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Cristian HR, Walshe M, Birch S, Sabic K, Korie U, Chasteau C, Miladinova VM, Sabol WB, Mengesha E, Hanna M, Pozdnyakova V, Datta L, Kohen R, Milgrom R, Stempak JM, Bitton A, Brant SR, Rioux JD, McGovern DPB, Duerr RH, Cho JH, Schumm PL, Silverberg MS, Lazarev M. Clinical predictors of early and late endoscopic recurrence following ileocolonic resection in Crohn's disease. J Crohns Colitis 2023:jjad186. [PMID: 37976264 DOI: 10.1093/ecco-jcc/jjad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND AND AIM Multiple factors are suggested to place Crohn's disease patients at risk of recurrence after ileocolic resection with conflicting associations. We aimed to identify clinical predictors of recurrence at first (early) and further (late) postoperative colonoscopy. METHODS Crohn's disease patients undergoing ileocolic resection were prospectively recruited at six North American centers. Clinical data was collected and endoscopic recurrence was defined as Rutgeerts score ≥i2. A multivariable model was fitted to analyze variables independently associated with recurrence. RESULTS A total of 365 patients undergoing 674 postoperative colonoscopies were included with a median age of 32 years, 189 (51.8%) were male and 37 (10.1%) non-Whites. Postoperatively, 133 (36.4%) used anti-TNF and 30 (8.2%) were smokers. At first colonoscopy, 109 (29.9%) had recurrence. Male gender (OR = 1.95, 95% CI 1.12 - 3.40), non-White ethnicity (OR = 2.48, 95% CI 1.09 - 5.63), longer interval between surgery and colonoscopy (OR = 1.09, 95% CI 1.002 - 1.18), and postoperative smoking (OR = 2.78, 95% CI 1.16 - 6.67) were associated with recurrence, while prophylactic anti-TNF reduced the risk (OR = 0.28, 95% CI 0.14 - 0.55). Postoperative anti-TNF prophylaxis had a protective effect on anti-TNF experienced patients but not on anti-TNF naïve patients. Among patients without recurrence at first colonoscopy, Rutgeerts score i1 was associated with subsequent recurrence (OR = 4.43, 95% CI 1.73 - 11.35). CONCLUSIONS We identified independent clinical predictors of early and late Crohn's disease postoperative endoscopic recurrence. Clinical factors traditionally used for risk stratification failed to predict recurrence and need to be revised.
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Affiliation(s)
- Hernandez-Rocha Cristian
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Margaret Walshe
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Sondra Birch
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Ksenija Sabic
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ujunwa Korie
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Colleen Chasteau
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vessela M Miladinova
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - William B Sabol
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Mary Hanna
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Lisa Datta
- Department of Gastroenterology, The John Hopkins Medical Institutions, Baltimore, MD, USA
| | - Rita Kohen
- Inflammatory Bowel Disease Centre, Division of Gastroenterology, McGill University Health Centre, Montréal, Quebec, Canada
| | - Raquel Milgrom
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Joanne M Stempak
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Alain Bitton
- Inflammatory Bowel Disease Centre, Division of Gastroenterology, McGill University Health Centre, Montréal, Quebec, Canada
| | - Steven R Brant
- Crohn's and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - John D Rioux
- Research Centre, Montreal Heart Institute, Montréal, Quebec, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Phil L Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Mark Lazarev
- Department of Gastroenterology, The John Hopkins Medical Institutions, Baltimore, MD, USA
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Astore C, Sharma S, Nagpal S, Cutler DJ, Rioux JD, Cho JH, McGovern DPB, Brant SR, Kugathasan S, Jordan IK, Gibson G. The role of admixture in the rare variant contribution to inflammatory bowel disease. Genome Med 2023; 15:97. [PMID: 37968638 PMCID: PMC10647102 DOI: 10.1186/s13073-023-01244-w] [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: 04/05/2023] [Accepted: 10/10/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Identification of rare variants involved in complex, polygenic diseases like Crohn's disease (CD) has accelerated with the introduction of whole exome/genome sequencing association studies. Rare variants can be used in both diagnostic and therapeutic assessments; however, since they are likely to be restricted to specific ancestry groups, their contributions to risk assessment need to be evaluated outside the discovery population. Prior studies implied that the three known rare variants in NOD2 are absent in West African and Asian populations and only contribute in African Americans via admixture. METHODS Whole genome sequencing (WGS) data from 3418 African American individuals, 1774 inflammatory bowel disease (IBD) cases, and 1644 controls were used to assess odds ratios and allele frequencies (AF), as well as haplotype-specific ancestral origins of European-derived CD variants discovered in a large exome-wide association study. Local and global ancestry was performed to assess the contribution of admixture to IBD contrasting European and African American cohorts. RESULTS Twenty-five rare variants associated with CD in European discovery cohorts are typically five-fold lower frequency in African Americans. Correspondingly, where comparisons could be made, the rare variants were found to have a predicted four-fold reduced burden for IBD in African Americans, when compared to European individuals. Almost all of the rare CD European variants were found on European haplotypes in the African American cohort, implying that they contribute to disease risk in African Americans primarily due to recent admixture. In addition, proportion of European ancestry correlates the number of rare CD European variants each African American individual carry, as well as their polygenic risk of disease. Similar findings were observed for 23 mutations affecting 10 other common complex diseases for which the rare variants were discovered in European cohorts. CONCLUSIONS European-derived Crohn's disease rare variants are even more rare in African Americans and contribute to disease risk mainly due to admixture, which needs to be accounted for when performing cross-ancestry genetic assessments.
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Affiliation(s)
- Courtney Astore
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Shivam Sharma
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Sini Nagpal
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - John D Rioux
- Department of Medicine, Université de Montréal and the Montreal Heart Institute Research Center, Montreal, QC, H1Y3N1, Canada
| | - Judy H Cho
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dermot P B McGovern
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, 08554, USA
- Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, 21287, USA
| | - Steven R Brant
- Immunology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Subra Kugathasan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - I King Jordan
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Greg Gibson
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA.
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Akhlaghpour M, Haritunians T, More SK, Thomas LS, Stamps DT, Dube S, Li D, Yang S, Landers CJ, Mengesha E, Hamade H, Murali R, Potdar AA, Wolf AJ, Botwin GJ, Khrom M, Ananthakrishnan AN, Faubion WA, Jabri B, Lira SA, Newberry RD, Sandler RS, Sartor RB, Xavier RJ, Brant SR, Cho JH, Duerr RH, Lazarev MG, Rioux JD, Schumm LP, Silverberg MS, Zaghiyan K, Fleshner P, Melmed GY, Vasiliauskas EA, Ha C, Rabizadeh S, Syal G, Bonthala NN, Ziring DA, Targan SR, Long MD, McGovern DPB, Michelsen KS. Genetic coding variant in complement factor B (CFB) is associated with increased risk for perianal Crohn's disease and leads to impaired CFB cleavage and phagocytosis. Gut 2023; 72:2068-2080. [PMID: 37080587 DOI: 10.1136/gutjnl-2023-329689] [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] [Received: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 04/22/2023]
Abstract
OBJECTIVE Perianal Crohn's disease (pCD) occurs in up to 40% of patients with CD and is associated with poor quality of life, limited treatment responses and poorly understood aetiology. We performed a genetic association study comparing CD subjects with and without perianal disease and subsequently performed functional follow-up studies for a pCD associated SNP in Complement Factor B (CFB). DESIGN Immunochip-based meta-analysis on 4056 pCD and 11 088 patients with CD from three independent cohorts was performed. Serological and clinical variables were analysed by regression analyses. Risk allele of rs4151651 was introduced into human CFB plasmid by site-directed mutagenesis. Binding of recombinant G252 or S252 CFB to C3b and its cleavage was determined in cell-free assays. Macrophage phagocytosis in presence of recombinant CFB or serum from CFB risk, or protective CD or healthy subjects was assessed by flow cytometry. RESULTS Perianal complications were associated with colonic involvement, OmpC and ASCA serology, and serology quartile sum score. We identified a genetic association for pCD (rs4151651), a non-synonymous SNP (G252S) in CFB, in all three cohorts. Recombinant S252 CFB had reduced binding to C3b, its cleavage was impaired, and complement-driven phagocytosis and cytokine secretion were reduced compared with G252 CFB. Serine 252 generates a de novo glycosylation site in CFB. Serum from homozygous risk patients displayed significantly decreased macrophage phagocytosis compared with non-risk serum. CONCLUSION pCD-associated rs4151651 in CFB is a loss-of-function mutation that impairs its cleavage, activation of alternative complement pathway, and pathogen phagocytosis thus implicating the alternative complement pathway and CFB in pCD aetiology.
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Affiliation(s)
- Marzieh Akhlaghpour
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shyam K More
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lisa S Thomas
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalton T Stamps
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Carol J Landers
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Hussein Hamade
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Alka A Potdar
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Andrea J Wolf
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | | | - Bana Jabri
- Biological Sciences Division, University of Chicago, Pritzker School of Medicine, Chicago, Illinois, USA
| | - Sergio A Lira
- Immunology Institute, Mount Sinai Medical Center, New York, New York, USA
| | - Rodney D Newberry
- Division of Gastroenterology, Washington Univ. Sch. of Medicine, Saint Louis, Missouri, USA
| | - Robert S Sandler
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Steven R Brant
- Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Judy H Cho
- Genetics and Genomics Sciences, Mt Sinai School of Medicine, New York, New York, USA
| | - Richard H Duerr
- Departments of Medicine and Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mark G Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John D Rioux
- Faculty of Medicine, Universite de Montreal, Montreal, Québec, Canada
| | - L Philip Schumm
- Dept of Health Studies, University of Chicago, Chicago, Illinois, USA
| | - Mark S Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Karen Zaghiyan
- Division of Colorectal Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Phillip Fleshner
- Division of Colorectal Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gil Y Melmed
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Eric A Vasiliauskas
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Christina Ha
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shervin Rabizadeh
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gaurav Syal
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nirupama N Bonthala
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - David A Ziring
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Millie D Long
- Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kathrin S Michelsen
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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Choi SH, Lee JG, Cho JH. The Role of Local Prostate and Metastasis-Directed Radiotherapy in the Treatment of Oligometastatic Prostate Cancer. Int J Radiat Oncol Biol Phys 2023; 117:e373. [PMID: 37785271 DOI: 10.1016/j.ijrobp.2023.06.2476] [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] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The local ablative therapy for oligometastatic disease (OMD) has the potential to delay further metastases and improve survival. However, it has not been fully elucidated how prostate primary radiotherapy (PPR) and metastasis-directed radiotherapy (MDR) affect prognosis in each different OMD scenario. Herein, we tried to provide efficacy and future perspectives for MDR in oligometastatic prostate cancer. MATERIALS/METHODS Patients diagnosed with prostate cancer between 2010 and 2019 and treated for OMD (≤5 active lesions), which occurred synchronously or metachronously, were included. All patients received MDR at all detected lesions (OMDRT). OMDRT which was performed as soon as OMD was detected was classified as early, and OMDRT for progressions after hormone therapy was classified as late. The primary endpoint was survival after OMDRT, and timing of progression after RT was also analyzed. RESULTS A total of 82 patients with oligometastatic prostate cancer received OMDRT. Among 36 patients with synchronous OMD, 58% received PPR at diagnosis, and 64% received early OMDRT. Among 46 patients with metachronous OMD, 80% received early OMDRT, and 28 received sequential OMDRT for repetitive OMD events. With a median follow-up of 32 months after OMDRT, 54 patients experienced progression and 5-year survival was 78%. Survival was highest in patients with synchronous OMD and early RT (5-year 86%), and 5-year survival of patients with metachronous OMD and early RT was significantly higher than those with late RT (78% vs. 44%, p = 0.003). Survival of patients with synchronous OMD and PPR was significantly higher than those without PPR or with metachronous OMD (5-year 90% vs. 66%, p = 0.030), by delaying progressions (17.9 vs. 7.0 months, p = 0.005). CONCLUSION Survival gain could be achieved through OMDRT in oligometastatic prostate cancer, especially in synchronous OMD status. Also, it was possible to improve the prognosis further when OMDRT was performed early and with PPR.
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Affiliation(s)
- S H Choi
- Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - J G Lee
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - J H Cho
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
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Choi H, Lee JG, Kim J, Byun HK, Kim KH, Koom WS, Cho JH, Lee IJ. Mapping the Anatomical Distribution of MRI-Identified Locoregional Recurrence following Robotic-Assisted Laparoscopic Prostatectomy for Prostate Adenocarcinoma. Int J Radiat Oncol Biol Phys 2023; 117:e373. [PMID: 37785270 DOI: 10.1016/j.ijrobp.2023.06.2475] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The pattern of locoregional recurrence specifically after robotic-assisted laparoscopic prostatectomy (RALP) for prostate adenocarcinoma is still unknown. In this study, we reviewed pelvic magnetic resonance images (MRI) after postoperative biochemical recurrence (BCR) and drew a map of locoregional recurrence to support evidence of determining the optimal target volume of salvage radiotherapy in a post-RALP BCR scenario. MATERIALS/METHODS We have retrospectively searched 7,583 prostate adenocarcinoma patients who have received RALP in our institution between January 2010 and December 2021, and found a pool of highly selected patients with gross tumor recurrence confirmed by post-BCR pelvic MRIs and did not have other histories of malignancy. BCR was defined as the serum PSA more or equal to 0.2 ng/mL, or three consecutive increases. Patients with serum PSA nadir more or equal to 0.2 ng/mL on the 90th postoperative day (POD 90) were excluded to guarantee successful tumor removal. We have reviewed serum PSA levels using R codes, MRI and pathological reports using Excel, and descriptive statistics using SPSS 25. The gross lesions were contoured on the correlating MRIs using MIM Maestro 7.1. The RT structure DICOM files were merged into a map using MATLAB 2022b. In addition, we have conducted Fisher exacted test, Mann-Whitney U test, and logistic regression to identify risk factors for regional recurrence. RESULTS A total of 173 patients were identified with locoregional recurrence from post-BCR pelvic MRIs, and 139 (80.3%) patients were in the high-risk group or very-high-risk group according to the NCCN guidelines: 57 (32.9%) patients with histological grade group 5, 50 (28.9%) patients with initial PSA over 20 ng/mL, 114 (65.9%) patients with extracapsular extension, 55 (31.8%) patients with seminal vesicle invasion, and 15 (9%) patients with pN1. The median follow-up was 4.7 (IQR 2.8-6.9) years for pelvic MRIs and 5.8 (IQR 4.0-8.6) years for serum PSA. The BCF survival was median of 10.7 (IQR 4.6-19.1) months, and the locoregional recurrence-free survival was median of 24.6 (IQR 9.7-49.4) months for this subgroup of patients. At first locoregional recurrence, 148 (85.5%) patients were local only, 20 (11.6%) patients were regional only, and 5 (2.9%) patients were both local and regional. Out of the 25 patients with regional recurrence, the incidence of gross tumor recurrence differed by nodal sites: 3 (12%) in perirectal space, 5 (20%) in internal iliac, 7 (28%) in obturator, 13 (52%) in external iliac, and 6 (24%) in common iliac lymph nodes. CONCLUSION We have found 173 patients and were able to map reliable gross tumor recurrence sites after RALP and confirmed by pelvic MRIs following BCR. The map supports evidence of using the existing consensus pelvic clinical target volume of salvage radiotherapy, in a post-RALP BCR scenario.
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Affiliation(s)
- H Choi
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - J G Lee
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - J Kim
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - H K Byun
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - K H Kim
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - W S Koom
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - J H Cho
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - I J Lee
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
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Moscati A, Faucon AB, Arnaiz-Yépez C, Lönn SL, Sundquist J, Sundquist K, Belbin GM, Nadkarni G, Cho JH, Loos RJF, Davis LK, Kendler KS. Life is pain: Fibromyalgia as a nexus of multiple liability distributions. Am J Med Genet B Neuropsychiatr Genet 2023; 192:171-182. [PMID: 37334860 DOI: 10.1002/ajmg.b.32949] [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] [Received: 01/08/2022] [Revised: 03/20/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Fibromyalgia is a complex disease of unclear etiology that is complicated by difficulties in diagnosis, treatment, and clinical heterogeneity. To clarify this etiology, healthcare-based data are leveraged to assess the influences on fibromyalgia in several domains. Prevalence is less than 1% of females in our population register data, and about 1/10th that in males. Fibromyalgia often presents with co-occurring conditions including back pain, rheumatoid arthritis, and anxiety. More comorbidities are identified with hospital-associated biobank data, falling into three broad categories of pain-related, autoimmune, and psychiatric disorders. Selecting representative phenotypes with published genome-wide association results for polygenic scoring, we confirm genetic predispositions to psychiatric, pain sensitivity, and autoimmune conditions show associations with fibromyalgia, although these may differ by ancestry group. We conduct a genome-wide association analysis of fibromyalgia in biobank samples, which did not result in any genome-wide significant loci; further studies with increased sample size are necessary to identify specific genetic effects on fibromyalgia. Overall, fibromyalgia appears to have strong clinical and likely genetic links to several disease categories, and could usefully be understood as a composite manifestation of these etiological sources.
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Affiliation(s)
- Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Annika B Faucon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cayetana Arnaiz-Yépez
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sara Larsson Lönn
- Center for Primary Health Care Research, Lund University, Lund, Sweden
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University, Lund, Sweden
- Department of Family Medicine and Community Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Functional Pathology, School of Medicine, Center for Community-based Healthcare Research and Education (CoHRE), Shimane University, Matsue, Japan
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University, Lund, Sweden
- Department of Family Medicine and Community Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Functional Pathology, School of Medicine, Center for Community-based Healthcare Research and Education (CoHRE), Shimane University, Matsue, Japan
| | - Gillian M Belbin
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lea K Davis
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, USA
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Lee HI, Kim J, Kim IA, Lee JH, Cho JH, Yoon HI, Wee CW. Choosing Wisely between Radiotherapy Dose-Fractionation Schedules: The Molecular Graded Prognostic Assessment (molGPA) for Elderly Glioblastoma (eGBM-molGPA). Int J Radiat Oncol Biol Phys 2023; 117:e125-e126. [PMID: 37784678 DOI: 10.1016/j.ijrobp.2023.06.919] [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] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) This study aimed to develop a graded prognostic assessment (GPA) model integrating genomic characteristics in patients with elderly glioblastoma (eGBM), and compare the efficacy between conventionally fractionated radiotherapy (CFRT) vs. hypofractionated radiotherapy (HFRT) in each risk group. MATERIALS/METHODS Patients aged ≥65 years who underwent surgical resection followed by radiotherapy (RT) with or without temozolomide (TMZ) for newly diagnosed IDH-wildtype eGBM between 2006 and 2021 were included in this multicenter cohort study. Patients who were planned for a ≥6-week or ≤4-week radiotherapy were regarded as being treated with CFRT or HFRT, respectively. Based on the prognostic factors significantly identified through multivariate analysis for overall survival (OS), we developed the molecular GPA for eGBM (eGBM-molGPA) and assigned 0.0, 0.5, and 1.0 points in proportion to the corresponding hazard ratio (HR) of each factor. Then, the survival outcomes by treatment groups were evaluated according to the eGBM-molGPA scores. RESULTS A total of 334 and 239 patients who underwent CFRT and HFRT were included, respectively, and 86% of patients were treated with TMZ-based chemoradiation. With a median follow-up of 17.4 months for survivors, the median OS was 18.7 months for CFRT plus TMZ group, 15.1 months for HFRT plus TMZ group, and 10.4 months for RT alone group, respectively (all p<0.001). In the multivariate analysis, Karnofsky performance scale, surgical extent, TMZ, and the methylation status of the MGMT promoter were identified as strong prognostic factors for OS, with an estimated HR of greater than 1.5 (all p<0.001). Additionally, subventricular zone involvement, temporalis muscle thickness, RT regimen, and the mutation status of TERT promoter and TP53 gene were found to be significant prognostic factors for OS, with an estimated HR of less than 1.5. The eGBM-molGPA was established based on these prognostic factors (Table 1) and patients were allocated to three risk groups, which included high risk (total score of 3.0-4.5), intermediate risk (1.5-2.5), and low risk (0.0-1.0). Patients treated with CFRT plus TMZ had significantly improved OS compared to those treated with HFRT plus TMZ or RT alone in the low and intermediate risk groups (p<0.001). However, in the high-risk group, there was no significant difference in OS between treatment options (p = 0.770). CONCLUSION CFRT plus TMZ can be a more effective strategy for selected eGBM patients compared to HFRT. For high-risk patients, a protracted treatment schedule might not be beneficial. The novel eGBM-molGPA can be used as a clinical tool for choosing wisely among treatment options. Further prospective studies are warranted to establish optimal RT guidelines for eGBM patients.
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Affiliation(s)
- H I Lee
- Department of Radiation Oncology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - J Kim
- Department of Radiation Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - I A Kim
- Department of Radiation Oncology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea, Republic of (South) Korea
| | - J H Lee
- Department of Radiation Oncology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - J H Cho
- Department of Radiation Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - H I Yoon
- Department of Radiation Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - C W Wee
- Department of Radiation Oncology, SMG-SNU Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea, Republic of (South) Korea
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8
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Paranjpe I, Wang X, Anandakrishnan N, Haydak JC, Van Vleck T, DeFronzo S, Li Z, Mendoza A, Liu R, Fu J, Forrest I, Zhou W, Lee K, O'Hagan R, Dellepiane S, Menon KM, Gulamali F, Kamat S, Gusella GL, Charney AW, Hofer I, Cho JH, Do R, Glicksberg BS, He JC, Nadkarni GN, Azeloglu EU. Deep learning on electronic medical records identifies distinct subphenotypes of diabetic kidney disease driven by genetic variations in the Rho pathway. medRxiv 2023:2023.09.06.23295120. [PMID: 37732187 PMCID: PMC10508814 DOI: 10.1101/2023.09.06.23295120] [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: 09/22/2023]
Abstract
Kidney disease affects 50% of all diabetic patients; however, prediction of disease progression has been challenging due to inherent disease heterogeneity. We use deep learning to identify novel genetic signatures prognostically associated with outcomes. Using autoencoders and unsupervised clustering of electronic health record data on 1,372 diabetic kidney disease patients, we establish two clusters with differential prevalence of end-stage kidney disease. Exome-wide associations identify a novel variant in ARHGEF18, a Rho guanine exchange factor specifically expressed in glomeruli. Overexpression of ARHGEF18 in human podocytes leads to impairments in focal adhesion architecture, cytoskeletal dynamics, cellular motility, and RhoA/Rac1 activation. Mutant GEF18 is resistant to ubiquitin mediated degradation leading to pathologically increased protein levels. Our findings uncover the first known disease-causing genetic variant that affects protein stability of a cytoskeletal regulator through impaired degradation, a potentially novel class of expression quantitative trait loci that can be therapeutically targeted.
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9
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Ibing S, Cho JH, Böttinger EP, Ungaro RC. Second-Line Biologic Therapy Following Tumor Necrosis Factor Antagonist Failure: A Real-World Propensity Score-Weighted Analysis. Clin Gastroenterol Hepatol 2023; 21:2629-2638. [PMID: 36787837 DOI: 10.1016/j.cgh.2023.01.038] [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] [Received: 07/21/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND& AIMS Tumor necrosis factor (TNF) antagonists often are used as first-line medications to treat moderate to severe inflammatory bowel disease (IBD), but many patients do not achieve or maintain response. Our aim was to compare the effectiveness of second-line treatments (ustekinumab, vedolizumab, or a second TNF antagonist) after TNF antagonist exposure in patients with Crohn's disease (CD) and ulcerative colitis (UC) from 2 electronic health records-based cohorts. METHODS We identified patients with prior TNF antagonist exposure who switched to a different biologic in the Mount Sinai Health System (MSHS) electronic health records (CD, n = 527; UC, n = 165) and the Study of a Prospective Adult Research Cohort (SPARC) from the Inflammatory Bowel Disease Plexus Program of the Crohn's & Colitis Foundation (CD, n = 412; UC, n = 129). Treatment failure was defined as the composite of any IBD-related surgery, IBD-related hospitalization, new prescription of oral/intravenous corticosteroids, or need to switch to a third biologic agent. Time-to-event analysis was conducted with inverse probability of treatment-weighted data. RESULTS Overall, treatment failure occurred in 85% of MSHS and 72% of SPARC CD patients. In SPARC, the likelihood of treatment failure was significantly lower with ustekinumab compared with vedolizumab as second-line treatment (adjusted hazard ratio, 0.66; 95% CI, 0.54-0.82; P < .001), a trend confirmed in MSHS (adjusted hazard ratio, 0.89; 95% CI, 0.77-1.04; P = .15). In both cohorts, the superiority of ustekinumab compared with vedolizumab was shown when considering treatment failure as prescription of steroids or a third biologic agent. In UC, no differences between second-line treatment groups were identified. CONCLUSIONS In 2 independent real-world cohort settings, second-line therapy in CD with ustekinumab after TNF antagonist treatment failure was associated with a lower likelihood of treatment failure than second-line vedolizumab.
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Affiliation(s)
- Susanne Ibing
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York; Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany
| | - Judy H Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Erwin P Böttinger
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York; Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany
| | - Ryan C Ungaro
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York.
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10
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Ferru-Clément R, Boucher G, Forest A, Bouchard B, Bitton A, Lesage S, Schumm P, Lazarev M, Brant S, Duerr RH, McGovern DPB, Silverberg M, Cho JH, Ananthakrishnan A, Xavier RJ, Rioux JD, Des Rosiers C. Serum Lipidomic Screen Identifies Key Metabolites, Pathways, and Disease Classifiers in Crohn's Disease. Inflamm Bowel Dis 2023; 29:1024-1037. [PMID: 36662167 PMCID: PMC10320374 DOI: 10.1093/ibd/izac281] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND There is an unmet medical need for biomarkers that capture host and environmental contributions in inflammatory bowel diseases (IBDs). This study aimed at testing the potential of circulating lipids as disease classifiers given their major roles in inflammation. METHODS We applied a previously validated comprehensive high-resolution liquid chromatography-mass spectrometry-based untargeted lipidomic workflow covering 25 lipid subclasses to serum samples from 100 Crohn's disease (CD) patients and 100 matched control subjects. Findings were replicated and expanded in another 200 CD patients and 200 control subjects. Key metabolites were tested for associations with disease behavior and location, and classification models were built and validated. Their association with disease activity was tested using an independent cohort of 42 CD patients. RESULTS We identified >70 metabolites with strong association (P < 1 × 10-4, q < 5 × 10-4) to CD. Highly performing classification models (area under the curve > 0.84-0.97) could be built with as few as 5 to 9 different metabolites, representing 6 major correlated lipid clusters. These classifiers included a phosphatidylethanolamine ether (O-16:0/20:4), a sphingomyelin (d18:1/21:0) and a cholesterol ester (14:1), a very long-chain dicarboxylic acid [28:1(OH)] and sitosterol sulfate. These classifiers and correlated lipids indicate a dysregulated metabolism in host cells, notably in peroxisomes, as well as dysbiosis, oxidative stress, compromised inflammation resolution, or intestinal membrane integrity. A subset of these were associated with disease behavior or location. CONCLUSIONS Untargeted lipidomic analyses uncovered perturbations in the circulating human CD lipidome, likely resulting from multiple pathogenic mechanisms. Models using as few as 5 biomarkers had strong disease classifier characteristics, supporting their potential use in diagnosis or prognosis.
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Affiliation(s)
- Romain Ferru-Clément
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Laboratoire Histocompatibilité et Immunogénétique, Établissement français du sang–Nouvelle-Aquitaine, site de Poitiers, Poitiers, France
| | | | - Anik Forest
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
| | | | - Alain Bitton
- Division of Gastroenterology, McGill University Health Centre, Montreal, QC, Canada
| | - Sylvie Lesage
- Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Phil Schumm
- Department of Public Health Sciences, University of Chicago, IL, USA
| | - Mark Lazarev
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steve Brant
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pennsylvania, PA, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Silverberg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Judy H Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ashwin Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Département de Médicine, Université de Montréal, Montreal, QC, Canada
| | - Christine Des Rosiers
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Département de Nutrition, Université de Montréal, Montreal, QC, Canada
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11
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Forrest IS, Petrazzini BO, Duffy Á, Park JK, O'Neal AJ, Jordan DM, Rocheleau G, Nadkarni GN, Cho JH, Blazer AD, Do R. A machine learning model identifies patients in need of autoimmune disease testing using electronic health records. Nat Commun 2023; 14:2385. [PMID: 37169741 PMCID: PMC10130143 DOI: 10.1038/s41467-023-37996-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 04/05/2023] [Indexed: 05/13/2023] Open
Abstract
Systemic autoimmune rheumatic diseases (SARDs) can lead to irreversible damage if left untreated, yet these patients often endure long diagnostic journeys before being diagnosed and treated. Machine learning may help overcome the challenges of diagnosing SARDs and inform clinical decision-making. Here, we developed and tested a machine learning model to identify patients who should receive rheumatological evaluation for SARDs using longitudinal electronic health records of 161,584 individuals from two institutions. The model demonstrated high performance for predicting cases of autoantibody-tested individuals in a validation set, an external test set, and an independent cohort with a broader case definition. This approach identified more individuals for autoantibody testing compared with current clinical standards and a greater proportion of autoantibody carriers among those tested. Diagnoses of SARDs and other autoimmune conditions increased with higher model probabilities. The model detected a need for autoantibody testing and rheumatology encounters up to five years before the test date and assessment date, respectively. Altogether, these findings illustrate that the clinical manifestations of a diverse array of autoimmune conditions are detectable in electronic health records using machine learning, which may help systematize and accelerate autoimmune testing.
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Affiliation(s)
- Iain S Forrest
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ben O Petrazzini
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Áine Duffy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua K Park
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anya J O'Neal
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Daniel M Jordan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ghislain Rocheleau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashira D Blazer
- Division of Rheumatology, Hospital for Special Surgery, New York, NY, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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12
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Wu Y, Gettler K, Kars ME, Giri M, Li D, Bayrak CS, Zhang P, Jain A, Maffucci P, Sabic K, Van Vleck T, Nadkarni G, Denson LA, Ostrer H, Levine AP, Schiff ER, Segal AW, Kugathasan S, Stenson PD, Cooper DN, Philip Schumm L, Snapper S, Daly MJ, Haritunians T, Duerr RH, Silverberg MS, Rioux JD, Brant SR, McGovern DPB, Cho JH, Itan Y. Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients. Nat Commun 2023; 14:2256. [PMID: 37080976 PMCID: PMC10119186 DOI: 10.1038/s41467-023-37849-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a group of chronic digestive tract inflammatory conditions whose genetic etiology is still poorly understood. The incidence of IBD is particularly high among Ashkenazi Jews. Here, we identify 8 novel and plausible IBD-causing genes from the exomes of 4453 genetically identified Ashkenazi Jewish IBD cases (1734) and controls (2719). Various biological pathway analyses are performed, along with bulk and single-cell RNA sequencing, to demonstrate the likely physiological relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of Ashkenazi Jewish adult IBD displays significant overlap with very early onset-IBD genetics. Moreover, by performing biobank phenome-wide analyses, we find that IBD genes have pleiotropic effects that involve other immune responses. Finally, we show that polygenic risk score analyses based on genome-wide high impact variants have high power to predict IBD susceptibility.
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Affiliation(s)
- Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kyle Gettler
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Meltem Ece Kars
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dalin Li
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cigdem Sevim Bayrak
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick Maffucci
- Immunology Institute, Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Ksenija Sabic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tielman Van Vleck
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Adam P Levine
- Division of Medicine, University College London (UCL), London, UK
- Research Department of Pathology, University College London (UCL), London, UK
| | - Elena R Schiff
- Division of Medicine, University College London (UCL), London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Anthony W Segal
- Division of Medicine, University College London (UCL), London, UK
| | | | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Scott Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Oncology Boston Children's Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Talin Haritunians
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Mark S Silverberg
- Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Steven R Brant
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dermot P B McGovern
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Ma H, Hu T, Tao W, Tong J, Han Z, Herndler-Brandstetter D, Wei Z, Liu R, Zhou T, Liu Q, Xu X, Zhang K, Zhou R, Cho JH, Li HB, Huang H, Flavell RA, Zhu S. A lncRNA from an inflammatory bowel disease risk locus maintains intestinal host-commensal homeostasis. Cell Res 2023; 33:372-388. [PMID: 37055591 PMCID: PMC10156687 DOI: 10.1038/s41422-023-00790-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/10/2023] [Indexed: 04/15/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are known to have complex, genetically influenced etiologies, involving dysfunctional interactions between the intestinal immune system and the microbiome. Here, we characterized how the RNA transcript from an IBD-associated long non-coding RNA locus ("CARINH-Colitis Associated IRF1 antisense Regulator of Intestinal Homeostasis") protects against IBD. We show that CARINH and its neighboring gene coding for the transcription factor IRF1 together form a feedforward loop in host myeloid cells. The loop activation is sustained by microbial factors, and functions to maintain the intestinal host-commensal homeostasis via the induction of the anti-inflammatory factor IL-18BP and anti-microbial factors called guanylate-binding proteins (GBPs). Extending these mechanistic insights back to humans, we demonstrate that the function of the CARINH/IRF1 loop is conserved between mice and humans. Genetically, the T allele of rs2188962, the most probable causal variant of IBD within the CARINH locus from the human genetics study, impairs the inducible expression of the CARINH/IRF1 loop and thus increases genetic predisposition to IBD. Our study thus illustrates how an IBD-associated lncRNA maintains intestinal homeostasis and protects the host against colitis.
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Affiliation(s)
- Hongdi Ma
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Taidou Hu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wanyin Tao
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jiyu Tong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Zili Han
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | | | - Zheng Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ruize Liu
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tingyue Zhou
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiuyuan Liu
- The Key Laboratory of Digestive Diseases of Anhui Province, Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xuemei Xu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Kaiguang Zhang
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Rongbin Zhou
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Judy H Cho
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hua-Bing Li
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China.
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.
| | - Shu Zhu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- School of Data Science, University of Science and Technology of China, Hefei, Anhui, China.
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China.
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14
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Hsu NY, Nayar S, Gettler K, Talware S, Giri M, Alter I, Argmann C, Sabic K, Thin TH, Ko HBM, Werner R, Tastad C, Stappenbeck T, Azabdaftari A, Uhlig HH, Chuang LS, Cho JH. NOX1 is essential for TNFα-induced intestinal epithelial ROS secretion and inhibits M cell signatures. Gut 2023; 72:654-662. [PMID: 36191961 PMCID: PMC9998338 DOI: 10.1136/gutjnl-2021-326305] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/20/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Loss-of-function mutations in genes generating reactive oxygen species (ROS), such as NOX1, are associated with IBD. Mechanisms whereby loss of ROS drive IBD are incompletely defined. DESIGN ROS measurements and single-cell transcriptomics were performed on colonoids stratified by NOX1 genotype and TNFα stimulation. Clustering of epithelial cells from human UC (inflamed and uninflamed) scRNASeq was performed. Validation of M cell induction was performed by immunohistochemistry using UEA1 (ulex europaeus agglutin-1 lectin) and in vivo with DSS injury. RESULTS TNFα induces ROS production more in NOX1-WT versus NOX1-deficient murine colonoids under a range of Wnt-mediated and Notch-mediated conditions. scRNASeq from inflamed and uninflamed human colitis versus TNFα stimulated, in vitro colonoids defines substantially shared, induced transcription factors; NOX1-deficient colonoids express substantially lower levels of STAT3 (signal transducer and activator of transcription 3), CEBPD (CCAAT enhancer-binding protein delta), DNMT1 (DNA methyltransferase) and HIF1A (hypoxia-inducible factor) baseline. Subclustering unexpectedly showed marked TNFα-mediated induction of M cells (sentinel cells overlying lymphoid aggregates) in NOX1-deficient colonoids. M cell induction by UEA1 staining is rescued with H2O2 and paraquat, defining extra- and intracellular ROS roles in maintenance of LGR5+ stem cells. DSS injury demonstrated GP2 (glycoprotein-2), basal lymphoplasmacytosis and UEA1 induction in NOX1-deficiency. Principal components analyses of M cell genes and decreased DNMT1 RNA velocity correlate with UC inflammation. CONCLUSIONS NOX1 deficiency plus TNFα stimulation contribute to colitis through dysregulation of the stem cell niche and altered cell differentiation, enhancing basal lymphoplasmacytosis. Our findings prioritise ROS modulation for future therapies.
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Affiliation(s)
- Nai-Yun Hsu
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shikha Nayar
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kyle Gettler
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sayali Talware
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai Department of Medicine, New York, New York, USA.,The Icahn Genomic Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mamta Giri
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Isaac Alter
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ksenija Sabic
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tin Htwe Thin
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Huai-Bin Mabel Ko
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Robert Werner
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christopher Tastad
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thaddeus Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, Ohio, USA
| | - Aline Azabdaftari
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Ling-Shiang Chuang
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy H Cho
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA .,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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15
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Forrest IS, Petrazzini BO, Duffy Á, Park JK, Marquez-Luna C, Jordan DM, Rocheleau G, Cho JH, Rosenson RS, Narula J, Nadkarni GN, Do R. Machine learning-based marker for coronary artery disease: derivation and validation in two longitudinal cohorts. Lancet 2023; 401:215-225. [PMID: 36563696 PMCID: PMC10069625 DOI: 10.1016/s0140-6736(22)02079-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Binary diagnosis of coronary artery disease does not preserve the complexity of disease or quantify its severity or its associated risk with death; hence, a quantitative marker of coronary artery disease is warranted. We evaluated a quantitative marker of coronary artery disease derived from probabilities of a machine learning model. METHODS In this cohort study, we developed and validated a coronary artery disease-predictive machine learning model using 95 935 electronic health records and assessed its probabilities as in-silico scores for coronary artery disease (ISCAD; range 0 [lowest probability] to 1 [highest probability]) in participants in two longitudinal biobank cohorts. We measured the association of ISCAD with clinical outcomes-namely, coronary artery stenosis, obstructive coronary artery disease, multivessel coronary artery disease, all-cause death, and coronary artery disease sequelae. FINDINGS Among 95 935 participants, 35 749 were from the BioMe Biobank (median age 61 years [IQR 18]; 14 599 [41%] were male and 21 150 [59%] were female; 5130 [14%] were with diagnosed coronary artery disease) and 60 186 were from the UK Biobank (median age 62 [15] years; 25 031 [42%] male and 35 155 [58%] female; 8128 [14%] with diagnosed coronary artery disease). The model predicted coronary artery disease with an area under the receiver operating characteristic curve of 0·95 (95% CI 0·94-0·95; sensitivity of 0·94 [0·94-0·95] and specificity of 0·82 [0·81-0·83]) and 0·93 (0·92-0·93; sensitivity of 0·90 [0·89-0·90] and specificity of 0·88 [0·87-0·88]) in the BioMe validation and holdout sets, respectively, and 0·91 (0·91-0·91; sensitivity of 0·84 [0·83-0·84] and specificity of 0·83 [0·82-0·83]) in the UK Biobank external test set. ISCAD captured coronary artery disease risk from known risk factors, pooled cohort equations, and polygenic risk scores. Coronary artery stenosis increased quantitatively with ascending ISCAD quartiles (increase per quartile of 12 percentage points), including risk of obstructive coronary artery disease, multivessel coronary artery disease, and stenosis of major coronary arteries. Hazard ratios (HRs) and prevalence of all-cause death increased stepwise over ISCAD deciles (decile 1: HR 1·0 [95% CI 1·0-1·0], 0·2% prevalence; decile 6: 11 [3·9-31], 3·1% prevalence; and decile 10: 56 [20-158], 11% prevalence). A similar trend was observed for recurrent myocardial infarction. 12 (46%) undiagnosed individuals with high ISCAD (≥0·9) had clinical evidence of coronary artery disease according to the 2014 American College of Cardiology/American Heart Association Task Force guidelines. INTERPRETATION Electronic health record-based machine learning was used to generate an in-silico marker for coronary artery disease that can non-invasively quantify atherosclerosis and risk of death on a continuous spectrum, and identify underdiagnosed individuals. FUNDING National Institutes of Health.
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Affiliation(s)
- Iain S Forrest
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ben O Petrazzini
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Áine Duffy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua K Park
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carla Marquez-Luna
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel M Jordan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ghislain Rocheleau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert S Rosenson
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Metabolism and Lipids Unit, Zena and Michael A Wiener Cardiovascular Institute, Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jagat Narula
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Data-Driven and Digital Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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16
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Lee S, Kim HJ, Kim JH, Kim TK, Kang CN, Lee JH, Cho JH, Kim SH, Moon SH. Evaluation of the efficacy and safety of NVP-1203 and aceclofenac in patients with acute low back pain and muscle spasm: A randomized, double-blind, active-controlled, parallel, multicenter, phase 3 clinical trial. Eur Rev Med Pharmacol Sci 2023; 27:315-324. [PMID: 36647880 DOI: 10.26355/eurrev_202301_30878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OBJECTIVE Acute low back pain (LBP) is a common condition that can be chronic if not properly treated. Aceclofenac and eperisone hydrochloride are commonly prescribed drugs for acute LBP and muscle spasms. Therefore, NVP-1203, a fixed-dose combination of 100 mg aceclofenac and 75 mg eperisone hydrochloride, is being developed. This study aimed to evaluate the efficacy and safety of NVP-1203 compared to those of a single administration of 100 mg aceclofenac in patients with acute LBP and muscle spasms. PATIENTS AND METHODS Overall, 455 patients with acute LBP and muscle spasms were enrolled. The patients were assigned to NVP-1203 or Airtal group (aceclofenac 100 mg). The primary efficacy endpoint was the mean change in the 100 mm pain movement and resting visual analog scale (VAS) scores on treatment day 7. RESULTS The mean change in the 100 mm pain movement/resting VAS scores from baseline to day 7 was -49.7 ± 21.5/-41.0 ± 19.4 mm and -38.8 ± 18.9/-33.8 ± 18.0 mm for the NVP-1203 and Airtal groups, respectively. The differences between the two groups were statistically significant (movement, p < 0.0001; resting, p = 0.0002). Differences in least-square (LS) mean change of the 100 mm pain movement/resting VAS score between the two groups using the analysis of covariance (ANCOVA) model was -10.2/-7.4 mm, and the upper limit of the 95% confidence interval was -6.44/-4.16 mm. CONCLUSIONS NVP-1203 is more effective in reducing pain than the 100 mg aceclofenac alone. However, the two drugs have similar safety profiles in patients with acute LBP and muscle spasms.
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Affiliation(s)
- S Lee
- Department of Orthopedic Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Gyeonggi-do, Republic of Korea.
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17
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Cho JH, Shin SY. Effects of smoking cessation on the risk of cardiovascular disease: a nationwide population-based study. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2384] [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: 11/13/2022] Open
Abstract
Abstract
Introduction
Cardiovascular disease (CVD) is the global leading cause of death, and the economic and social burden of CVD is still increasing, Smoking is one of the top three leading risk factors for the disease and one of the well-established and important modifiable risk factors for CVD. However, the time course of CVD risk after smoking cessation is unclear.
Purpose
We assess the association between smoking and CVD and the incidence of CVD with years quitting smoking.
Methods
This study used the Korean National Health Insurance Service (NHIS) database. Self-reported smoking habit data were used to classify participants as current, former or never smokers and to investigate the duration and intensity of smoking. Smoking records of participants were updated every 2 years, and all participants whose smoking records were changed or unclear were excluded. The primary outcome was the development of CVD, including myocardial infarction, stroke, heart failure, and cardiovascular death.
Results
Total 5,391,231 participants (953,756 subjects were current smokers, 104,604 subjects were former smokers, 4,432,871 subjects never smoker) were followed-up for an average of 4.2 years. The mean age was 45.8 years, 39.9% were male. Cumulative pack-year (PY) were 14 in current smoker, 10.5 in former smokers at baseline. The median years of quitting smoking for former smoker was 4.
Regardless of whether smoking continues or not, a dose-dependent relationship exists between smoking and CVD (Fig. 1). For those smoked less than 8PY, smoking cessation significantly lowered the CVD risk within 10 years compared to current smokers, and the CVD risk was not significantly different from never smokers (Fig. 2A). However, in the case of smokers over 8PY, although smoking cessation affects the reduction of CVD, the CVD risk decreases slowly over decades, and it takes more than 20 years for the effect of smoking on the CVD risk to disappear (Fig. 2B).
Conclusion
Smoking and CVD have a dose-dependent relationship, and mild smokers with less than 8PY had a similar CVD risk to never smokers when quitting smoking. However, for heavy smokers over 8PY, it takes a long time for the CVD risk from smoking to disappear
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- J H Cho
- Chung-Ang University Hospital , Seoul , Korea (Republic of)
| | - S Y Shin
- Chung-Ang University Hospital , Seoul , Korea (Republic of)
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18
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Mortha A, Remark R, Del Valle DM, Chuang LS, Chai Z, Alves I, Azevedo C, Gaifem J, Martin J, Petralia F, Tuballes K, Barcessat V, Tai SL, Huang HH, Laface I, Jerez YA, Boschetti G, Villaverde N, Wang MD, Korie UM, Murray J, Choung RS, Sato T, Laird RM, Plevy S, Rahman A, Torres J, Porter C, Riddle MS, Kenigsberg E, Pinho SS, Cho JH, Merad M, Colombel JF, Gnjatic S. Neutralizing Anti-Granulocyte Macrophage-Colony Stimulating Factor Autoantibodies Recognize Post-Translational Glycosylations on Granulocyte Macrophage-Colony Stimulating Factor Years Before Diagnosis and Predict Complicated Crohn's Disease. Gastroenterology 2022; 163:659-670. [PMID: 35623454 PMCID: PMC10127946 DOI: 10.1053/j.gastro.2022.05.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Anti-granulocyte macrophage-colony stimulating factor autoantibodies (aGMAbs) are detected in patients with ileal Crohn's disease (CD). Their induction and mode of action during or before disease are not well understood. We aimed to investigate the underlying mechanisms associated with aGMAb induction, from functional orientation to recognized epitopes, for their impact on intestinal immune homeostasis and use as a predictive biomarker for complicated CD. METHODS We characterized using enzyme-linked immunosorbent assay naturally occurring aGMAbs in longitudinal serum samples from patients archived before the diagnosis of CD (n = 220) as well as from 400 healthy individuals (matched controls) as part of the US Defense Medical Surveillance System. We used biochemical, cellular, and transcriptional analysis to uncover a mechanism that governs the impaired immune balance in CD mucosa after diagnosis. RESULTS Neutralizing aGMAbs were found to be specific for post-translational glycosylation on granulocyte macrophage-colony stimulating factor (GM-CSF), detectable years before diagnosis, and associated with complicated CD at presentation. Glycosylation of GM-CSF was altered in patients with CD, and aGMAb affected myeloid homeostasis and promoted group 1 innate lymphoid cells. Perturbations in immune homeostasis preceded the diagnosis in the serum of patients with CD presenting with aGMAb and were detectable in the noninflamed CD mucosa. CONCLUSIONS Anti-GMAbs predict the diagnosis of complicated CD long before the diagnosis of disease, recognize uniquely glycosylated epitopes, and impair myeloid cell and innate lymphoid cell balance associated with altered intestinal immune homeostasis.
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Affiliation(s)
- Arthur Mortha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Tisch Cancer Institute, Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Immunology, University of Toronto, Toronto, Canada.
| | - Romain Remark
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Innate Pharma, Marseille, France
| | - Diane Marie Del Valle
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Tisch Cancer Institute, Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ling-Shiang Chuang
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zhi Chai
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Inês Alves
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal; Faculty of Medicine, University of Porto, Porto, Portugal
| | - Catarina Azevedo
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal; Faculty of Medicine, University of Porto, Porto, Portugal
| | - Joana Gaifem
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Jerome Martin
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, Nantes, France; CHU Nantes, Laboratoire d'Immunologie, CIMNA, Nantes, France
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Tisch Cancer Institute, Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Vanessa Barcessat
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Tisch Cancer Institute, Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Siu Ling Tai
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Hsin-Hui Huang
- Tisch Cancer Institute, Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ilaria Laface
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Tisch Cancer Institute, Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yeray Arteaga Jerez
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gilles Boschetti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Hépato-Gastroentérologue, Hospices Civils de Lyon, Université Claude Bernard, Lyon, France
| | - Nicole Villaverde
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mona D Wang
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Ujunwa M Korie
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Joseph Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Rok-Seon Choung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Renee M Laird
- Naval Medical Research Center, Silver Spring, Maryland
| | | | - Adeeb Rahman
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center at Mount Sinai, New York, New York
| | - Joana Torres
- Department of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York; Gastroenterology Division, Hospital Beatriz Ângelo, Loures, Portugal
| | - Chad Porter
- Naval Medical Research Center, Silver Spring, Maryland
| | - Mark S Riddle
- Naval Medical Research Center, Silver Spring, Maryland
| | - Ephraim Kenigsberg
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center at Mount Sinai, New York, New York
| | - Salomé S Pinho
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal; Faculty of Medicine, University of Porto, Porto, Portugal; School of Medicine and Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Judy H Cho
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Tisch Cancer Institute, Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center at Mount Sinai, New York, New York
| | - Jean-Frederic Colombel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Tisch Cancer Institute, Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center at Mount Sinai, New York, New York
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Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Morrison JK, DeRossi C, Alter IL, Nayar S, Giri M, Zhang C, Cho JH, Chu J. Single-cell transcriptomics reveals conserved cell identities and fibrogenic phenotypes in zebrafish and human liver. Hepatol Commun 2022; 6:1711-1724. [PMID: 35315595 PMCID: PMC9234649 DOI: 10.1002/hep4.1930] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 12/16/2022] Open
Abstract
The mechanisms underlying liver fibrosis are multifaceted and remain elusive with no approved antifibrotic treatments available. The adult zebrafish has been an underutilized tool to study liver fibrosis. We aimed to characterize the single-cell transcriptome of the adult zebrafish liver to determine its utility as a model for studying liver fibrosis. We used single-cell RNA sequencing (scRNA-seq) of adult zebrafish liver to study the molecular and cellular dynamics at a single-cell level. We performed a comparative analysis to scRNA-seq of human liver with a focus on hepatic stellate cells (HSCs), the driver cells in liver fibrosis. scRNA-seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA-seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish. Human and zebrafish HSCs show conservation of transcriptional profiles, and we uncover collectin subfamily member 11 (colec11) as a novel, conserved marker for zebrafish HSCs. To demonstrate the power of scRNA-seq to study liver fibrosis using zebrafish, we performed scRNA-seq on our zebrafish model of a pediatric liver disease with mutation in mannose phosphate isomerase (MPI) and characteristic early liver fibrosis. We found fibrosis signaling pathways and upstream regulators conserved across MPI-depleted zebrafish and human HSCs. CellPhoneDB analysis of zebrafish transcriptome identified neuropilin 1 as a potential driver of liver fibrosis. Conclusion: This study establishes the first scRNA-seq atlas of the adult zebrafish liver, highlights the high degree of similarity to human liver, and strengthens its value as a model to study liver fibrosis.
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Affiliation(s)
- Joshua K Morrison
- Department of PediatricsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Charles DeRossi
- Department of PediatricsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Isaac L Alter
- Department of PediatricsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Shikha Nayar
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Mamta Giri
- The Charles Bronfman Institute of Personalized MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Chi Zhang
- Department of Cell BiologyAlbert Einstein College of MedicineNew YorkNew YorkUSA
| | - Judy H Cho
- The Charles Bronfman Institute of Personalized MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Jaime Chu
- Department of PediatricsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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Khan A, Turchin MC, Patki A, Srinivasasainagendra V, Shang N, Nadukuru R, Jones AC, Malolepsza E, Dikilitas O, Kullo IJ, Schaid DJ, Karlson E, Ge T, Meigs JB, Smoller JW, Lange C, Crosslin DR, Jarvik GP, Bhatraju PK, Hellwege JN, Chandler P, Torvik LR, Fedotov A, Liu C, Kachulis C, Lennon N, Abul-Husn NS, Cho JH, Ionita-Laza I, Gharavi AG, Chung WK, Hripcsak G, Weng C, Nadkarni G, Irvin MR, Tiwari HK, Kenny EE, Limdi NA, Kiryluk K. Genome-wide polygenic score to predict chronic kidney disease across ancestries. Nat Med 2022; 28:1412-1420. [PMID: 35710995 PMCID: PMC9329233 DOI: 10.1038/s41591-022-01869-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [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: 11/09/2021] [Accepted: 05/11/2022] [Indexed: 01/03/2023]
Abstract
Chronic kidney disease (CKD) is a common complex condition associated with high morbidity and mortality. Polygenic prediction could enhance CKD screening and prevention; however, this approach has not been optimized for ancestrally diverse populations. By combining APOL1 risk genotypes with genome-wide association studies (GWAS) of kidney function, we designed, optimized and validated a genome-wide polygenic score (GPS) for CKD. The new GPS was tested in 15 independent cohorts, including 3 cohorts of European ancestry (n = 97,050), 6 cohorts of African ancestry (n = 14,544), 4 cohorts of Asian ancestry (n = 8,625) and 2 admixed Latinx cohorts (n = 3,625). We demonstrated score transferability with reproducible performance across all tested cohorts. The top 2% of the GPS was associated with nearly threefold increased risk of CKD across ancestries. In African ancestry cohorts, the APOL1 risk genotype and polygenic component of the GPS had additive effects on the risk of CKD.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Michael C Turchin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amit Patki
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Rajiv Nadukuru
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alana C Jones
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Ozan Dikilitas
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Daniel J Schaid
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Tian Ge
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - James B Meigs
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jordan W Smoller
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jacklyn N Hellwege
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paulette Chandler
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Laura Rasmussen Torvik
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alex Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Cong Liu
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | | | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nita A Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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Forrest IS, Chaudhary K, Vy HMT, Petrazzini BO, Bafna S, Jordan DM, Rocheleau G, Loos RJF, Nadkarni GN, Cho JH, Do R. Population-Based Penetrance of Deleterious Clinical Variants. JAMA 2022; 327:350-359. [PMID: 35076666 PMCID: PMC8790667 DOI: 10.1001/jama.2021.23686] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
IMPORTANCE Population-based assessment of disease risk associated with gene variants informs clinical decisions and risk stratification approaches. OBJECTIVE To evaluate the population-based disease risk of clinical variants in known disease predisposition genes. DESIGN, SETTING, AND PARTICIPANTS This cohort study included 72 434 individuals with 37 780 clinical variants who were enrolled in the BioMe Biobank from 2007 onwards with follow-up until December 2020 and the UK Biobank from 2006 to 2010 with follow-up until June 2020. Participants had linked exome and electronic health record data, were older than 20 years, and were of diverse ancestral backgrounds. EXPOSURES Variants previously reported as pathogenic or predicted to cause a loss of protein function by bioinformatic algorithms (pathogenic/loss-of-function variants). MAIN OUTCOMES AND MEASURES The primary outcome was the disease risk associated with clinical variants. The risk difference (RD) between the prevalence of disease in individuals with a variant allele (penetrance) vs in individuals with a normal allele was measured. RESULTS Among 72 434 study participants, 43 395 were from the UK Biobank (mean [SD] age, 57 [8.0] years; 24 065 [55%] women; 2948 [7%] non-European) and 29 039 were from the BioMe Biobank (mean [SD] age, 56 [16] years; 17 355 [60%] women; 19 663 [68%] non-European). Of 5360 pathogenic/loss-of-function variants, 4795 (89%) were associated with an RD less than or equal to 0.05. Mean penetrance was 6.9% (95% CI, 6.0%-7.8%) for pathogenic variants and 0.85% (95% CI, 0.76%-0.95%) for benign variants reported in ClinVar (difference, 6.0 [95% CI, 5.6-6.4] percentage points), with a median of 0% for both groups due to large numbers of nonpenetrant variants. Penetrance of pathogenic/loss-of-function variants for late-onset diseases was modified by age: mean penetrance was 10.3% (95% CI, 9.0%-11.6%) in individuals 70 years or older and 8.5% (95% CI, 7.9%-9.1%) in individuals 20 years or older (difference, 1.8 [95% CI, 0.40-3.3] percentage points). Penetrance of pathogenic/loss-of-function variants was heterogeneous even in known disease predisposition genes, including BRCA1 (mean [range], 38% [0%-100%]), BRCA2 (mean [range], 38% [0%-100%]), and PALB2 (mean [range], 26% [0%-100%]). CONCLUSIONS AND RELEVANCE In 2 large biobank cohorts, the estimated penetrance of pathogenic/loss-of-function variants was variable but generally low. Further research of population-based penetrance is needed to refine variant interpretation and clinical evaluation of individuals with these variant alleles.
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Affiliation(s)
- Iain S. Forrest
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, New York
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kumardeep Chaudhary
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ha My T. Vy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ben O. Petrazzini
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Shantanu Bafna
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Daniel M. Jordan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ghislain Rocheleau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Girish N. Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Judy H. Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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23
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Nayar S, Cho JH. From single-target to cellular niche targeting in Crohn's disease: intercepting bad communications. EBioMedicine 2021; 74:103690. [PMID: 34773892 PMCID: PMC8601974 DOI: 10.1016/j.ebiom.2021.103690] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 02/07/2023] Open
Abstract
The mainstay of moderate to severe Crohn's disease (CD), anti-TNF treatment, shows no clinical benefit in ∼40% of patients, likely due to incomplete cellular targeting and delayed treatment institution. While single-target therapeutics have been highly effective for some CD patients, substantial limitations with respect to safety, efficacy, and long-term, complete remission remain. Deconvolution of the cellular and molecular circuitry of tissue lesions underscores the importance of combinatorial strategies targeting cellular niches. This review aims to evaluate current therapeutic approaches used to manage CD, and highlight recent advances to our cellular, genetic, and molecular understanding of mechanisms driving pathogenic niche activation in CD. We propose new frameworks outlining that combinatorial therapies, along with serial tissue sampling and studies guided by genetics and genomics, can advance on current treatment approaches and will inform newer strategies upon which we can move towards precision therapeutics in IBD.
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Affiliation(s)
- Shikha Nayar
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, Hess CSM Building Room 8-201, New York, NY 10029, USA.
| | - Judy H Cho
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, Hess CSM Building Room 8-201, New York, NY 10029, USA
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24
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Walshe M, Nayeri S, Ji J, Hernandez-Rocha C, Sabic K, Hu L, Giri M, Nayar S, Brant S, McGovern DPB, Rioux JD, Duerr RH, Cho JH, Schumm PL, Lazarev M, Silverberg MS. A Role for CXCR3 Ligands as Biomarkers of Post-Operative Crohn's Disease Recurrence. J Crohns Colitis 2021; 16:900-910. [PMID: 34698823 PMCID: PMC9282882 DOI: 10.1093/ecco-jcc/jjab186] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] recurrence following ileocolic resection [ICR] is common. We sought to identify blood-based biomarkers associated with CD recurrence. METHODS CD patients undergoing ICR were recruited across six centres. Serum samples were obtained at post-operative colonoscopy. A multiplex immunoassay was used to analyse 92 inflammation-related proteins [Olink Proteomics]. Bayesian analysis was used to identify proteins associated with increasing Rutgeerts score. Identified proteins were used in receiver operating characteristic [ROC] analysis to examine the ability to identify CD recurrence [Rutgeerts score ≥i2]. Existing single cell data were interrogated to further elucidate the role of the identified proteins. RESULTS Data from 276 colonoscopies in 213 patients were available. Median time from surgery to first and second colonoscopy was 7 (interquartile range [IQR] 6-9) and 19 [IQR 16-23] months, respectively. Disease recurrence was evident at 60 [30%] first and 36 [49%] second colonoscopies. Of 14 proteins significantly associated with Rutgeerts score, the strongest signal was seen for CXCL9 and MMP1. Among patients on anti-tumour necrosis factor drugs, CXCL9 and CXCL11 were most strongly associated with Rutgeerts score. Both are CXCR3 ligands. Incorporation of identified proteins into ROC analysis improved the ability to identify disease recurrence as compared to C-reactive protein alone: area under the curve [AUC] 0.75 (95% confidence interval [CI]: 0.66-0.82] vs 0.64 [95% CI 0.56-0.72], p = 0.012. Single cell transcriptomic data provide evidence that innate immune cells are the primary source of the identified proteins. CONCLUSIONS CXCR3 ligands are associated with CD recurrence following ICR. Incorporation of novel blood-based candidate biomarkers may aid in identification of CD recurrence.
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Affiliation(s)
- Margaret Walshe
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada,Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Shadi Nayeri
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cristian Hernandez-Rocha
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada,Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Ksenija Sabic
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shikha Nayar
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Brant
- Crohn’s and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - John D Rioux
- Research Centre, Montreal Heart Institute, Montréal, QC, Canada,Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA,USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Phil L Schumm
- Department of Health Sciences, University of Chicago, Chicago, IL, USA
| | | | - Mark S Silverberg
- Corresponding author: Dr Mark Silverberg, MD, PhD, FRCPC, University of Toronto, Division of Gastroenterology, Mount Sinai Hospital Inflammatory Bowel Disease Centre, 441–600 University Avenue, Toronto, Ontario, M5G1X5, Canada. Tel: +1-416-586-4800 ext 8236; Fax: +1-416-619-5524;
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25
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Lencz T, Backenroth D, Granot-Hershkovitz E, Green A, Gettler K, Cho JH, Weissbrod O, Zuk O, Carmi S. Utility of polygenic embryo screening for disease depends on the selection strategy. eLife 2021; 10:64716. [PMID: 34635206 PMCID: PMC8510582 DOI: 10.7554/elife.64716] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 11/09/2020] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
Polygenic risk scores (PRSs) have been offered since 2019 to screen in vitro fertilization embryos for genetic liability to adult diseases, despite a lack of comprehensive modeling of expected outcomes. Here we predict, based on the liability threshold model, the expected reduction in complex disease risk following polygenic embryo screening for a single disease. A strong determinant of the potential utility of such screening is the selection strategy, a factor that has not been previously studied. When only embryos with a very high PRS are excluded, the achieved risk reduction is minimal. In contrast, selecting the embryo with the lowest PRS can lead to substantial relative risk reductions, given a sufficient number of viable embryos. We systematically examine the impact of several factors on the utility of screening, including: variance explained by the PRS, number of embryos, disease prevalence, parental PRSs, and parental disease status. We consider both relative and absolute risk reductions, as well as population-averaged and per-couple risk reductions, and also examine the risk of pleiotropic effects. Finally, we confirm our theoretical predictions by simulating ‘virtual’ couples and offspring based on real genomes from schizophrenia and Crohn’s disease case-control studies. We discuss the assumptions and limitations of our model, as well as the potential emerging ethical concerns.
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Affiliation(s)
- Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, United States.,Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, United States.,Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, United States
| | - Daniel Backenroth
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Einat Granot-Hershkovitz
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adam Green
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kyle Gettler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Judy H Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Omer Weissbrod
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Or Zuk
- Department of Statistics and Data Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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26
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Mo A, Nagpal S, Gettler K, Haritunians T, Giri M, Haberman Y, Karns R, Prince J, Arafat D, Hsu NY, Chuang LS, Argmann C, Kasarskis A, Suarez-Farinas M, Gotman N, Mengesha E, Venkateswaran S, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, LeLeiko NS, Heyman MB, Griffiths AM, Patel AS, Noe JD, Davis Thomas S, Aronow BJ, Walters TD, McGovern DPB, Hyams JS, Kugathasan S, Cho JH, Denson LA, Gibson G. Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression. Am J Hum Genet 2021; 108:1765-1779. [PMID: 34450030 DOI: 10.1016/j.ajhg.2021.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
An important goal of clinical genomics is to be able to estimate the risk of adverse disease outcomes. Between 5% and 10% of individuals with ulcerative colitis (UC) require colectomy within 5 years of diagnosis, but polygenic risk scores (PRSs) utilizing findings from genome-wide association studies (GWASs) are unable to provide meaningful prediction of this adverse status. By contrast, in Crohn disease, gene expression profiling of GWAS-significant genes does provide some stratification of risk of progression to complicated disease in the form of a transcriptional risk score (TRS). Here, we demonstrate that a measured TRS based on bulk rectal gene expression in the PROTECT inception cohort study has a positive predictive value approaching 50% for colectomy. Single-cell profiling demonstrates that the genes are active in multiple diverse cell types from both the epithelial and immune compartments. Expression quantitative trait locus (QTL) analysis identifies genes with differential effects at baseline and week 52 follow-up, but for the most part, differential expression associated with colectomy risk is independent of local genetic regulation. Nevertheless, a predicted polygenic transcriptional risk score (PPTRS) derived by summation of transcriptome-wide association study (TWAS) effects identifies UC-affected individuals at 5-fold elevated risk of colectomy with data from the UK Biobank population cohort studies, independently replicated in an NIDDK-IBDGC dataset. Prediction of gene expression from relatively small transcriptome datasets can thus be used in conjunction with TWASs for stratification of risk of disease complications.
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Affiliation(s)
- Angela Mo
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sini Nagpal
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kyle Gettler
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mamta Giri
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Yael Haberman
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Sheba Medical Center, Tel Hashomer, Tel Aviv University, Tel Aviv 5265601, Israel
| | - Rebekah Karns
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dalia Arafat
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nai-Yun Hsu
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ling-Shiang Chuang
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Carmen Argmann
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Andrew Kasarskis
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Mayte Suarez-Farinas
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Nathan Gotman
- University of North Carolina, Chapel Hill, NC 27516, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Paul A Rufo
- Harvard University-Children's Hospital Boston, Boston, MA 02115, USA
| | - Susan S Baker
- Women & Children's Hospital of Buffalo, Buffalo, NY 14222, USA
| | | | - James Markowitz
- Cohen Children's Medical Center of New York, New Hyde Park, NY 11040, USA
| | | | - Joel R Rosh
- Goryeb Children's Hospital-Atlantic Health, Morristown, NJ 07960, USA
| | | | - David R Mack
- Children's Hospital of East Ontario, Ottawa, ON K1P 1J1, Canada
| | | | - Sapana Shah
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Neal S LeLeiko
- Department of Pediatrics, Columbia University, New York City, NY 10032, USA
| | - Melvin B Heyman
- University of California at San Francisco, San Francisco, CA 94143, USA
| | | | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Bruce J Aronow
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, CT 06106, USA
| | | | - Judy H Cho
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Lee A Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Greg Gibson
- Georgia Institute of Technology, Atlanta, GA 30332, USA.
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27
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Belbin GM, Cullina S, Wenric S, Soper ER, Glicksberg BS, Torre D, Moscati A, Wojcik GL, Shemirani R, Beckmann ND, Cohain A, Sorokin EP, Park DS, Ambite JL, Ellis S, Auton A, Bottinger EP, Cho JH, Loos RJF, Abul-Husn NS, Zaitlen NA, Gignoux CR, Kenny EE. Toward a fine-scale population health monitoring system. Cell 2021; 184:2068-2083.e11. [PMID: 33861964 DOI: 10.1016/j.cell.2021.03.034] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/18/2020] [Accepted: 03/12/2021] [Indexed: 12/22/2022]
Abstract
Understanding population health disparities is an essential component of equitable precision health efforts. Epidemiology research often relies on definitions of race and ethnicity, but these population labels may not adequately capture disease burdens and environmental factors impacting specific sub-populations. Here, we propose a framework for repurposing data from electronic health records (EHRs) in concert with genomic data to explore the demographic ties that can impact disease burdens. Using data from a diverse biobank in New York City, we identified 17 communities sharing recent genetic ancestry. We observed 1,177 health outcomes that were statistically associated with a specific group and demonstrated significant differences in the segregation of genetic variants contributing to Mendelian diseases. We also demonstrated that fine-scale population structure can impact the prediction of complex disease risk within groups. This work reinforces the utility of linking genomic data to EHRs and provides a framework toward fine-scale monitoring of population health.
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Affiliation(s)
- Gillian M Belbin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sinead Cullina
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stephane Wenric
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily R Soper
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Denis Torre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arden Moscati
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ruhollah Shemirani
- Information Science Institute, University of Southern California, Marina del Rey, CA 90089, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ariella Cohain
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena P Sorokin
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Danny S Park
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jose-Luis Ambite
- Information Science Institute, University of Southern California, Marina del Rey, CA 90089, USA
| | - Steve Ellis
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Auton
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
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- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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- Regeneron Genetics Center, Tarrytown, New York, NY 10591, USA
| | - Erwin P Bottinger
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Judy H Cho
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth J F Loos
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noah A Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90033, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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28
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Chen E, Chuang LS, Giri M, Villaverde N, Hsu NY, Sabic K, Joshowitz S, Gettler K, Nayar S, Chai Z, Alter IL, Chasteau CC, Korie UM, Dzedzik S, Thin TH, Jain A, Moscati A, Bongers G, Duerr RH, Silverberg MS, Brant SR, Rioux JD, Peter I, Schumm LP, Haritunians T, McGovern DP, Itan Y, Cho JH. Inflamed Ulcerative Colitis Regions Associated With MRGPRX2-Mediated Mast Cell Degranulation and Cell Activation Modules, Defining a New Therapeutic Target. Gastroenterology 2021; 160:1709-1724. [PMID: 33421512 PMCID: PMC8494017 DOI: 10.1053/j.gastro.2020.12.076] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Recent literature has implicated a key role for mast cells in murine models of colonic inflammation, but their role in human ulcerative colitis (UC) is not well established. A major advance has been the identification of mrgprb2 (human orthologue, MRGPX2) as mediating IgE-independent mast cell activation. We sought to define mechanisms of mast cell activation and MRGPRX2 in human UC. METHODS Colon tissues were collected from patients with UC for bulk RNA sequencing and lamina propria cells were isolated for MRGPRX2 activation studies and single-cell RNA sequencing. Genetic association of all protein-altering G-protein coupled receptor single-nucleotide polymorphism was performed in an Ashkenazi Jewish UC case-control cohort. Variants of MRGPRX2 were transfected into Chinese hamster ovary (CHO) and human mast cell (HMC) 1.1 cells to detect genotype-dependent effects on β-arrestin recruitment, IP-1 accumulation, and phosphorylated extracellular signal-regulated kinase. RESULTS Mast cell-specific mediators and adrenomedullin (proteolytic precursor of PAMP-12, an MRGPRX2 agonist) are up-regulated in inflamed compared to uninflamed UC. MRGPRX2 stimulation induces carboxypeptidase secretion from inflamed UC. Of all protein-altering GPCR alleles, a unique variant of MRGPRX2, Asn62Ser, was most associated with and was bioinformatically predicted to alter arrestin recruitment. We validated that the UC protective serine allele enhances β-arrestin recruitment, decreases IP-1, and increases phosphorylated extracellular signal-regulated kinase with MRGPRX2 agonists. Single-cell RNA sequencing defines that adrenomedullin is expressed by activated fibroblasts and epithelial cells and that interferon gamma is a key upstream regulator of mast cell gene expression. CONCLUSION Inflamed UC regions are distinguished by MRGPRX2-mediated activation of mast cells, with decreased activation observed with a UC-protective genetic variant. These results define cell modules of UC activation and a new therapeutic target.
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Affiliation(s)
- Ernie Chen
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ling-shiang Chuang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Mamta Giri
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nicole Villaverde
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nai-yun Hsu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ksenija Sabic
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Sari Joshowitz
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Kyle Gettler
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Shikha Nayar
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Zhi Chai
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Isaac L. Alter
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Colleen C. Chasteau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ujunwa M. Korie
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Siarhei Dzedzik
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Tin Htwe Thin
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Gerardus Bongers
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mark S. Silverberg
- Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Ontario, Canada, Toronto, Ontario, Canada
| | - Steven R. Brant
- Crohns and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States
| | - John D. Rioux
- Research Centre, Montreal Heart Institute, Montréal, QC, Canada. Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Inga Peter
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - L. Philip Schumm
- Department of Health Sciences, University of Chicago, Chicago, Illinois, United States
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Dermot P. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Judy H. Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States,To whom correspondence should be addressed: Judy Cho, Hess CSM Building Floor 8th Room 118, 1470 Madison Avenue, New York, NY 10029, TEL. (212) 824-8940, FAX. (646) 537-9452,
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29
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Gettler K, Levantovsky R, Moscati A, Giri M, Wu Y, Hsu NY, Chuang LS, Sazonovs A, Venkateswaran S, Korie U, Chasteau C, Duerr RH, Silverberg MS, Snapper SB, Daly MJ, McGovern DP, Brant SR, Kugathasan S, Anderson CA, Itan Y, Cho JH, Cho JH. Common and Rare Variant Prediction and Penetrance of IBD in a Large, Multi-ethnic, Health System-based Biobank Cohort. Gastroenterology 2021; 160:1546-1557. [PMID: 33359885 PMCID: PMC8237248 DOI: 10.1053/j.gastro.2020.12.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Polygenic risk scores (PRS) may soon be used to predict inflammatory bowel disease (IBD) risk in prevention efforts. We leveraged exome-sequence and single nucleotide polymorphism (SNP) array data from 29,358 individuals in the multiethnic, randomly ascertained health system-based BioMe biobank to define effects of common and rare IBD variants on disease prediction and pathophysiology. METHODS PRS were calculated from European, African American, and Ashkenazi Jewish (AJ) reference case-control studies, and a meta-GWAS run using all three association datasets. PRS were then combined using regression to assess which combination of scores best predicted IBD status in European, AJ, Hispanic, and African American cohorts in BioMe. Additionally, rare variants were assessed in genes associated with very early-onset IBD (VEO-IBD), by estimating genetic penetrance in each BioMe population. RESULTS Combining risk scores based on association data from distinct ancestral populations improved IBD prediction for every population in BioMe and significantly improved prediction among European ancestry UK Biobank individuals. Lower predictive power for non-Europeans was observed, reflecting in part substantially lower African IBD case-control reference sizes. We replicated associations for two VEO-IBD genes, ADAM17 and LRBA, with high dominant model penetrance in BioMe. Autosomal recessive LRBA risk alleles are associated with severe, early-onset autoimmunity; we show that heterozygous carriage of an African-predominant LRBA protein-altering allele is associated with significantly decreased LRBA and CTLA-4 expression with T-cell activation. CONCLUSIONS Greater genetic diversity in African populations improves prediction across populations, and generalizes some VEO-IBD genes. Increasing African American IBD case-collections should be prioritized to reduce health disparities and enhance pathophysiological insight.
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Affiliation(s)
- Kyle Gettler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Levantovsky
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksejs Sazonovs
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Emory University School of Medicine, Atlanta, GA, USA
| | - Ujunwa Korie
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Colleen Chasteau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Richard H. Duerr
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark S. Silverberg
- Division of Gastroenterology, Mount Sinai Hospital Inflammatory Bowel Disease Centre, Toronto, ON
| | - Scott B. Snapper
- Division of Gastroenterology, Hepatology & Nutrition, Boston Children’s Hospital, Boston, MA, USA
| | - Mark J. Daly
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | - Steven R. Brant
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, and Department of Genetics and The Human Genetics Institute of New Jersey, Rutgers University, New Brunswick, New Jersey, USA,Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Emory University School of Medicine, Atlanta, GA, USA,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Carl A. Anderson
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H. Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Judy H Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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30
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Lencz T, Yu J, Khan RR, Flaherty E, Carmi S, Lam M, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Vijai J, Klein RJ, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Malhotra AK, Maniatis T, Atzmon G, Pe'er I. Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. Neuron 2021; 109:1465-1478.e4. [PMID: 33756103 DOI: 10.1016/j.neuron.2021.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
The identification of rare variants associated with schizophrenia has proven challenging due to genetic heterogeneity, which is reduced in founder populations. In samples from the Ashkenazi Jewish population, we report that schizophrenia cases had a greater frequency of novel missense or loss of function (MisLoF) ultra-rare variants (URVs) compared to controls, and the MisLoF URV burden was inversely correlated with polygenic risk scores in cases. Characterizing 141 "case-only" genes (MisLoF URVs in ≥3 cases with none in controls), the cadherin gene set was associated with schizophrenia. We report a recurrent case mutation in PCDHA3 that results in the formation of cytoplasmic aggregates and failure to engage in homophilic interactions on the plasma membrane in cultured cells. Modeling purifying selection, we demonstrate that deleterious URVs are greatly overrepresented in the Ashkenazi population, yielding enhanced power for association studies. Identification of the cadherin/protocadherin family as risk genes helps specify the synaptic abnormalities central to schizophrenia.
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Affiliation(s)
- Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA.
| | - Jin Yu
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Raiyan Rashid Khan
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Erin Flaherty
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel
| | - Max Lam
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Danny Ben-Avraham
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan Bressman
- Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Steven Lipkin
- Departments of Medicine, Genetic Medicine and Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie J Ozelius
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anil K Malhotra
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; New York Genome Center, New York, NY 10013, USA
| | - Gil Atzmon
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Human Biology, Haifa University, Haifa, Israel
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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31
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Somineni HK, Nagpal S, Venkateswaran S, Cutler DJ, Okou DT, Haritunians T, Simpson CL, Begum F, Datta LW, Quiros AJ, Seminerio J, Mengesha E, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Iskandar H, Dryden GW, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kuemmerle JF, Lazarev M, Li E, Mannon P, Moulton DE, Newberry RD, Patel AS, Pekow J, Saeed SA, Valentine JF, Wang MH, McCauley JL, Abreu MT, Jester T, Molle-Rios Z, Palle S, Scherl EJ, Kwon J, Rioux JD, Duerr RH, Silverberg MS, Zwick ME, Stevens C, Daly MJ, Cho JH, Gibson G, McGovern DP, Brant SR, Kugathasan S. Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease. Am J Hum Genet 2021; 108:431-445. [PMID: 33600772 PMCID: PMC8008495 DOI: 10.1016/j.ajhg.2021.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/01/2021] [Indexed: 12/20/2022] Open
Abstract
Whether or not populations diverge with respect to the genetic contribution to risk of specific complex diseases is relevant to understanding the evolution of susceptibility and origins of health disparities. Here, we describe a large-scale whole-genome sequencing study of inflammatory bowel disease encompassing 1,774 affected individuals and 1,644 healthy control Americans with African ancestry (African Americans). Although no new loci for inflammatory bowel disease are discovered at genome-wide significance levels, we identify numerous instances of differential effect sizes in combination with divergent allele frequencies. For example, the major effect at PTGER4 fine maps to a single credible interval of 22 SNPs corresponding to one of four independent associations at the locus in European ancestry individuals but with an elevated odds ratio for Crohn disease in African Americans. A rare variant aggregate analysis implicates Ca2+-binding neuro-immunomodulator CALB2 in ulcerative colitis. Highly significant overall overlap of common variant risk for inflammatory bowel disease susceptibility between individuals with African and European ancestries was observed, with 41 of 241 previously known lead variants replicated and overall correlations in effect sizes of 0.68 for combined inflammatory bowel disease. Nevertheless, subtle differences influence the performance of polygenic risk scores, and we show that ancestry-appropriate weights significantly improve polygenic prediction in the highest percentiles of risk. The median amount of variance explained per locus remains the same in African and European cohorts, providing evidence for compensation of effect sizes as allele frequencies diverge, as expected under a highly polygenic model of disease.
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32
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Abul-Husn NS, Soper ER, Braganza GT, Rodriguez JE, Zeid N, Cullina S, Bobo D, Moscati A, Merkelson A, Loos RJF, Cho JH, Belbin GM, Suckiel SA, Kenny EE. Implementing genomic screening in diverse populations. Genome Med 2021; 13:17. [PMID: 33546753 PMCID: PMC7863616 DOI: 10.1186/s13073-021-00832-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/14/2021] [Indexed: 12/11/2022] Open
Abstract
Background Population-based genomic screening has the predicted ability to reduce morbidity and mortality associated with medically actionable conditions. However, much research is needed to develop standards for genomic screening and to understand the perspectives of people offered this new testing modality. This is particularly true for non-European ancestry populations who are vastly underrepresented in genomic medicine research. Therefore, we implemented a pilot genomic screening program in the BioMe Biobank in New York City, where the majority of participants are of non-European ancestry. Methods We initiated genomic screening for well-established genes associated with hereditary breast and ovarian cancer syndrome (HBOC), Lynch syndrome (LS), and familial hypercholesterolemia (FH). We evaluated and included an additional gene (TTR) associated with hereditary transthyretin amyloidosis (hATTR), which has a common founder variant in African ancestry populations. We evaluated the characteristics of 74 participants who received results associated with these conditions. We also assessed the preferences of 7461 newly enrolled BioMe participants to receive genomic results. Results In the pilot genomic screening program, 74 consented participants received results related to HBOC (N = 26), LS (N = 6), FH (N = 8), and hATTR (N = 34). Thirty-three of 34 (97.1%) participants who received a result related to hATTR were self-reported African American/African (AA) or Hispanic/Latinx (HL), compared to 14 of 40 (35.0%) participants who received a result related to HBOC, LS, or FH. Among the 7461 participants enrolled after the BioMe protocol modification to allow the return of genomic results, 93.4% indicated that they would want to receive results. Younger participants, women, and HL participants were more likely to opt to receive results. Conclusions The addition of TTR to a pilot genomic screening program meant that we returned results to a higher proportion of AA and HL participants, in comparison with genes traditionally included in genomic screening programs in the USA. We found that the majority of participants in a multi-ethnic biobank are interested in receiving genomic results for medically actionable conditions. These findings increase knowledge about the perspectives of diverse research participants on receiving genomic results and inform the broader implementation of genomic medicine in underrepresented patient populations. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00832-y.
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Affiliation(s)
- Noura S Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Emily R Soper
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giovanna T Braganza
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica E Rodriguez
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natasha Zeid
- Cardiogenetics, GeneDx Inc., Gaithersburg, MD, USA
| | - Sinead Cullina
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dean Bobo
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arden Moscati
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Merkelson
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gillian M Belbin
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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33
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Shapiro JM, de Zoete MR, Palm NW, Laenen Y, Bright R, Mallette M, Bu K, Bielecka AA, Xu F, Hurtado-Lorenzo A, Shah SA, Cho JH, LeLeiko NS, Sands BE, Flavell RA, Clemente JC. Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease. Cell Host Microbe 2021; 29:83-93.e3. [PMID: 33385335 PMCID: PMC10477929 DOI: 10.1016/j.chom.2020.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 04/20/2020] [Revised: 09/18/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022]
Abstract
The immunopathogenesis of inflammatory bowel disease (IBD) has been attributed to a combination of host genetics and intestinal dysbiosis. Previous work in a small cohort of IBD patients suggested that pro-inflammatory bacterial taxa are highly coated with secretory immunoglobulin IgA. Using bacterial fluorescence-activated cell sorting coupled with 16S rRNA gene sequencing (IgA-SEQ), we profiled IgA coating of intestinal microbiota in a large cohort of IBD patients and identified bacteria associated with disease and treatment. Forty-three bacterial taxa displayed significantly higher IgA coating in IBD compared with controls, including 8 taxa exhibiting differential IgA coating but similar relative abundance. Patients treated with anti-TNF-α therapies exhibited dramatically altered microbiota-specific IgA responses compared with controls. Furthermore, increased IgA coating of Oscillospira was associated with a delay in time to surgery. These results demonstrate that investigating IgA responses to microbiota can uncover potential disease-modifying taxa and reveal improved biomarkers of clinical course in IBD.
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Affiliation(s)
- Jason M Shapiro
- Division of Pediatric Gastroenterology, Nutrition and Liver Diseases, Hasbro Children's Hospital, Providence, RI 02903, USA; Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Marcel R de Zoete
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Noah W Palm
- Human and Translational Immunobiology Program, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Yaro Laenen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rene Bright
- Division of Gastroenterology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Meaghan Mallette
- Division of Gastroenterology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Agata A Bielecka
- Human and Translational Immunobiology Program, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Fang Xu
- Division of Population Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | | | - Samir A Shah
- Alpert Medical School of Brown University, Providence, RI 02903, USA; Division of Gastroenterology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Neal S LeLeiko
- Division of Pediatric Gastroenterology, Nutrition and Liver Diseases, Hasbro Children's Hospital, Providence, RI 02903, USA; Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Bruce E Sands
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard A Flavell
- Human and Translational Immunobiology Program, Yale University School of Medicine, New Haven, CT 06519, USA
| | - J C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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34
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Ungaro RC, Hu L, Ji J, Nayar S, Kugathasan S, Denson LA, Hyams J, Dubinsky MC, Sands BE, Cho JH. Machine learning identifies novel blood protein predictors of penetrating and stricturing complications in newly diagnosed paediatric Crohn's disease. Aliment Pharmacol Ther 2021; 53:281-290. [PMID: 33131065 PMCID: PMC7770008 DOI: 10.1111/apt.16136] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/23/2020] [Accepted: 10/11/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND There is a need for improved risk stratification in Crohn's disease. AIM To identify novel blood protein biomarkers associated with future Crohn's disease complications METHODS: We performed a case-cohort study utilising a paediatric inception cohort, the Risk Stratification and Identification of Immunogenetic and Microbial Markers of Rapid Disease Progression in Children with Crohn's disease (RISK) study. All patients had inflammatory disease (B1) at baseline. Outcomes were development of stricturing (B2) or penetrating (B3) complications. We assayed 92 inflammation-related proteins in baseline plasma using a proximity extension assay (Olink Proteomics). An ensemble machine learning technique, random survival forests (RSF), selected variables predicting B2 and B3 complications. Selected analytes were compared to clinical variables and serology only models. We examined selected proteins in a single-cell sequencing cohort to analyse differential cell expression in blood and ileum. RESULTS We included 265 patients with mean age 11.6 years (standard deviation [SD] 3.2). Seventy-three and 34 patients, respectively, had B2 and B3 complications within mean 1123 (SD 477) days for B2 and 1251 (442) for B3. A model with 5 protein markers predicted B3 complications with an area under the curve (AUC) of 0.79 (95% confidence interval [CI] 0.76-0.82) compared to 0.69 (95% CI 0.66-0.72) for serologies and 0.74 (95% CI 0.71-0.77) for clinical variables. A model with 4 protein markers predicted B2 complications with an AUC of 0.68 (95% CI 0.65-0.71) compared to 0.62 (95% CI 0.59-0.65) for serologies and 0.52 (95% CI 0.50-0.55) for clinical variables. B2 analytes were highly expressed in ileal stromal cells while B3 analytes were prominent in peripheral blood and ileal T cells. CONCLUSIONS We identified novel blood proteomic markers, distinct for B2 and B3, associated with progression of paediatric Crohn's disease.
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Affiliation(s)
- Ryan C. Ungaro
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shikha Nayar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lee A. Denson
- Division of Pediatric Gastroenterology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Jeffrey Hyams
- Division of Gastroenterology, Hepatology, and Nutrition, Connecticut Children’s Medical Center, Hartford, CT, USA
| | - Marla C. Dubinsky
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce E. Sands
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H. Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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35
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Vaid A, Somani S, Russak AJ, De Freitas JK, Chaudhry FF, Paranjpe I, Johnson KW, Lee SJ, Miotto R, Richter F, Zhao S, Beckmann ND, Naik N, Kia A, Timsina P, Lala A, Paranjpe M, Golden E, Danieletto M, Singh M, Meyer D, O'Reilly PF, Huckins L, Kovatch P, Finkelstein J, Freeman RM, Argulian E, Kasarskis A, Percha B, Aberg JA, Bagiella E, Horowitz CR, Murphy B, Nestler EJ, Schadt EE, Cho JH, Cordon-Cardo C, Fuster V, Charney DS, Reich DL, Bottinger EP, Levin MA, Narula J, Fayad ZA, Just AC, Charney AW, Nadkarni GN, Glicksberg BS. Machine Learning to Predict Mortality and Critical Events in a Cohort of Patients With COVID-19 in New York City: Model Development and Validation. J Med Internet Res 2020; 22:e24018. [PMID: 33027032 PMCID: PMC7652593 DOI: 10.2196/24018] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND COVID-19 has infected millions of people worldwide and is responsible for several hundred thousand fatalities. The COVID-19 pandemic has necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods to meet these needs are lacking. OBJECTIVE The aims of this study were to analyze the electronic health records (EHRs) of patients who tested positive for COVID-19 and were admitted to hospitals in the Mount Sinai Health System in New York City; to develop machine learning models for making predictions about the hospital course of the patients over clinically meaningful time horizons based on patient characteristics at admission; and to assess the performance of these models at multiple hospitals and time points. METHODS We used Extreme Gradient Boosting (XGBoost) and baseline comparator models to predict in-hospital mortality and critical events at time windows of 3, 5, 7, and 10 days from admission. Our study population included harmonized EHR data from five hospitals in New York City for 4098 COVID-19-positive patients admitted from March 15 to May 22, 2020. The models were first trained on patients from a single hospital (n=1514) before or on May 1, externally validated on patients from four other hospitals (n=2201) before or on May 1, and prospectively validated on all patients after May 1 (n=383). Finally, we established model interpretability to identify and rank variables that drive model predictions. RESULTS Upon cross-validation, the XGBoost classifier outperformed baseline models, with an area under the receiver operating characteristic curve (AUC-ROC) for mortality of 0.89 at 3 days, 0.85 at 5 and 7 days, and 0.84 at 10 days. XGBoost also performed well for critical event prediction, with an AUC-ROC of 0.80 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. In external validation, XGBoost achieved an AUC-ROC of 0.88 at 3 days, 0.86 at 5 days, 0.86 at 7 days, and 0.84 at 10 days for mortality prediction. Similarly, the unimputed XGBoost model achieved an AUC-ROC of 0.78 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. Trends in performance on prospective validation sets were similar. At 7 days, acute kidney injury on admission, elevated LDH, tachypnea, and hyperglycemia were the strongest drivers of critical event prediction, while higher age, anion gap, and C-reactive protein were the strongest drivers of mortality prediction. CONCLUSIONS We externally and prospectively trained and validated machine learning models for mortality and critical events for patients with COVID-19 at different time horizons. These models identified at-risk patients and uncovered underlying relationships that predicted outcomes.
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Affiliation(s)
- Akhil Vaid
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sulaiman Somani
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Adam J Russak
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jessica K De Freitas
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Fayzan F Chaudhry
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ishan Paranjpe
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Kipp W Johnson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Samuel J Lee
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Riccardo Miotto
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Felix Richter
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Shan Zhao
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nidhi Naik
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Arash Kia
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Healthcare Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Prem Timsina
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Healthcare Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Anuradha Lala
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Eddye Golden
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Matteo Danieletto
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Manbir Singh
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Dara Meyer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Paul F O'Reilly
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Laura Huckins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Patricia Kovatch
- Mount Sinai Data Warehouse, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Joseph Finkelstein
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Robert M Freeman
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Healthcare Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Edgar Argulian
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Data Office, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bethany Percha
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Judith A Aberg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Emilia Bagiella
- Institute for Healthcare Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Carol R Horowitz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Barbara Murphy
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eric J Nestler
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Valentin Fuster
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Dennis S Charney
- Office of the Dean, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David L Reich
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Erwin P Bottinger
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany
| | - Matthew A Levin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jagat Narula
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zahi A Fayad
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Allan C Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alexander W Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Girish N Nadkarni
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Benjamin S Glicksberg
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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36
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Cho JH, Han KD, Jung HY, Bond A. National health screening may reduce cardiovascular morbidity and mortality among the elderly. Public Health 2020; 187:172-176. [PMID: 32992163 DOI: 10.1016/j.puhe.2020.08.010] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 08/04/2020] [Accepted: 08/09/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVES Since 2007, the Korean government has provided a free health screening to the elderly starting at the age of 66 years. The purpose of this study was to evaluate the association between this general health screening and the incidences of stroke and myocardial infarction and mortality. STUDY DESIGN The study design used in this study is a retrospective cohort study. METHODS The study was conducted using the universe of insurance claims data of Korea and followed a cohort of individuals aged 66 years in 2009 from 2006 through 2016 (n = 354,194). We assessed the association between receipt of the national health screening and health outcomes using propensity matching and Cox proportional hazard models. RESULTS We found that the receipt of the national health screening was associated with a reduction in negative health outcomes. The hazard ratio for stroke was 0.89 (P < 0.001), 0.88 (P < 0.001) for myocardial infarction and 0.58 for death (P < 0.001). CONCLUSION Korea's national health screening was associated with reductions in cardiovascular morbidity and mortality in the elderly.
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Affiliation(s)
- J H Cho
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Konkuk University, Seoul, Republic of Korea.
| | - K D Han
- Department of Biostatistics, Catholic University College of Medicine, Seoul, Republic of Korea
| | - H-Y Jung
- Department of Healthcare Policy and Research, Weill Cornell Medical College, New York, NY, USA
| | - A Bond
- Department of Healthcare Policy and Research, Weill Cornell Medical College, New York, NY, USA
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37
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Stahl E, Roda G, Dobbyn A, Hu J, Zhang Z, Westerlind H, Bonfiglio F, Raj T, Torres J, Chen A, Petras R, Pardi DS, Iuga AC, Levi GS, Cao W, Jain P, Rieder F, Gordon IO, Cho JH, D’Amato M, Harpaz N, Hao K, Colombel JF, Peter I. Collagenous Colitis Is Associated With HLA Signature and Shares Genetic Risks With Other Immune-Mediated Diseases. Gastroenterology 2020; 159:549-561.e8. [PMID: 32371109 PMCID: PMC7483815 DOI: 10.1053/j.gastro.2020.04.063] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 04/17/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Collagenous colitis (CC) is an inflammatory bowel disorder with unknown etiopathogenesis involving HLA-related immune-mediated responses and environmental and genetic risk factors. We carried out an array-based genetic association study in a cohort of patients with CC and investigated the common genetic basis between CC and Crohn's disease (CD), ulcerative colitis (UC), and celiac disease. METHODS DNA from 804 CC formalin-fixed, paraffin-embedded tissue samples was genotyped with Illumina Immunochip. Matching genotype data on control samples and CD, UC, and celiac disease cases were provided by the respective consortia. A discovery association study followed by meta-analysis with an independent cohort, polygenic risk score calculation, and cross-phenotype analyses were performed. Enrichment of regulatory expression quantitative trait loci among the CC variants was assessed in hemopoietic and intestinal cells. RESULTS Three HLA alleles (HLA-B∗08:01, HLA-DRB1∗03:01, and HLA-DQB1∗02:01), related to the ancestral haplotype 8.1, were significantly associated with increased CC risk. We also identified an independent protective effect of HLA-DRB1∗04:01 on CC risk. Polygenic risk score quantifying the risk across multiple susceptibility loci was strongly associated with CC risk. An enrichment of expression quantitative trait loci was detected among the CC-susceptibility variants in various cell types. The cross-phenotype analysis identified a complex pattern of polygenic pleiotropy between CC and other immune-mediated diseases. CONCLUSIONS In this largest genetic study of CC to date with histologically confirmed diagnosis, we strongly implicated the HLA locus and proposed potential non-HLA mechanisms in disease pathogenesis. We also detected a shared genetic risk between CC, celiac disease, CD, and UC, which supports clinical observations of comorbidity.
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Affiliation(s)
- Eli Stahl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giulia Roda
- IBD Center, Humanitas Research Hospital, Milan, Italy
| | - Amanda Dobbyn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Helga Westerlind
- Department of Medicine, Karolinska Institutet, Solna, SE-17176, Stockholm, Sweden
| | - Ferdinando Bonfiglio
- Department of Medicine, Karolinska Institutet, Solna, SE-17176, Stockholm, Sweden
| | - Towfique Raj
- Ronald M. Loeb Center for Alzheimer’s Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joana Torres
- Department of Gastroenterology, Hospital Beatriz Angelo, Loures, Portugal
| | - Anli Chen
- Department of Pathology, Icahn School of Medicine, New York, NY, USA
| | - Robert Petras
- AmeriPath Institute of Gastrointestinal Pathology and Digestive Disease, Cleveland, OH, USA
| | - Darrell S. Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Alina C. Iuga
- Department of Biology and Cell Pathology, Columbia University, New York, NY, USA
| | - Gabriel S. Levi
- Department of Pathology, Icahn School of Medicine, New York, NY, USA
| | - Wenqing Cao
- Division of Anatomic Pathology, New York University Langone Medical Center, New York, NY, USA
| | - Prantesh Jain
- Department of Hematology and Oncology, University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Florian Rieder
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic
| | - Ilyssa O. Gordon
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic
| | - Judy H. Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mauro D’Amato
- Department of Medicine, Karolinska Institutet, Solna, SE-17176, Stockholm, Sweden,School of Biological Sciences, Monash University, Clayton, VIC Australia
| | - Noam Harpaz
- Department of Pathology, Icahn School of Medicine, New York, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean Frederic Colombel
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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38
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Aragam KG, Dobbyn A, Judy R, Chaffin M, Chaudhary K, Hindy G, Cagan A, Finneran P, Weng LC, Loos RJ, Nadkarni G, Cho JH, Kember RL, Baras A, Reid J, Overton J, Philippakis A, Ellinor PT, Weiss ST, Rader DJ, Lubitz SA, Smoller JW, Karlson EW, Khera AV, Kathiresan S, Do R, Damrauer SM, Natarajan P. Limitations of Contemporary Guidelines for Managing Patients at High Genetic Risk of Coronary Artery Disease. J Am Coll Cardiol 2020; 75:2769-2780. [PMID: 32498804 PMCID: PMC7346975 DOI: 10.1016/j.jacc.2020.04.027] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Polygenic risk scores (PRS) for coronary artery disease (CAD) identify high-risk individuals more likely to benefit from primary prevention statin therapy. Whether polygenic CAD risk is captured by conventional paradigms for assessing clinical cardiovascular risk remains unclear. OBJECTIVES This study sought to intersect polygenic risk with guideline-based recommendations and management patterns for CAD primary prevention. METHODS A genome-wide CAD PRS was applied to 47,108 individuals across 3 U.S. health care systems. The authors then assessed whether primary prevention patients at high polygenic risk might be distinguished on the basis of greater guideline-recommended statin eligibility and higher rates of statin therapy. RESULTS Of 47,108 study participants, the mean age was 60 years, and 11,020 (23.4%) had CAD. The CAD PRS strongly associated with prevalent CAD (odds ratio: 1.4 per SD increase in PRS; p < 0.0001). High polygenic risk (top 20% of PRS) conferred 1.9-fold odds of developing CAD (p < 0.0001). However, among primary prevention patients (n = 33,251), high polygenic risk did not correspond with increased recommendations for statin therapy per the American College of Cardiology/American Heart Association (46.2% for those with high PRS vs. 46.8% for all others, p = 0.54) or U.S. Preventive Services Task Force (43.7% vs. 43.7%, p = 0.99) or higher rates of statin prescriptions (25.0% vs. 23.8%, p = 0.04). An additional 4.1% of primary prevention patients may be recommended for statin therapy if high CAD PRS were considered a guideline-based risk-enhancing factor. CONCLUSIONS Current paradigms for primary cardiovascular prevention incompletely capture a polygenic susceptibility to CAD. An opportunity may exist to improve CAD prevention efforts by integrating both genetic and clinical risk.
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Affiliation(s)
- Krishna G. Aragam
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Amanda Dobbyn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Renae Judy
- Department of Surgery, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark Chaffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Kumardeep Chaudhary
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - George Hindy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Andrew Cagan
- Research Computing, Partners HealthCare, Charlestown, MA, USA
| | - Phoebe Finneran
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Lu-Chen Weng
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy H. Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel L. Kember
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Anthony Philippakis
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Patrick T. Ellinor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Scott T. Weiss
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Daniel J. Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Steven A. Lubitz
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Jordan W. Smoller
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute, Boston, MA, USA
| | - Elizabeth W. Karlson
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA
| | - Amit V. Khera
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Sekar Kathiresan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Scott M. Damrauer
- Department of Surgery, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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39
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Claussnitzer M, Cho JH, Collins R, Cox NJ, Dermitzakis ET, Hurles ME, Kathiresan S, Kenny EE, Lindgren CM, MacArthur DG, North KN, Plon SE, Rehm HL, Risch N, Rotimi CN, Shendure J, Soranzo N, McCarthy MI. A brief history of human disease genetics. Nature 2020; 577:179-189. [PMID: 31915397 DOI: 10.1038/s41586-019-1879-7] [Citation(s) in RCA: 307] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022]
Abstract
A primary goal of human genetics is to identify DNA sequence variants that influence biomedical traits, particularly those related to the onset and progression of human disease. Over the past 25 years, progress in realizing this objective has been transformed by advances in technology, foundational genomic resources and analytical tools, and by access to vast amounts of genotype and phenotype data. Genetic discoveries have substantially improved our understanding of the mechanisms responsible for many rare and common diseases and driven development of novel preventative and therapeutic strategies. Medical innovation will increasingly focus on delivering care tailored to individual patterns of genetic predisposition.
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Affiliation(s)
- Melina Claussnitzer
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA.,Institute of Nutritional Science, University of Hohenheim, Stuttgart, Germany
| | - Judy H Cho
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rory Collins
- Nuffield Department of Population Health (NDPH), University of Oxford, Oxford, UK.,UK Biobank, Stockport, UK
| | - Nancy J Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Health 2030 Genome Center, Geneva, Switzerland
| | | | - Sekar Kathiresan
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Verve Therapeutics, Cambridge, MA, USA
| | - Eimear E Kenny
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cecilia M Lindgren
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA.,Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel G MacArthur
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn N North
- Murdoch Children's Research Institute, Parkville, Victoria, Australia.,University of Melbourne, Parkville, Victoria, Australia
| | - Sharon E Plon
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Magnuson Health Sciences Building, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,Oxford Centre for Diabetes, Endocrinology and Metabolism, Oxford, UK. .,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK. .,Human Genetics, Genentech, South San Francisco, CA, USA.
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40
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Abul-Husn NS, Soper ER, Odgis JA, Cullina S, Bobo D, Moscati A, Rodriguez JE, Loos RJF, Cho JH, Belbin GM, Suckiel SA, Kenny EE. Exome sequencing reveals a high prevalence of BRCA1 and BRCA2 founder variants in a diverse population-based biobank. Genome Med 2019; 12:2. [PMID: 31892343 PMCID: PMC6938627 DOI: 10.1186/s13073-019-0691-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/13/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Pathogenic variants in BRCA1 and BRCA2 (BRCA1/2) lead to increased risk of breast, ovarian, and other cancers, but most variant-positive individuals in the general population are unaware of their risk, and little is known about prevalence in non-European populations. We investigated BRCA1/2 prevalence and impact in the electronic health record (EHR)-linked BioMe Biobank in New York City. METHODS Exome sequence data from 30,223 adult BioMe participants were evaluated for pathogenic variants in BRCA1/2. Prevalence estimates were made in population groups defined by genetic ancestry and self-report. EHR data were used to evaluate clinical characteristics of variant-positive individuals. RESULTS There were 218 (0.7%) individuals harboring expected pathogenic variants, resulting in an overall prevalence of 1 in 139. The highest prevalence was in individuals with Ashkenazi Jewish (AJ; 1 in 49), Filipino and other Southeast Asian (1 in 81), and non-AJ European (1 in 103) ancestry. Among 218 variant-positive individuals, 112 (51.4%) harbored known founder variants: 80 had AJ founder variants (BRCA1 c.5266dupC and c.68_69delAG, and BRCA2 c.5946delT), 8 had a Puerto Rican founder variant (BRCA2 c.3922G>T), and 24 had one of 19 other founder variants. Non-European populations were more likely to harbor BRCA1/2 variants that were not classified in ClinVar or that had uncertain or conflicting evidence for pathogenicity (uncertain/conflicting). Within mixed ancestry populations, such as Hispanic/Latinos with genetic ancestry from Africa, Europe, and the Americas, there was a strong correlation between the proportion of African genetic ancestry and the likelihood of harboring an uncertain/conflicting variant. Approximately 28% of variant-positive individuals had a personal history, and 45% had a personal or family history of BRCA1/2-associated cancers. Approximately 27% of variant-positive individuals had prior clinical genetic testing for BRCA1/2. However, individuals with AJ founder variants were twice as likely to have had a clinical test (39%) than those with other pathogenic variants (20%). CONCLUSIONS These findings deepen our knowledge about BRCA1/2 variants and associated cancer risk in diverse populations, indicate a gap in knowledge about potential cancer-related variants in non-European populations, and suggest that genomic screening in diverse patient populations may be an effective tool to identify at-risk individuals.
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Affiliation(s)
- Noura S Abul-Husn
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Emily R Soper
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacqueline A Odgis
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sinead Cullina
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dean Bobo
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arden Moscati
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica E Rodriguez
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gillian M Belbin
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabrina A Suckiel
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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41
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Damrauer SM, Chaudhary K, Cho JH, Liang LW, Argulian E, Chan L, Dobbyn A, Guerraty MA, Judy R, Kay J, Kember RL, Levin MG, Saha A, Van Vleck T, Verma SS, Weaver J, Abul-Husn NS, Baras A, Chirinos JA, Drachman B, Kenny EE, Loos RJF, Narula J, Overton J, Reid J, Ritchie M, Sirugo G, Nadkarni G, Rader DJ, Do R. Association of the V122I Hereditary Transthyretin Amyloidosis Genetic Variant With Heart Failure Among Individuals of African or Hispanic/Latino Ancestry. JAMA 2019; 322:2191-2202. [PMID: 31821430 PMCID: PMC7081752 DOI: 10.1001/jama.2019.17935] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
Importance Hereditary transthyretin (TTR) amyloid cardiomyopathy (hATTR-CM) due to the TTR V122I variant is an autosomal-dominant disorder that causes heart failure in elderly individuals of African ancestry. The clinical associations of carrying the variant, its effect in other African ancestry populations including Hispanic/Latino individuals, and the rates of achieving a clinical diagnosis in carriers are unknown. Objective To assess the association between the TTR V122I variant and heart failure and identify rates of hATTR-CM diagnosis among carriers with heart failure. Design, Setting, and Participants Cross-sectional analysis of carriers and noncarriers of TTR V122I of African ancestry aged 50 years or older enrolled in the Penn Medicine Biobank between 2008 and 2017 using electronic health record data from 1996 to 2017. Case-control study in participants of African and Hispanic/Latino ancestry with and without heart failure in the Mount Sinai BioMe Biobank enrolled between 2007 and 2015 using electronic health record data from 2007 to 2018. Exposures TTR V122I carrier status. Main Outcomes and Measures The primary outcome was prevalent heart failure. The rate of diagnosis with hATTR-CM among TTR V122I carriers with heart failure was measured. Results The cross-sectional cohort included 3724 individuals of African ancestry with a median age of 64 years (interquartile range, 57-71); 1755 (47%) were male, 2896 (78%) had a diagnosis of hypertension, and 753 (20%) had a history of myocardial infarction or coronary revascularization. There were 116 TTR V122I carriers (3.1%); 1121 participants (30%) had heart failure. The case-control study consisted of 2307 individuals of African ancestry and 3663 Hispanic/Latino individuals; the median age was 73 years (interquartile range, 68-80), 2271 (38%) were male, 4709 (79%) had a diagnosis of hypertension, and 1008 (17%) had a history of myocardial infarction or coronary revascularization. There were 1376 cases of heart failure. TTR V122I was associated with higher rates of heart failure (cross-sectional cohort: n = 51/116 TTR V122I carriers [44%], n = 1070/3608 noncarriers [30%], adjusted odds ratio, 1.7 [95% CI, 1.2-2.4], P = .006; case-control study: n = 36/1376 heart failure cases [2.6%], n = 82/4594 controls [1.8%], adjusted odds ratio, 1.8 [95% CI, 1.2-2.7], P = .008). Ten of 92 TTR V122I carriers with heart failure (11%) were diagnosed as having hATTR-CM; the median time from onset of symptoms to clinical diagnosis was 3 years. Conclusions and Relevance Among individuals of African or Hispanic/Latino ancestry enrolled in 2 academic medical center-based biobanks, the TTR V122I genetic variant was significantly associated with heart failure.
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Affiliation(s)
- Scott M. Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Department of Surgery, Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania
| | - Kumardeep Chaudhary
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Judy H. Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lusha W. Liang
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Edgar Argulian
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lili Chan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Amanda Dobbyn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marie A. Guerraty
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Renae Judy
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Jenna Kay
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Rachel L. Kember
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- MIRECC, Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania
| | - Michael G. Levin
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Aparna Saha
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tielman Van Vleck
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Shefali S. Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - JoEllen Weaver
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Noura S. Abul-Husn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York
| | - Julio A. Chirinos
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Brian Drachman
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Eimear E. Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jagat Narula
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Marylyn Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Giorgio Sirugo
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Pennsylvania
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Daniel J. Rader
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Pennsylvania
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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42
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Park HJ, Cho JH, Kim HJ, Park JY, Lee HS, Byun MK. The effect of low body mass index on the development of chronic obstructive pulmonary disease and mortality. J Intern Med 2019; 286:573-582. [PMID: 31215064 DOI: 10.1111/joim.12949] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Sarcopenia may worsen disease progression and lead to poor outcomes in chronic obstructive pulmonary disease (COPD). OBJECTIVES We aimed to determine the effect of BMI on the development of COPD and mortality. METHODS We enrolled 437 584 participants registered in the physical health check-up cohort database of the Korean National Health Interview Survey from 2002 to 2003, and we defined COPD diagnosis based on the ICD-10 code and prescribed medication. BMI (kg m-2 ) classified them to five groups (low BMI < 18.5, normal BMI 18.5-23, overweight 23-25, obesity 25-30, severe obesity ≥30) at baseline. RESULTS Participants in the low BMI group had a significantly higher rate of COPD development for 13 years (7.6%) than those in other groups (3.4-4.1%, P < 0.0001). Amongst never or light smokers, COPD development in the low BMI group (5.6-6.7%) was significantly higher than that in other groups (2.8-4.7%). Similarly, amongst participants with a smoking history of ≥30 years, COPD development in the low BMI group (20.1%) was higher than those in other groups (8.4-12.4%). On multivariable analysis, normal or higher than normal body weight was significantly protective against the development of COPD (hazard ratio [HR], 0.609-0.739,) compared to low BMI. COPD-free-survival (HR, 0.491-0.622) and overall survival (HR, 0.440-0.585) were also better in them compared to those with low BMI (all P < 0.0001). CONCLUSIONS Low BMI is an important risk factor for COPD development and mortality. Maintaining adequate body weight may reduce the risk for COPD development and mortality.
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Affiliation(s)
- H J Park
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - J H Cho
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - H J Kim
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - J-Y Park
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, Korea
| | - H S Lee
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, Korea
| | - M K Byun
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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43
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Martin JC, Chang C, Boschetti G, Ungaro R, Giri M, Grout JA, Gettler K, Chuang LS, Nayar S, Greenstein AJ, Dubinsky M, Walker L, Leader A, Fine JS, Whitehurst CE, Mbow ML, Kugathasan S, Denson LA, Hyams JS, Friedman JR, Desai PT, Ko HM, Laface I, Akturk G, Schadt EE, Salmon H, Gnjatic S, Rahman AH, Merad M, Cho JH, Kenigsberg E. Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy. Cell 2019; 178:1493-1508.e20. [PMID: 31474370 DOI: 10.1016/j.cell.2019.08.008] [Citation(s) in RCA: 412] [Impact Index Per Article: 82.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/06/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Abstract
Clinical benefits of cytokine blockade in ileal Crohn's disease (iCD) are limited to a subset of patients. Here, we applied single-cell technologies to iCD lesions to address whether cellular heterogeneity contributes to treatment resistance. We found that a subset of patients expressed a unique cellular module in inflamed tissues that consisted of IgG plasma cells, inflammatory mononuclear phagocytes, activated T cells, and stromal cells, which we named the GIMATS module. Analysis of ligand-receptor interaction pairs identified a distinct network connectivity that likely drives the GIMATS module. Strikingly, the GIMATS module was also present in a subset of patients in four independent iCD cohorts (n = 441), and its presence at diagnosis correlated with failure to achieve durable corticosteroid-free remission upon anti-TNF therapy. These results emphasize the limitations of current diagnostic assays and the potential for single-cell mapping tools to identify novel biomarkers of treatment response and tailored therapeutic opportunities.
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Affiliation(s)
- Jerome C Martin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christie Chang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gilles Boschetti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ryan Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Mamta Giri
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John A Grout
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kyle Gettler
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ling-Shiang Chuang
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shikha Nayar
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander J Greenstein
- Department of Colorectal Surgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marla Dubinsky
- Department of Pediatrics, Susan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Walker
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew Leader
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jay S Fine
- Boehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Diseases Research, Ridgefield, CT 06877, USA
| | - Charles E Whitehurst
- Boehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Diseases Research, Ridgefield, CT 06877, USA
| | - M Lamine Mbow
- Boehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Diseases Research, Ridgefield, CT 06877, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA
| | | | | | - Huaibin M Ko
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ilaria Laface
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Guray Akturk
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Helene Salmon
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adeeb H Rahman
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Judy H Cho
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Ephraim Kenigsberg
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Chuang LS, Morrison J, Hsu NY, Labrias PR, Nayar S, Chen E, Villaverde N, Facey JA, Boschetti G, Giri M, Castillo-Martin M, Thin TH, Sharma Y, Chu J, Cho JH. Zebrafish modeling of intestinal injury, bacterial exposures and medications defines epithelial in vivo responses relevant to human inflammatory bowel disease. Dis Model Mech 2019; 12:dmm.037432. [PMID: 31337664 PMCID: PMC6737949 DOI: 10.1242/dmm.037432] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 07/11/2019] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified over 200 genomic loci associated with inflammatory bowel disease (IBD). High-effect risk alleles define key roles for genes involved in bacterial response and innate defense. More high-throughput in vivo systems are required to rapidly evaluate therapeutic agents. We visualize, in zebrafish, the effects on epithelial barrier function and intestinal autophagy of one-course and repetitive injury. Repetitive injury induces increased mortality, impaired recovery of intestinal barrier function, failure to contain bacteria within the intestine and impaired autophagy. Prostaglandin E2 (PGE2) administration protected against injury by enhancing epithelial barrier function and limiting systemic infection. Effects of IBD therapeutic agents were defined: mesalamine showed protective features during injury, whereas 6-mercaptopurine displayed marked induction of autophagy during recovery. Given the highly conserved nature of innate defense in zebrafish, it represents an ideal model system with which to test established and new IBD therapies targeted to the epithelial barrier.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua Morrison
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Philippe Ronel Labrias
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shikha Nayar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ernie Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Villaverde
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jody Ann Facey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gilles Boschetti
- Department of Oncological Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mireia Castillo-Martin
- Departments of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tin Htwe Thin
- Departments of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yashoda Sharma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaime Chu
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Judy H Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA .,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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45
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Cohen LJ, Cho JH, Gevers D, Chu H. Genetic Factors and the Intestinal Microbiome Guide Development of Microbe-Based Therapies for Inflammatory Bowel Diseases. Gastroenterology 2019; 156:2174-2189. [PMID: 30880022 PMCID: PMC6568267 DOI: 10.1053/j.gastro.2019.03.017] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 02/28/2019] [Accepted: 03/02/2019] [Indexed: 12/22/2022]
Abstract
The intestinal microbiota is a dynamic community of bacteria, fungi, and viruses that mediates mucosal homeostasis and physiology. Imbalances in the microbiome and aberrant immune responses to gut bacteria can disrupt homeostasis and are associated with inflammatory bowel diseases (IBDs) in humans and colitis in mice. We review genetic variants associated with IBD and their effects on the intestinal microbiome, the immune response, and disease pathogenesis. The intestinal microbiome, which includes microbial antigens, adjuvants, and metabolic products, affects the development and function of the intestinal mucosa, influencing inflammatory responses in the gut. Therefore, strategies to manipulate the microbiome might be used in treatment of IBD. We review microbe-based therapies for IBD and the potential to engineer patients' intestinal microbiota. We discuss how studies of patients with IBD and mouse models have advanced our understanding of the interactions between genetic factors and the gut microbiome, and challenges to the development of microbe-based therapies for IBD.
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Affiliation(s)
- Louis J. Cohen
- Division of Gastroenterology, Department of Medicine, Icahn
School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Correspondence:
(L.J.C.),
(H.C.)
| | - Judy H. Cho
- Division of Gastroenterology, Department of Medicine, Icahn
School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai; The Charles Bronfman Institute for Personalized
Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, 10029,
USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research &
Development, Cambridge, MA, 02142, USA
| | - Hiutung Chu
- Department of Pathology, University of California-San Diego, La Jolla, California; Chiba University and University of California-San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, California.
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46
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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet 2019; 15:e1008190. [PMID: 31145742 PMCID: PMC6542503 DOI: 10.1371/journal.pgen.1008190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Rosenblum R, Suckiel SA, Belbin GM, Cullina S, Cho JH, Kenny EE, Lucas AL, Ang C, Abul-Husn NS. Genetic identification and characterization of Lynch syndrome in a multi-ethnic biobank. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.1520] [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] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1520 Background: Lynch syndrome (LS), caused by germline pathogenic variants in mismatch repair (MMR) genes, results in increased risk of colorectal, endometrial, and other cancers. LS has a prevalence of ~1 in 440 in European ancestry populations; prevalence data in other populations are limited. We identified and characterized carriers of pathogenic MMR gene variants in the multi-ethnic Bio Me Biobank in New York City. Methods: Exome sequence data from ~31,000 Bio Me participants were evaluated for known (per ClinVar) and predicted (loss-of-function) pathogenic variants in MMR genes. Population groups were defined by genetic ancestry. Participant questionnaires and electronic health records (EHRs) of carriers were reviewed for personal or family history of malignancy. Results: We identified 48 carriers of 33 distinct pathogenic variants in PMS2 (48%), MLH1 (27%), MSH6 (15%), and MSH2 (10%), for an estimated prevalence of ~1/640 in the Bio Me Biobank. Prevalence was higher among individuals of Non-Jewish European (N = 14; 1/400) and African (N = 14; 1/490) ancestries, compared to Puerto Rican (N = 8; 1/640), Ashkenazi Jewish (N = 6; 1/690), and other/mixed (N = 6) ancestries. Carriers had a median age of 56 (range 27 to 77) years and were 50% female. Overall rate of malignancy among carriers was 38%, with the lowest rate in PMS2 (26%) and the highest rate in MSH6 (57%) variant carriers. We found a high prevalence of endometrial cancer (21% of female carriers) and a lower prevalence of colorectal cancer (4% of all carriers). Only 2 carriers (4%) had a diagnosis of LS in their EHRs, and only 1 carrier met Amsterdam diagnostic criteria for LS. Conclusions: These data show that ~0.15% of participants in a multi-ethnic biobank are carriers of pathogenic MMR gene variants and suggest that the prevalence is higher in European and lower in non-European ancestry populations. Notably, most carriers do not have a clinical diagnosis of LS and do not meet diagnostic criteria for LS. Carriers demonstrate variable rates of cancer, which may contribute to under-diagnosis of LS. Genomic screening for pathogenic MMR variants may lead to earlier diagnosis of LS and improved outcomes.
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Affiliation(s)
- Rachel Rosenblum
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sabrina A. Suckiel
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gillian M. Belbin
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sinead Cullina
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Judy H. Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eimear E. Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Aimee L. Lucas
- Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Celina Ang
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S. Abul-Husn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
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Denson LA, Curran M, McGovern DPB, Koltun WA, Duerr RH, Kim SC, Sartor RB, Sylvester FA, Abraham C, de Zoeten EF, Siegel CA, Burns RM, Dobes AM, Shtraizent N, Honig G, Heller CA, Hurtado-Lorenzo A, Cho JH. Challenges in IBD Research: Precision Medicine. Inflamm Bowel Dis 2019; 25:S31-S39. [PMID: 31095701 DOI: 10.1093/ibd/izz078] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Indexed: 12/12/2022]
Abstract
Precision medicine is part of five focus areas of the Challenges in IBD research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. The Challenges in IBD Research document provides a comprehensive overview of current gaps in inflammatory bowel diseases (IBD) research and delivers actionable approaches to address them. It is the result of a multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient centric research prioritization. In particular, the precision medicine section is focused on highlighting the main gap areas that must be addressed to get closer to treatments tailored to the biological and clinical characteristics of each patient, which is the aim of precision medicine. The main gaps were identified in: 1) understanding and predicting the natural history of IBD: disease susceptibility, activity, and behavior; 2) predicting disease course and treatment response; and 3) optimizing current and developing new molecular technologies. Suggested approaches to bridge these gaps include prospective longitudinal cohort studies to identify and validate precision biomarkers for prognostication of disease course, and prediction and monitoring of treatment response. To achieve this, harmonization across studies is key as well as development of standardized methods and infrastructure. The implementation of state-of-the-art molecular technologies, systems biology and machine learning approaches for multi-omics and clinical data integration and analysis will be also fundamental. Finally, randomized biomarker-stratified trials will be critical to evaluate the clinical utility of validated signatures and biomarkers in improving patient outcomes and cost-effective care.
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Affiliation(s)
- Lee A Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Mark Curran
- Janssen Research and Development, Spring House, PA, USA
| | - Dermot P B McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Walter A Koltun
- Department of Surgery, Division of Colon and Rectal Surgery, Pennsylvania State University, Hershey, PA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sandra C Kim
- Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - R Balfour Sartor
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Francisco A Sylvester
- Division of Pediatric Gastroenterology, University of North Carolina at Chapel Hil, Chapel Hill, NC, USA
| | | | - Edwin F de Zoeten
- University of Colorado School of Medicine, Childrens Hospital Colorado, Aurora, CO, USA
| | - Corey A Siegel
- Dartmouth Hitchcock Medical Center, Section of Gastroenterology and Hepatology, Lebanon NH, USA
| | - Richéal M Burns
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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49
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Hirten RP, Grinspan A, Fu SC, Luo Y, Suarez-Farinas M, Rowland J, Contijoch EJ, Mogno I, Yang N, Luong T, Labrias PR, Peter I, Cho JH, Sands BE, Colombel JF, Faith JJ, Clemente JC. Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease. Inflamm Bowel Dis 2019; 25:969-979. [PMID: 30852592 PMCID: PMC6499938 DOI: 10.1093/ibd/izy398] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 08/27/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recurrent and severe Clostridium difficile infections (CDI) are treated with fecal microbiota transplant (FMT). Uncertainty exists regarding FMT effectiveness for CDI with underlying inflammatory bowel disease (IBD) and regarding its effects on disease activity and effectiveness in transferring the donor microbiota to patients with and without IBD. METHODS Subjects with and without IBD who underwent FMT for recurrent or severe CDI between 2013 and 2016 at The Mount Sinai Hospital were followed for up to 6 months. The primary outcome was CDI recurrence 6 months after FMT. Secondary outcomes were (1) CDI recurrence 2 months after FMT; (2) frequency of IBD flare after FMT; (3) microbiota engraftment after FMT; (and 4) predictors of CDI recurrence. RESULTS One hundred thirty-four patients, 46 with IBD, were treated with FMT. Follow-up was available in 83 and 118 patients at 6 and 2 months, respectively. There was no difference in recurrence in patients with and without IBD at 6 months (38.7% vs 36.5%; P > 0.99) and 2 months (22.5% vs 17.9%; P = 0.63). Proton pump inhibitor use, severe CDI, and comorbid conditions were predictors of recurrence. Pre-FMT microbiota was not predictive of CDI recurrence. Subjects with active disease requiring medication escalation had reduced engraftment, with no difference in engraftment based on CDI recurrence or IBD endoscopic severity at FMT. CONCLUSIONS Inflammatory bowel disease did not affect CDI recurrence rates 6 months after FMT. Pre-FMT microbiota was not predictive of recurrence, and microbial engraftment was impacted in those requiring IBD treatment escalation, though not by CDI recurrence or IBD disease severity.
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Affiliation(s)
- Robert P Hirten
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shih-Chen Fu
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Yuying Luo
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Rowland
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eduardo J Contijoch
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Ilaria Mogno
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Nancy Yang
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tramy Luong
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Philippe R Labrias
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Inga Peter
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Judy H Cho
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Bruce E Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Jose C Clemente
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Address correspondence to: Jose C. Clemente, 1470 Madison Avenue, New York NY, USA 10029. E-mail:
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Liu SD, Song MH, Yun W, Lee JH, Kim HB, Cho JH. Effect of carvacrol essential oils on immune response and inflammation-related genes expression in broilers challenged by lipopolysaccharide. Poult Sci 2019; 98:2026-2033. [PMID: 30590708 DOI: 10.3382/ps/pey575] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 12/08/2018] [Indexed: 02/06/2023] Open
Abstract
This experiment was conducted to study the effects of orally administered carvacrol essential oils on immune response and inflammation-related genes expression in broilers challenged by lipopolysaccharide (LPS). Eighty 28-day-old (1.28 ± 0.15 kg) ROSS 308 broilers were assigned to a 2 × 2 factorial arrangement of treatments (20 pens of 1 chick/trt). Factors were carvacrol essential oil (orally administered or non-orally administered) and LPS (challenged or non-challenged). Individually housed broilers were randomly assigned (n = 20 broilers per treatment: 10 males and 10 females) to four treatments: (1) basic diet (CTR), (2) basic diet + carvacrol (CAR), (3) basic diet + LPS-challenge (LPS), (4) basic diet + carvacrol + LPS-challenge (CAR+LPS). All were fed with the same diet. The experimental period was for 15 d, after which injecting LPS significantly up-regulated the gene expression levels of TNF-α (P < 0.05), IL-1β (P < 0.05), IL-6 (P < 0.05), IL-8 (P < 0.05), TLR2 (P < 0.05), TLR4 (P < 0.05), NF-κB p65 (P < 0.05), AVBD-9 (P < 0.05), and SIgA(P < 0.05) compared with the CTR group; the broilers were challenged by LPS after oral administration of carvacrol, they had significant lower on the gene expression levels of TNF-α (P < 0.05), IL-1β (P < 0.05), IL-6 (P < 0.05), TLR4 (P < 0.05), NF-κB p65 (P < 0.05), and AVBD-9 (P < 0.05) than the LPS group. In conclusion, the broilers orally administrated carvacrol essential oils inhibited the secretion of inflammatory cytokines caused by LPS, affected the pathway of TLRs/NF-κB, and showed an anti-inflammatory function.
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Affiliation(s)
- S D Liu
- Division of Food and Animal Science, Chungbuk National University, Cheongju-si 361-763, Republic of Korea.,College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071000, China
| | - M H Song
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - W Yun
- Division of Food and Animal Science, Chungbuk National University, Cheongju-si 361-763, Republic of Korea
| | - J H Lee
- Division of Food and Animal Science, Chungbuk National University, Cheongju-si 361-763, Republic of Korea
| | - H B Kim
- Department of Animal Resource and Science, Dankook University, Cheonan 330-714, Republic of Korea
| | - J H Cho
- Division of Food and Animal Science, Chungbuk National University, Cheongju-si 361-763, Republic of Korea
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