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Amro C, Niu EF, Deianni E, Smith L, Qiu M, Torkington J, Broach RB, Maguire LH, Damrauer SM, Itani K, Fischer JP. Genetic and biologic risk factors associated with hernia formation: A review. Am J Surg 2024; 234:41-57. [PMID: 38519402 DOI: 10.1016/j.amjsurg.2024.02.029] [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: 11/20/2023] [Revised: 01/28/2024] [Accepted: 02/15/2024] [Indexed: 03/24/2024]
Abstract
BACKGROUND This systematic review aims to identify genetic and biologic markers associated with abdominal hernia formation. METHODS Following PRIMSA-guidelines, we searched PubMed, MEDLINE, Embase, Scopus, and COCHRANE databases. RESULTS Of 5946 studies, 65 were selected, excluding parastomal hernias due to insufficient data. For inguinal hernias, five studies unveiled 92 susceptible loci across 66 genes, predominantly linked to immune responses. Eleven studies observed elevated MMP-2 levels, with seven highlighting greater MMP-2 in direct compared to indirect inguinal hernias. One incisional hernia study identified unique gene-expression profiles in 174 genes associated with inflammation and cell-adhesion. In hiatal hernias, several genetic risk loci were identified. For all hernia categories, type I/III collagen ratios diminished. CONCLUSIONS Biological markers in inguinal hernias appears consistent. Yet, the genetic predisposition in incisional hernias remains elusive. Further research to elucidate these genetic and biological intricacies can pave the way for more individualized patient care.
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Affiliation(s)
- Chris Amro
- Division of Plastic Surgery, Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA; Hansjörg Wyss Department of Plastic Surgery, NYU Langone, New York, NY.
| | - Ellen F Niu
- Division of Plastic Surgery, Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Ellie Deianni
- Division of Plastic Surgery, Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Laurie Smith
- Department of Colorectal Surgery, Cardiff and Vale University Health Board, Cardiff, UK
| | - Maylene Qiu
- Biomedical Library, University of Pennsylvania, Philadelphia, PA, USA
| | - Jared Torkington
- Department of Colorectal Surgery, Cardiff and Vale University Health Board, Cardiff, UK
| | - Robyn B Broach
- Division of Plastic Surgery, Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Lillias H Maguire
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott M Damrauer
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Kamal Itani
- Department of Surgery, VA Boston Health Care System, Boston, MA, USA; Department of Surgery, Boston University, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - John P Fischer
- Division of Plastic Surgery, Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
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2
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Shoji K, Hikino K, Saito J, Matsui T, Utano T, Takebayashi A, Tomizawa D, Kato M, Matsumoto K, Ishikawa T, Kawai T, Nakamura H, Miyairi I, Terao C, Mushiroda T. Pharmacogenetic implementation for CYP2C19 and pharmacokinetics of voriconazole in children with malignancy or inborn errors of immunity. J Infect Chemother 2024:S1341-321X(24)00164-8. [PMID: 38897411 DOI: 10.1016/j.jiac.2024.06.009] [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: 03/16/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Voriconazole pharmacokinetics (PK) are known to be affected by genetic polymorphisms of drug-metabolizing enzymes such as CYP2C19; however, such information is limited for the pediatric population. The primary aim of this study is to establish a voriconazole PK model incorporating CYP2C19 phenotypes in Japanese children with malignancy or inborn errors of immunity. METHODS CYP2C19 genotypes were assessed by whole-genome genotyping and defined as follows: *17/*17: ultrarapid metabolizer (URM), *1/*17: rapid metabolizer (RM), *1/*1:normal metabolizer (NM), *1/*2, *1/*3, *2/*17:intermediate metabolizer (IM), and *2/*2, *2/*3, *3/*3: poor metabolizer (PM). Population PK analysis was performed. The voriconazole serum concentration profile was described by a two-compartment model with first-order absorption, mixed linear and nonlinear (Michaelis-Menten) elimination. RESULTS Voriconazole concentration data were available from 60 patients with a median age of 5.3 years. The phenotypes predicted from CYP2C19 genotypes were RM in 1 (2 %), NM in 21 (35 %) patients, IM in 27 (45 %) patients, and PM in 11 (18 %) patients. Underlying diseases included 38 (63%) patients with hematological malignancy and 18 (30 %) patients with inborn errors of immunity. Among the CYP2C19 phenotypes, PM was predicted to show complete inhibition (the degree of Vmax inhibition [Vmax, inh] = 100 %; Vmax = 0). The estimated parameters of Vmax,inh were +0.8 higher in patients with gamma-glutamyl transpeptidase (γ-GTP) Grade 2 or higher and +2.7 higher when C-reactive protein (CRP) levels were 2.0 mg/dL or higher. CONCLUSION CYP2C19 genetic polymorphisms, γ-GTP, and CRP affect Vmax,inh of voriconazole in children with malignancy or inborn errors of immunity.
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Affiliation(s)
- Kensuke Shoji
- Division of Infectious Diseases, Department of Medical Subspecialties, National Center for Child Health and Development, Tokyo, Japan.
| | - Keiko Hikino
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jumpei Saito
- Department of Pharmacy, National Center for Child Health and Development, Tokyo, Japan
| | - Toshihiro Matsui
- Division of Infectious Diseases, Department of Medical Subspecialties, National Center for Child Health and Development, Tokyo, Japan; Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoyuki Utano
- Department of Pharmacy, National Center for Child Health and Development, Tokyo, Japan
| | - Akira Takebayashi
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Daisuke Tomizawa
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Kimikazu Matsumoto
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Takashi Ishikawa
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Toshinao Kawai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Hidefumi Nakamura
- Department of Research and Development Supervision, National Center for Child Health and Development, Tokyo, Japan
| | - Isao Miyairi
- Division of Infectious Diseases, Department of Medical Subspecialties, National Center for Child Health and Development, Tokyo, Japan; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Pediatrics, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan; The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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3
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Tsukanov AV, Ivanov IS, Ponomareva IV, Tarabrin DV, Panarina NV, Bushueva OY. [Genetic architecture of anterior abdominal wall hernias]. Khirurgiia (Mosk) 2024:118-124. [PMID: 39140953 DOI: 10.17116/hirurgia2024081118] [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] [Indexed: 08/15/2024]
Abstract
OBJECTIVE To analyze genome-wide studies devoted to polymorphisms of factors of anterior abdominal wall hernias, to study the association of the most common polymorphism In Russian population. MATERIAL AND METHODS Searching for literature data was carried out in the RSCI and PubMed databases. We enrolled national and foreign reports. The study on Russian population included 577 people. RESULTS We found 5 genome-wide studies performed by foreign authors. We identified the loci responsible for genetic predisposition to inguinal hernias: WT1, EFEMP1, EBF2 and ADAMTS6. The Japanese scientists revealed an important role of loci TGFB2, RNA5SP214/VGLL2, LOC646588, HMCN2, ATP5F1CP1/CDKN3. In other studies, loci 1q41 (ZC3H11B), 2p16.1 (EFEMP1), 6p22.1 (MHC region), 7q33 (CALD1) and 11p13 (WT1) determined different hernias. The EFEMP1 gene polymorphism was among genes most associated with anterior abdominal wall hernias in all studies. Analysis of this polymorphism In Russian population revealed significant association with anterior abdominal wall hernias. CONCLUSION The obtained data on target correction of DNA chains can significantly reduce the incidence of anterior abdominal wall hernias. In turn, this will significantly reduce the cost of surgical treatment and risk of complications with recurrences of hernias. Moreover, identifying the most associated polymorphisms may be valuable to determine the most appropriate surgical treatment.
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Affiliation(s)
| | - I S Ivanov
- Kursk State Medical University, Kursk, Russia
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4
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Park CL, Chan PH, Prentice HA, Sucher K, Brill ER, Paxton EW, Laxa B. Risk factors for reoperation following inguinal hernia repair: results from a cohort of patients from an integrated healthcare system. Hernia 2023; 27:1515-1524. [PMID: 38007413 DOI: 10.1007/s10029-023-02922-9] [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: 08/16/2023] [Accepted: 10/27/2023] [Indexed: 11/27/2023]
Abstract
PURPOSE Inguinal hernia repair is one of the most common operations performed globally. Identification of risk factors that contribute to hernia recurrence following an index inguinal hernia repair, especially those that are modifiable, is of paramount importance. Therefore, we sought to investigate risk factors for reoperation following index inguinal hernia repair. METHODS 125,133 patients aged ≥ 18 years who underwent their first inguinal hernia repair with mesh within a large US integrated healthcare system were identified for a cohort study (2010-2020). Laparoscopic, robotic, and open procedures were included. The system's integrated electronic health record was used to obtain data on demographics, patient characteristics, surgical characteristics, and reoperations. The association of these characteristics with ipsilateral reoperation during follow-up was modeled using Cox proportional-hazards regression. Risk factors were selected into the final model by stepwise regression with Akaike Information Criteria, which quantifies the amount of information lost if a factor is left out of the model. Factors associated with reoperation with p < 0.05 were considered statistically significant. RESULTS The cumulative incidence of reoperation at 5-year follow-up was 2.4% (95% CI 2.3-2.5). Increasing age, female gender, increasing body mass index, White race, chronic pulmonary disease, diabetes, drug abuse, peripheral vascular disease, and bilateral procedures all associated with a higher risk for reoperation during follow-up. CONCLUSION This study identifies several risk factors associated with reoperation following inguinal hernia repair. These risk factors may serve as targets for optimization protocols prior to elective inguinal hernia repair, with the goal of reducing reoperation risk.
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Affiliation(s)
- Cheryl L Park
- Department of General Surgery, Southern California Permanente Medical Group, 5601 De Soto Ave, Woodland Hills, CA, 91367, USA.
| | - P H Chan
- Medical Device Surveillance and Assessment, Kaiser Permanente, San Diego, CA, USA
| | - H A Prentice
- Medical Device Surveillance and Assessment, Kaiser Permanente, San Diego, CA, USA
| | - K Sucher
- Medical Device Surveillance and Assessment, Kaiser Permanente, San Diego, CA, USA
| | - E R Brill
- Department of Surgery, The Permanente Medical Group, Santa Clara, CA, USA
| | - E W Paxton
- Medical Device Surveillance and Assessment, Kaiser Permanente, San Diego, CA, USA
| | - B Laxa
- Department of General Surgery, Southern California Permanente Medical Group, Downey, CA, USA
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5
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Zhang HY, Xiao M, Zhang Y. Novel mutation in ELN gene causes cardiac abnormalities and inguinal hernia: case report. BMC Pediatr 2023; 23:580. [PMID: 37980465 PMCID: PMC10656980 DOI: 10.1186/s12887-023-04408-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/03/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND Elastin-driven genetic diseases are a group of complex diseases driven by elastin protein insufficiency and dominant-negative production of aberrant protein, including supravalvular aortic stenosis (SVAS) and autosomal dominant cutis laxa. Here, a Chinese boy with a novel nonsense mutation in the ELN gene is reported. CASE PRESENTATION We report a 1-year-old boy who presented with exercise intolerance, weight growth restriction with age, a 1-year history of heart murmur, and inguinal hernia. Gene sequencing revealed a novel nonsense mutation in the ELN gene (c.757 C > T (p.Gln253Ter), NM_000501.4). Due to severe branch pulmonary artery stenosis, the reconstruction of the branch pulmonary artery with autologous pericardium was performed. The inguinal hernia repair was performed 3 months postoperatively. After six months of outpatient follow-up, the child recovered well, gained weight with age, and had no special clinical symptoms. CONCLUSION We identified a de novo nonsense mutation in the ELN gene leading to mild SVAS and severe branch pulmonary artery stenosis. A new phenotype of inguinal hernia was also needed to be considered for possible association with the ELN gene. Still, further confirmation will be necessary.
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Affiliation(s)
- Hua-Yong Zhang
- Department of Cardiology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430016, China
| | - Min Xiao
- Department of Rheumatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Yong Zhang
- Department of Cardiology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430016, China.
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6
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Yen HC, Chen IC, Lin GC, Ke YY, Lin MC, Chen YM, Hsu CC. Sex-specific genetic variants associated with adult-onset inguinal hernia in a Taiwanese population. Int J Med Sci 2023; 20:607-615. [PMID: 37082733 PMCID: PMC10110472 DOI: 10.7150/ijms.82331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/16/2023] [Indexed: 04/22/2023] Open
Abstract
Introduction: Inguinal hernia repair is one of the most common surgeries worldwide. However, there is limited information on its underlying genetic mechanism. Studies on the genetic factors related to inguinal hernia in Han Chinese are lacking. Therefore, we aimed to conduct a hospital-based study to assess the genetic factors and comorbidities underlying inguinal hernia in Taiwan. Materials and Methods: This was a retrospective case-control study. Utilizing data from the Taiwan Precision Medicine Initiative, we identified 1000 patients with inguinal hernia and 10,021 matched controls without inguinal hernia between June 2019 and June 2020. Four susceptibility loci (rs2009262, rs13091322, rs6991952, and rs3809060) associated with inguinal hernia were genotyped by the Taiwan Biobank version 2 (TWBv2) array. Inguinal hernia, surgery types, and comorbidities were obtained from the electronic health records of Taichung Veterans General Hospital. Results: Adult-onset inguinal hernia was associated with WT1 rs3809060 GT/TT genotype in males and EFEMP1 rs2009262 TC/CC genotype in females. In addition, we identified sex-specific risk factors associated with inguinal hernia; benign prostatic hyperplasia in males (OR: 3.19, 95% CI: 2.73 - 3.73, p< 0.001), chronic obstructive pulmonary disease in females (OR: 2.34, 95% CI: 1.33 - 4.11, p = 0.003) and overweight, defined by body mass index ≧24 kg/m2 (OR: 0.75, 95% CI: 0.65 - 0.86, p<0.001 in males, and OR: 0.60, 95% CI:0.37 - 0.98, p = 0.042 in females), were inversely associated with inguinal hernia. After stratifying BMI, overweight males with EFEMP1 rs2009262 TC/CC genotype exhibited a higher risk of inguinal hernia (OR: 1.31, 95% CI: 1.07 - 1.61, p = 0.01). Additionally, rs3809060 was specifically associated with male patients with direct-type inguinal hernia (OR: 1.62, 95% CI: 1.19 - 2.22, p = 0.002). Conclusion: Genetic susceptibility appears to participate in the pathogenesis of inguinal hernia in the Taiwanese population in a sex-specific manner. Future studies are needed to illuminate the complex interplay between heredity and comorbidities.
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Affiliation(s)
- Hsin-Chien Yen
- Division of Pediatric Genetics and Metabolism, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - I-Chieh Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Guan-Cheng Lin
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Yuan Ke
- Division of Pediatric Genetics and Metabolism, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ming-Chih Lin
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Food and Nutrition, Providence University, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yi-Ming Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- Institute of Biomedical Science and Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taiwan
- ✉ Corresponding authors: Yi-Ming Chen, M.D., Ph.D. Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, Taichung Veterans General Hospital, 1650, Section 4, Taiwan Boulevard, Xitun Dist., Taichung City 40705, Taiwan. Tel.: +886-4-2359-2525 ext. 3354; Fax: +886-4-2350-3285; E-mail: . Chia-Chi Hsu, M.D. Division of Pediatric Genetics and Metabolism, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan. Tel.: +886-4-2359-2525 ext. 5987; Fax: +886-4-2359-5046; E-mail:
| | - Chia-Chi Hsu
- Division of Pediatric Genetics and Metabolism, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- ✉ Corresponding authors: Yi-Ming Chen, M.D., Ph.D. Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, Taichung Veterans General Hospital, 1650, Section 4, Taiwan Boulevard, Xitun Dist., Taichung City 40705, Taiwan. Tel.: +886-4-2359-2525 ext. 3354; Fax: +886-4-2350-3285; E-mail: . Chia-Chi Hsu, M.D. Division of Pediatric Genetics and Metabolism, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan. Tel.: +886-4-2359-2525 ext. 5987; Fax: +886-4-2359-5046; E-mail:
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Ahmed WUR, Patel MIA, Ng M, McVeigh J, Zondervan K, Wiberg A, Furniss D. Shared genetic architecture of hernias: A genome-wide association study with multivariable meta-analysis of multiple hernia phenotypes. PLoS One 2022; 17:e0272261. [PMID: 36584111 PMCID: PMC9803250 DOI: 10.1371/journal.pone.0272261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/14/2022] [Indexed: 12/31/2022] Open
Abstract
Abdominal hernias are common and characterised by the abnormal protrusion of a viscus through the wall of the abdominal cavity. The global incidence is 18.5 million annually and there are limited non-surgical treatments. To improve understanding of common hernia aetiopathology, we performed a six-stage genome-wide association study (GWAS) of 62,637 UK Biobank participants with either single or multiple hernia phenotypes including inguinal, femoral, umbilical and hiatus hernia. Additionally, we performed multivariable meta-analysis with metaUSAT, to allow integration of summary data across traits to generate combined effect estimates. On individual hernia analysis, we identified 3404 variants across 38 genome-wide significant (p < 5×10-8) loci of which 11 are previously unreported. Robust evidence for five shared susceptibility loci was discovered: ZC3H11B, EFEMP1, MHC region, WT1 and CALD1. Combined hernia phenotype analyses with additional multivariable meta-analysis of summary statistics in metaUSAT revealed 28 independent (seven previously unreported) shared susceptibility loci. These clustered in functional categories related to connective tissue and elastic fibre homeostasis. Weighted genetic risk scores also correlated with disease severity suggesting a phenotypic-genotypic severity correlation, an important finding to inform future personalised therapeutic approaches to hernia.
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Affiliation(s)
- Waheed Ul-Rahman Ahmed
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Manal I. A. Patel
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael Ng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - James McVeigh
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Krina Zondervan
- Nuffield Department of Women’s & Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Akira Wiberg
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
- Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Dominic Furniss
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
- Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- * E-mail:
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8
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Koido M, Hon CC, Koyama S, Kawaji H, Murakawa Y, Ishigaki K, Ito K, Sese J, Parrish NF, Kamatani Y, Carninci P, Terao C. Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning. Nat Biomed Eng 2022:10.1038/s41551-022-00961-8. [PMID: 36411359 DOI: 10.1038/s41551-022-00961-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/12/2022] [Indexed: 11/22/2022]
Abstract
Gene transcription is regulated through complex mechanisms involving non-coding RNAs (ncRNAs). As the transcription of ncRNAs, especially of enhancer RNAs, is often low and cell type specific, how the levels of RNA transcription depend on genotype remains largely unexplored. Here we report the development and utility of a machine-learning model (MENTR) that reliably links genome sequence and ncRNA expression at the cell type level. Effects on ncRNA transcription predicted by the model were concordant with estimates from published studies in a cell-type-dependent manner, regardless of allele frequency and genetic linkage. Among 41,223 variants from genome-wide association studies, the model identified 7,775 enhancer RNAs and 3,548 long ncRNAs causally associated with complex traits across 348 major human primary cells and tissues, such as rare variants plausibly altering the transcription of enhancer RNAs to influence the risks of Crohn's disease and asthma. The model may aid the discovery of causal variants and the generation of testable hypotheses for biological mechanisms driving complex traits.
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Affiliation(s)
- Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Chung-Chau Hon
- Laboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hideya Kawaji
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.,Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo, Japan.,Humanome Lab Inc., Tokyo, Japan
| | - Nicholas F Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory for Single Cell Technologies, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Human Technopole, Milan, Italy
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. .,Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan. .,The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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9
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Choquet H, Li W, Yin J, Bradley R, Hoffmann TJ, Nandakumar P, Mostaedi R, Tian C, Ahituv N, Jorgenson E. Ancestry- and sex-specific effects underlying inguinal hernia susceptibility identified in a multiethnic genome-wide association study meta-analysis. Hum Mol Genet 2022; 31:2279-2293. [PMID: 35022708 PMCID: PMC9262393 DOI: 10.1093/hmg/ddac003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/06/2021] [Accepted: 01/04/2022] [Indexed: 12/03/2022] Open
Abstract
Inguinal hernias are some of the most frequently diagnosed conditions in clinical practice and inguinal hernia repair is the most common procedure performed by general surgeons. Studies of inguinal hernias in non-European populations are lacking, though it is expected that such studies could identify novel loci. Further, the cumulative lifetime incidence of inguinal hernia is nine times greater in men than women, however, it is not clear why this difference exists. We conducted a genome-wide association meta-analysis of inguinal hernia risk across 513 120 individuals (35 774 cases and 477 346 controls) of Hispanic/Latino, African, Asian and European descent, with replication in 728 418 participants (33 491 cases and 694 927 controls) from the 23andMe, Inc dataset. We identified 63 genome-wide significant loci (P < 5 × 10−8), including 41 novel. Ancestry-specific analyses identified two loci (LYPLAL1-AS1/SLC30A10 and STXBP6-NOVA1) in African ancestry individuals. Sex-stratified analyses identified two loci (MYO1D and ZBTB7C) that are specific to women, and four (EBF2, EMX2/RAB11FIP2, VCL and FAM9A/FAM9B) that are specific to men. Functional experiments demonstrated that several of the associated regions (EFEMP1 and LYPLAL1-SLC30A10) function as enhancers and show differential activity between risk and reference alleles. Our study highlights the importance of large-scale genomic studies in ancestrally diverse populations for identifying ancestry-specific inguinal hernia susceptibility loci and provides novel biological insights into inguinal hernia etiology.
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Affiliation(s)
- Hélène Choquet
- To whom correspondence should be addressed at: KPNC, Division of Research, 2000 Broadway, Oakland, CA 94612, USA. Tel: +1 5108915972; Fax: +1 5108913508;
| | - Weiyu Li
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Jie Yin
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA 94612, USA
| | - Rachael Bradley
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Thomas J Hoffmann
- Institute for Human Genetics, UCSF, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA 94158, USA
| | | | | | | | - Chao Tian
- 23andMe Inc, Sunnyvale, CA 94086, USA
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Ramkhalawan D, Makki N. New insights into the genetic architecture of inguinal hernia. EBioMedicine 2021; 71:103564. [PMID: 34455395 PMCID: PMC8399045 DOI: 10.1016/j.ebiom.2021.103564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Darius Ramkhalawan
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Nadja Makki
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida, USA.
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