DNA samples in 197 patients with SCZ spectrum disorder and 82 healthy controls (HC), and performed exome sequencing. The AAO variable was ascertained in the majority of SCZ participants for identify the early-onset (EOS, AAO<=18) and adult-onset (AOS, AAO>18) subgroups. We examined the overall association of rare/low-frequency, damaging variants in SCZ versus HC, EOS versus HC, and AOS versus HC at the gene and gene-set levels using Sequence Kernel Association Test. The quantitative rare-variant association test of AAO was conducted. Resampling was used to obtain empirical p-values and to control for family-wise error rate (FWER). In binary-trait association tests, we identified 5 potential candidate risk genes and 10 gene ontology biological processes (GOBP) terms, among which PADI2 reached FWER-adjusted significance. In quantitative rare-variant association tests, we found marginally significant correlations of AAO with alterations in 4 candidate risk genes, and 5 GOBP pathways. Together, the biological and functional profiles of these genes and gene sets supported the involvement of perturbations of neural systems in SCZ, and altered immune functions in EOS.
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Affiliation(s)
- Yuanxin Zhong
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Justin D Tubbs
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Perry B M Leung
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Na Zhan
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Tomy C K Hui
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Karen K Y Ho
- Department of General Adult Psychiatry, Castle Peak Hospital, Hong Kong Special Administrative Region of China
| | - Karen S Y Hung
- Department of General Adult Psychiatry, Castle Peak Hospital, Hong Kong Special Administrative Region of China
| | - Eric F C Cheung
- Department of General Adult Psychiatry, Castle Peak Hospital, Hong Kong Special Administrative Region of China
| | - Hon-Cheong So
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China; Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China.
| | - Simon S Y Lui
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China.
| | - Pak C Sham
- Department of Psychiatry, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong Special Administrative Region of China.
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Cristina-Marianini-Rios, Sanchez MEC, de Paredes AGG, Rodríguez M, Barreto E, López JV, Fuentes R, Beltrán MM, Sanjuanbenito A, Lobo E, Caminoa A, Ruz-Caracuel I, Durán SL, Olcina JRF, Blázquez J, Sequeros EV, Carrato A, Ávila JCM, Earl J. The best linear unbiased prediction (BLUP) method as a tool to estimate the lifetime risk of pancreatic ductal adenocarcinoma in high-risk individuals with no known pathogenic germline variants. Fam Cancer 2024:10.1007/s10689-024-00397-w. [PMID: 38780705 DOI: 10.1007/s10689-024-00397-w] [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: 02/02/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related death in the Western world. The number of diagnosed cases and the mortality rate are almost equal as the majority of patients present with advanced disease at diagnosis. Between 4 and 10% of pancreatic cancer cases have an apparent hereditary background, known as hereditary pancreatic cancer (HPC) and familial pancreatic cancer (FPC), when the genetic basis is unknown. Surveillance of high-risk individuals (HRI) from these families by imaging aims to detect PDAC at an early stage to improve prognosis. However, the genetic basis is unknown in the majority of HRIs, with only around 10-13% of families carrying known pathogenic germline mutations. The aim of this study was to assess an individual's genetic cancer risk based on sex and personal and family history of cancer. The Best Linear Unbiased Prediction (BLUP) methodology was used to estimate an individual's predicted risk of developing cancer during their lifetime. The model uses different demographic factors in order to estimate heritability. A reliable estimation of heritability for pancreatic cancer of 0.27 on the liability scale, and 0.07 at the observed data scale as obtained, which is different from zero, indicating a polygenic inheritance pattern of PDAC. BLUP was able to correctly discriminate PDAC cases from healthy individuals and those with other cancer types. Thus, providing an additional tool to assess PDAC risk HRI with an assumed genetic predisposition in the absence of known pathogenic germline mutations.
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Affiliation(s)
- Cristina-Marianini-Rios
- Department of Agricultural Economics, Statistics and Business Management, Universidad Politécnica de Madrid, Madrid, Spain
| | - María E Castillo Sanchez
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
| | - Ana García García de Paredes
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- Gastroenterology and Hepatology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Mercedes Rodríguez
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- Medical Oncology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, 28034, Spain
- The Biomedical Research Network in Cancer (CIBERONC), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, Madrid, 28029, Spain
- University of Alcalá, Madrid, Spain
| | - Emma Barreto
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- The Biomedical Research Network in Cancer (CIBERONC), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, Madrid, 28029, Spain
- University of Alcalá, Madrid, Spain
| | - Jorge Villalón López
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
| | - Raquel Fuentes
- Medical Oncology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, 28034, Spain
| | | | - Alfonso Sanjuanbenito
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- The Biomedical Research Network in Cancer (CIBERONC), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, Madrid, 28029, Spain
- Pancreatic and Biliopancreatic Surgery Unit, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Eduardo Lobo
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- Pancreatic and Biliopancreatic Surgery Unit, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Alejandra Caminoa
- Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, 28034, Spain
| | - Ignacio Ruz-Caracuel
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- The Biomedical Research Network in Cancer (CIBERONC), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, Madrid, 28029, Spain
- Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, 28034, Spain
| | - Sergio López Durán
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- Gastroenterology and Hepatology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - José Ramón Foruny Olcina
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- Gastroenterology and Hepatology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Javier Blázquez
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- Radiology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Enrique Vázquez Sequeros
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- Gastroenterology and Hepatology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
- The Biomedical Research Network in Cancer (CIBERONC), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, Madrid, 28029, Spain
| | - Alfredo Carrato
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain
- The Biomedical Research Network in Cancer (CIBERONC), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, Madrid, 28029, Spain
- University of Alcalá, Madrid, Spain
- Pancreatic Cancer Europe, Brussels, Belgium
| | - Jose Carlos Martínez Ávila
- Department of Agricultural Economics, Statistics and Business Management, Universidad Politécnica de Madrid, Madrid, Spain.
| | - Julie Earl
- Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9, 100, Madrid, 28034, Spain.
- The Biomedical Research Network in Cancer (CIBERONC), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, Madrid, 28029, Spain.
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Zhong Y, Tubbs JD, Leung PBM, Zhan N, Hui TCK, Ho KKY, Hung KSY, Cheung EFC, So HC, Lui SSY, Sham PC. Early-onset schizophrenia is associated with immune-related rare variants in a Chinese sample. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.21.23298115. [PMID: 38045317 PMCID: PMC10690336 DOI: 10.1101/2023.11.21.23298115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Background Rare variants are likely to contribute to schizophrenia (SCZ), given the large discrepancy between the heritability estimated from twin and GWAS studies. Furthermore, the nature of the rare-variant contribution to SCZ may vary with the "age-at-onset" (AAO), since early-onset has been suggested as being indicative of neurodevelopment deviance. Objective To examine the association of rare deleterious coding variants in early- and adult-onset SCZ in a Chinese sample. Method Exome sequencing was performed on DNA from 197 patients with SCZ spectrum disorder and 82 healthy controls (HC) of Chinese ancestry recruited in Hong Kong. We also gathered AAO information in the majority of SCZ samples. Patients were classified into early-onset (EOS, AAO<18) and adult-onset (AOS, AAO>18). We collapsed the rare variants to improve statistical power and examined the overall association of rare variants in SCZ versus HC, EOS versus HC, and AOS versus HC at the gene and gene-set levels by Sequence Kernel Association Test. The quantitative rare-variant association test of AAO was also conducted. We focused on variants which were predicted to have a medium or high impact on the protein-encoding process as defined by Ensembl. We applied a 100000-time permutation test to obtain empirical p-values, with significance threshold set at p < 1e -3 to control family-wise error rates. Moreover, we compared the burden of targeted rare variants in significant risk genes and gene sets in cases and controls. Results Based on several binary-trait association tests (i.e., SCZ vs HC, EOS vs HC and AOS vs HC), we identified 7 candidate risk genes and 20 gene ontology biological processes (GOBP) terms, which exhibited higher burdens in SCZ than in controls. Based on quantitative rare-variant association tests, we found that alterations in 5 candidate risk genes and 7 GOBP pathways were significantly correlated with AAO. Based on biological and functional profiles of the candidate risk genes and gene sets, our findings suggested that, in addition to the involvement of perturbations in neural systems in SCZ in general, altered immune responses may be specifically implicated in EOS. Conclusion Disrupted immune responses may exacerbate abnormal perturbations during neurodevelopment and trigger the early onset of SCZ. We provided evidence of rare variants increasing SCZ risk in the Chinese population.
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