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Iyer PG, Slettedahl SW, Mahoney DW, Giakoumopoulos M, Olson MC, Krockenberger M, Taylor WR, Foote P, Berger C, Leggett C, Wu TT, Antpack E, Falk GW, Ginsberg GG, Abrams JA, Lightdale CJ, Ramirez F, Kahn A, Wolfsen H, Konda V, Trindade AJ, Kisiel JB. Algorithm Training and Testing for a Nonendoscopic Barrett's Esophagus Detection Test in Prospective Multicenter Cohorts. Clin Gastroenterol Hepatol 2024; 22:1596-1604.e4. [PMID: 38513982 PMCID: PMC11272429 DOI: 10.1016/j.cgh.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND & AIMS Endoscopic Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) detection is invasive and expensive. Nonendoscopic BE/EAC detection tools are guideline-endorsed alternatives. We previously described a 5-methylated DNA marker (MDM) panel assayed on encapsulated sponge cell collection device (CCD) specimens. We aimed to train a new algorithm using a 3-MDM panel and test its performance in an independent cohort. METHODS Algorithm training and test samples were from 2 prospective multicenter cohorts. All BE cases had esophageal intestinal metaplasia (with or without dysplasia/EAC); control subjects had no endoscopic evidence of BE. The CCD procedure was followed by endoscopy. From CCD cell lysates, DNA was extracted, bisulfite treated, and MDMs were blindly assayed. The algorithm was set and locked using cross-validated logistic regression (training set) and its performance was assessed in an independent test set. RESULTS Training (N = 352) and test (N = 125) set clinical characteristics were comparable. The final panel included 3 MDMs (NDRG4, VAV3, ZNF682). Overall sensitivity was 82% (95% CI, 68%-94%) at 90% (79%-98%) specificity and 88% (78%-94%) sensitivity at 84% (70%-93%) specificity in training and test sets, respectively. Sensitivity was 90% and 68% for all long- and short-segment BE, respectively. Sensitivity for BE with high-grade dysplasia and EAC was 100% in training and test sets. Overall sensitivity for nondysplastic BE was 82%. Areas under the receiver operating characteristic curves for BE detection were 0.92 and 0.94 in the training and test sets, respectively. CONCLUSIONS A locked 3-MDM panel algorithm for BE/EAC detection using a nonendoscopic CCD demonstrated excellent sensitivity for high-risk BE cases in independent validation samples. (Clinical trials.gov: NCT02560623, NCT03060642.).
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Affiliation(s)
- Prasad G Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Seth W Slettedahl
- Division of Clinical Trials, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Division of Clinical Trials, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | | | | | | | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Patrick Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Calise Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Cadman Leggett
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Tsung-Teh Wu
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eduardo Antpack
- Department of Surgery, Mayo Clinic Health System, Austin, Minnesota
| | - Gary W Falk
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Gregory G Ginsberg
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, New York
| | - Charles J Lightdale
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, New York
| | - Francisco Ramirez
- Division of Gastroenterology and Hepatology, Mayo Clinic, Phoenix, Arizona
| | - Allon Kahn
- Division of Gastroenterology and Hepatology, Mayo Clinic, Phoenix, Arizona
| | - Herbert Wolfsen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida
| | - Vani Konda
- Division of Gastroenterology and Hepatology, Baylor University Medical Center, Dallas, Texas
| | - Arvind J Trindade
- Division of Gastroenterology and Hepatology, Zucker School of Medicine at Hofstra/Northwell, Long Island Jewish Medical Center, New Hyde Park, New York
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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2
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Kalra A, Meltzer SJ. The Role of DNA Methylation in Gastrointestinal Disease: An Expanded Review of Malignant and Nonmalignant Gastrointestinal Diseases. Gastroenterology 2024:S0016-5085(24)05185-0. [PMID: 38971197 DOI: 10.1053/j.gastro.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
Esophageal, colorectal, pancreatic, hepatocellular, and gastric cancer together impact millions of patients worldwide each year, with high overall mortality rates, and are increasing in incidence. Additionally, premalignant gastrointestinal diseases, such as Barrett's esophagus and inflammatory bowel disease, are also increasing in incidence. However, involvement of aberrant DNA methylation in these diseases is incompletely understood, especially given recent research advancements in this field. Here, we review knowledge of this epigenetic mechanism in gastrointestinal preneoplasia and neoplasia, considering mechanisms of action, genetic and environmental factors, and 5'-C-phosphate-G-3' island methylator phenotype. We also highlight developments in translational research, focusing on genomic-wide database data, methylation-based biomarkers and diagnostic tests, machine learning, and therapeutic epigenetic strategies.
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Affiliation(s)
- Andrew Kalra
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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3
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Tu R, Zhong D, Li P, Li Y, Chen Z, Hu F, Yuan G, Chen Z, Yu S, Song J. PTPN13 rs989902 and CHEK2 rs738722 are associated with esophageal cancer. Ann Med 2023; 55:2281659. [PMID: 38039548 PMCID: PMC10836260 DOI: 10.1080/07853890.2023.2281659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023] Open
Abstract
PURPOSE Individual genetic background can play an essential role in determining the development of esophageal squamous cell carcinoma (ESCC). PTPN13 and CHEK2 play important roles in the pathogenesis of ESCC. This case-control study aimed to analyze the association between gene polymorphisms and ESCC susceptibility. METHODS DNA was extracted from the peripheral blood of patients. The Agena MassARRAY platform was used for the genotyping. Statistical analysis was conducted using the chi-squared test or Fisher's exact test, logistic regression analysis, and stratification analysis. RESULTS The 'G' allele of rs989902 (PTPN13) and the 'T' allele of rs738722 (CHEK2) were both associated with an increased risk of ESCC (rs989902: OR = 1.23, 95% CI = 1.02-1.47, p = 0.028; rs738722: OR = 1.28, 95% CI = 1.06-1.55, p = 0.011). Stratification analysis showed that SNPs (rs989902 and rs738722) were notably correlated with an increased risk of ESCC after stratification for age, sex, smoking, and drinking status. In addition, rs738722 might be associated with lower stage, while rs989902 had a lower risk of metastasis. CONCLUSION Our findings display that PTPN13 rs989902 and CHEK2 rs738722 are associated with an increased risk of ESCC in the Chinese Han population.
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Affiliation(s)
- Ruisha Tu
- Department of Gastrointestinal Surgery, Hainan Cancer Hospital, Haikou, Hainan, China
| | - Dunjing Zhong
- Department of Gastroenterology, Hainan Cancer Hospital, Haikou, Hainan, China
| | - Ping Li
- Department of Digestive Endoscopy Center, Hainan Cancer Hospital, Haikou, Hainan, China
| | - Yongyu Li
- Department of Gastroenterology, Hainan Cancer Hospital, Haikou, Hainan, China
| | - Zhuang Chen
- Department of Gastroenterology, Hainan Cancer Hospital, Haikou, Hainan, China
| | - Feixiang Hu
- Department of Gastrointestinal Surgery, Hainan Cancer Hospital, Haikou, Hainan, China
| | - Guihong Yuan
- Department of Gastroenterology, Hainan Cancer Hospital, Haikou, Hainan, China
| | - Zhaowei Chen
- Department of Gastroenterology, Hainan Cancer Hospital, Haikou, Hainan, China
| | - Shuyong Yu
- Department of Gastrointestinal Surgery, Hainan Cancer Hospital, Haikou, Hainan, China
| | - Jian Song
- Department of Digestive Endoscopy Center, Hainan Cancer Hospital, Haikou, Hainan, China
- Department of Gastroenterology, Southern University of Science and Technology Hospital, Shenzhen, Guangdong, China
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4
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Zheng Y, Ziman B, Ho AS, Sinha UK, Xu LY, Li EM, Koeffler HP, Berman BP, Lin DC. Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation. Genome Biol 2023; 24:193. [PMID: 37620896 PMCID: PMC10463844 DOI: 10.1186/s13059-023-03035-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND As one of the most common malignancies, esophageal cancer has two subtypes, squamous cell carcinoma and adenocarcinoma, arising from distinct cells-of-origin. Distinguishing cell-type-specific molecular features from cancer-specific characteristics is challenging. RESULTS We analyze whole-genome bisulfite sequencing data on 45 esophageal tumor and nonmalignant samples from both subtypes. We develop a novel sequence-aware method to identify large partially methylated domains (PMDs), revealing profound heterogeneity at both methylation level and genomic distribution of PMDs across tumor samples. We identify subtype-specific PMDs that are associated with repressive transcription, chromatin B compartments and high somatic mutation rate. While genomic locations of these PMDs are pre-established in normal cells, the degree of loss is significantly higher in tumors. We find that cell-type-specific deposition of H3K36me2 may underlie genomic distribution of PMDs. At a smaller genomic scale, both cell-type- and cancer-specific differentially methylated regions (DMRs) are identified for each subtype. Using binding motif analysis within these DMRs, we show that a cell-type-specific transcription factor HNF4A maintains the binding sites that it generates in normal cells, while establishing new binding sites cooperatively with novel partners such as FOSL1 in esophageal adenocarcinoma. Finally, leveraging pan-tissue single-cell and pan-cancer epigenomic datasets, we demonstrate that a substantial fraction of cell-type-specific PMDs and DMRs identified here in esophageal cancer are actually markers that co-occur in other cancers originating from related cell types. CONCLUSIONS These findings advance our understanding of DNA methylation dynamics at various genomic scales in normal and malignant states, providing novel mechanistic insights into cell-type- and cancer-specific epigenetic regulations.
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Affiliation(s)
- Yueyuan Zheng
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Benjamin Ziman
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, 2250 Alcazar Street - CSA 207D, Los Angeles, CA, 90033, USA
| | - Allen S Ho
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Uttam K Sinha
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Guangdong, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Guangdong, China
| | - H Phillip Koeffler
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Benjamin P Berman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - De-Chen Lin
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA.
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, 2250 Alcazar Street - CSA 207D, Los Angeles, CA, 90033, USA.
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5
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Shijimaya T, Tahara T, Yamazaki J, Kobayashi S, Horitani A, Matsumoto Y, Nakamura N, Okazaki T, Takahashi Y, Tomiyama T, Honzawa Y, Fukata N, Fukui T, Naganuma M. Microarchitectures of Barrett's esophagus associated with DNA methylation status. Epigenomics 2023; 15:759-767. [PMID: 37661863 DOI: 10.2217/epi-2023-0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Abstract
Aim: DNA methylation is involved in esophageal adenocarcinoma (EAC) and Barrett's esophagus (BE). Microarchitectures of on-neoplastic BE associated with DNA methylation status were examined using magnifying narrow-band imaging (NBI) endoscopy. Patients and methods: Using biopsies from non-neoplastic BE without cancer (n = 66; N group), with EAC (n = 27; ADJ group) and EAC tissue (n = 22; T group), methylation of N33, DPYS, SLC16A12, miR124a3 and miR34bc genes were quantified. Magnifying NBI features of non-neoplastic BE were classified according to their morphologies. Results: The ADJ and T groups presented higher DNA methylation compared with the N group. Magnifying NBI endoscopic features of non-neoplastic BE also correlated with DNA methylation as an independent factor. Conclusion: Microarchitectures of BE visualized by magnifying NBI endoscopy correlated with DNA methylation.
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Affiliation(s)
- Takuya Shijimaya
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Tomomitsu Tahara
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
- One Health Research Center and Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Sanshiro Kobayashi
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Anna Horitani
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Yasushi Matsumoto
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Naohiro Nakamura
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Takashi Okazaki
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Yu Takahashi
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Takashi Tomiyama
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Yusuke Honzawa
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Norimasa Fukata
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Toshiro Fukui
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Makoto Naganuma
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
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6
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Yi Q, Zhao Y, Xia R, Wei Q, Chao F, Zhang R, Bian P, Lv L. TRIM29 hypermethylation drives esophageal cancer progression via suppression of ZNF750. Cell Death Discov 2023; 9:191. [PMID: 37365152 DOI: 10.1038/s41420-023-01491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Esophageal cancer (ESCA) is the seventh most frequent and deadly neoplasm. Due to the lack of early diagnosis and high invasion/metastasis, the prognosis of ESCA remains very poor. Herein, we identify skin-related signatures as the most deficient signatures in invasive ESCA, which are regulated by the transcription factor ZNF750. Of note, we find that TRIM29 level strongly correlated with the expression of many genes in the skin-related signatures, including ZNF750. TRIM29 is significantly down-regulated due to hypermethylation of its promoter in both ESCA and precancerous lesions compared to normal tissues. Low TRIM29 expression and high methylation levels of its promoter are associated with malignant progression and poor clinical outcomes in ESCA patients. Functionally, TRIM29 overexpression markedly hinders proliferation, migration, invasion, and epithelial-mesenchymal transition of esophageal cancer cells, whereas opposing results are observed when TRIM29 is silenced in vitro. In addition, TRIM29 inhibits metastasis in vivo. Mechanistically, TRIM29 downregulation suppresses the expression of the tumor suppressor ZNF750 by activating the STAT3 signaling pathway. Overall, our study demonstrates that TRIM29 expression and its promoter methylation status could be potential early diagnostic and prognostic markers. It highlights the role of the TRIM29-ZNF750 signaling axis in modulating tumorigenesis and metastasis of esophageal cancer.
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Affiliation(s)
- Qiyi Yi
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, Anhui, China
| | - Yujia Zhao
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, Anhui, China
- Department of education training, The First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Ran Xia
- Department of Cancer Epigenetics Program, Anhui Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230031, Hefei, Anhui, China
| | - Qinqin Wei
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, Anhui, China
| | - Fengmei Chao
- Department of Cancer Epigenetics Program, Anhui Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230031, Hefei, Anhui, China
| | - Rui Zhang
- Department of Oncology, The First Affiliated Hospital of Anhui University of Chinese Medicine, 230031, Hefei, Anhui, China
| | - Po Bian
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, Anhui, China.
| | - Lei Lv
- Department of Cancer Epigenetics Program, Anhui Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230031, Hefei, Anhui, China.
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7
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Li HS, Chu CL. Intestinal metaplasia in progression of Barrett's esophagus to esophageal adenocarcinoma. Shijie Huaren Xiaohua Zazhi 2023; 31:41-47. [DOI: 10.11569/wcjd.v31.i2.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The incidence of esophageal adenocarcinoma (EAC) has been increasing year by year. The prognosis of EAC is poor, and the 5-year survival rate is less than 20%. Barrett's esophagus (BE) is the only known precancerous lesion of EAC. BE with intestinal metaplasia (IM) has a higher risk of progressing to EAC. Exploring the mechanism of IM and finding targeted therapeutic targets for BE has become an important measure for tumor prevention. Bile acid reflux is considered an important factor in the occurrence of IM and promotes the progression of BE to EAC. However, the molecular regulatory mechanism of bile reflux induced IM and carcinogenesis remains unclear. This article reviews the environment, significance, and cell origin theory of IM, toxic effects of bile reflux, and molecular changes of IM progression to tumor, aiming to improve clinicians' understanding of IM in BE and provide evidence for early intervention of BE and prevention and treatment of EAC.
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Affiliation(s)
- Hai-Su Li
- Jinan Central Hospital, Jinan Key Translational Gastroenterology Laboratory, Jinan Digestive Diseases Clinical Research Center, Jinan 250013, Shandong Province, China
| | - Chuan-Lian Chu
- Jinan Central Hospital, Jinan Key Translational Gastroenterology Laboratory, Jinan Digestive Diseases Clinical Research Center, Jinan 250013, Shandong Province, China
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8
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Yu H, Wang X, Bai L, Tang G, Carter KT, Cui J, Huang P, Liang L, Ding Y, Cai M, Huang M, Liu H, Cao G, Gallinger S, Pai RK, Buchanan DD, Win AK, Newcomb PA, Wang J, Grady WM, Luo Y. DNA methylation profile in CpG-depleted regions uncovers a high-risk subtype of early-stage colorectal cancer. J Natl Cancer Inst 2023; 115:52-61. [PMID: 36171645 PMCID: PMC10089593 DOI: 10.1093/jnci/djac183] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/27/2022] [Accepted: 08/23/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The current risk stratification system defined by clinicopathological features does not identify the risk of recurrence in early-stage (stage I-II) colorectal cancer (CRC) with sufficient accuracy. We aimed to investigate whether DNA methylation could serve as a novel biomarker for predicting prognosis in early-stage CRC patients. METHODS We analyzed the genome-wide methylation status of CpG loci using Infinium MethylationEPIC array run on primary tumor tissues and normal mucosa of early-stage CRC patients to identify potential methylation markers for prognosis. The machine-learning approach was applied to construct a DNA methylation-based prognostic classifier for early-stage CRC (MePEC) using the 4 gene methylation markers FAT3, KAZN, TLE4, and DUSP3. The prognostic value of the classifier was evaluated in 2 independent cohorts (n = 438 and 359, respectively). RESULTS The comprehensive analysis identified an epigenetic subtype with high risk of recurrence based on a group of CpG loci in the CpG-depleted region. In multivariable analysis, the MePEC classifier was independently and statistically significantly associated with time to recurrence in validation cohort 1 (hazard ratio = 2.35, 95% confidence interval = 1.47 to 3.76, P < .001) and cohort 2 (hazard ratio = 3.20, 95% confidence interval = 1.92 to 5.33, P < .001). All results were further confirmed after each cohort was stratified by clinicopathological variables and molecular subtypes. CONCLUSIONS We demonstrated the prognostic statistical significance of a DNA methylation profile in the CpG-depleted region, which may serve as a valuable source for tumor biomarkers. MePEC could identify an epigenetic subtype with high risk of recurrence and improve the prognostic accuracy of current clinical variables in early-stage CRC.
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Affiliation(s)
- Huichuan Yu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
| | - Xiaolin Wang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
| | - Liangliang Bai
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
| | - Guannan Tang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
| | - Kelly T Carter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Ji Cui
- Departments of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pinzhu Huang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Yanqing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Muyan Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Meijin Huang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
| | - Huanliang Liu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Steven Gallinger
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, ON, Canada
| | - Rish K Pai
- Department of laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Polly A Newcomb
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jianping Wang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, China
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Yanxin Luo
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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9
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Yu M, Moinova HR, Willbanks A, Canon VK, Wang T, Carter K, Kaz A, Reddi D, Inadomi J, Luebeck G, Iyer PG, Canto MI, Wang JS, Shaheen NJ, Thota PN, Willis JE, LaFramboise T, Chak A, Markowitz SD, Grady WM. Novel DNA Methylation Biomarker Panel for Detection of Esophageal Adenocarcinoma and High-Grade Dysplasia. Clin Cancer Res 2022; 28:3761-3769. [PMID: 35705525 PMCID: PMC9444948 DOI: 10.1158/1078-0432.ccr-22-0445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/10/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Current endoscopy-based screening and surveillance programs have not been proven effective at decreasing esophageal adenocarcinoma (EAC) mortality, creating an unmet need for effective molecular tests for early detection of this highly lethal cancer. We conducted a genome-wide methylation screen to identify novel methylation markers that distinguish EAC and high-grade dysplasia (HGD) from normal squamous epithelium (SQ) or nondysplastic Barrett's esophagus (NDBE). EXPERIMENTAL DESIGN DNA methylation profiling of samples from SQ, NDBE, HGD, and EAC was performed using HM450 methylation arrays (Illumina) and reduced-representation bisulfate sequencing. Ultrasensitive methylation-specific droplet digital PCR and next-generation sequencing (NGS)-based bisulfite-sequencing assays were developed to detect the methylation level of candidate CpGs in independent esophageal biopsy and endoscopic brushing samples. RESULTS Five candidate methylation markers were significantly hypermethylated in HGD/EAC samples compared with SQ or NDBE (P < 0.01) in both esophageal biopsy and endoscopic brushing samples. In an independent set of brushing samples used to construct biomarker panels, a four-marker panel (model 1) demonstrated sensitivity of 85.0% and 90.8% for HGD and EACs respectively, with 84.2% and 97.9% specificity for NDBE and SQ respectively. In a validation set of brushing samples, the panel achieved sensitivity of 80% and 82.5% for HGD and EAC respectively, at specificity of 67.6% and 96.3% for NDBE and SQ samples. CONCLUSIONS A novel DNA methylation marker panel differentiates HGD/EAC from SQ/NDBE. DNA-methylation-based molecular assays hold promise for the detection of HGD/EAC using esophageal brushing samples.
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Affiliation(s)
- Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Helen R. Moinova
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Amber Willbanks
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Victoria K. Canon
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ting Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kelly Carter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew Kaz
- Gastroenterology Section, VA Puget Sound Health Care System, WA, USA,Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Deepti Reddi
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - John Inadomi
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Georg Luebeck
- Public Heath Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Prasad G. Iyer
- Barrett’s Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Marcia I. Canto
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Medical Institutions, Baltimore, MD
| | - Jean S. Wang
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Nicholas J. Shaheen
- Center for Esophageal Diseases and Swallowing, Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC
| | | | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA,Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Amitabh Chak
- Gastroenterology Division, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sanford D. Markowitz
- Seidman Cancer Center, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
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10
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Sugano K, Spechler SJ, El-Omar EM, McColl KEL, Takubo K, Gotoda T, Fujishiro M, Iijima K, Inoue H, Kawai T, Kinoshita Y, Miwa H, Mukaisho KI, Murakami K, Seto Y, Tajiri H, Bhatia S, Choi MG, Fitzgerald RC, Fock KM, Goh KL, Ho KY, Mahachai V, O'Donovan M, Odze R, Peek R, Rugge M, Sharma P, Sollano JD, Vieth M, Wu J, Wu MS, Zou D, Kaminishi M, Malfertheiner P. Kyoto international consensus report on anatomy, pathophysiology and clinical significance of the gastro-oesophageal junction. Gut 2022; 71:1488-1514. [PMID: 35725291 PMCID: PMC9279854 DOI: 10.1136/gutjnl-2022-327281] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/03/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVE An international meeting was organised to develop consensus on (1) the landmarks to define the gastro-oesophageal junction (GOJ), (2) the occurrence and pathophysiological significance of the cardiac gland, (3) the definition of the gastro-oesophageal junctional zone (GOJZ) and (4) the causes of inflammation, metaplasia and neoplasia occurring in the GOJZ. DESIGN Clinical questions relevant to the afore-mentioned major issues were drafted for which expert panels formulated relevant statements and textural explanations.A Delphi method using an anonymous system was employed to develop the consensus, the level of which was predefined as ≥80% of agreement. Two rounds of voting and amendments were completed before the meeting at which clinical questions and consensus were finalised. RESULTS Twenty eight clinical questions and statements were finalised after extensive amendments. Critical consensus was achieved: (1) definition for the GOJ, (2) definition of the GOJZ spanning 1 cm proximal and distal to the GOJ as defined by the end of palisade vessels was accepted based on the anatomical distribution of cardiac type gland, (3) chemical and bacterial (Helicobacter pylori) factors as the primary causes of inflammation, metaplasia and neoplasia occurring in the GOJZ, (4) a new definition of Barrett's oesophagus (BO). CONCLUSIONS This international consensus on the new definitions of BO, GOJ and the GOJZ will be instrumental in future studies aiming to resolve many issues on this important anatomic area and hopefully will lead to better classification and management of the diseases surrounding the GOJ.
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Affiliation(s)
- Kentaro Sugano
- Division of Gastroenterology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Stuart Jon Spechler
- Division of Gastroenterology, Center for Esophageal Diseases, Baylor University Medical Center, Dallas, Texas, USA
| | - Emad M El-Omar
- Microbiome Research Centre, St George & Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine & Health, Sydney, New South Wales, Australia
| | - Kenneth E L McColl
- Division of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Kaiyo Takubo
- Research Team for Geriatric Pathology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Takuji Gotoda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsunori Iijima
- Department of Gastroenterology, Akita University Graduate School of Medicine, Akita, Japan
| | - Haruhiro Inoue
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Tokyo, Japan
| | - Takashi Kawai
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan
| | | | - Hiroto Miwa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Hyogo College of Medicine, Kobe, Japan
| | - Ken-Ichi Mukaisho
- Education Center for Medicine and Nursing, Shiga University of Medical Science, Otsu, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Faculty of Medicine, Yuhu, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hisao Tajiri
- Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | | | - Myung-Gyu Choi
- Gastroenterology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, The Republic of Korea
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
| | - Kwong Ming Fock
- Department of Gastroenterology and Hepatology, Duke NUS School of Medicine, National University of Singapore, Singapore
| | | | - Khek Yu Ho
- Department of Medicine, National University of Singapore, Singapore
| | - Varocha Mahachai
- Center of Excellence in Digestive Diseases, Thammasat University and Science Resarch and Innovation, Bangkok, Thailand
| | - Maria O'Donovan
- Department of Histopathology, Cambridge University Hospital NHS Trust UK, Cambridge, UK
| | - Robert Odze
- Department of Pathology, Tuft University School of Medicine, Boston, Massachusetts, USA
| | - Richard Peek
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Massimo Rugge
- Department of Medicine DIMED, Surgical Pathology and Cytopathology Unit, University of Padova, Padova, Italy
| | - Prateek Sharma
- Department of Gastroenterology and Hepatology, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Jose D Sollano
- Department of Medicine, University of Santo Tomas, Manila, Philippines
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth, Friedrich-Alexander University Erlangen, Nurenberg, Germany
| | - Justin Wu
- Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Ming-Shiang Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Duowu Zou
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Peter Malfertheiner
- Medizinixhe Klinik und Poliklinik II, Ludwig Maximillian University Klinikum, Munich, Germany
- Klinik und Poliklinik für Radiologie, Ludwig Maximillian University Klinikum, Munich, Germany
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11
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Paulson TG, Galipeau PC, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Hadi K, Shah M, Arora K, Shelton J, Johnson M, Corvelo A, Maley CC, Yao X, Sanghvi R, Venturini E, Emde AK, Hubert B, Imielinski M, Robine N, Reid BJ, Li X. Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression. Nat Commun 2022; 13:2300. [PMID: 35484108 PMCID: PMC9050715 DOI: 10.1038/s41467-022-29767-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
While the genomes of normal tissues undergo dynamic changes over time, little is understood about the temporal-spatial dynamics of genomes in premalignant tissues that progress to cancer compared to those that remain cancer-free. Here we use whole genome sequencing to contrast genomic alterations in 427 longitudinal samples from 40 patients with stable Barrett’s esophagus compared to 40 Barrett’s patients who progressed to esophageal adenocarcinoma (ESAD). We show the same somatic mutational processes are active in Barrett’s tissue regardless of outcome, with high levels of mutation, ESAD gene and focal chromosomal alterations, and similar mutational signatures. The critical distinction between stable Barrett’s versus those who progress to cancer is acquisition and expansion of TP53−/− cell populations having complex structural variants and high-level amplifications, which are detectable up to six years prior to a cancer diagnosis. These findings reveal the timing of common somatic genome dynamics in stable Barrett’s esophagus and define key genomic features specific to progression to esophageal adenocarcinoma, both of which are critical for cancer prevention and early detection strategies. Barrett’s esophagus is a pre-malignant condition that can progress to esophageal cancer. Here, the authors carry out whole genome sequencing of samples from patients who did or did not progress to cancer and find that mutations in many genes occur regardless of progression status, but also find features associated with progressive disease.
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Affiliation(s)
- Thomas G Paulson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.
| | - Patricia C Galipeau
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Kenji M Oman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Carissa A Sanchez
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Mary K Kuhner
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195-5065, USA
| | - Lucian P Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA
| | - Kevin Hadi
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Minita Shah
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Kanika Arora
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | | | - Molly Johnson
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Andre Corvelo
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | - Xiaotong Yao
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | | | | | | | | | - Marcin Imielinski
- New York Genome Center (NYGC), New York, NY, 10013, USA.,Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine and Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10065, USA
| | | | - Brian J Reid
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195-5065, USA.,Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Xiaohong Li
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.
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12
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Bregni G, Beck B. Toward Targeted Therapies in Oesophageal Cancers: An Overview. Cancers (Basel) 2022; 14:1522. [PMID: 35326673 PMCID: PMC8946490 DOI: 10.3390/cancers14061522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Oesophageal cancer is one of the leading causes of cancer-related death worldwide. Oesophageal cancer occurs as squamous cell carcinoma (ESCC) or adenocarcinoma (EAC). Prognosis for patients with either ESCC or EAC is poor, with less than 20% of patients surviving more than 5 years after diagnosis. A major progress has been made in the development of biomarker-driven targeted therapies against breast and lung cancers, as well as melanoma. However, precision oncology for patients with oesophageal cancer is still virtually non-existent. In this review, we outline the recent advances in oesophageal cancer profiling and clinical trials based on targeted therapies in this disease.
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Affiliation(s)
- Giacomo Bregni
- Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium;
| | - Benjamin Beck
- Welbio and FNRS Investigator at IRIBHM, Faculty of Medicine, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
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13
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Saller JJ, Mora LB, Nasir A, Mayer Z, Shahid M, Coppola D. Expression of DNA Mismatch Repair Proteins, PD1 and PDL1 in Barrett's Neoplasia. Cancer Genomics Proteomics 2022; 19:145-150. [PMID: 35181584 DOI: 10.21873/cgp.20310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND/AIM Cancers with a microsatellite instability-high (MSI-H) or deficient mismatch repair (dMMR) status respond to immune checkpoint inhibition (ICI). Regardless of the tumor type, MSI-H/dMMR status is a reliable biomarker for ICI responsiveness. This study aimed at determining the MSI-H status in precursor lesions to esophageal adenocarcinoma (EAC) such as Barrett's esophagus (BE) and BE with either low-grade dysplasia (LGD) or high-grade dysplasia (HGD). PATIENTS AND METHODS We performed immunohistochemical staining (IHC) for PMS2, MSH6, PD1, and PD-L1. RESULTS All cases of BE (50), LGD (48), and HGD (50) had intact PMS2 and MSH6 nuclear expression; were negative for PD1; and had a PD-L1 combined positive score (CPS) score <1. One EAC case (2%) was negative for PMS2 nuclear expression. One HGD case (2%) and two EAC cases (4%) were PD1 positive (CPS score <1 applied to PD1). One EAC case (2%) had a CPS score >1, and one EAC case (2%) was MSI-H. MSI-H tumors usually show PD-L1 expression, although the MSI-H EAC in this study had a PD-L1 CPS score of <1. CONCLUSION Further studies investigating EAC and its precursor lesions for PD1, PD-L1, and dMMR status may be informative regarding the immunogenicity of the evolution of EAC.
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Affiliation(s)
- James J Saller
- Department of Pathology, Moffitt Cancer Center, Tampa, FL, U.S.A
| | - Linda B Mora
- Pathology Laboratory, Florida Digestive Health Specialists, Bradenton, FL, U.S.A
| | - Aejaz Nasir
- Pathology Laboratory, Florida Digestive Health Specialists, Bradenton, FL, U.S.A
| | - Zachary Mayer
- College of Medicine, University of Florida, Gainesville, FL, U.S.A
| | - Mohammad Shahid
- Pathology Laboratory, Florida Digestive Health Specialists, Bradenton, FL, U.S.A
| | - Domenico Coppola
- Department of Pathology, Moffitt Cancer Center, Tampa, FL, U.S.A.; .,Pathology Laboratory, Florida Digestive Health Specialists, Bradenton, FL, U.S.A
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14
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Maslyonkina KS, Konyukova AK, Alexeeva DY, Sinelnikov MY, Mikhaleva LM. Barrett's esophagus: The pathomorphological and molecular genetic keystones of neoplastic progression. Cancer Med 2022; 11:447-478. [PMID: 34870375 PMCID: PMC8729054 DOI: 10.1002/cam4.4447] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023] Open
Abstract
Barrett's esophagus is a widespread chronically progressing disease of heterogeneous nature. A life threatening complication of this condition is neoplastic transformation, which is often overlooked due to lack of standardized approaches in diagnosis, preventative measures and treatment. In this essay, we aim to stratify existing data to show specific associations between neoplastic transformation and the underlying processes which predate cancerous transition. We discuss pathomorphological, genetic, epigenetic, molecular and immunohistochemical methods related to neoplasia detection on the basis of Barrett's esophagus. Our review sheds light on pathways of such neoplastic progression in the distal esophagus, providing valuable insight into progression assessment, preventative targets and treatment modalities. Our results suggest that molecular, genetic and epigenetic alterations in the esophagus arise earlier than cancerous transformation, meaning the discussed targets can help form preventative strategies in at-risk patient groups.
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15
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Wang H, DeFina SM, Bajpai M, Yan Q, Yang L, Zhou Z. DNA methylation markers in esophageal cancer: an emerging tool for cancer surveillance and treatment. Am J Cancer Res 2021; 11:5644-5658. [PMID: 34873485 PMCID: PMC8640794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023] Open
Abstract
Esophageal carcinoma (EC) is one of the most pervasive cancers in the world, with upwards of 500,000 new diagnoses, annually. Despite its prominence, advancements in the detection and treatment of EC have been marginal over the past 30 years and the survival rate continues to stay below 20%. This is due to the uncommonly heterogeneous presentation of EC which presents unprecedented challenges in improving patient survival and quality of care. However, distinct epigenetic alterations to the DNA methylome may provide an avenue to drastically improve the detection and treatment of EC. Specifically, the creation of novel biomarker panels that consist of EC-specific methylation markers have shown promise as a potential alternative to the more invasive, contemporary diagnostic methods. Additionally, growing insight into the biological and clinical properties of EC-specific methylation patterns have opened a window of opportunity for enhanced treatment; of growing interest is the application of "DNMT inhibitors" - a class of drugs which inhibit excessive methylation and have been shown to re-sensitize chemoresistant tumors. Here we provide a comprehensive review of the current advancements in EC DNA methylation to underscore a potential approach to its detection and treatment.
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Affiliation(s)
- He Wang
- Department of Pathology, Yale School of Medicine, Yale UniversityNew Haven, Connecticut, United States
| | - Samuel M DeFina
- Department of Pathology, Yale School of Medicine, Yale UniversityNew Haven, Connecticut, United States
| | - Manisha Bajpai
- Department of Medicine-Gastroenterology and Hepatology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New JerseyNew Brunswick, NJ, United States
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, Yale UniversityNew Haven, Connecticut, United States
| | - Lei Yang
- Department of Pathology, Yale School of Medicine, Yale UniversityNew Haven, Connecticut, United States
| | - Zhongren Zhou
- Department of Pathology & Laboratory Medicine, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New JerseyNew Brunswick, NJ, United States
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16
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Sharma S, George P, Waddell N. Precision diagnostics: Integration of tissue pathology and genomics in cancer. Pathology 2021; 53:809-817. [PMID: 34635323 DOI: 10.1016/j.pathol.2021.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/09/2022]
Abstract
Traditionally, cancer diagnosis and management has been reactionary in that symptoms lead to investigations, then a diagnosis is followed by clinical management. This process is heavily dependent on tissue diagnosis mainly by histopathology and to a lesser extent, cytopathology. However, in recent times there has been a shift towards precision medicine to enable prevention, prediction and personalisation in healthcare. The core of precision medicine is optimising therapeutic benefit for patients, by using genomic and molecular profiling, analogously termed precision pathology. This review explores (1) the evolution of pathology from a para-clinical discipline to a mainstream medical field integral to oncology tumour boards; (2) its critical role in preventative, diagnostic, therapeutic and follow-up cancer care; (3) the future of tissue pathology in the era of precision oncology; and (4) how pathologists may evolve to future-proof their profession.
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Affiliation(s)
- Sowmya Sharma
- Medlab Pathology, Auburn, NSW, Australia; QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, Qld, Australia; Faculty of Medicine, University of Queensland, Brisbane, Qld, Australia.
| | - Peter George
- Medlab Pathology, Auburn, NSW, Australia; genomiQa, Brisbane, Qld, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, Qld, Australia; Faculty of Medicine, University of Queensland, Brisbane, Qld, Australia; genomiQa, Brisbane, Qld, Australia
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17
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Guccione C, Yadlapati R, Shah S, Knight R, Curtius K. Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma. Microorganisms 2021; 9:2003. [PMID: 34683324 PMCID: PMC8541168 DOI: 10.3390/microorganisms9102003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) claims the lives of half of patients within the first year of diagnosis, and its incidence has rapidly increased since the 1970s despite extensive research into etiological factors. The changes in the microbiome within the distal esophagus in modern populations may help explain the growth in cases that other common EAC risk factors together cannot fully explain. The precursor to EAC is Barrett's esophagus (BE), a metaplasia adapted to a reflux-mediated microenvironment that can be challenging to diagnose in patients who do not undergo endoscopic screening. Non-invasive procedures to detect microbial communities in saliva, oral swabs and brushings from the distal esophagus allow us to characterize taxonomic differences in bacterial population abundances within patients with BE versus controls, and may provide an alternative means of BE detection. Unique microbial communities have been identified across healthy esophagus, BE, and various stages of progression to EAC, but studies determining dynamic changes in these communities, including migration from proximal stomach and oral cavity niches, and their potential causal role in cancer formation are lacking. Helicobacter pylori is negatively associated with EAC, and the absence of this species has been implicated in the evolution of chromosomal instability, a main driver of EAC, but joint analyses of microbiome and host genomes are needed. Acknowledging technical challenges, future studies on the prediction of microbial dynamics and evolution within BE and the progression to EAC will require larger esophageal microbiome datasets, improved bioinformatics pipelines, and specialized mathematical models for analysis.
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Affiliation(s)
- Caitlin Guccione
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Rena Yadlapati
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (R.Y.); (S.S.)
| | - Shailja Shah
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (R.Y.); (S.S.)
- Veterans Affairs, San Diego Healthcare System, San Diego, CA 92161, USA
| | - Rob Knight
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
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18
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Validation of a methylated DNA marker panel for the nonendoscopic detection of Barrett's esophagus in a multisite case-control study. Gastrointest Endosc 2021; 94:498-505. [PMID: 33857451 PMCID: PMC8380660 DOI: 10.1016/j.gie.2021.03.937] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/30/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS We previously identified a 5 methylated DNA marker (MDM) panel for the detection of nonendoscopic Barrett's esophagus (BE). In this study, we aimed to recalibrate the performance of the 5 MDM panel using a simplified assay in a training cohort, validate the panel in an independent test cohort, and explore the accuracy of an MDM panel with only 3 markers. METHODS Participants were recruited from 3 medical centers. The sponge on a string device (EsophaCap; CapNostics, Concord, NC, USA) was swallowed and withdrawn, followed by endoscopy, in BE cases and control subjects. A 5 MDM panel was blindly assayed using a simplified assay. Random forest modeling analysis was performed, in silico cross-validated in the training set, and then locked down, before test set analysis. RESULTS The training set had 199 patients: 110 BE cases and 89 control subjects, and the test set had 89 patients: 60 BE cases and 29 control subjects. Sensitivity of the 5 MDM panel for BE diagnosis was 93% at 90% specificity in the training set and 93% at 93% specificity in the test set. Areas under the receiver operating characteristic curves were .96 and .97 in the training and test sets, respectively. Model accuracy was not influenced by age, sex, or smoking history. Multiple 3 MDM panels achieved similar accuracy. CONCLUSIONS A 5 MDM panel for BE is highly accurate in training and test sets in a blinded multisite case-control analysis using a simplified assay. This panel may be reduced to only 3 MDMs in the future. (Clinical trial registration number: NCT02560623.).
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Bornschein J, Quante M, Jansen M. The complexity of cancer origins at the gastro-oesophageal junction. Best Pract Res Clin Gastroenterol 2021; 50-51:101729. [PMID: 33975686 DOI: 10.1016/j.bpg.2021.101729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/08/2021] [Indexed: 01/31/2023]
Abstract
Chronic acid-biliary reflux and Helicobacter pylori infection are instrumental environmental drivers of cancer initiation and progression in the upper gastrointestinal tract. Remarkably, although these environmental carcinogens are quite dissimilar, the tumour progression cascade these carcinogens engender is highly comparable. For this reason, studies of malignant progression occurring at the anatomic borderland between the oesophagus and the stomach have traditionally lumped junctional adenocarcinomas with either oesophageal adenocarcinoma or gastric adenocarcinoma. Whilst studies have revealed remarkable epidemiological and genetic similarities of these cancers and their associated premalignant conditions, these works have also revealed some key differences. This highlights that further scientific effort demands a dedicated focus on the understanding of the cell-cell interaction between the epithelium and the local microenvironment in this anatomic region. We here review available evidence with regards to tumour progression occurring at the gastro-oesophageal junction and contrast it with available data on cancer evolution in the metaplastic oesophagus and distal stomach.
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Affiliation(s)
- Jan Bornschein
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, United Kingdom and NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
| | - Michael Quante
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg, Germany
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20
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Grady WM, Yu M, Markowitz SD. Epigenetic Alterations in the Gastrointestinal Tract: Current and Emerging Use for Biomarkers of Cancer. Gastroenterology 2021; 160:690-709. [PMID: 33279516 PMCID: PMC7878343 DOI: 10.1053/j.gastro.2020.09.058] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer, liver cancer, stomach cancer, pancreatic cancer, and esophageal cancer are leading causes of cancer-related deaths worldwide. A fundamental trait of virtually all gastrointestinal cancers is genomic and epigenomic DNA alterations. Cancer cells acquire genetic and epigenetic alterations that drive the initiation and progression of the cancers by altering the molecular and cell biological processes of the cells. These alterations, as well as other host and microenvironment factors, ultimately mediate the clinical behavior of the precancers and cancers and can be used as biomarkers for cancer risk determination, early detection of cancer and precancer, determination of the prognosis of cancer and prediction of the response to therapy. Epigenetic alterations have emerged as one of most robust classes of biomarkers and are the basis for a growing number of clinical tests for cancer screening and surveillance.
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Affiliation(s)
- William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
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21
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Dual Role of the PTPN13 Tyrosine Phosphatase in Cancer. Biomolecules 2020; 10:biom10121659. [PMID: 33322542 PMCID: PMC7763032 DOI: 10.3390/biom10121659] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/08/2023] Open
Abstract
In this review article, we present the current knowledge on PTPN13, a class I non-receptor protein tyrosine phosphatase identified in 1994. We focus particularly on its role in cancer, where PTPN13 acts as an oncogenic protein and also a tumor suppressor. To try to understand these apparent contradictory functions, we discuss PTPN13 implication in the FAS and oncogenic tyrosine kinase signaling pathways and in the associated biological activities, as well as its post-transcriptional and epigenetic regulation. Then, we describe PTPN13 clinical significance as a prognostic marker in different cancer types and its impact on anti-cancer treatment sensitivity. Finally, we present future research axes following recent findings on its role in cell junction regulation that implicate PTPN13 in cell death and cell migration, two major hallmarks of tumor formation and progression.
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22
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Curtius K, Rubenstein JH, Chak A, Inadomi JM. Computational modelling suggests that Barrett's oesophagus may be the precursor of all oesophageal adenocarcinomas. Gut 2020; 70:gutjnl-2020-321598. [PMID: 33234525 PMCID: PMC8292551 DOI: 10.1136/gutjnl-2020-321598] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Barrett's oesophagus (BE) is a known precursor to oesophageal adenocarcinoma (OAC) but current clinical data have not been consolidated to address whether BE is the origin of all incident OAC, which would reinforce evidence for BE screening efforts. We aimed to answer whether all expected prevalent BE, diagnosed and undiagnosed, could account for all incident OACs in the US cancer registry data. DESIGN We used a multiscale computational model of OAC that includes the evolutionary process from normal oesophagus through BE in individuals from the US population. The model was previously calibrated to fit Surveillance, Epidemiology and End Results cancer incidence curves. Here, we also utilised age-specific and sex-specific US census data for numbers at-risk. The primary outcome for model validation was the expected number of OAC cases for a given calendar year. Secondary outcomes included the comparisons of resulting model-predicted prevalence of BE and BE-to-OAC progression to the observed prevalence and progression rates. RESULTS The model estimated the total number of OAC cases from BE in 2010 was 9970 (95% CI: 9140 to 11 980), which recapitulates nearly all OAC cases from population data. The model simultaneously predicted 8%-9% BE prevalence in high-risk males age 45-55, and 0.1%-0.2% non-dysplastic BE-to-OAC annual progression in males, consistent with clinical studies. CONCLUSION There are likely few additional OAC cases arising in the US population outside those expected from individuals with BE. Effective screening of high-risk patients could capture the majority of population destined for OAC progression and potentially decrease mortality through early detection and curative removal of small (pre)cancers during surveillance.
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Affiliation(s)
- Kit Curtius
- Centre for Genomics and Computational Biology, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Joel H Rubenstein
- Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
- Center for Clinical Management Research, Ann Arbor Veterans Affairs Medical Center, Ann Arbor, Michigan, USA
| | - Amitabh Chak
- Division of Gastroenterology and Liver Disease, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - John M Inadomi
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
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23
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Mashimo H, Gordon SR, Singh SK. Advanced endoscopic imaging for detecting and guiding therapy of early neoplasias of the esophagus. Ann N Y Acad Sci 2020; 1482:61-76. [PMID: 33184872 DOI: 10.1111/nyas.14523] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022]
Abstract
Esophageal cancers, largely adenocarcinoma in Western countries and squamous cell cancer in Asia, present a significant burden of disease and remain one of the most lethal of cancers. Key to improving survival is the development and adoption of new imaging modalities to identify early neoplastic lesions, which may be small, multifocal, subsurface, and difficult to detect by standard endoscopy. Such advanced imaging is particularly relevant with the emergence of ablative techniques that often require multiple endoscopic sessions and may be complicated by bleeding, pain, strictures, and recurrences. Assessing the specific location, depth of involvement, and features correlated with neoplastic progression or incomplete treatment may optimize treatments. While not comprehensive of all endoscopic imaging modalities, we review here some of the recent advances in endoscopic luminal imaging, particularly with surface contrast enhancement using virtual chromoendoscopy, highly magnified subsurface imaging with confocal endomicroscopy, optical coherence tomography, elastic scattering spectroscopy, angle-resolved low-coherence interferometry, and light scattering spectroscopy. While there is no single ideal imaging modality, various multimodal instruments are also being investigated. The future of combining computer-aided assessments, molecular markers, and improved imaging technologies to help localize and ablate early neoplastic lesions shed hope for improved disease outcome.
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Affiliation(s)
- Hiroshi Mashimo
- VA Boston Healthcare System, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Stuart R Gordon
- Dartmouth-Hitchcock Medical Center, Dartmouth University, Lebanon, New Hampshire
| | - Satish K Singh
- VA Boston Healthcare System, Boston, Massachusetts.,Boston University School of Medicine, Boston, Massachusetts
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Grady WM, Yu M, Markowitz SD, Chak A. Barrett's Esophagus and Esophageal Adenocarcinoma Biomarkers. Cancer Epidemiol Biomarkers Prev 2020; 29:2486-2494. [PMID: 33093162 DOI: 10.1158/1055-9965.epi-20-0223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/31/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
Esophageal adenocarcinoma is a major cause of cancer-related morbidity and mortality in Western countries. The incidences of esophageal adenocarcinoma and its precursor Barrett's esophagus have increased substantially in the last four decades. Current care guidelines recommend that endoscopy be used for the early detection and monitoring of patients with Barrett's esophagus; however, the efficacy of this approach is unclear. To prevent the increasing morbidity and mortality from esophageal adenocarcinoma, there is a tremendous need for early detection and surveillance biomarker assays that are accurate, low-cost, and clinically feasible to implement. The last decade has seen remarkable advances in the development of minimally invasive molecular biomarkers, an effort led in large part by the Early Detection Research Network (EDRN). Advances in multi-omics analysis, the development of swallowable cytology collection devices, and emerging technology have led to promising assays that are likely to be implemented into clinical care in the next decade. In this review, an updated overview of the molecular pathology of Barrett's esophagus and esophageal adenocarcinoma and emerging molecular biomarker assays, as well as the role of EDRN in biomarker discovery and validation, will be discussed.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- William M Grady
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington. .,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sanford D Markowitz
- Oncology Division, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Amitabh Chak
- Gastroenterology Division, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
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25
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Jammula S, Katz-Summercorn AC, Li X, Linossi C, Smyth E, Killcoyne S, Biasci D, Subash VV, Abbas S, Blasko A, Devonshire G, Grantham A, Wronowski F, O'Donovan M, Grehan N, Eldridge MD, Tavaré S, Fitzgerald RC. Identification of Subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data. Gastroenterology 2020; 158:1682-1697.e1. [PMID: 32032585 PMCID: PMC7305027 DOI: 10.1053/j.gastro.2020.01.044] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Esophageal adenocarcinomas (EACs) are heterogeneous and often preceded by Barrett's esophagus (BE). Many genomic changes have been associated with development of BE and EAC, but little is known about epigenetic alterations. We performed epigenetic analyses of BE and EAC tissues and combined these data with transcriptome and genomic data to identify mechanisms that control gene expression and genome integrity. METHODS In a retrospective cohort study, we collected tissue samples and clinical data from 150 BE and 285 EAC cases from the Oesophageal Cancer Classification and Molecular Stratification consortium in the United Kingdom. We analyzed methylation profiles of all BE and EAC tissues and assigned them to subgroups using non-negative matrix factorization with k-means clustering. Data from whole-genome sequencing and transcriptome studies were then incorporated; we performed integrative methylation and RNA-sequencing analyses to identify genes that were suppressed with increased methylation in promoter regions. Levels of different immune cell types were computed using single-sample gene set enrichment methods. We derived 8 organoids from 8 EAC tissues and tested their sensitivity to different drugs. RESULTS BE and EAC samples shared genome-wide methylation features, compared with normal tissues (esophageal, gastric, and duodenum; controls) from the same patients and grouped into 4 subtypes. Subtype 1 was characterized by DNA hypermethylation with a high mutation burden and multiple mutations in genes in cell cycle and receptor tyrosine signaling pathways. Subtype 2 was characterized by a gene expression pattern associated with metabolic processes (ATP synthesis and fatty acid oxidation) and lack methylation at specific binding sites for transcription factors; 83% of samples of this subtype were BE and 17% were EAC. The third subtype did not have changes in methylation pattern, compared with control tissue, but had a gene expression pattern that indicated immune cell infiltration; this tumor type was associated with the shortest time of patient survival. The fourth subtype was characterized by DNA hypomethylation associated with structure rearrangements, copy number alterations, with preferential amplification of CCNE1 (cells with this gene amplification have been reported to be sensitive to CDK2 inhibitors). Organoids with reduced levels of MGMT and CHFR expression were sensitive to temozolomide and taxane drugs. CONCLUSIONS In a comprehensive integrated analysis of methylation, transcriptome, and genome profiles of more than 400 BE and EAC tissues, along with clinical data, we identified 4 subtypes that were associated with patient outcomes and potential responses to therapy.
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Affiliation(s)
- SriGanesh Jammula
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Xiaodun Li
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Constanza Linossi
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth Smyth
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Killcoyne
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Daniele Biasci
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Vinod V Subash
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sujath Abbas
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Adrienn Blasko
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ginny Devonshire
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Amber Grantham
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Filip Wronowski
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Maria O'Donovan
- Department of Histopathology, Cambridge University Hospital NHS Trust, Cambridge, United Kingdom
| | - Nicola Grehan
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Matthew D Eldridge
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Simon Tavaré
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom; Irving Institute for Cancer Dynamics, Columbia University, New York, New York
| | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom.
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26
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Teng H, Xue M, Liang J, Wang X, Wang L, Wei W, Li C, Zhang Z, Li Q, Ran X, Shi X, Cai W, Wang W, Gao H, Sun Z. Inter- and intratumor DNA methylation heterogeneity associated with lymph node metastasis and prognosis of esophageal squamous cell carcinoma. Am J Cancer Res 2020; 10:3035-3048. [PMID: 32194853 PMCID: PMC7053185 DOI: 10.7150/thno.42559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/22/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Esophageal squamous cell carcinoma (ESCC), one of the leading causes of cancer mortality worldwide, is a heterogeneous cancer with diverse clinical manifestations. However, little is known about the epigenetic heterogeneity and its clinical relevance for this prevalent cancer. Methods: We generated 7.56 Tb single-base resolution whole-genome bisulfite sequencing data for 84 ESCC and paired paraneoplastic tissues. The analysis identified inter- and intratumor DNA methylation (DNAm) heterogeneity, epigenome-wide DNAm alterations together with the functional regulators involved in the hyper- or hypomethylated regions, and their association with clinical features. We then validated the correlation between the methylation level of specific regions and clinical outcomes of 96 ESCC patients in an independent cohort. Results: ESCC manifested substantial inter- and intratumor DNAm heterogeneity. The high intratumor DNAm heterogeneity was associated with lymph node metastasis and worse overall survival. Interestingly, hypermethylated regions in ESCC were enriched in promoters of numerous transcription factors, and demethylated noncoding regions related to RXR transcription factor binding appeared to contribute to the development of ESCC. Furthermore, we identified numerous DNAm alterations associated with carcinogenesis and lymph node metastasis of ESCC. We also validated three novel prognostic markers for ESCC, including one each in the promoter of CLK1, the 3' untranslated region of ZEB2, and the intergenic locus surrounded by several lncRNAs. Conclusions: This study presents the first population-level resource for dissecting base-resolution DNAm variation in ESCC and provides novel insights into the ESCC pathogenesis and progression, which might facilitate diagnosis and prognosis for this prevalent malignancy.
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27
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Abstract
Tumor-specific DNA methylation can be used for cancer diagnostics and monitoring. We have recently reported a set of DNA methylation biomarkers that can distinguish plasma samples from lung cancer patients versus healthy controls with high sensitivity and specificity. Furthermore, the DNA methylation signal from the biomarker loci detected in plasma samples correlated with tumor size and decreased after surgical resection of lung tumors. In order to determine the timing of DNA methylation of these loci during carcinogenesis and thus the potential of the biomarkers to detect early stages of the disease we analyzed the DNA methylation of the biomarker loci in five precancerous conditions using available data from the GEO database. We found that the DNA methylation of the biomarker loci is gained early in carcinogenesis since most of the precancerous conditions already have biomarker loci hypermethylated. Moreover, these DNA methylation biomarkers are able to distinguish between precancerous lesions with malignant potential and those that stay benign where data is available. Taken together, the biomarkers have the potential to detect the earliest cancer stages; the only limitation to detection of cancer from plasma samples or other liquid biopsies is the timing when tumors start to shed enough DNA into body fluids.
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Affiliation(s)
- Lukas Vrba
- The University of Arizona Cancer Center, The University of Arizona, Tucson, Arizona, 85724, USA
| | - Bernard W Futscher
- The University of Arizona Cancer Center, The University of Arizona, Tucson, Arizona, 85724, USA.,Department of Pharmacology & Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona, 85724, USA
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28
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Specific DNA methylation markers in the diagnosis and prognosis of esophageal cancer. Aging (Albany NY) 2019; 11:11640-11658. [PMID: 31834866 PMCID: PMC6932928 DOI: 10.18632/aging.102569] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/23/2019] [Indexed: 12/14/2022]
Abstract
The early diagnosis and accurate prognosis prediction of esophageal cancer is an essential part of improving survival. However, these diseases lack effective and specific markers. A total of 1,744 samples of HumanMethylation450 data were integrated to identify and validate specific methylation markers for esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC) as well as for Barrett's esophagus (BE) using The Cancer Genome Atlas and the Gene Expression Omnibus. The diagnostic and prognostic methylation classifiers were constructed by moderated t-statistics and the least absolute shrinkage and selection operator method. The diagnostic methylation classifier using 12 CpG sites was constructed in training set (377 samples) that could effectively discriminate samples of BE, EAC, and ESCC from normal tissue (AUC = 0.992), which achieved highly predictive ability in both internal (187 samples, AUC = 0.990) and external validation (184 samples, AUC = 0.978). The prognostic methylation classifier with 3 CpG and 2 CpG sites for EAC and ESCC respectively, could accurately estimate the prognosis of an individual patient and improved the predictive ability of the tumor node metastasis staging system. Overall, our study systematically analyzed large-scale methylation data and provided promising markers for the diagnosis and prognosis of esophageal cancer.
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29
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Yu M, Hazelton WD, Luebeck GE, Grady WM. Epigenetic Aging: More Than Just a Clock When It Comes to Cancer. Cancer Res 2019; 80:367-374. [PMID: 31694907 DOI: 10.1158/0008-5472.can-19-0924] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/26/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022]
Abstract
The incidence of cancer, adjusted for secular trends, is directly related to age, and advanced chronologic age is one of the most significant risk factors for cancer. Organismal aging is associated with changes at the molecular, cellular, and tissue levels and is affected by both genetic and environmental factors. The specific mechanisms through which these age-associated molecular changes contribute to the increased risk of aging-related disease, such as cancer, are incompletely understood. DNA methylation, a prominent epigenetic mark, also changes over a lifetime as part of an "epigenetic aging" process. Here, we give an update and review of epigenetic aging, in particular, the phenomena of epigenetic drift and epigenetic clock, with regard to its implication in cancer etiology. We discuss the discovery of the DNA methylation-based biomarkers for biological tissue age and the construction of various epigenetic age estimators for human clinical outcomes and health/life span. Recent studies in various types of cancer point to the significance of epigenetic aging in tumorigenesis and its potential use for cancer risk prediction. Future studies are needed to assess the potential clinical impact of strategies focused on lowering cancer risk by preventing premature aging or promoting healthy aging.
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Affiliation(s)
- Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
| | - William D Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Georg E Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. .,Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington.,GI Cancer Prevention Program, Seattle Cancer Care Alliance, Seattle, Washington
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Abstract
An organ-specific chronic inflammation–remodeling–carcinoma sequence has been proposed, mainly for the alimentary tract. As representative diseases, gastroesophageal reflux disease, chronic gastritis and inflammatory bowel disease (ulcerative colitis and Crohn’s disease of the colitis type) were adopted for this discussion. Tissue remodeling is such an important part of tumorigenesis in this sequence that an organ-specific chronic inflammation–remodeling–carcinoma sequence has been proposed in detail. Chronic inflammation accelerates the cycle of tissue injury and regeneration; in other words, cell necrosis (or apoptosis) and proliferation result in tissue remodeling in long-standing cases of inflammation. Remodeling encompasses epithelial cell metaplasia and stromal fibrosis, and modifies epithelial–stromal cell interactions. Further, the accumulation of genetic, epigenetic and molecular changes—as well as morphologic disorganization—also occurs during tissue remodeling. The expression of mucosal tissue adapted to chronic inflammatory injury is thought to occur at an early stage. Subsequently, dysplasia and carcinoma develop on a background of remodeling due to continuous, active inflammation. Accordingly, organ-specific chronic inflammation should be ameliorated or well controlled with appropriate monitoring if complete healing is unachievable.
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