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Peters BA, Pass HI, Burk RD, Xue X, Goparaju C, Sollecito CC, Grassi E, Segal LN, Tsay JCJ, Hayes RB, Ahn J. The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer. Genome Med 2022; 14:121. [PMID: 36303210 PMCID: PMC9609265 DOI: 10.1186/s13073-022-01126-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Cancer recurrence after tumor resection in early-stage non-small cell lung cancer (NSCLC) is common, yet difficult to predict. The lung microbiota and systemic immunity may be important modulators of risk for lung cancer recurrence, yet biomarkers from the lung microbiome and peripheral immune environment are understudied. Such markers may hold promise for prediction as well as improved etiologic understanding of lung cancer recurrence. METHODS In tumor and distant normal lung samples from 46 stage II NSCLC patients with curative resection (39 tumor samples, 41 normal lung samples), we conducted 16S rRNA gene sequencing. We also measured peripheral blood immune gene expression with nanoString®. We examined associations of lung microbiota and peripheral gene expression with recurrence-free survival (RFS) and disease-free survival (DFS) using 500 × 10-fold cross-validated elastic-net penalized Cox regression, and examined predictive accuracy using time-dependent receiver operating characteristic (ROC) curves. RESULTS Over a median of 4.8 years of follow-up (range 0.2-12.2 years), 43% of patients experienced a recurrence, and 50% died. In normal lung tissue, a higher abundance of classes Bacteroidia and Clostridia, and orders Bacteroidales and Clostridiales, were associated with worse RFS, while a higher abundance of classes Alphaproteobacteria and Betaproteobacteria, and orders Burkholderiales and Neisseriales, were associated with better RFS. In tumor tissue, a higher abundance of orders Actinomycetales and Pseudomonadales were associated with worse DFS. Among these taxa, normal lung Clostridiales and Bacteroidales were also related to worse survival in a previous small pilot study and an additional independent validation cohort. In peripheral blood, higher expression of genes TAP1, TAPBP, CSF2RB, and IFITM2 were associated with better DFS. Analysis of ROC curves revealed that lung microbiome and peripheral gene expression biomarkers provided significant additional recurrence risk discrimination over standard demographic and clinical covariates, with microbiome biomarkers contributing more to short-term (1-year) prediction and gene biomarkers contributing to longer-term (2-5-year) prediction. CONCLUSIONS We identified compelling biomarkers in under-explored data types, the lung microbiome, and peripheral blood gene expression, which may improve risk prediction of recurrence in early-stage NSCLC patients. These findings will require validation in a larger cohort.
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Affiliation(s)
- Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, #1315AB, The Bronx, New York, NY, 10461, USA.
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, NYU Langone Health, New York, NY, USA
- NYU Perlmutter Cancer Center, New York, NY, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, #1315AB, The Bronx, New York, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, The Bronx, New York, NY, USA
- Department of Microbiology & Immunology, and Obstetrics & Gynecology & Women's Health, Albert Einstein College of Medicine, The Bronx, New York, NY, USA
| | - Xiaonan Xue
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, #1315AB, The Bronx, New York, NY, 10461, USA
| | - Chandra Goparaju
- Department of Cardiothoracic Surgery, NYU Langone Health, New York, NY, USA
| | | | - Evan Grassi
- Department of Pediatrics, Albert Einstein College of Medicine, The Bronx, New York, NY, USA
| | | | | | - Richard B Hayes
- NYU Perlmutter Cancer Center, New York, NY, USA
- Department of Population Health, NYU Langone Health, New York, NY, USA
| | - Jiyoung Ahn
- NYU Perlmutter Cancer Center, New York, NY, USA
- Department of Population Health, NYU Langone Health, New York, NY, USA
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Ho PJ, Khng AJ, Tan BKT, Tan EY, Tan SM, Tan VKM, Lim GH, Aronson KJ, Chan TL, Choi JY, Dennis J, Ho WK, Hou MF, Ito H, Iwasaki M, John EM, Kang D, Kim SW, Kurian AW, Kwong A, Lophatananon A, Matsuo K, Mohd-Taib NA, Muir K, Murphy RA, Park SK, Shen CY, Shu XO, Teo SH, Wang Q, Yamaji T, Zheng W, Bolla MK, Dunning AM, Easton DF, Pharoah PDP, Hartman M, Li J. Relevance of the MHC region for breast cancer susceptibility in Asians. Breast Cancer 2022; 29:869-879. [PMID: 35543923 PMCID: PMC9385763 DOI: 10.1007/s12282-022-01366-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Human leukocyte antigen (HLA) genes play critical roles in immune surveillance, an important defence against tumors. Imputing HLA genotypes from existing single-nucleotide polymorphism datasets is low-cost and efficient. We investigate the relevance of the major histocompatibility complex region in breast cancer susceptibility, using imputed class I and II HLA alleles, in 25,484 women of Asian ancestry. METHODS A total of 12,901 breast cancer cases and 12,583 controls from 12 case-control studies were included in our pooled analysis. HLA imputation was performed using SNP2HLA on 10,886 quality-controlled variants within the 15-55 Mb region on chromosome 6. HLA alleles (n = 175) with info scores greater than 0.8 and frequencies greater than 0.01 were included (resolution at two-digit level: 71; four-digit level: 104). We studied the associations between HLA alleles and breast cancer risk using logistic regression, adjusting for population structure and age. Associations between HLA alleles and the risk of subtypes of breast cancer (ER-positive, ER-negative, HER2-positive, HER2-negative, early-stage, and late-stage) were examined. RESULTS We did not observe associations between any HLA allele and breast cancer risk at P < 5e-8; the smallest p value was observed for HLA-C*12:03 (OR = 1.29, P = 1.08e-3). Ninety-five percent of the effect sizes (OR) observed were between 0.90 and 1.23. Similar results were observed when different subtypes of breast cancer were studied (95% of ORs were between 0.85 and 1.18). CONCLUSIONS No imputed HLA allele was associated with breast cancer risk in our large Asian study. Direct measurement of HLA gene expressions may be required to further explore the associations between HLA genes and breast cancer risk.
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Affiliation(s)
- Peh Joo Ho
- Women’s Health and Genetics, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672 Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 119077 Singapore
- Department of Surgery, National University Health System, Singapore, 119228 Singapore
| | - Alexis Jiaying Khng
- Women’s Health and Genetics, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672 Singapore
| | - Benita Kiat-Tee Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore, Singapore
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of General Surgery, Sengkang General Hospital, Singapore, Singapore
| | - Ern Yu Tan
- Department of General Surgery, Tan Tock Seng Hospital, Singapore, 308433 Singapore
- Lee Kong Chian School of Medicine, Singapore, Singapore
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Su-Ming Tan
- Division of Breast Surgery, Changi General Hospital, Singapore, Singapore
| | - Veronique Kiak Mien Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore, Singapore
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Geok Hoon Lim
- KK Breast Department, KK Women’s and Children’s Hospital, Singapore, 229899 Singapore
| | - Kristan J. Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen’s University, Kingston, ON K7L 3N6 Canada
| | - Tsun L. Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong
- Department of Molecular Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, Hong Kong
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, 03080 Korea
- Cancer Research Institute, Seoul National University, Seoul, 03080 Korea
- Institute of Health Policy and Management, Seoul National University Medical Research Center, Seoul, 03080 Korea
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN UK
| | - Weang-Kee Ho
- Department of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor Malaysia
- Breast Cancer Research Programme, Cancer Research Malaysia, 47500 Subang Jaya, Selangor Malaysia
| | - Ming-Feng Hou
- Department of Surgery, Kaohsiung Municipal Hsiao-Kang Hospital, Kao-hsiung, 812 Taiwan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, 464-8681 Japan
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, 104-0045 Japan
| | - Esther M. John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94304 USA
| | - Daehee Kang
- Cancer Research Institute, Seoul National University, Seoul, 03080 Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, 03080 Korea
| | - Sung-Won Kim
- Department of Surgery, Daerim Saint Mary’s Hospital, Seoul, 07442 Korea
| | - Allison W. Kurian
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94304 USA
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
- Department of Surgery and Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong, Hong Kong
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL UK
| | - Keitaro Matsuo
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, 464-8681 Japan
| | - Nur Aishah Mohd-Taib
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL UK
| | - Rachel A. Murphy
- School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Cancer Control Research, BC Cancer, Vancouver, BC V5Z 1L3 Canada
| | - Sue K. Park
- Cancer Research Institute, Seoul National University, Seoul, 03080 Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, 03080 Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, 03080 South Korea
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115 Taiwan
- School of Public Health, China Medical University, Taichung, Taiwan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, 47500 Subang Jaya, Selangor Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN UK
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, 104-0045 Japan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| | - Manjeet K. Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN UK
| | - Alison M. Dunning
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN UK
| | - Douglas F. Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN UK
| | - Paul D. P. Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB1 8RN UK
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 119077 Singapore
- Department of Surgery, National University Health System, Singapore, 119228 Singapore
| | - Jingmei Li
- Women’s Health and Genetics, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672 Singapore
- Department of Surgery, National University Health System, Singapore, 119228 Singapore
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