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Wang Q, Xu J, Luo M, Jiang Y, Gu Y, Wang Q, He J, Sun Y, Lin Y, Feng L, Chen S, Hou T. Fasting mimicking diet extends lifespan and improves intestinal and cognitive health. Food Funct 2024; 15:4503-4514. [PMID: 38567489 DOI: 10.1039/d4fo00483c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Caloric restriction is an effective means of extending a healthy lifespan. Fasting mimicking diet (FMD) is a growing pattern of caloric restriction. We found that FMD significantly prolonged the lifespan of prematurely aging mice. In naturally aging mice, FMD improved cognitive and intestinal health. Through a series of behavioral experiments, we found that FMD relieved anxiety and enhanced cognition in aged mice. In the intestine, the FMD cycles enhanced the barrier function, reduced senescence markers, and maintained T cell naïve-memory balance in the lamina propria mucosa. To further explore the causes of immune alterations, we examined changes in the stool microbiota using 16S rRNA sequencing. We found that FMD remodeled gut bacterial composition and significantly expanded the abundance of Lactobacillus johnsonii. Our research revealed that FMD has in-depth investigative value as an anti-aging intervention for extending longevity and improving cognition, intestinal function, and gut microbiota composition.
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Affiliation(s)
- Qingyi Wang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Jilei Xu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Man Luo
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
- Department of Clinical Nutrition, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yao Jiang
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
- Department of Gastroenterology, Second Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yanrou Gu
- Department of Gastroenterology, Wenzhou No. 3 Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People's Hospital, Wenzhou, China
| | - Qiwen Wang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Jiamin He
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yong Sun
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
- Department of Gastroenterology, Second Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yifeng Lin
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
- Department of Gastroenterology, Second Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Lijun Feng
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
- Department of Clinical Nutrition, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Shujie Chen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Tongyao Hou
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
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Stangis MM, Chen Z, Min J, Glass SE, Jackson JO, Radyk MD, Hoi XP, Brennen WN, Yu M, Dinh HQ, Coffey RJ, Shrubsole MJ, Chan KS, Grady WM, Yegnasubramanian S, Lyssiotis CA, Maitra A, Halberg RB, Dey N, Lau KS. The Hallmarks of Precancer. Cancer Discov 2024; 14:683-689. [PMID: 38571435 DOI: 10.1158/2159-8290.cd-23-1550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Research on precancers, as defined as at-risk tissues and early lesions, is of high significance given the effectiveness of early intervention. We discuss the need for risk stratification to prevent overtreatment, an emphasis on the role of genetic and epigenetic aging when considering risk, and the importance of integrating macroenvironmental risk factors with molecules and cells in lesions and at-risk normal tissues for developing effective intervention and health policy strategies.
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Affiliation(s)
- Mary M Stangis
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Gastroenterology Division, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Zhengyi Chen
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jimin Min
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah E Glass
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jordan O Jackson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Megan D Radyk
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Xen Ping Hoi
- Department of Urology, Houston Methodist Research Institute, Houston, Texas
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas
| | - W Nathaniel Brennen
- Genitourinary Cancer Disease Division, Department of Oncology, Johns Hopkins Medicine, Baltimore, Maryland
- Department of Pharmacology and Molecular Sciences, Johns Hopkins Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins Medicine, Baltimore, Maryland
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Division of Gastroenterology, Hepatology, & Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Martha J Shrubsole
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Keith S Chan
- Department of Urology, Houston Methodist Research Institute, Houston, Texas
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas
| | - William M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Srinivasan Yegnasubramanian
- Genitourinary Cancer Disease Division, Department of Oncology, Johns Hopkins Medicine, Baltimore, Maryland
- Molecular Radiation Science Division, Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, Maryland
- Kidney-Urologic Pathology Division, Department of Pathology, Johns Hopkins Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
- Division of Gastroenterology, Internal Medicine, University of Washington, Seattle, Washington
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - Anirban Maitra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Richard B Halberg
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Gastroenterology Division, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Neelendu Dey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
| | - Ken S Lau
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
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Fritz CDL, Oduyale O, Cao Y. Overcoming Racial and Ethnic Disparities in Rectal Cancer Treatment. JAMA Netw Open 2024; 7:e240018. [PMID: 38421655 DOI: 10.1001/jamanetworkopen.2024.0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Affiliation(s)
- Cassandra D L Fritz
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Editorial Fellow, JAMA Network Open
| | - Oluseye Oduyale
- Department of Surgery, Washington University School of Medicine, St Louis, Missouri
| | - Yin Cao
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Surgery, Washington University School of Medicine, St Louis, Missouri
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Nwaokorie A, Kolch W, Fey D. A Systems Biology Approach to Understand the Racial Disparities in Colorectal Cancer. Cancer Res Commun 2024; 4:103-117. [PMID: 38051091 PMCID: PMC10785768 DOI: 10.1158/2767-9764.crc-22-0464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/04/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023]
Abstract
Racial disparities between Black/African Americans (AA) and White patients in colorectal cancer are an ever-growing area of concern. Black/AA show the highest incidence and have the highest mortality among major U.S. racial groups. There is no definite cause other than possible sociodemographic, socioeconomic, education, nutrition, delivery of healthcare, screening, and cultural factors. A primary limitation in this field is the lack of and small sample size of Black/AA studies. Thus, this study aimed to investigate whether differences in gene expression contribute to this ongoing unanswered racial disparity issue. In this study, we examined transcriptomic data of Black/AA and White patient cohorts using a bioinformatic and systems biology approach. We performed a Kaplan-Meier overall survival analysis between both patient cohorts across critical colorectal cancer signal transduction networks (STN), to determine the differences in significant genes across each cohort. Other bioinformatic analyses performed included PROGENy (pathway responsive genes for activity inference), RNA sequencing differential expression using DESeq2, multivariable-adjusted regression, and other associated Kaplan-Meier analyses. These analyses identified novel prognostic genes independent from each cohort, 176 differentially expressed genes, and specific patient cohort STN survival associations. Despite the overarching limitation, the results revealed several novel differences in gene expression between the colorectal cancer Black/AA and White patient cohorts, which allows one to dive deeper into and understand the behavior on a systems level of what could be driving this racial difference across colorectal cancer. Concretely, this information can guide precision medicine approaches tailored specifically for colorectal cancer racial disparities. SIGNIFICANCE The purpose of this work is to investigate the racial disparities in colorectal cancer between Black/AA and White patient cohorts using a systems biology and bioinformatic approach. Our study investigates the underlying biology of each patient cohort. Concretely, the findings of this study include disparity-associated genes and pathways, which provide a tangible starting point to guide precision medicine approaches tailored specifically for colorectal cancer racial disparities.
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Affiliation(s)
- Annabelle Nwaokorie
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Dirk Fey
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, Ireland
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Widayati TA, Schneider J, Panteleeva K, Chernysheva E, Hrbkova N, Beck S, Voloshin V, Chervova O. Open access-enabled evaluation of epigenetic age acceleration in colorectal cancer and development of a classifier with diagnostic potential. Front Genet 2023; 14:1258648. [PMID: 37953923 PMCID: PMC10634722 DOI: 10.3389/fgene.2023.1258648] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
Aberrant DNA methylation (DNAm) is known to be associated with the aetiology of cancer, including colorectal cancer (CRC). In the past, the availability of open access data has been the main driver of innovative method development and research training. However, this is increasingly being eroded by the move to controlled access, particularly of medical data, including cancer DNAm data. To rejuvenate this valuable tradition, we leveraged DNAm data from 1,845 samples (535 CRC tumours, 522 normal colon tissues adjacent to tumours, 72 colorectal adenomas, and 716 normal colon tissues from healthy individuals) from 14 open access studies deposited in NCBI GEO and ArrayExpress. We calculated each sample's epigenetic age (EA) using eleven epigenetic clock models and derived the corresponding epigenetic age acceleration (EAA). For EA, we observed that most first- and second-generation epigenetic clocks reflect the chronological age in normal tissues adjacent to tumours and healthy individuals [e.g., Horvath (r = 0.77 and 0.79), Zhang elastic net (EN) (r = 0.70 and 0.73)] unlike the epigenetic mitotic clocks (EpiTOC, HypoClock, MiAge) (r < 0.3). For EAA, we used PhenoAge, Wu, and the above mitotic clocks and found them to have distinct distributions in different tissue types, particularly between normal colon tissues adjacent to tumours and cancerous tumours, as well as between normal colon tissues adjacent to tumours and normal colon tissue from healthy individuals. Finally, we harnessed these associations to develop a classifier using elastic net regression (with lasso and ridge regularisations) that predicts CRC diagnosis based on a patient's sex and EAAs calculated from histologically normal controls (i.e., normal colon tissues adjacent to tumours and normal colon tissue from healthy individuals). The classifier demonstrated good diagnostic potential with ROC-AUC = 0.886, which suggests that an EAA-based classifier trained on relevant data could become a tool to support diagnostic/prognostic decisions in CRC for clinical professionals. Our study also reemphasises the importance of open access clinical data for method development and training of young scientists. Obtaining the required approvals for controlled access data would not have been possible in the timeframe of this study.
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Affiliation(s)
- Tyas Arum Widayati
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
| | - Jadesada Schneider
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Kseniia Panteleeva
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth Chernysheva
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Natalie Hrbkova
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
| | - Stephan Beck
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
| | - Vitaly Voloshin
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Olga Chervova
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
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Seagle HM, Keller SR, Tavtigian SV, Horton C, Holowatyj AN. Clinical Multigene Panel Testing Identifies Racial and Ethnic Differences in Germline Pathogenic Variants Among Patients With Early-Onset Colorectal Cancer. J Clin Oncol 2023; 41:4279-4289. [PMID: 37319387 PMCID: PMC10852379 DOI: 10.1200/jco.22.02378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/03/2023] [Accepted: 03/06/2023] [Indexed: 06/17/2023] Open
Abstract
PURPOSE The early-onset colorectal cancer (EOCRC) burden differs across racial/ethnic groups, yet the role of germline genetic predisposition in EOCRC disparities remains uncharacterized. We defined the prevalence and spectrum of inherited colorectal cancer (CRC) susceptibility gene variations among patients with EOCRC by race and ethnicity. PATIENTS AND METHODS We included individuals diagnosed with a first primary CRC between age 15 and 49 years who identified as Ashkenazi Jewish, Asian, Black, Hispanic, or White and underwent germline genetic testing of 14 CRC susceptibility genes performed by a clinical testing laboratory. Variant comparisons by racial and ethnic groups were evaluated using chi-square tests and multivariable logistic regression adjusted for sex, age, CRC site, and number of primary colorectal tumors. RESULTS Among 3,980 patients with EOCRC, a total of 530 germline pathogenic or likely pathogenic variants were identified in 485 individuals (12.2%). By race/ethnicity, 12.7% of Ashkenazim patients, 9.5% of Asian patients, 10.3% of Black patients, 14.0% of Hispanic patients, and 12.4% of White patients carried a germline variant. The prevalence of Lynch syndrome (P = .037), as well as APC, CHEK2, MLH1, monoallelic MUTYH, and PTEN variants, varied by race/ethnicity among patients with EOCRC (all P < .026). Ashkenazim and Hispanic patients had significantly higher odds of presenting with a pathogenic APC variant, which included p.I1307K (odds ratio [OR], 2.67; 95% CI, 1.30 to 5.49; P = .007) and MLH1 variant (OR, 8.69; 95% CI, 2.68 to 28.20; P = .0003), respectively, versus White patients in adjusted models. CONCLUSION Germline genetic features differed by race/ethnicity in young patients with CRC, suggesting that current multigene panel tests may not be representative of EOCRC risk in diverse populations. Further study is needed to optimize genes selected for genetic testing in EOCRC via ancestry-specific gene and variant discovery to yield equitable clinical benefits for all patients and to mitigate inequities in disease burden.
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Affiliation(s)
- Hannah M. Seagle
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
| | - Samantha R. Keller
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT
| | - Carolyn Horton
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA
| | - Andreana N. Holowatyj
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT
- Vanderbilt-Ingram Cancer Center, Nashville, TN
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Hao J, Liu T, Xiu Y, Yuan H, Xu D. High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma. Front Immunol 2023; 14:1208223. [PMID: 37388735 PMCID: PMC10303802 DOI: 10.3389/fimmu.2023.1208223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
Like telomere shortening, global DNA hypomethylation occurs progressively with cellular divisions or in vivo aging and functions as a mitotic clock to restrain malignant transformation/progression. Several DNA-methylation (DNAm) age clocks have been established to precisely predict chronological age using normal tissues, but show DNAm age drift in tumors, which suggests disruption of this mitotic clock during carcinogenesis. Little is known about DNAm age alterations and biological/clinical implications in endometrial cancer (EC). Here we address these issues by analyzing TCGA and GSE67116 cohorts of ECs. Horvath clock analysis of these tumors unexpectedly revealed that almost 90% of them exhibited DNAm age deceleration (DNAmad) compared to patient chronological age. Combined with an additional clock named Phenoage, we identified a subset of tumors (82/429) with high DNAmad (hDNAmad+) as assessed by both clocks. Clinically, hDNAmad+ tumors were associated with advanced diseases and shorter patient survival, compared to hDNAmad- ones. Genetically, hDNAmad+ tumors were characterized by higher copy number alterations (CNAs) whereas lower tumor mutation burden. Functionally, hDNAmad+ tumors were enriched with cell cycle and DNA mismatch repair pathways. Increased PIK3CA alterations and downregulation of SCGB2A1, the inhibitor of PI3K kinase, in hDNAmad+ tumors, might promote tumor growth/proliferation and stemness. In addition, the inactivation of aging drivers/tumor suppressors (TP53, RB1, and CDKN2A) while enhanced telomere maintenance occurred more frequently in hDNAmad+ tumors, which supports sustained tumor growth. Prominently, hDNAmad+ tumors were featured with immunoexclusion microenvironments, accompanied by significantly higher levels of VTCN1 expression while lower PD-L1 and CTLA4 expression, which indicates their poor response to immune checkpoint inhibitor (ICI)-based immunotherapy. We further showed significantly higher levels of DNMT3A and 3B expression in hDNAmad+ than in hDNAmad- tumors. Thus, the tumor suppressive function of aging-like DNA hypomethylation is severely impaired in hDNAmad+ tumors, likely due to enhanced expression of DNMT3A/3B and dysregulated aging regulators. Our findings not only enrich biological knowledge of EC pathogenesis but also help improve EC risk stratification and precision ICI immunotherapy.
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Affiliation(s)
- Jing Hao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, China
| | - Tiantian Liu
- Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuchen Xiu
- Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Huiyang Yuan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Dawei Xu
- Department of Medicine, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
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Devall MA, Eaton S, Hu G, Sun X, Jakum E, Venkatesh S, Powell SM, Yoshida C, Weisenberger DJ, Cooper GS, Willis J, Ebrahim S, Zoellner J, Casey G, Li L. Potential role of fructose on human colon DNA methylation in racial disparities observed for colorectal cancer risk. medRxiv 2023:2023.05.31.23290777. [PMID: 37398462 PMCID: PMC10312841 DOI: 10.1101/2023.05.31.23290777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background and aims An increasing body of observational studies has linked fructose intake to colorectal cancer (CRC). African Americans (AAs) are significantly more likely than European Americans to consume greater quantities of fructose and to develop right-side colon cancer. Yet, a mechanistic link between these two associations remains poorly defined. We aimed to identify differentially methylated regions (DMRs) associated with dietary fructose consumption measures obtained from food frequency questionnaires in a cohort of normal colon biopsies derived from AA men and women (n=79). Methods DNA methylation data from this study was obtained using the Illumina Infinium MethylationEPIC kit and is housed under accession GSE151732. DMR analysis was carried out using DMRcate in right and matched left colon, separately. Secondary analysis of CRC tumors was carried out using data derived from TCGA-COAD, GSE101764 and GSE193535. Differential expression analysis was carried out on CRC tumors from TCGA-COAD using DESeq2 . Results We identified 4,263 right-side fructose-DMRs. In contrast, only 24 DMRs survived multiple testing corrections (FDR<0.05) in matched, left colon. To identify targets by which dietary fructose drives CRC risk, we overlaid these findings with data from three CRC tumor datasets. Remarkably, almost 50% of right-side fructose-DMRs overlapped regions associated with CRC in at least one of three datasets. TNXB and CDX2 ranked among the most significant fructose risk DMRs in right and left colon respectively that also displayed altered gene expression in CRC tumors. Conclusions Our mechanistic data support the notion that fructose has a greater CRC-related effect in right than left AA colon, alluding to a potential role for fructose in contributing to racial disparities in CRC.
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Yang G, Yu XR, Weisenberger DJ, Lu T, Liang G. A Multi-Omics Overview of Colorectal Cancer to Address Mechanisms of Disease, Metastasis, Patient Disparities and Outcomes. Cancers (Basel) 2023; 15:cancers15112934. [PMID: 37296894 DOI: 10.3390/cancers15112934] [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] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Human colorectal cancer (CRC) is one of the most common malignancies in men and women across the globe, albeit CRC incidence and mortality shows a substantial racial and ethnic disparity, with the highest burden in African American patients. Even with effective screening tools such as colonoscopy and diagnostic detection assays, CRC remains a substantial health burden. In addition, primary tumors located in the proximal (right) or distal (left) sides of the colorectum have been shown to be unique tumor types that require unique treatment schema. Distal metastases in the liver and other organ systems are the major causes of mortality in CRC patients. Characterizing genomic, epigenomic, transcriptomic and proteomic (multi-omics) alterations has led to a better understanding of primary tumor biology, resulting in targeted therapeutic advancements. In this regard, molecular-based CRC subgroups have been developed that show correlations with patient outcomes. Molecular characterization of CRC metastases has highlighted similarities and differences between metastases and primary tumors; however, our understanding as to how to improve patient outcomes based on metastasis biology is lagging and remains a major obstacle to improving CRC patient outcomes. In this review, we will summarize the multi-omics features of primary CRC tumors and their metastases across racial and ethnic groups, the differences in proximal and distal tumor biology, molecular-based CRC subgroups, treatment strategies and challenges for improving patient outcomes.
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Affiliation(s)
- Guang Yang
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- China Grand Enterprises, Beijing 100101, China
| | - Xi Richard Yu
- China Grand Enterprises, Beijing 100101, China
- Huadong Medicine Co., Ltd., Hangzhou 310011, China
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- USC Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- State Key Laboratory of Natural Sciences, China Pharmaceutical University, Nanjing 211121, China
| | - Gangning Liang
- USC Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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10
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Vidotto T, Imada EL, Faisal F, Murali S, Mendes AA, Kaur H, Zheng S, Xu J, Schaeffer EM, Isaacs WB, Sfanos KS, Marchionni L, Lotan TL. Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer. JCI Insight 2023; 8:e162409. [PMID: 36752203 PMCID: PMC9977441 DOI: 10.1172/jci.insight.162409] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/27/2022] [Indexed: 02/09/2023] Open
Abstract
The genomic and immune landscapes of prostate cancer differ by self-identified race. However, few studies have examined the genome-wide copy number landscape and immune content of matched cohorts with genetic ancestry data and clinical outcomes. Here, we assessed prostate cancer somatic copy number alterations (sCNA) and tumor immune content of a grade-matched, surgically treated cohort of 145 self-identified Black (BL) and 145 self-identified White (WH) patients with genetic ancestry estimation. A generalized linear model adjusted with age, preoperative prostate-specific antigen (PSA), and Gleason Grade Group and filtered for germline copy number variations (gCNV) identified 143 loci where copy number varied significantly by percent African ancestry, clustering on chromosomes 6p, 10q, 11p, 12p, and 17p. Multivariable Cox regression models adjusted for age, preoperative PSA levels, and Gleason Grade Group revealed that chromosome 8q gains (including MYC) were significantly associated with biochemical recurrence and metastasis, independent of genetic ancestry. Finally, Treg density in BL and WH patients was significantly correlated with percent genome altered, and these findings were validated in the TCGA cohort. Taken together, our findings identify specific sCNA linked to genetic ancestry and outcome in primary prostate cancer and demonstrate that Treg infiltration varies by global sCNA burden in primary disease.
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Affiliation(s)
- Thiago Vidotto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eddie L. Imada
- Department of Pathology, Weill-Cornell School of Medicine, New York, New York, USA
| | - Farzana Faisal
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sanjana Murali
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adrianna A. Mendes
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harsimar Kaur
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Siqun Zheng
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Edward M. Schaeffer
- Department of Urology, Northwestern University School of Medicine, Chicago, Illinois, USA
| | | | - Karen S. Sfanos
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Luigi Marchionni
- Department of Pathology, Weill-Cornell School of Medicine, New York, New York, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology and
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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11
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Aukema SM, Glaser S, van den Hout MFCM, Dahlum S, Blok MJ, Hillmer M, Kolarova J, Sciot R, Schott DA, Siebert R, Stumpel CTRM. Molecular characterization of an embryonal rhabdomyosarcoma occurring in a patient with Kabuki syndrome: report and literature review in the light of tumor predisposition syndromes. Fam Cancer 2023; 22:103-118. [PMID: 35856126 PMCID: PMC9829644 DOI: 10.1007/s10689-022-00306-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/05/2022] [Indexed: 01/13/2023]
Abstract
Kabuki syndrome is a well-recognized syndrome characterized by facial dysmorphism and developmental delay/intellectual disability and in the majority of patients a germline variant in KMT2D is found. As somatic KMT2D variants can be found in 5-10% of tumors a tumor predisposition in Kabuki syndrome is discussed. So far less than 20 patients with Kabuki syndrome and a concomitant malignancy have been published. Here we report on a female patient with Kabuki syndrome and a c.2558_2559delCT germline variant in KMT2D who developed an embryonal rhabdomyosarcoma (ERMS) at 10 years. On tumor tissue we performed DNA-methylation profiling and exome sequencing (ES). Copy number analyses revealed aneuploidies typical for ERMS including (partial) gains of chromosomes 2, 3, 7, 8, 12, 15, and 20 and 3 focal deletions of chromosome 11p. DNA methylation profiling mapped the case to ERMS by a DNA methylation-based sarcoma classifier. Sequencing suggested gain of the wild-type KMT2D allele in the trisomy 12. Including our patient literature review identified 18 patients with Kabuki syndrome and a malignancy. Overall, the landscape of malignancies in patients with Kabuki syndrome was reminiscent of that of the pediatric population in general. Histopathological and molecular data were only infrequently reported and no report included next generation sequencing and/or DNA-methylation profiling. Although we found no strong arguments pointing towards KS as a tumor predisposition syndrome, based on the small numbers any relation cannot be fully excluded. Further planned studies including profiling of additional tumors and long term follow-up of KS-patients into adulthood could provide further insights.
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Affiliation(s)
- Sietse M Aukema
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Mari F C M van den Hout
- Department of Pathology, Research Institute GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sonja Dahlum
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Morten Hillmer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Raf Sciot
- Department of Pathology, University Hospital, University of Leuven, 3000, Louvain, Belgium
| | - Dina A Schott
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands
- Department of Pediatrics, Zuyderland Medical Center, Heerlen, The Netherlands
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
- Department of Clinical Genetics and GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands.
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12
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Devall MA, Sun X, Eaton S, Cooper GS, Willis JE, Weisenberger DJ, Casey G, Li L. A Race-Specific, DNA Methylation Analysis of Aging in Normal Rectum: Implications for the Biology of Aging and Its Relationship to Rectal Cancer. Cancers (Basel) 2022; 15:cancers15010045. [PMID: 36612042 PMCID: PMC9817986 DOI: 10.3390/cancers15010045] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/01/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Approximately 90% of colorectal cancer (CRC) develop over the age of 50, highlighting the important role of aging in CRC risk. African Americans (AAs) shoulder a greater CRC burden than European Americans (EA) and are more likely to develop CRC at a younger age. The effects of aging in AA and EA normal rectal tissue have yet to be defined. Here, we performed epigenome-wide DNA methylation analysis in the first, large-scale biracial cohort of normal rectum (n = 140 samples). We identified increased epigenetic age acceleration in EA than AA rectum (p = 3.91 × 10-4) using linear regression. We also identified differentially methylated regions (DMRs) associated with chronological aging in AA and EA, separately using DMRcate. Next, a consensus set of regions associated with cancer was identified through DMR analysis of two rectal cancer cohorts. The vast majority of AA DMRs were present in our analysis of aging in rectum of EA subjects, though rates of epigenetic drift were significantly greater in AA (p = 1.94 × 10-45). However, 3.66-fold more DMRs were associated with aging in rectum of EA subjects, many of which were also associated with rectal cancer. Our findings reveal a novel relationship between race, age, DNA methylation and rectal cancer risk that warrants further investigation.
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Affiliation(s)
- Matthew A. Devall
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Xiangqing Sun
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gregory S. Cooper
- Department of Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: ; Tel.: +1-434-982-3975
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13
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Ulanja MB, Ntafam C, Beutler BD, Antwi‐Amoabeng D, Rahman GA, Ulanja RN, Mabrouk T, Governor SB, Djankpa FT, Alese OB. Race, age, and sex differences on the influence of obesity on colorectal cancer sidedness and mortality: A national cross‐sectional study. J Surg Oncol 2022; 127:109-118. [PMID: 36112396 PMCID: PMC10086849 DOI: 10.1002/jso.27096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/17/2022] [Accepted: 09/03/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND AND OBJECTIVES Colorectal cancer (CRC) sidedness is recognized as a prognostic factor for survival; left-sided colorectal cancer is associated with better outcomes than right-sided colon cancer (RsCC). We aimed to evaluate the influence of obesity on CRC sidedness and determine how race, age, and sex affect mortality among overweight and obese individuals. METHODS A survey-weighted analysis was conducted using data obtained from the National Inpatient Sample between 2016 and 2019. RESULTS Of the 24 549 patients with a diagnosis of CRC and a reported body mass index (BMI), 13.6% were overweight and 49.9% were obese. The race distribution was predominantly non-Hispanic Whites (69.7%), followed by Black (15.6%), Hispanic (8.7%), and other race (6.1%). Overweight (BMI: 25-29.9) and obese (BMI: ≥30) individuals were more likely to have RsCC (adjusted OR [aOR] = 1.28; 95% CI: 1.17-1.39, p < 0.001 and aOR = 1.45; 95% CI: 1.37-1.54, p < 0.001, respectively). Obese Black individuals were more likely to have RsCC as compared to their White counterparts (aOR = 1.23; 95% CI: 1.09-1.38). CONCLUSIONS Obesity is associated with an increased risk of RsCC. In addition, racial disparities in CRC sidedness and outcomes are most pronounced among obese patients.
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Affiliation(s)
- Mark B. Ulanja
- Christus Ochsner St. Patrick Hospital Lake Charles Louisiana USA
| | - Carnot Ntafam
- Department of Radiology Children's Hospital Los Angeles Los Angeles California USA
| | - Bryce D. Beutler
- Department of Radiology, Keck School of Medicine University of Southern California Los Angeles California USA
| | | | - Ganiyu A. Rahman
- Department of Surgery, School of Medical Sciences University of Cape Coast Cape Coast Ghana
| | - Reginald N. Ulanja
- Department of Physiology, School of Medical Sciences University of Cape Coast Cape Coast Ghana
| | - Tarig Mabrouk
- Christus Ochsner St. Patrick Hospital Lake Charles Louisiana USA
| | - Samuel B. Governor
- Department of Biostatistics, College for Public Health and Social Justice Saint Louis University St Louis Missouri USA
- Washington University School of Medicine St. Louis Missouri USA
| | - Francis T. Djankpa
- Department of Physiology, School of Medical Sciences University of Cape Coast Cape Coast Ghana
| | - Olatunji B. Alese
- Department of Hematology and Oncology, Winship Cancer Institute Emory University Atlanta Georgia USA
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14
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Devall MA, Eaton S, Ali MW, Dampier CH, Weisenberger D, Powell SM, Li L, Casey G. DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development. Clin Epigenetics 2022; 14:104. [PMID: 35999641 PMCID: PMC9396789 DOI: 10.1186/s13148-022-01324-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/05/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Familial adenomatous polyposis (FAP) is an inherited colorectal cancer (CRC) syndrome resulting from germ line mutations in the adenomatous polyposis coli (APC) gene. While FAP accounts for less than 1% of all CRC cases, loss of APC expression is seen in > 80% of non-hereditary CRCs. To better understand molecular mechanisms underlying APC-driven CRC, we performed an epigenome-wide analysis of colon organoids derived from normal-appearing colons of FAP patients versus healthy subjects to identify differentially methylated regions (DMRs) that may precede the onset of CRC. RESULTS We identified 358 DMRs when comparing colon organoids of FAP patients to those of healthy subjects (FDR < 0.05, |mean beta difference| = 5%). Of these, nearly 50% of DMRs were also differentially methylated in at least one of three CRC tumor and normal adjacent tissue (NAT) cohorts (TCGA-COAD, GSE193535 and ColoCare). Moreover, 27 of the DMRs mapped to CRC genome-wide association study (GWAS) loci. We provide evidence suggesting that some of these DMRs led to significant differences in gene expression of adjacent genes using quantitative PCR. For example, we identified significantly greater expression of five genes: Kazal-type serine peptidase inhibitor domain 1 (KAZALD1, P = 0.032), F-Box and leucine-rich repeat protein 8 (FBXL8, P = 0.036), TRIM31 antisense RNA 1 (TRIM31-AS1, P = 0.036), Fas apoptotic inhibitory molecule 2 (FAIM2, P = 0.049) and (Collagen beta (1-0)galactosyltransferase 2 (COLGALT2, P = 0.049). Importantly, both FBXL8 and TRIM31-AS1 were also significantly differentially expressed in TCGA-COAD tumor versus matched NAT, supporting a role for these genes in CRC tumor development. CONCLUSIONS We performed the first DNA methylome-wide analysis of normal colon organoids derived from FAP patients compared to those of healthy subjects. Our results reveal that normal colon organoids from FAP patients exhibit extensive epigenetic differences compared to those of healthy subjects that appear similar to those exhibited in CRC tumor. Our analyses therefore identify DMRs and candidate target genes that are potentially important in CRC tumor development in FAP, with potential implications for non-hereditary CRC.
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Affiliation(s)
- Matthew A. Devall
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Stephen Eaton
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Mourad Wagdy Ali
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Christopher H. Dampier
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Daniel Weisenberger
- grid.42505.360000 0001 2156 6853Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA USA
| | - Steven M. Powell
- grid.27755.320000 0000 9136 933XDigestive Health Center, University of Virginia, Charlottesville, VA USA
| | - Li Li
- grid.27755.320000 0000 9136 933XDepartment of Family Medicine, University of Virginia, Charlottesville, VA USA
| | - Graham Casey
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA ,grid.27755.320000 0000 9136 933XDepartment of Public Health Sciences, University of Virginia, Charlottesville, VA USA
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15
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Kalyanaraman B. Exploiting the tumor immune microenvironment and immunometabolism using mitochondria-targeted drugs: Challenges and opportunities in racial disparity and cancer outcome research. FASEB J 2022; 36:e22226. [PMID: 35233843 PMCID: PMC9242412 DOI: 10.1096/fj.202101862r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 12/03/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 12/16/2022]
Abstract
Black and Hispanic cancer patients have a higher incidence of cancer mortality. Many factors (e.g., socioeconomic differences, insufficient access to healthcare) contribute to racial disparity. Emerging research implicates biological disparity in cancer outcomes. Studies show distinct differences in the tumor immune microenvironment (TIME) in Black cancer patients. Studies also have linked altered mitochondrial metabolism to changes in immune cell activation in TIME. Recent publications revealed a novel immunomodulatory role for triphenylphosphonium‐based mitochondrial‐targeted drugs (MTDs). These are synthetically modified, naturally occurring molecules (e.g., honokiol, magnolol, metformin) or FDA‐approved small molecule drugs (e.g., atovaquone, hydroxyurea). Modifications involve conjugating the parent molecule via an alkyl linker chain to a triphenylphosphonium moiety. These modified molecules (e.g., Mito‐honokiol, Mito‐magnolol, Mito‐metformin, Mito‐atovaquone, Mito‐hydroxyurea) accumulate in tumor cell mitochondria more effectively than in normal cells and inhibit mitochondrial respiration, induce reactive oxygen species, activate AMPK and redox transcription factors, and inhibit cancer cell proliferation. Besides these intrinsic effects of MTDs in redox signaling and proliferation in tumors, MTDs induced extrinsic effects in the TIME of mouse xenografts. MTD treatment inhibited tumor‐suppressive immune cells, myeloid‐derived suppressor cells, and regulatory T cells, and activated T cells and antitumor immune effects. One key biological disparity in Black cancer patients was related to altered mitochondrial oxidative metabolism; MTDs targeting vulnerabilities in tumor cells and the TIME may help us understand this biological disparity. Clinical trials should include an appropriate number of Black and Hispanic cancer patients and should validate the intratumoral, antihypoxic effects of MTDs with imaging.
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Affiliation(s)
- Balaraman Kalyanaraman
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Center for Disease Prevention Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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16
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Abstract
Health care disparities are defined as health differences between groups that are avoidable, unnecessary, and unjust. Racial disparities in colorectal cancer mortality, particularly for Black patients, are well-described. Disparities in preventative measures, early detection, effective treatment, and posttreatment services contribute to these differences. Underlying these issues are patient, provider, health care system, and policy-level factors that lead to these disparities. Multilevel interventions designed to address each level of care can provide an effective means to mitigate these disparities.
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17
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Keenan JI, Frizelle FA. Biomarkers to Detect Early-Stage Colorectal Cancer. Biomedicines 2022; 10:255. [PMID: 35203465 DOI: 10.3390/biomedicines10020255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is a leading cause of mortality worldwide. The high incidence and the acceleration of incidence in younger people reinforces the need for better techniques of early detection. The use of noninvasive biomarkers has potential to more accurately inform how patients are prioritised for clinical investigation, which, in turn, may ultimately translate into improved survival for those subsequently found to have curable-stage CRC. This review surveys a wide range of CRC biomarkers that may (alone or in combination) identify symptomatic patients presenting in primary care who should be progressed for clinical investigation.
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Nwanaji-Enwerem JC, Nze C, Cardenas A. Long-term Aspirin Use and Epigenetic Mitotic Clocks for Cancer Risk Prediction: Findings in Healthy Colon Mucosa and Recommendations for Future Epigenetic Aging Studies. Epigenetics Commun 2021; 1:5. [PMID: 35493198 PMCID: PMC9053330 DOI: 10.1186/s43682-021-00004-4] [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] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/20/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Despite the known role of mitosis in colorectal cancer, previous associations of long-term aspirin use with suppressed cancer-related epigenetic aging did not involve epigenetic mitotic clocks. We investigated these relationships using three epigenetic mitotic clocks developed for cancer risk prediction: EpiTOC, EpiTOC2, and MiAge. We utilized publicly available HumanMethylationEPIC BeadChip data from 112 healthy colon (proximal and distal) mucosal samples taken at baseline (T1) and at 10-years follow-up (T2) from a screening cohort of 28 Polish women (11 non-users and 17 long-term [≥ 2 years] aspirin users). Mitotic clock values were divided by chronological age at each timepoint to obtain intrinsic rates (IRs). We evaluated differences in residuals of the mitotic clock IRs taken from linear mixed effects models adjusted for BMI, polyp status, and DNA methylation batch. FINDINGS EpiTOC, EpiTOC2 and MiAge were significantly correlated with chronological age (P < 0.05) with correlations ranging from 0.41 to 0.63. The EpiTOC, EpiTOC2 and MiAge clocks were strongly correlated with each other in proximal and distal samples (r > 0.79, P < 0.0001). We observed proximal within group median clock IR deceleration for EpiTOC (-0.0004 DNAm, P = 0.008), EpiTOC2 (-16 cell divisions, P = 0.009), and MiAge (-3 cell divisions, P = 0.002) for long-term aspirin users from T1 to T2 but not for non-users. In distal samples, only the long-term user MiAge IR was significantly deaccelerated (-3 cell divisions, P = 0.009). CONCLUSIONS Our observed findings support previously reported longitudinal associations of aspirin use with deceleration of other epigenetic age measures in the proximal colon. Our mitotic clock results suggest that cell proliferation could play a role in some aspirin relationships with epigenetic aging. Furthermore, the findings provide added impetus for establishing gold standards for epigenetic aging and consensus guidelines for more comprehensive reporting in future epigenetic aging cancer studies.
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Affiliation(s)
- Jamaji C. Nwanaji-Enwerem
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, and MD/PhD Program, Harvard Medical School, Boston, MA, USA
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Chijioke Nze
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
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Liu T, Wang J, Xiu Y, Wu Y, Xu D. DNA Methylation Age Drift Is Associated with Poor Outcomes and De-Differentiation in Papillary and Follicular Thyroid Carcinomas. Cancers (Basel) 2021; 13:cancers13194827. [PMID: 34638311 PMCID: PMC8508076 DOI: 10.3390/cancers13194827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Normal human tissues contain an epigenetic clock resulting from the age-dependent DNA methylation signature, which is the so-called DNA methylation (DNAm) age and can be used to precisely predict chronological age of healthy individuals. Abnormal DNAm age drift has been implicated in cancer risk and pathogenesis. Here, we observed that highly drifted DNAm age (HDDA) occurred in approximately 1/3 tumors derived from patients with papillary and follicular thyroid carcinomas. HDDA is significantly associated with dedifferentiation of tumor cells and poor patient outcomes. Thus, HDDA may serve as a new prognostic factor for thyroid carcinoma. Abstract Alterations in global DNA methylation play a critical role in both aging and cancer, and DNA methylation (DNAm) age drift has been implicated in cancer risk and pathogenesis. In the present study, we analyzed the TCGA cohort of papillary and follicular thyroid carcinoma (PTC and FTC) for their DNAm age and association with clinic-pathological features. In 54 noncancerous thyroid (NT) samples, DNAm age was highly correlated with patient chronological age (R2 = 0.928, p = 2.6 × 10−31), but drifted to younger than chronological age in most specimens, especially those from patients >50 years old. DNAm age in 502 tumors was also correlated with patient chronological age, but to a much lesser extent (R2 = 0.403). Highly drifted DNAm age (HDDA) was identified in 161 tumors, among which were 101 with DNAm age acceleration while 60 with DNAm age deceleration. Tumors with HDDA were characterized by the robust aberrations in metabolic activities, extracellular microenvironment components and inflammation/immunology responses, and dedifferentiation. Importantly, HDDA in tumors independently predicted shorter disease-free survival of patients. Collectively, NT thyroids from TC patients have younger DNAm age, while HDDA frequently occurs in TCs, and contributes to the TC progression and poor patient outcomes. HDDA may serve as a new prognostic factor for TCs.
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Affiliation(s)
- Tiantian Liu
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
- Correspondence:
| | - Jiansheng Wang
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
| | - Yuchen Xiu
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
| | - Yujiao Wu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska University Hospital Solna, Karolinsk Institutet, SE-171 76 Stockholm, Sweden; (Y.W.); (D.X.)
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska University Hospital Solna, Karolinsk Institutet, SE-171 76 Stockholm, Sweden; (Y.W.); (D.X.)
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Tanaka R, Inoue K, Yamada Y, Yoshida M, Shima H, Ito J, Okita H, Miwa T, Kato M, Shimada H. A case of primary CNS embryonal rhabdomyosarcoma with PAX3-NCOA2 fusion and systematic meta-review. J Neurooncol 2021; 154:247-256. [PMID: 34398431 DOI: 10.1007/s11060-021-03823-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/06/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE Primary central nervous system (CNS) rhabdomyosarcoma is a rare mesenchymal tumor predominantly seen in children and associated with a poor outcome. We report a case of primary CNS rhabdomyosarcoma with PAX3-NCOA2 fusion and present a systematic meta-review of primary CNS rhabdomyosarcoma to characterize this rare tumor. METHODS We present the case of a 6-year-old boy with primary CNS rhabdomyosarcoma in the posterior fossa. In a systematic meta-review, we compare the demographic data of primary CNS rhabdomyosarcoma with data of rhabdomyosarcoma at all sites from the SEER database and analyze clinical factors associated with survival outcome. RESULTS Our patient underwent gross total resection and received vincristine, actinomycin-D, cyclophosphamide with early introduction of concurrent focal radiation and remained alive with no evidence of disease for 2 years after the end of therapy. Histopathological review revealed embryonal-type rhabdomyosarcoma, and whole-transcriptome analysis revealed PAX3 (EX6)-NCOA2 (EX12) fusion. In all, 77 cases of primary CNS rhabdomyosarcoma were identified through the meta-review. The demographic data of primary CNS rhabdomyosarcoma were similar to data of rhabdomyosarcoma at all sites. Overall and event-free survival outcomes were available for 64 and 56 patients, respectively, with a 3-year OS of 29.0% and a 3-year EFS of 25.7%. The group that received trimodal treatment exhibited better survival outcomes, with a 3-year OS of 57.4% and a 3-year EFS of 46.3%. CONCLUSIONS Primary CNS rhabdomyosarcoma shares common histological, molecular, and demographic features with non-CNS rhabdomyosarcoma. A trimodal treatment approach with early introduction of radiation therapy may result in favorable survival outcomes.
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Affiliation(s)
- Ryuma Tanaka
- Division of Hem/Onc/BMT, Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, MFRC3018, Milwaukee, WI, 53226, USA. .,Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.
| | - Kyohei Inoue
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Yuji Yamada
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.,Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development, Tokyo, Japan
| | - Masanori Yoshida
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Haruko Shima
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Jumpei Ito
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Hajime Okita
- Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Tomoru Miwa
- Department of Neurosurgery, Keio University School of Medicine, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Shimada
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
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21
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Abstract
Colorectal cancer (CRC) incidence among individuals age younger than 50 years continues to rise with etiologies unknown. Synchronously, early-onset CRC disparities have grown more pronounced. As translational research across diverse populations has been limited, we advocate for mechanistic studies that address this challenge to mitigate CRC disparities among young adults.
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Affiliation(s)
- Andreana N Holowatyj
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA.
| | - Jose Perea
- Fundación Jiménez Díaz University Hospital, Madrid, Spain
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22
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Muller C, Ihionkhan E, Stoffel EM, Kupfer SS. Disparities in Early-Onset Colorectal Cancer. Cells 2021; 10:1018. [PMID: 33925893 DOI: 10.3390/cells10051018] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 03/02/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
The incidence and mortality of early-onset colorectal cancer (CRC) are increasing in the United States (US) and worldwide. In the US, there are notable disparities in early-onset CRC burden by race/ethnicity and geography. African Americans, Hispanic/Latinos, and populations residing in specific regions of the Southern U.S. are disproportionately affected with CRC diagnosed at younger ages, while less is known about disparities in other countries. Reasons for these disparities are likely multi-factorial and potentially implicate differences in health determinants including biology/genetics, diet/environment, individual health behaviors, and access to high-quality health services, as well as social and policy factors. This review summarizes current understanding of early-onset CRC disparities and identifies specific research areas that will inform evidence-based interventions at individual, practice, and policy levels to reduce the global burden of this disease.
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23
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Abstract
Colorectal cancer (CRC) is characterized by genetic-environmental interplay leading to diffuse changes in the entire colonic mucosa (field carcinogenesis or field of injury) and to a pro-neoplastic genetic/epigenetic/physiological milieu. The clinical consequences are increased risk of synchronous and metachronous neoplasia. Factors such as genetics, race, ethnicity, age, and socioeconomic status are thought to influence neoplasia development. Here, we explore the potential improvement to CRC screening through exploiting field carcinogenesis, with particular focus on racial disparities and chemoprevention strategies. Also, we discuss future directions for field carcinogenesis/risk stratification using molecular and novel biophotonic techniques for personalized CRC screening.
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