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Kamal UH, Jamil A, Fatima E, Khurram A, Khan Z, Kamdi ZA, Ahmed S, Farooq MZ, Jaglal M. Mortality Patterns of Esophageal Cancer in the United States: A 21-Year Retrospective Analysis. Am J Clin Oncol 2024:00000421-990000000-00230. [PMID: 39359061 DOI: 10.1097/coc.0000000000001147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
OBJECTIVES Esophageal cancer (EC) is the sixth leading cause of cancer-related deaths in the United States, with a mere 20% survival rate in the first 5 years, making it a significant public health concern. Considering the lack of comprehensive evaluations of mortality trends, this study aims to provide an update on the mortality rates of esophageal cancer and its trends in the United States. METHODS The mortality trends among adults with EC were analyzed using data from the CDC WONDER database. Crude and age-adjusted mortality rates (AAMRs) per 100,000 people were extracted. Annual percent changes (APCs) in AAMRs with 95% CI were obtained using joinpoint regression analysis across different demographic (sex, race/ethnicity, and age) and geographic (state, urban-rural, and regional) subgroups. RESULTS Between 1999 and 2020, 309,725 documented deaths were attributed to esophageal cancer. The overall AAMR decreased from 1999 to 2020 (6.69 to 5.68). Males had higher consistently higher AAMRs than females (10.96 vs. 2.24). NH White had the highest overall AAMR (6.88), followed by NH Black (6.46), NH American Indian (4.95), Hispanic or Latino (3.31), and NH Asian or Pacific Islander (2.57). AAMR also varied by region (overall AAMR: Midwest: 7.18; Northeast: 6.75; South: 6.07; West: 5.76), and nonmetropolitan areas had higher AAMR (non-core areas: 7.09; micropolitan areas: 7.19) than metropolitan areas (large central metropolitan areas: 5.75; large fringe areas: 6.33). The states in the upper 90th percentile of esophageal cancer-related AAMR were Vermont, District of Columbia, West Virginia, Ohio, New Hampshire, and Maine, and exhibited an approximately two-fold increase in AAMRs, compared with states falling in the lower 10th percentile. CONCLUSIONS Over the last 2 decades, there has been an overall decline in mortality related to EC in the United States. However, demographic and geographic discrepancies in EC-related mortality persist, necessitating additional exploration and development of specifically directed treatments.
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Affiliation(s)
| | - Adeena Jamil
- Department of Medicine, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Eeshal Fatima
- Department of Medicine, Services Institute of Medical Sciences, Lahore
| | - Abiha Khurram
- Department of Medicine, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Zoha Khan
- Department of Medicine, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Zainab Anwar Kamdi
- Department of Medicine, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Sana Ahmed
- Department of Medicine, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
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Engl W, Kunstar-Thomas A, Chen S, Ng WS, Sielaff H, Zhao ZW. Single-molecule imaging of SWI/SNF chromatin remodelers reveals bromodomain-mediated and cancer-mutants-specific landscape of multi-modal DNA-binding dynamics. Nat Commun 2024; 15:7646. [PMID: 39223123 PMCID: PMC11369179 DOI: 10.1038/s41467-024-52040-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Despite their prevalent cancer implications, the in vivo dynamics of SWI/SNF chromatin remodelers and how misregulation of such dynamics underpins cancer remain poorly understood. Using live-cell single-molecule tracking, we quantify the intranuclear diffusion and chromatin-binding of three key subunits common to all major human SWI/SNF remodeler complexes (BAF57, BAF155 and BRG1), and resolve two temporally distinct stable binding modes for the fully assembled complex. Super-resolved density mapping reveals heterogeneous, nanoscale remodeler binding "hotspots" across the nucleoplasm where multiple binding events (especially longer-lived ones) preferentially cluster. Importantly, we uncover distinct roles of the bromodomain in modulating chromatin binding/targeting in a DNA-accessibility-dependent manner, pointing to a model where successive longer-lived binding within "hotspots" leads to sustained productive remodeling. Finally, systematic comparison of six common BRG1 mutants implicated in various cancers unveils alterations in chromatin-binding dynamics unique to each mutant, shedding insight into a multi-modal landscape regulating the spatio-temporal organizational dynamics of SWI/SNF remodelers.
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Affiliation(s)
- Wilfried Engl
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Aliz Kunstar-Thomas
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Siyi Chen
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Woei Shyuan Ng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Hendrik Sielaff
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Ziqing Winston Zhao
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore.
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore, 119077, Singapore.
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Tomuleasa C, Tigu AB, Munteanu R, Moldovan CS, Kegyes D, Onaciu A, Gulei D, Ghiaur G, Einsele H, Croce CM. Therapeutic advances of targeting receptor tyrosine kinases in cancer. Signal Transduct Target Ther 2024; 9:201. [PMID: 39138146 PMCID: PMC11323831 DOI: 10.1038/s41392-024-01899-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/29/2024] [Accepted: 06/14/2024] [Indexed: 08/15/2024] Open
Abstract
Receptor tyrosine kinases (RTKs), a category of transmembrane receptors, have gained significant clinical attention in oncology due to their central role in cancer pathogenesis. Genetic alterations, including mutations, amplifications, and overexpression of certain RTKs, are critical in creating environments conducive to tumor development. Following their discovery, extensive research has revealed how RTK dysregulation contributes to oncogenesis, with many cancer subtypes showing dependency on aberrant RTK signaling for their proliferation, survival and progression. These findings paved the way for targeted therapies that aim to inhibit crucial biological pathways in cancer. As a result, RTKs have emerged as primary targets in anticancer therapeutic development. Over the past two decades, this has led to the synthesis and clinical validation of numerous small molecule tyrosine kinase inhibitors (TKIs), now effectively utilized in treating various cancer types. In this manuscript we aim to provide a comprehensive understanding of the RTKs in the context of cancer. We explored the various alterations and overexpression of specific receptors across different malignancies, with special attention dedicated to the examination of current RTK inhibitors, highlighting their role as potential targeted therapies. By integrating the latest research findings and clinical evidence, we seek to elucidate the pivotal role of RTKs in cancer biology and the therapeutic efficacy of RTK inhibition with promising treatment outcomes.
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Affiliation(s)
- Ciprian Tomuleasa
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania.
- Academy of Romanian Scientists, Ilfov 3, 050044, Bucharest, Romania.
| | - Adrian-Bogdan Tigu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Academy of Romanian Scientists, Ilfov 3, 050044, Bucharest, Romania
| | - Raluca Munteanu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
- Academy of Romanian Scientists, Ilfov 3, 050044, Bucharest, Romania
| | - Cristian-Silviu Moldovan
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - David Kegyes
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
- Academy of Romanian Scientists, Ilfov 3, 050044, Bucharest, Romania
| | - Anca Onaciu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Diana Gulei
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Gabriel Ghiaur
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
- Department of Leukemia, Sidney Kimmel Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hermann Einsele
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
- Universitätsklinikum Würzburg, Medizinische Klinik II, Würzburg, Germany
| | - Carlo M Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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Kumar A, Rara M, Yu M, Wen KW, Grady WM, Chak A, Iyer PG, Rustgi AK, Wang TC, Rubenstein JH, Liu Y, Kresty L, Westerhoff M, Kwon RS, Wamsteker E, Wang T, Berry L, Canto MI, Shaheen NJ, Wang KK, Abrams JA, Stachler MD. Molecular Analysis of Persistent and Recurrent Barrett's Esophagus in the Setting of Endoscopic Therapy. Clin Transl Gastroenterol 2024; 15:e00751. [PMID: 39007490 PMCID: PMC11346883 DOI: 10.14309/ctg.0000000000000751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
INTRODUCTION Early neoplastic progression of Barrett's esophagus (BE) is often treated with endoscopic therapy. Although effective, some patients are refractory to therapy or recur after apparent eradication of the BE. The goal of this study was to determine whether genomic alterations within the treated BE may be associated with persistent or recurrent disease. METHODS We performed DNA sequencing on pre-treatment esophageal samples from 45 patients who were successfully treated by endoscopic therapy and did not recur as well as pre-treatment and post-treatment samples from 40 patients who had persistent neoplasia and 21 patients who had recurrent neoplasia. The genomic alterations were compared between groups. RESULTS The genomic landscape was similar between all groups. Patients with persistent disease were more likely to have pre-treatment alterations involving the receptor tyrosine kinase pathway ( P = 0.01), amplifications of oncogenes ( P = 0.01), and deletions of tumor suppressor genes ( P = 0.02). These associations were no longer significant after adjusting for patient age and BE length. More than half of patients with persistent (52.5%) or recurrent (57.2%) disease showed pre-treatment and post-treatment samples that shared at least 50% of their driver mutations. DISCUSSION Pre-treatment samples were genomically similar between those who responded to endoscopic therapy and those who had persistent or recurrent disease, suggesting there is not a strong genomic component to treatment response. Although it was expected to find shared driver mutations in pre-treatment and post-treatment samples in patients with persistent disease, the finding that an equal number of patients with recurrent disease also showed this relation suggests that many recurrences represent undetected minimal residual disease.
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Affiliation(s)
- Aarti Kumar
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Marianne Rara
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Ming Yu
- Translation Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kwun Wah Wen
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - William M. Grady
- Translation Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Amitabh Chak
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Prasad G. Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Anil K. Rustgi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Timothy C. Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Joel H. Rubenstein
- Barrett's Esophagus Program, Division of Gastroenterology and Rogel Cancer Research Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Center for Clinical Management Research, LTC Charles S. Kettles Veterans Affairs Medical Center, Ann Arbor, Michigan, USA
| | - Yue Liu
- Barrett's Esophagus Program, Division of Gastroenterology and Rogel Cancer Research Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Laura Kresty
- Department of Surgery, Section of Thoracic Surgery, and Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Maria Westerhoff
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Richard S. Kwon
- Barrett's Esophagus Program, Division of Gastroenterology and Rogel Cancer Research Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Erik Wamsteker
- Barrett's Esophagus Program, Division of Gastroenterology and Rogel Cancer Research Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tom Wang
- Barrett's Esophagus Program, Division of Gastroenterology and Rogel Cancer Research Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lynne Berry
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Marcia I. Canto
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicholas J. Shaheen
- Division of Gastroenterology & Hepatology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Kenneth K. Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Julian A. Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Matthew D. Stachler
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
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Wang M, Miao H. Disease burden and related risk factors of esophageal cancer in China and globally from 1990 to 2021, with forecast to 2035: An analysis and comparison. Tob Induc Dis 2024; 22:TID-22-140. [PMID: 39091891 PMCID: PMC11292605 DOI: 10.18332/tid/191389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/18/2024] [Accepted: 07/21/2024] [Indexed: 08/04/2024] Open
Abstract
INTRODUCTION In this study we estimate the burden of esophageal cancer (EC) in China and globally from 1990 to 2021, with a forecast to 2035, using Global Burden of Disease (GBD) data. We also analyze the related risk factors to investigate burden trends. METHODS Mortality, disability-adjusted life years (DALYs), crude rates, and age-standardized rates of EC were analyzed in China and globally from 1990 to 2035, utilizing GBD open data as a secondary dataset analysis of GBD data. Temporal change trends of EC risk factors were analyzed from 1990 to 2021. Joinpoint regression determined average annual percentage change (AAPC) of age-standardized rates. Descriptive analysis compared mortality and DALYs by age groups. Bayesian age-period-cohort (BAPC) predicted age-standardized mortality and DALYs rates for the next 14 years. RESULTS The ASMR and ASDR fluctuations in EC were significant in China, showing an overall downward trend. Globally, although there was also a downward trend, the fluctuations were relatively mild. The number of deaths and DALYs related to EC in China and globally showed a significant upward trend. Age-specific burden trends in China for EC indicated that the age group with the peak number of EC deaths shifted to the 70-74 years age group in 2021, while DALYs peaked in the 65-69 years age group. The crude mortality rate (CMR) peaked consistently in 1990 and 2021, both within the 90-94 years age range, while the crude DALY rate (CDR) shifted to the 85-89 years age group. Overall, the burden of EC deaths and DALYs in the population aged <40 years was relatively low, increasing rapidly after the age of 40 years, reaching a peak and gradually declining, and reaching a lower level after the age of 85 years. The predictive results of the BAPC model indicated that over the next 14 years, both ASMR and ASDR for EC in China and globally would show a slight overall increase. The GBD 2021 study identified smoking, high alcohol use, chewing tobacco, and diet low in vegetables as the main risk factors affecting EC mortality rate and DALYs. Among these, smoking and alcohol use were the most significant risk factors, with a higher impact on EC in China compared to the global level. From 1990 to 2021, the overall changes in ASMR and ASDR indicate a decreasing trend in the impact of these four risk factors on EC mortality rate and DALYs. CONCLUSIONS The burden of EC is expected to steadily increase in China and globally until 2035, posing a significant challenge. Targeted prevention and control policies, such as calling on people to quit smoking and reduce alcohol use, may help curb this upward trend.
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Affiliation(s)
- Mimi Wang
- Science and Education Information Section, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Huiwen Miao
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhejiang, University School of Medicine, Hangzhou, China
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Brosda S, Aoude LG, Bonazzi VF, Patel K, Lonie JM, Belle CJ, Newell F, Koufariotis LT, Addala V, Naeini MM, Pearson JV, Krause L, Waddell N, Barbour AP. Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy. Genome Med 2024; 16:90. [PMID: 39020404 PMCID: PMC11253399 DOI: 10.1186/s13073-024-01362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Oesophageal adenocarcinoma (OAC) is a highly heterogeneous cancer with poor survival. Standard curative treatment is chemotherapy with or without radiotherapy followed by oesophagectomy. Genomic heterogeneity is a feature of OAC and has been linked to treatment resistance. METHODS Whole-genome sequencing data from 59 treatment-naïve and 18 post-treatment samples from 29 OAC patients was analysed. Twenty-seven of these were enrolled in the DOCTOR trial, sponsored by the Australasian Gastro-Intestinal Trials Group. Two biopsies from each treatment-naïve tumour were assessed to define 'shared' (between both samples) and 'private' (present in one sample) mutations. RESULTS Mutational signatures SBS2/13 (APOBEC) and SBS3 (BRCA) were almost exclusively detected in private mutation populations of treatment-naïve tumours. Patients presenting these signatures had significantly worse disease specific survival. Furthermore, mutational signatures associated with platinum-based chemotherapy treatment as well as high platinum enrichment scores were only detected in post-treatment samples. Additionally, clones with high putative neoantigen binding scores were detected in some treatment-naïve samples suggesting immunoediting of clones. CONCLUSIONS This study demonstrates the high intra-tumour heterogeneity in OAC, as well as indicators for treatment-induced changes during tumour evolution. Intra-tumour heterogeneity remains a problem for successful treatment strategies in OAC.
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Affiliation(s)
- Sandra Brosda
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
| | - Lauren G Aoude
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Vanessa F Bonazzi
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Kalpana Patel
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - James M Lonie
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Clemence J Belle
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | | | - Venkateswar Addala
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Marjan M Naeini
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Lutz Krause
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
- Microba Life Sciences, Brisbane, QLD, 4000, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Andrew P Barbour
- Frazer Institute, The University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
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Hirose T, Yamamoto S, Honma Y, Yokoyama K, Hirano H, Okita N, Shoji H, Iwasa S, Takashima A, Ishiyama K, Oguma J, Daiko H, Maeda S, Kato K. Preoperative docetaxel, cisplatin, and 5-fluorouracil for resectable locally advanced esophageal and esophagogastric junctional adenocarcinoma. Esophagus 2024; 21:328-335. [PMID: 38467986 PMCID: PMC11199255 DOI: 10.1007/s10388-024-01050-2] [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: 10/26/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND Chemotherapy consisting of 5-fluorouracil, leucovorin, oxaliplatin, and docetaxel is the standard perioperative treatment for resectable esophageal adenocarcinoma and esophagogastric junctional adenocarcinoma (EGJ-AC) in Western countries. Meanwhile, preoperative chemotherapy consisting of docetaxel, cisplatin, and 5-fluorouracil (DCF) has been developed for esophageal squamous cell carcinoma in Japan. However, there are few reports on the safety and efficacy of preoperative DCF for resectable EGJ-AC in the Japanese population. METHODS Patients with histologically confirmed resectable EGJ-AC who received preoperative DCF (docetaxel 70 mg/m2 and cisplatin 70 mg/m2 on day 1 and continuous infusion of 5-fluorouracil 750 mg/m2/day on days 1-5 every 3 weeks with a maximum of three cycles) between January 2015 and April 2020 were retrospectively evaluated. We assessed the rates of completion of ≥ 2 courses of DCF and R0 resection, histopathological response, progression-free survival (PFS), overall survival (OS), and adverse events. RESULTS Thirty-two patients were included. Median follow-up was 28.7 (range, 5.2-70.8) months and median age was 63 (range, 42-80) years. Twenty-one patients (66%) had a performance status of 0. The proportions of clinical stage IIA/IIB/III/IVA/IVB disease were 3%/0%/44%/44%/9%, respectively. The treatment completion rate was 84%. A histopathological response of grade 1a/1b/2/3 was obtained in 58%/26%/13%/3% of cases. Median PFS was 40.7 months (95% confidence interval 11.8-NA). Median OS was not reached (80.8% at 3 years). Grade ≥ 3 adverse events were observed in 63% of cases (neutropenia, 44%; febrile neutropenia, 13%). No treatment-related deaths occurred. CONCLUSIONS Preoperative DCF for resectable EGJ-AC was well tolerated and has promising efficacy.
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Affiliation(s)
- Toshiharu Hirose
- Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
- Department of Gastroenterology, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Shun Yamamoto
- Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshitaka Honma
- Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kazuki Yokoyama
- Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hidekazu Hirano
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Natsuko Okita
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Hirokazu Shoji
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Satoru Iwasa
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Atsuo Takashima
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Koshiro Ishiyama
- Department of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Junya Oguma
- Department of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyuki Daiko
- Department of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Shin Maeda
- Department of Gastroenterology, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Ken Kato
- Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan.
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Choi Y, Bedford A, Pollack S. The Aberrant Expression of Biomarkers and Risk Prediction for Neoplastic Changes in Barrett's Esophagus-Dysplasia. Cancers (Basel) 2024; 16:2386. [PMID: 39001449 PMCID: PMC11240336 DOI: 10.3390/cancers16132386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Background: Barrett's esophagus (BE) is a pre-neoplastic condition associated with an increased risk of esophageal adenocarcinoma (EAC). The accurate diagnosis of BE and grading of dysplasia can help to optimize the management of patients with BE. However, BE may be missed and the accurate grading of dysplasia based on a routine histology has a considerable intra- and interobserver variability. Thus, well-defined biomarker testing remains indispensable. The aim of our study was to identify routinely applicable and relatively specific biomarkers for an accurate diagnosis of BE, as well as determining biomarkers to predict the risk of progression in BE-dysplasia. Methods: Retrospectively, we performed immunohistochemistry to test mucin 2(MUC2), trefoil factor 3 (TFF3), p53, p16, cyclin D1, Ki-67, beta-catenin, and minichromosome maintenance (MCM2) in biopsies. Prospectively, to identify chromosomal alterations, we conducted fluorescent in situ hybridization testing on fresh brush samples collected at the time of endoscopy surveillance. Results: We discovered that MUC2 and TFF3 are specific markers for the diagnosis of BE. Aberrant expression, including the loss and strong overexpression of p53, Ki-67, p16, beta-catenin, cyclin D1, and MCM2, was significantly associated with low-grade dysplasia (LGD), high-grade dysplasia (HGD), and EAC histology, with a relatively high risk of neoplastic changes. Furthermore, the aberrant expressions of p53 and p16 in BE-indefinite dysplasia (IND) progressor cohorts predicted the risk of progression. Conclusions: Assessing the biomarkers would be a suitable adjunct to accurate BE histology diagnoses and improve the accuracy of BE-dysplasia grading, thus reducing interobserver variability, particularly of LGD and risk prediction.
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Affiliation(s)
- Young Choi
- Department of Pathology, Yale School of Medicine, 434 Pine Grove Lane, Hartsdale, NY 10530, USA
| | - Andrew Bedford
- Department of Internal Medicine, Yale School of Medicine, Bridgeport Hospital, 267 Grant St., Bridgeport, CT 06610, USA;
| | - Simcha Pollack
- Department of Business Analytics Statistics, St. John’s University Tobin College of Business, Queens, NY 11423, USA;
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9
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Deboever N, Jones CM, Yamashita K, Ajani JA, Hofstetter WL. Advances in diagnosis and management of cancer of the esophagus. BMJ 2024; 385:e074962. [PMID: 38830686 DOI: 10.1136/bmj-2023-074962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Esophageal cancer is the seventh most common malignancy worldwide, with over 470 000 new cases diagnosed each year. Two distinct histological subtypes predominate, and should be considered biologically separate disease entities.1 These subtypes are esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC). Outcomes remain poor regardless of subtype, with most patients presenting with late stage disease.2 Novel strategies to improve early detection of the respective precursor lesions, squamous dysplasia, and Barrett's esophagus offer the potential to improve outcomes. The introduction of a limited number of biologic agents, as well as immune checkpoint inhibitors, is resulting in improvements in the systemic treatment of locally advanced and metastatic esophageal cancer. These developments, coupled with improvements in minimally invasive surgical and endoscopic treatment approaches, as well as adaptive and precision radiotherapy technologies, offer the potential to improve outcomes still further. This review summarizes the latest advances in the diagnosis and management of esophageal cancer, and the developments in understanding of the biology of this disease.
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Affiliation(s)
- Nathaniel Deboever
- Department of Thoracic and Cardiovascular Surgery, MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher M Jones
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kohei Yamashita
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, MD Anderson Cancer Center, Houston, TX, USA
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10
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Stachler MD, Jin RU. Molecular Pathology of Gastroesophageal Cancer. Clin Lab Med 2024; 44:239-254. [PMID: 38821643 DOI: 10.1016/j.cll.2023.08.005] [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: 06/02/2024]
Abstract
Upper gastroesophageal carcinomas consist of cancers arising from the esophagus and stomach. Squamous cell carcinomas and adenocarcinomas are seen in the esophagus and despite arising from the same organ have different biology. Gastric adenocarcinomas are categorized into 4 molecular subtypes: high Epstein-Barr virus load, microsatellite unstable cancers, chromosomal unstable (CIN) cancers, and genomically stable cancers. Genomically stable gastric cancers correlate highly with histologically defined diffuse-type cancers. Esophageal carcinomas and CIN gastric cancers often are driven by high-level amplifications of oncogenes and contain a high degree of intratumoral heterogeneity. Targeted therapeutics is an active area of research for gastroesophageal cancers.
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Affiliation(s)
- Matthew D Stachler
- Department of Pathology, University of California San Francisco, 513 Parnassus Avenue HSW450B, San Francisco, CA 94143, USA.
| | - Ramon U Jin
- Section of Hematology/Oncology, Department of Medicine, Baylor College of Medicine, 7200 Cambridge Street, Suite 7B, MS: BCM904, Houston, TX 77030, USA
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11
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Jalali P, Yaghoobi A, Rezaee M, Zabihi MR, Piroozkhah M, Aliyari S, Salehi Z. Decoding common genetic alterations between Barrett's esophagus and esophageal adenocarcinoma: A bioinformatics analysis. Heliyon 2024; 10:e31194. [PMID: 38803922 PMCID: PMC11128929 DOI: 10.1016/j.heliyon.2024.e31194] [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: 11/08/2023] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Background Esophageal adenocarcinoma (EAC) is a common cancer with a poor prognosis in advanced stages. Therefore, early EAC diagnosis and treatment have gained attention in recent decades. It has been found that various pathological changes, particularly Barrett's Esophagus (BE), can occur in the esophageal tissue before the development of EAC. In this study, we aimed to identify the molecular contributor in BE to EAC progression by detecting the essential regulatory genes that are differentially expressed in both BE and EAC. Materials and methods We conducted a comprehensive bioinformatics analysis to detect BE and EAC-associated genes. The common differentially expressed genes (DEGs) and common single nucleotide polymorphisms (SNPs) were detected using the GEO and DisGeNET databases, respectively. Then, hub genes and the top modules within the protein-protein interaction network were identified. Moreover, the co-expression network of the top module by the HIPPIE database was constructed. Additionally, the gene regulatory network was constructed based on miRNAs and circRNAs. Lastly, we inspected the DGIdb database for possible interacted drugs. Results Our microarray dataset analysis identified 92 common DEGs between BE and EAC with significant enrichment in skin and epidermis development genes. The study also identified 22 common SNPs between BE and EAC. The top module of PPI network analysis included SCEL, KRT6A, SPRR1A, SPRR1B, SPRR3, PPL, SPRR2B, EVPL, and CSTA. We constructed a ceRNA network involving three specific mRNAs, 23 miRNAs, and 101 selected circRNAs. According to the results from the DGIdb database, TD101 was found to interact with the KRT6A gene. Conclusion The present study provides novel potential candidate genes that may be involved in the molecular association between Esophageal adenocarcinoma and Barrett's Esophagus, resulting in developing the diagnostic tools and therapeutic targets to prevent progression of BE to EAC.
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Affiliation(s)
- Pooya Jalali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Yaghoobi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Malihe Rezaee
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zabihi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Moein Piroozkhah
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahram Aliyari
- Division of Applied Bioinformatics, German Cancer Research Center DKFZ Heidelberg, Iran
| | - Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran
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12
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Zhu Z, Dong S, Qin S, Gu K, Zhou Y. ANOS1 accelerates the progression of esophageal cancer identified by multi-omic approaches. Am J Cancer Res 2024; 14:2343-2370. [PMID: 38859828 PMCID: PMC11162658 DOI: 10.62347/spcp3536] [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: 12/19/2023] [Accepted: 04/27/2024] [Indexed: 06/12/2024] Open
Abstract
To assess the role of ANOS1 in esophageal cancer (ESCA) progression, multi-omic analysis and experimental validation were employed. It was revealed that ANOS1 expression is significantly enhanced in ESCA patients and cell lines. The expression level of ANOS1 in ESCA patients can distinguish the malignancy from normal tissue with an area under curve (AUC) >0.75. Moreover, increased expression of ANOS1 is associated with advanced T stage and worse disease-free survival of ESCA patients. Therefore, a clinically applicable nomogram with ANOS1 was established with strong predictive power. Furthermore, high expression of ANOS1 in ESCA is correlated with (i) the enrichment of epithelial-mesenchymal transition by gene set enrichment analysis, (ii) the involvement in hypoxia, angiogenesis, WNT signaling pathway, and TGFβ signaling pathway by gene set variation analysis, (iii) the presence of the small insertion and deletion mutational signature ID9, associated with chromothripsis, in the single-nucleotide polymorphism analysis, (iv) the amplification of 11q13.3 in the copy number variants analysis, (v) the enrichment of cancer-associated fibroblasts and mesenchymal stromal cells in the tumor microenvironment. All the results from multi-omic analysis indicate that ANOS1 plays a pivotal role in accelerating the progression of ESCA. Results from in vivo and in vitro experiments show that the knockdown of ANOS1 hampers the proliferation of ESCA cells, further validating the oncogenic role of ANOS1 in ESCA. Additionally, potential chemotherapeutics with sensitivity were identified in the high-ANOS1 group. In conclusion, ANOS1 accelerates the progression of ESCA.
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Affiliation(s)
- Zuoquan Zhu
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Shikun Dong
- Department of Otorhinolaryngology, Zhongda Hospital, Southeast UniversityNanjing 210009, Jiangsu, China
| | - Shaolei Qin
- Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Ke Gu
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Yanjun Zhou
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
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13
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Lim H, Gingras MC, Zhao J, Byun J, Castro PD, Tsavachidis S, Hu J, Doddapaneni H, Han Y, Muzny DM, Gibbs RA, Amos CI, Thrift AP. Somatic mutations of esophageal adenocarcinoma: a comparison between Black and White patients. Sci Rep 2024; 14:8988. [PMID: 38637560 PMCID: PMC11026501 DOI: 10.1038/s41598-024-59257-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Esophageal adenocarcinoma is the most common histological subtype of esophageal cancer in Western countries and shows poor prognosis with rapid growth. EAC is characterized by a strong male predominance and racial disparity. EAC is up to fivefold more common among Whites than Blacks, yet Black patients with EAC have poorer survival rates. The racial disparity remains largely unknown, and there is limited knowledge of mutations in EAC regarding racial disparities. We used whole-exome sequencing to show somatic mutation profiles derived from tumor samples from 18 EAC male patients. We identified three molecular subgroups based on the pre-defined esophageal cancer-specific mutational signatures. Group 1 is associated with age and NTHL1 deficiency-related signatures. Group 2 occurs primarily in Black patients and is associated with signatures related to DNA damage from oxidative stress and NTHL1 deficiency-related signatures. Group 3 is associated with defective homologous recombination-based DNA often caused by BRCA mutation in White patients. We observed significantly mutated race related genes (LCE2B in Black, SDR39U1 in White) were (q-value < 0.1). Our findings underscore the possibility of distinct molecular mutation patterns in EAC among different races. Further studies are needed to validate our findings, which could contribute to precision medicine in EAC.
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Affiliation(s)
- Hyeyeun Lim
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jing Zhao
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Patricia D Castro
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Spiridon Tsavachidis
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, MS: BCM451, Suite 100D, Houston, TX, 77030, USA.
| | - Aaron P Thrift
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, MS: BCM307, Room 621D, Houston, TX, 77030, USA.
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14
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Papadakos SP, Argyrou A, Lekakis V, Arvanitakis K, Kalisperati P, Stergiou IE, Konstantinidis I, Schizas D, Koufakis T, Germanidis G, Theocharis S. Metformin in Esophageal Carcinoma: Exploring Molecular Mechanisms and Therapeutic Insights. Int J Mol Sci 2024; 25:2978. [PMID: 38474224 DOI: 10.3390/ijms25052978] [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: 02/10/2024] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024] Open
Abstract
Esophageal cancer (EC) remains a formidable malignancy with limited treatment options and high mortality rates, necessitating the exploration of innovative therapeutic avenues. Through a systematic analysis of a multitude of studies, we synthesize the diverse findings related to metformin's influence on EC. This review comprehensively elucidates the intricate metabolic pathways and molecular mechanisms through which metformin may exert its anti-cancer effects. Key focus areas include its impact on insulin signaling, AMP-activated protein kinase (AMPK) activation, and the mTOR pathway, which collectively contribute to its role in mitigating esophageal cancer progression. This review critically examines the body of clinical and preclinical evidence surrounding the potential role of metformin, a widely prescribed anti-diabetic medication, in EC management. Our examination extends to the modulation of inflammation, oxidative stress and angiogenesis, revealing metformin's potential as a metabolic intervention in esophageal cancer pathogenesis. By consolidating epidemiological and clinical data, we assess the evidence that supports metformin's candidacy as an adjuvant therapy for esophageal cancer. By summarizing clinical and preclinical findings, our review aims to enhance our understanding of metformin's role in EC management, potentially improving patient care and outcomes.
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Affiliation(s)
- Stavros P Papadakos
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, Goudi, 11527 Athens, Greece
| | - Alexandra Argyrou
- Academic Department of Gastroenterology, Laikon General Hospital, Athens University Medical School, 11527 Athens, Greece
| | - Vasileios Lekakis
- Academic Department of Gastroenterology, Laikon General Hospital, Athens University Medical School, 11527 Athens, Greece
| | - Konstantinos Arvanitakis
- First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
- Basic and Translational Research Unit (BTRU), Special Unit for Biomedical Research and Education (BRESU), Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Polyxeni Kalisperati
- Pathophysiology Department, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Ioanna E Stergiou
- Pathophysiology Department, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | - Dimitrios Schizas
- First Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Theocharis Koufakis
- Second Propaedeutic Department of Internal Medicine, General Hospital "Hippokration", Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
| | - Georgios Germanidis
- First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
- Basic and Translational Research Unit (BTRU), Special Unit for Biomedical Research and Education (BRESU), Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, Goudi, 11527 Athens, Greece
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15
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Cheng YQ, Wang GF, Zhou XL, Lin M, Zhang XW, Huang Q. Early adenocarcinoma mixed with a neuroendocrine carcinoma component arising in the gastroesophageal junction: A case report. World J Gastrointest Oncol 2024; 16:563-570. [PMID: 38425401 PMCID: PMC10900165 DOI: 10.4251/wjgo.v16.i2.563] [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] [Received: 11/07/2023] [Revised: 12/09/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Early adenocarcinoma mixed with a neuroendocrine carcinoma (NEC) component arising in the gastroesophageal junctional (GEJ) region is rare and even rarer in young patients. Here, we report such a case in a 29-year-old Chinese man. CASE SUMMARY This patient presented to our hospital with a 3-mo history of dysphagia and regurgitation. Upper endoscopy revealed an elevated nodule in the distal esophagus 1.6 cm above the GEJ line, without Barrett's esophagus or involvement of the gastric cardia. The nodule was completely resected by endoscopic submucosal dissection (ESD). Pathological examination confirmed diagnosis of intramucosal adenocarcinoma mixed with an NEC component, measuring 1.5 cm. Immunohistochemically, both adenocarcinoma and NEC components were positive for P53 with a Ki67 index of 90%; NEC was positive for synaptophysin and chromogranin. Next-generation sequencing of 196 genes demonstrated a novel germline mutation of the ERCC3 gene in the DNA repair pathway and a germline mutation of the RNF43 gene, a common gastric cancer driver gene, in addition to pathogenic somatic mutations in P53 and CHEK2 genes. The patient was alive without evidence of the disease 36 mo after ESD. CONCLUSION Early adenocarcinoma with an NEC component arising in the distal esophageal side of the GEJ region showed evidence of gastric origin.
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Affiliation(s)
- Yu-Qing Cheng
- Department of Pathology, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213164, Jiangsu Province, China
| | - Geng-Fang Wang
- Department of Pathology, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213164, Jiangsu Province, China
| | - Xiao-Li Zhou
- Department of Pathology, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213164, Jiangsu Province, China
| | - Min Lin
- Gastroenterology Center, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213164, Jiangsu Province, China
| | - Xin-Wen Zhang
- Department of Pathology, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213164, Jiangsu Province, China
- Graduate School, Dalian Medical University, Dalian 116044, Liaoning Province, China
| | - Qin Huang
- Department of Pathology, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213164, Jiangsu Province, China
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, United States
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16
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Song XQ, Chen BB, Jin YM, Wang CY. DNMT1-mediated epigenetic suppression of FBXO32 expression promoting cyclin dependent kinase 9 (CDK9) survival and esophageal cancer cell growth. Cell Cycle 2024; 23:262-278. [PMID: 38597826 PMCID: PMC11057636 DOI: 10.1080/15384101.2024.2309022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/25/2023] [Indexed: 04/11/2024] Open
Abstract
Esophageal cancer (EC) is a common and serious form of cancer, and while DNA methyltransferase-1 (DNMT1) promotes DNA methylation and carcinogenesis, the role of F-box protein 32 (FBXO32) in EC and its regulation by DNMT1-mediated methylation is still unclear. FBXO32 expression was examined in EC cells with high DNMT1 expression using GSE163735 dataset. RT-qPCR assessed FBXO32 expression in normal and EC cells, and impact of higher FBXO32 expression on cell proliferation, migration, and invasion was evaluated, along with EMT-related proteins. The xenograft model established by injecting EC cells transfected with FBXO32 was used to evaluate tumor growth, apoptosis, and tumor cells proliferation and metastasis. Chromatin immunoprecipitation (ChIP) assay was employed to study the interaction between DNMT1 and FBXO32. HitPredict, co-immunoprecipitation (Co-IP), and Glutathione-S-transferase (GST) pulldown assay analyzed the interaction between FBXO32 and cyclin dependent kinase 9 (CDK9). Finally, the ubiquitination assay identified CDK9 ubiquitination, and its half-life was measured using cycloheximide and confirmed through western blotting. DNMT1 negatively correlated with FBXO32 expression in esophageal cells. High FBXO32 expression was associated with better overall survival in patients. Knockdown of DNMT1 in EC cells increased FBXO32 expression and suppressed malignant phenotypes. FBXO32 repressed EC tumor growth and metastasis in mice. Enrichment of DNMT1 in FBXO32 promoter region led to increased DNA methylation and reduced transcription. Mechanistically, FBXO32 degraded CDK9 through promoting its ubiquitination.
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Affiliation(s)
- Xian-Qiang Song
- Department of Radiotherapy, Qinhuai Medical District, General Hospital of Eastern Theater Command, Nanjing, PR China
| | - Bin-Bin Chen
- Departments of Laboratory Medicine, Qinhuai Medical District, General Hospital of Eastern Theater Command, Nanjing, PR China
| | - Yong-Mei Jin
- Department of Cardiothoracic Surgery, Qinhuai Medical District, General Hospital of Eastern Theater Command, Nanjing, PR China
| | - Chang-Yong Wang
- Department of Cardiothoracic Surgery, Qinhuai Medical District, General Hospital of Eastern Theater Command, Nanjing, PR China
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17
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Greathouse KL, Stone JK, Vargas AJ, Choudhury A, Padgett RN, White JR, Jung A, Harris CC. Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue. Sci Rep 2024; 14:2574. [PMID: 38296990 PMCID: PMC10831118 DOI: 10.1038/s41598-023-48862-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/30/2023] [Indexed: 02/02/2024] Open
Abstract
Esophageal carcinoma (ESCA) is a leading cause of cancer-related death worldwide, and certain oral and intestinal pathogens have been associated with cancer development and progression. We asked if esophageal microbiomes had shared alterations that could provide novel biomarkers for ESCA risk. We extracted DNA from tumor and non-tumor tissue of 212 patients in the NCI-MD case control study and sequenced the 16S rRNA gene (V3-4), with TCGA ESCA RNA-seq (n = 172) and WGS (n = 123) non-human reads used as validation. We identified four taxa, Campylobacter, Prevotella, Streptococcus, and Fusobacterium as highly enriched in esophageal cancer across all cohorts. Using SparCC, we discovered that Fusobacterium and Prevotella were also co-enriched across all cohorts. We then analyzed immune cell infiltration to determine if these dysbiotic taxa were associated with immune signatures. Using xCell to obtain predicted immune infiltrates, we identified a depletion of megakaryocyte-erythroid progenitor (MEP) cells in tumors with presence of any of the four taxa, along with enrichment of platelets in tumors with Campylobactor or Fusobacterium. Taken together, our results suggest that intratumoral presence of these co-occurring bacterial genera may confer tumor promoting immune alterations that allow disease progression in esophageal cancer.
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Affiliation(s)
- K L Greathouse
- Department of Biology, Baylor University, Waco, TX, USA.
- Nutrition Division, Human Sciences and Design, Baylor University, Waco, TX, USA.
| | - J K Stone
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - A J Vargas
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - A Choudhury
- Department of Biology, Baylor University, Waco, TX, USA
| | - R N Padgett
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - J R White
- Resphera Biosciences, LLC, Baltimore, MD, USA
| | - A Jung
- Department of Biology, Baylor University, Waco, TX, USA
| | - C C Harris
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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18
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Bozzarelli I, Orsini A, Isidori F, Mastracci L, Malvi D, Lugaresi M, Fittipaldi S, Gozzellino L, Astolfi A, Räsänen J, D’Errico A, Rosati R, Fiocca R, Seri M, Krishnadath KK, Bonora E, Mattioli S. miRNA-221 and miRNA-483-3p Dysregulation in Esophageal Adenocarcinoma. Cancers (Basel) 2024; 16:591. [PMID: 38339342 PMCID: PMC10854562 DOI: 10.3390/cancers16030591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Alterations in microRNA (miRNA) expression have been reported in different cancers. We assessed the expression of 754 oncology-related miRNAs in esophageal adenocarcinoma (EAC) samples and evaluated their correlations with clinical parameters. We found that miR-221 and 483-3p were consistently upregulated in EAC patients vs. controls (Wilcoxon signed-rank test: miR-221 p < 0.0001; miR-483-3p p < 0.0001). Kaplan-Meier analysis showed worse cancer-related survival among all EAC patients expressing high miR-221 or miR-483-3p levels (log-rank p = 0.0025 and p = 0.0235, respectively). Higher miR-221 or miR-483-3p levels also correlated with advanced tumor stages (Mann-Whitney p = 0.0195 and p = 0.0085, respectively), and overexpression of miR-221 was associated with worse survival in low-risk EAC patients. Moreover, a significantly worse outcome was associated with the combined overexpression of miR-221 and miR-483-3p (log-rank p = 0.0410). To identify target genes affected by miRNA overexpression, we transfected the corresponding mimic RNA (miRVANA) for either miR-221 or miR-483-3p in a well-characterized esophageal adenocarcinoma cell line (OE19) and performed RNA-seq analysis. In the miRNA-overexpressing cells, we discovered a convergent dysregulation of genes linked to apoptosis, ATP synthesis, angiogenesis, and cancer progression, including a long non-coding RNA associated with oncogenesis, i.e., MALAT1. In conclusion, dysregulated miRNA expression, especially overexpression of miR-221 and 483-3p, was found in EAC samples. These alterations were connected with a lower cancer-specific patient survival, suggesting that these miRNAs could be useful for patient stratification and prognosis.
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Affiliation(s)
- Isotta Bozzarelli
- Gastrointestinal Genetics Lab, CIC bioGUNE—BRTA, 48160 Derio, Spain;
| | - Arianna Orsini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, via Massarenti 9, 40138 Bologna, Italy (L.G.); (M.S.)
| | - Federica Isidori
- Dipartimento di Genetica Medica, IRCCS Azienda Ospedaliero–Universitaria di Bologna, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; (F.I.); (D.M.); (M.L.); (S.F.); (A.D.)
| | - Luca Mastracci
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16100 Genoa, Italy; (L.M.); (R.F.)
- IRCCS Ospedale Policlinico San Martino, 16100 Genoa, Italy
| | - Deborah Malvi
- Dipartimento di Genetica Medica, IRCCS Azienda Ospedaliero–Universitaria di Bologna, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; (F.I.); (D.M.); (M.L.); (S.F.); (A.D.)
- Institute of Oncology and Transplant Pathology, University of Bologna, 40126 Bologna, Italy
| | - Marialuisa Lugaresi
- Dipartimento di Genetica Medica, IRCCS Azienda Ospedaliero–Universitaria di Bologna, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; (F.I.); (D.M.); (M.L.); (S.F.); (A.D.)
| | - Silvia Fittipaldi
- Dipartimento di Genetica Medica, IRCCS Azienda Ospedaliero–Universitaria di Bologna, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; (F.I.); (D.M.); (M.L.); (S.F.); (A.D.)
| | - Livia Gozzellino
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, via Massarenti 9, 40138 Bologna, Italy (L.G.); (M.S.)
| | - Annalisa Astolfi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, via Massarenti 9, 40138 Bologna, Italy (L.G.); (M.S.)
| | - Jari Räsänen
- Department of Cardiothoracic Surgery, University of Helsinki and Helsinki University Hospital, 00100 Helsinki, Finland;
| | - Antonia D’Errico
- Dipartimento di Genetica Medica, IRCCS Azienda Ospedaliero–Universitaria di Bologna, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; (F.I.); (D.M.); (M.L.); (S.F.); (A.D.)
- Institute of Oncology and Transplant Pathology, University of Bologna, 40126 Bologna, Italy
| | - Riccardo Rosati
- Department of Gastrointestinal Surgery, San Raffaele Hospital, Vita–Salute San Raffaele University, 20132 Milan, Italy;
| | - Roberto Fiocca
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16100 Genoa, Italy; (L.M.); (R.F.)
- IRCCS Ospedale Policlinico San Martino, 16100 Genoa, Italy
| | - Marco Seri
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, via Massarenti 9, 40138 Bologna, Italy (L.G.); (M.S.)
- Dipartimento di Genetica Medica, IRCCS Azienda Ospedaliero–Universitaria di Bologna, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; (F.I.); (D.M.); (M.L.); (S.F.); (A.D.)
| | - Kausilia K. Krishnadath
- Laboratory of Experimental Medicine and Pediatrics (LEMP), Department of Gastroenterology and Hepatology, University Hospital Antwerp, University of Antwerp, 2180 Antwerp, Belgium;
| | - Elena Bonora
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, via Massarenti 9, 40138 Bologna, Italy (L.G.); (M.S.)
- Dipartimento di Genetica Medica, IRCCS Azienda Ospedaliero–Universitaria di Bologna, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; (F.I.); (D.M.); (M.L.); (S.F.); (A.D.)
| | - Sandro Mattioli
- Division of Thoracic Surgery, Maria Cecilia Hospital, 48010 Cotignola, Italy;
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Sun J, Sepulveda JL, Komissarova EV, Hills C, Seckar TD, LeFevre NM, Simonyan H, Young C, Su G, Del Portillo A, Wang TC, Sepulveda AR. CDKN2A-p16 Deletion and Activated KRAS G12D Drive Barrett's-Like Gland Hyperplasia-Metaplasia and Synergize in the Development of Dysplasia Precancer Lesions. Cell Mol Gastroenterol Hepatol 2024; 17:769-784. [PMID: 38296052 PMCID: PMC10966774 DOI: 10.1016/j.jcmgh.2024.01.014] [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: 05/01/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND & AIMS Barrett's esophagus is the precursor of esophageal dysplasia and esophageal adenocarcinoma. CDKN2A-p16 deletions were reported in 34%-74% of patients with Barrett's esophagus who progressed to dysplasia and esophageal adenocarcinoma, suggesting that p16 loss may drive neoplastic progression. KRAS activation frequently occurs in esophageal adenocarcinoma and precancer lesions. LGR5+ stem cells in the squamocolumnar-junction (SCJ) of mouse stomach contribute as Barrett's esophagus progenitors. We aimed to determine the functional effects of p16 loss and KRAS activation in Barrett's-like metaplasia and dysplasia development. METHODS We established mouse models with conditional knockout of CDKN2A-p16 (p16KO) and/or activated KRASG12D expression targeting SCJ LGR5+ cells in interleukin 1b transgenic mice and characterized histologic alterations (mucous-gland hyperplasia/metaplasia, inflammation, and dysplasia) in mouse SCJ. Gene expression was determined by microarray, RNA sequencing, and immunohistochemistry of SCJ tissues and cultured 3-dimensional organoids. RESULTS p16KO mice exhibited increased mucous-gland hyperplasia/metaplasia versus control mice (P = .0051). Combined p16KO+KRASG12D resulted in more frequent dysplasia and higher dysplasia scores (P = .0036), with 82% of p16KO+KRASG12D mice developing high-grade dysplasia. SCJ transcriptome analysis showed several activated pathways in p16KO versus control mice (apoptosis, tumor necrosis factor-α/nuclear factor-kB, proteasome degradation, p53 signaling, MAPK, KRAS, and G1-to-S transition). CONCLUSIONS p16 deletion in LGR5+ cell precursors triggers increased SCJ mucous-gland hyperplasia/metaplasia. KRASG12D synergizes with p16 deletion resulting in higher grades of SCJ glandular dysplasia, mimicking Barrett's high-grade dysplasia. These genetically modified mouse models establish a functional role of p16 and activated KRAS in the progression of Barrett's-like lesions to dysplasia in mice, representing an in vivo model of esophageal adenocarcinoma precancer. Derived 3-dimensional organoid models further provide in vitro modeling opportunities of esophageal precancer stages.
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Affiliation(s)
- Jing Sun
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Jorge L Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Elena V Komissarova
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Caitlin Hills
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Tyler D Seckar
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Narine M LeFevre
- Department of Pharmacology & Physiology, George Washington University, School of Medicine and Health Sciences, Washington, DC
| | - Hayk Simonyan
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Colin Young
- Department of Pharmacology & Physiology, George Washington University, School of Medicine and Health Sciences, Washington, DC
| | - Gloria Su
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Timothy C Wang
- Division of Digestive and Liver diseases, Department of Medicine, Columbia University, New York, New York
| | - Antonia R Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC.
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20
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Sanjai C, Hakkimane SS, Guru BR, Gaonkar SL. A comprehensive review on anticancer evaluation techniques. Bioorg Chem 2024; 142:106973. [PMID: 37984104 DOI: 10.1016/j.bioorg.2023.106973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The development of effective anticancer strategies and the improvement of our understanding of cancer need analytical tools. Utilizing a variety of analytical approaches while investigating anti-cancer medicines gives us a thorough understanding of the traits and mechanisms concerned to cancer cells, which enables us to develop potent treatments to combat them. The importance of anticancer research may be attributed to various analytical techniques that contributes to the identification of therapeutic targets and the assessment of medication efficacy, which are crucial things in expanding our understanding of cancer biology. The study looks at methods that are often used in cancer research, including cell viability assays, clonogenic assay, flow cytometry, 2D electrophoresis, microarray, immunofluorescence, western blot caspase activation assay, bioinformatics, etc. The fundamentals, applications, and how each technique analytical advances our understanding of cancer are briefly reviewed.
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Affiliation(s)
- Chetana Sanjai
- Department of Biotechnology, Manipal Institute of Technology Bengaluru, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sushruta S Hakkimane
- Department of Biotechnology, Manipal Institute of Technology Bengaluru, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Bharath Raja Guru
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Santosh L Gaonkar
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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21
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Saikia S, Postwala H, Athilingam VP, Anandan A, Padma VV, Kalita PP, Chorawala M, Prajapati B. Single Nucleotide Polymorphisms (SNPs) in the Shadows: Uncovering their Function in Non-Coding Region of Esophageal Cancer. Curr Pharm Biotechnol 2024; 25:1915-1938. [PMID: 38310451 DOI: 10.2174/0113892010265004231116092802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 02/05/2024]
Abstract
Esophageal cancer is a complex disease influenced by genetic and environmental factors. Single nucleotide polymorphisms (SNPs) in non-coding regions of the genome have emerged as crucial contributors to esophageal cancer susceptibility. This review provides a comprehensive overview of the role of SNPs in non-coding regions and their association with esophageal cancer. The accumulation of SNPs in the genome has been implicated in esophageal cancer risk. Various studies have identified specific locations in the genome where SNPs are more likely to occur, suggesting a location-specific response. Chromatin conformational studies have shed light on the localization of SNPs and their impact on gene transcription, posttranscriptional modifications, gene expression regulation, and histone modification. Furthermore, miRNA-related SNPs have been found to play a significant role in esophageal squamous cell carcinoma (ESCC). These SNPs can affect miRNA binding sites, thereby altering target gene regulation and contributing to ESCC development. Additionally, the risk of ESCC has been linked to base excision repair, suggesting that SNPs in this pathway may influence disease susceptibility. Somatic DNA segment alterations and modified expression quantitative trait loci (eQTL) have also been associated with ESCC. These alterations can lead to disrupted gene expression and cellular processes, ultimately contributing to cancer development and progression. Moreover, SNPs have been found to be associated with the long non-coding RNA HOTAIR, which plays a crucial role in ESCC pathogenesis. This review concludes with a discussion of the current and future perspectives in the field of SNPs in non-coding regions and their relevance to esophageal cancer. Understanding the functional implications of these SNPs may lead to the identification of novel therapeutic targets and the development of personalized approaches for esophageal cancer prevention and treatment.
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Affiliation(s)
- Surovi Saikia
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Humzah Postwala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad, India
| | - Vishnu Prabhu Athilingam
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Aparna Anandan
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - V Vijaya Padma
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Partha P Kalita
- Program of Biotechnology, Assam Down Town University, Panikhaiti, Guwahati 781026, Assam, India
| | - Mehul Chorawala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad, India
| | - Bhupendra Prajapati
- Department of Pharmaceutics and Pharmaceutical Technology, Shree. S. K. Patel College of Pharmaceutical Education and Research, Ganpat University, Kherva, Gujarat, India
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22
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Al-Nattah S, Matkovic E, Schwalbe M, Matkowskyj KA. Pathologic Features of Esophageal and Gastric Malignancies. Cancer Treat Res 2024; 192:19-48. [PMID: 39212914 DOI: 10.1007/978-3-031-61238-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Esophageal cancer is the eighth most common cancer globally, affecting approximately 570,000 people worldwide and currently ranking sixth among cancer-related mortality (Uhlenhopp et al. in, Clin J Gastroenterol 13:1010-1021, 2020). The prognosis is poor as many patients present with locally incurable or metastatic disease. In spite of advancements in treatment, the overall 5-year survival rates are in the realm of 10% whereas the 5-year post-esophagectomy survival rates are in the realm of 15-40% [2]. The incidence rates vary dramatically worldwide, which can be attributed to demographic and socioeconomic factors. Although the vast majority of esophageal neoplasms arise from the epithelial layer and include squamous cell carcinoma (SCC) and adenocarcinoma (AC), a subset of neuroendocrine and soft tissue tumors can also occur in the esophagus. Several tasks are presented to the surgical pathologist when dealing with esophageal carcinoma that include rendering a diagnosis, classifying the histological type, and assessing prognostic factors. This narrative review aims to evaluate current literature on various esophageal neoplasms and highlight pathological factors that impact clinical decision making and prognosis.
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Affiliation(s)
- Sanaa Al-Nattah
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Quest Diagnostics, Las Vegas, NV, USA
| | - Eduard Matkovic
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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23
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Zhang Y, Weh KM, Tripp BA, Clarke JL, Howard CL, Sunilkumar S, Howell AB, Kresty LA. Cranberry Proanthocyanidins Mitigate Reflux-Induced Transporter Dysregulation in an Esophageal Adenocarcinoma Model. Pharmaceuticals (Basel) 2023; 16:1697. [PMID: 38139823 PMCID: PMC10747310 DOI: 10.3390/ph16121697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
We recently reported that cranberry proanthocyanidins (C-PACs) inhibit esophageal adenocarcinoma (EAC) by 83% through reversing reflux-induced bacterial, inflammatory and immune-implicated proteins and genes as well as reducing esophageal bile acids, which drive EAC progression. This study investigated whether C-PACs' mitigation of bile reflux-induced transporter dysregulation mechanistically contributes to EAC prevention. RNA was isolated from water-, C-PAC- and reflux-exposed rat esophagi with and without C-PAC treatment. Differential gene expression was determined by means of RNA sequencing and RT-PCR, followed by protein assessments. The literature, coupled with the publicly available Gene Expression Omnibus dataset GSE26886, was used to assess transporter expression levels in normal and EAC patient biopsies for translational relevance. Significant changes in ATP-binding cassette (ABC) transporters implicated in therapeutic resistance in humans (i.e., Abcb1, Abcb4, Abcc1, Abcc3, Abcc4, Abcc6 and Abcc10) and the transport of drugs, xenobiotics, lipids, and bile were altered in the reflux model with C-PACs' mitigating changes. Additionally, C-PACs restored reflux-induced changes in solute carrier (SLC), aquaporin, proton and cation transporters (i.e., Slc2a1, Slc7a11, Slc9a1, Slco2a1 and Atp6v0c). This research supports the suggestion that transporters merit investigation not only for their roles in metabolism and therapeutic resistance, but as targets for cancer prevention and targeting preventive agents in combination with chemotherapeutics.
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Affiliation(s)
- Yun Zhang
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
| | - Katherine M. Weh
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
| | - Bridget A. Tripp
- Bioinformatics Core Research Facility, Center for Biotechnology, University of Nebraska—Lincoln, N300 Beadle Center, Lincoln, NE 68588, USA;
| | - Jennifer L. Clarke
- Department of Statistics and Department of Food Science Technology, Quantitative Life Sciences Initiative, University of Nebraska—Lincoln, 253 Food Innovation Center, Lincoln, NE 68583, USA;
| | - Connor L. Howard
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
| | - Shruthi Sunilkumar
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
| | - Amy B. Howell
- Marucci Center for Blueberry and Cranberry Research, Rutgers University, 125A Lake Oswego Road, Chatsworth, NJ 08019, USA;
| | - Laura A. Kresty
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
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Li S, Hoefnagel SJM, Krishnadath KK. Molecular Biology and Clinical Management of Esophageal Adenocarcinoma. Cancers (Basel) 2023; 15:5410. [PMID: 38001670 PMCID: PMC10670638 DOI: 10.3390/cancers15225410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) is a highly lethal malignancy. Due to its rising incidence, EAC has become a severe health challenge in Western countries. Current treatment strategies are mainly chosen based on disease stage and clinical features, whereas the biological background is hardly considered. In this study, we performed a comprehensive review of existing studies and discussed how etiology, genetics and epigenetic characteristics, together with the tumor microenvironment, contribute to the malignant behavior and dismal prognosis of EAC. During the development of EAC, several intestinal-type proteins and signaling cascades are induced. The anti-inflammatory and immunosuppressive microenvironment is associated with poor survival. The accumulation of somatic mutations at the early phase and chromosomal structural rearrangements at relatively later time points contribute to the dynamic and heterogeneous genetic landscape of EAC. EAC is also characterized by frequent DNA methylation and dysregulation of microRNAs. We summarize the findings of dysregulations of specific cytokines, chemokines and immune cells in the tumor microenvironment and conclude that DNA methylation and microRNAs vary with each different phase of BE, LGD, HGD, early EAC and invasive EAC. Furthermore, we discuss the suitability of the currently employed therapies in the clinic and possible new therapies in the future. The development of targeted and immune therapies has been hampered by the heterogeneous genetic characteristics of EAC. In view of this, the up-to-date knowledge revealed by this work is absolutely important for future EAC studies and the discovery of new therapeutics.
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Affiliation(s)
- Shulin Li
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | | | - Kausilia Krishnawatie Krishnadath
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, 2650 Edegem, Belgium
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, 2000 Antwerpen, Belgium
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25
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Zhang L, Zheng Y, Chien W, Ziman B, Billet S, Koeffler HP, Lin DC, Bhowmick NA. ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma. Cancers (Basel) 2023; 15:5377. [PMID: 38001638 PMCID: PMC10670331 DOI: 10.3390/cancers15225377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
ARID1A, a member of the chromatin remodeling SWI/SNF complex, is frequently lost in many cancer types, including esophageal adenocarcinoma (EAC). Here, we study the impact of ARID1A deficiency on the anti-tumor immune response in EAC. We find that EAC tumors with ARID1A mutations are associated with enhanced tumor-infiltrating CD8+ T cell levels. ARID1A-deficient EAC cells exhibit heightened IFN response signaling and promote CD8+ T cell recruitment and cytolytic activity. Moreover, we demonstrate that ARID1A regulates fatty acid metabolism genes in EAC, showing that fatty acid metabolism could also regulate CD8+ T cell recruitment and CD8+ T cell cytolytic activity in EAC cells. These results suggest that ARID1A deficiency shapes both tumor immunity and lipid metabolism in EAC, with significant implications for immune checkpoint blockade therapy in EAC.
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Affiliation(s)
- Le Zhang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - Wenwen Chien
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - Benjamin Ziman
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
- Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Sandrine Billet
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - H. Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
- Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Neil A. Bhowmick
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
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26
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Yasar HA. Genomic Variations in Esophageal Squamous Cell Carcinoma and Esophageal Adenocarcinoma. Cureus 2023; 15:e45689. [PMID: 37745740 PMCID: PMC10512880 DOI: 10.7759/cureus.45689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2023] [Indexed: 09/26/2023] Open
Abstract
Objectives Using a comprehensive dataset derived from the American Association for Cancer Research (AACR) Project Genomics, Evidence, Neoplasia, Information, and Exchange (GENIE), we sought to demonstrate the genetic characteristics of esophageal squamous cell cancer (ESCC) and esophageal adenocarcinoma (EAC). Methodology Data were extracted from cBioPortal for cancer genomics (genie.cbioportal.org). Patients with EAC and squamous cell carcinoma were selected. To compare categorical variables, either the chi-square or Kruskal-Wallis test was used. The Benjamini-Hochberg method was applied to correct P-values, and consequently, false discovery rate-adjusted q-values were computed. When the q-value was <0.05, the P-value < 0.05 was accepted as statistically significant. Results In this study, 1,381 patients with EAC and 312 patients with ESCC were analyzed. Gene alterations were different between the two groups. In EAC, genetic alterations were detected in ERBB2, KRAS, SMAD4, and TACC3 genes, whereas ESCC exhibited alterations in CCDN1, NFE2L2, FGF19, FGF3, FGF4, NOTCH1, and CDKN2B genes. Conclusions Notably, this study showed distinct differences in gene alterations between ESCC and EAC, thereby enhancing our understanding of the genetic landscape of these tumors. Further research is required to elucidate the functional implications of these genetic variations to develop targeted therapies that can improve the prognosis of patients with esophageal cancer.
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Affiliation(s)
- Hatime A Yasar
- Medical Oncology, Ankara University School of Medicine, Ankara, TUR
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Poulsgaard GA, Sørensen SG, Juul RI, Nielsen MM, Pedersen JS. Sequence dependencies and mutation rates of localized mutational processes in cancer. Genome Med 2023; 15:63. [PMID: 37592287 PMCID: PMC10436389 DOI: 10.1186/s13073-023-01217-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a result, some sequence contexts mutate at much higher rates than others, with additional variation found between functional regions. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes. METHODS We count the 11-mer genomic sequences across the genome, and using the PCAWG set of 2583 pan-cancer whole genomes, we associate 11-mers with mutational signatures, hotspots of single nucleotide variants, and specific genomic regions. We evaluate the mutation rates of individual and combined sets of 11-mers and derive mutational sequence motifs. RESULTS We show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE deficiency), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate and sequence preference increase further when focusing on certain genomic regions, such as signature 62 in transcribed regions, where the mutation rate is increased up to 9-folds over cancer type and mutational signature average. CONCLUSIONS We summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.
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Affiliation(s)
- Gustav Alexander Poulsgaard
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Simon Grund Sørensen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Randi Istrup Juul
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Morten Muhlig Nielsen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Jakob Skou Pedersen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark.
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
- Bioinformatics Research Centre (BiRC), Aarhus University, University City 81, Building 1872, 3Rd Floor, 8000, Aarhus C, Denmark.
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Cui M, Lemmon K, Jin Z, Uboha NV. Esophageal carcinoma with SMARCA4 mutation: Unique diagnostic challenges. Pathol Res Pract 2023; 248:154692. [PMID: 37459679 DOI: 10.1016/j.prp.2023.154692] [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: 04/26/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 08/16/2023]
Abstract
Esophageal carcinoma with SMARCA4 deficiency or dysfunction is a recently recognized entity. This study describes the clinicopathologic features of four cases of esophageal carcinoma with SMARCA4 mutation, three with deep deletion and one with missense mutation. Patients include 3 males and 1 female, with an age range of 45-68 years old. Histologically, the neoplasms showed frequent mitotic activity, large nucleus and prominent nucleoli. Glandular differentiation was variable from not identifiable to approximately 20% in the biopsy material. Percentage of rhabdoid morphology was also variable from not identifiable to 20% of the biopsy material. For these cases, one case was diagnosed SMARCA4 deficient esophageal carcinoma based on the biopsy of a retroperitoneal lymph node showing loss of BRG1 by immunostain, and next generation sequencing confirmed deep deletion of SMARCA4. The other three cases had diagnosis of undifferentiated carcinoma or poorly differentiated carcinoma, and the SMARCA4 deep deletion or mutation was discovered by next generation sequencing. Molecular analysis showed TP53 mutation in all the three cases with SMARCA4 deep deletion. Two of the patients deceased 72 and 78 days after diagnosis, and the other two patients showed limited or no treatment response to chemotherapy. In conclusion, esophageal carcinoma with SMARCA4 mutation may pose significant diagnostic challenge for surgical pathologists due to its variable morphology and immunoprofile, and accurate classification of this entity requires recognition of the spectrum of morphology and utilization of BRG1 immunostain and next generating sequencing.
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Affiliation(s)
- Min Cui
- Department of Pathology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.
| | - Kayla Lemmon
- Division of Hematology and Oncology, Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Zhicheng Jin
- Department of Pathology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Nataliya V Uboha
- Division of Hematology and Oncology, Department of Medicine, University of Wisconsin, Madison, WI, USA
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29
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Carroll TM, Chadwick JA, Owen RP, White MJ, Kaplinsky J, Peneva I, Frangou A, Xie PF, Chang J, Roth A, Amess B, James SA, Rei M, Fuchs HS, McCann KJ, Omiyale AO, Jacobs BA, Lord SR, Norris-Bulpitt S, Dobbie ST, Griffiths L, Ramirez KA, Ricciardi T, Macri MJ, Ryan A, Venhaus RR, Van den Eynde BJ, Karydis I, Schuster-Böckler B, Middleton MR, Lu X. Tumor monocyte content predicts immunochemotherapy outcomes in esophageal adenocarcinoma. Cancer Cell 2023; 41:1222-1241.e7. [PMID: 37433281 DOI: 10.1016/j.ccell.2023.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 04/07/2023] [Accepted: 06/14/2023] [Indexed: 07/13/2023]
Abstract
For inoperable esophageal adenocarcinoma (EAC), identifying patients likely to benefit from recently approved immunochemotherapy (ICI+CTX) treatments remains a key challenge. We address this using a uniquely designed window-of-opportunity trial (LUD2015-005), in which 35 inoperable EAC patients received first-line immune checkpoint inhibitors for four weeks (ICI-4W), followed by ICI+CTX. Comprehensive biomarker profiling, including generation of a 65,000-cell single-cell RNA-sequencing atlas of esophageal cancer, as well as multi-timepoint transcriptomic profiling of EAC during ICI-4W, reveals a novel T cell inflammation signature (INCITE) whose upregulation correlates with ICI-induced tumor shrinkage. Deconvolution of pre-treatment gastro-esophageal cancer transcriptomes using our single-cell atlas identifies high tumor monocyte content (TMC) as an unexpected ICI+CTX-specific predictor of greater overall survival (OS) in LUD2015-005 patients and of ICI response in prevalent gastric cancer subtypes from independent cohorts. Tumor mutational burden is an additional independent and additive predictor of LUD2015-005 OS. TMC can improve patient selection for emerging ICI+CTX therapies in gastro-esophageal cancer.
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Affiliation(s)
- Thomas M Carroll
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Joseph A Chadwick
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Richard P Owen
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Michael J White
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Joseph Kaplinsky
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Iliana Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Anna Frangou
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
| | - Phil F Xie
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Jaeho Chang
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Andrew Roth
- Department of Pathology and Molecular Medicine, University of British Columbia, Vancouver, Canada; Department of Computer Science, University of British Columbia, Vancouver, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, Canada
| | - Bob Amess
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Sabrina A James
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Margarida Rei
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Hannah S Fuchs
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Katy J McCann
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ayo O Omiyale
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | | | - Simon R Lord
- Department of Oncology, University of Oxford, Oxford, UK
| | - Stewart Norris-Bulpitt
- Early Phase Clinical Trials Unit, Cancer & Haematology Centre, Churchill Hospital, Oxford, UK
| | - Sam T Dobbie
- Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, UK
| | - Lucinda Griffiths
- Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Benoit J Van den Eynde
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK; Ludwig Institute for Cancer Research, Brussels, Belgium; de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Ioannis Karydis
- Cancer Sciences Unit, University of Southampton and Cancer Care Group, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Mark R Middleton
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK; Early Phase Clinical Trials Unit, Cancer & Haematology Centre, Churchill Hospital, Oxford, UK.
| | - Xin Lu
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.
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30
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Yang H, Almadani N, Thompson EF, Tessier-Cloutier B, Chen J, Ho J, Senz J, McConechy MK, Chow C, Ta M, Cheng A, Karnezis A, Huvila J, McAlpine JN, Gilks B, Jamieson A, Hoang LN. Classification of Vulvar Squamous Cell Carcinoma and Precursor Lesions by p16 and p53 Immunohistochemistry: Considerations, Caveats, and an Algorithmic Approach. Mod Pathol 2023; 36:100145. [PMID: 36828360 DOI: 10.1016/j.modpat.2023.100145] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
There is emerging evidence that vulvar squamous cell carcinoma (VSCC) can be prognostically subclassified into 3 groups based on human papillomavirus (HPV) and p53 status: HPV-associated (HPV+), HPV-independent/p53 wild-type (HPV-/p53wt), or HPV-independent/p53 abnormal (HPV-/p53abn). Our goal was to assess the feasibility of separating VSCC and its precursors into these 3 groups using p16 and p53 immunohistochemistry (IHC). A tissue microarray containing 225 VSCC, 43 usual vulvar intraepithelial neoplasia (uVIN/HSIL), 10 verruciform acanthotic vulvar intraepithelial neoplasia (vaVIN), and 34 differentiated VIN (dVIN), was stained for p16 and p53. Noncomplementary p16 and p53 patterns were resolved by repeating p53 IHC and HPV RNA in situ hybridization (ISH) on whole sections, and sequencing for TP53. Of 82 p16-positive VSCC, 73 (89%) had complementary p16 and p53 patterns and were classified into the HPV+ group, 4 (4.9%) had wild-type p53 staining, positive HPV ISH and were classified into the HPV+ group, whereas 5 (6.1%) had p53 abnormal IHC patterns (1 null, 4 overexpression), negativity for HPV ISH, and harbored TP53 mutations (1 splice site, 4 missense); they were classified as HPV-/p53abn. Of 143 p16-negative VSCC, 142 (99.3%) had complementary p53 and p16 patterns: 115 (80.4%) HPV-/p53abn and 27 (18.9%) HPV-/p53wt. One had a basal-sparing p53 pattern, positivity for HPV ISH and was negative for TP53 mutations-HPV+ category. The use of IHC also led to revised diagnoses-HSIL to dVIN (3/43), dVIN to vaVIN (8/34), and dVIN to HSIL (3/34). Overall, 215/225 VSCC (95.6%) could be easily classifiable into 3 groups with p16 and p53 IHC. We identified several caveats, with the major caveat being that "double-positive" p16/p53 should be classified as HPV-/p53abn. We propose an algorithm that will facilitate the application of p16 and p53 IHC to classify VSCC in pathology practice.
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Affiliation(s)
- Hang Yang
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada
| | - Noorah Almadani
- Department of Pathology, Ministry of the National Guard - Health Affairs, and King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Emily F Thompson
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada
| | | | - Julia Chen
- Medical Undergraduate Program, University of British Columbia, British Columbia, Canada
| | - Julie Ho
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada; Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Janine Senz
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | | | - Christine Chow
- Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Monica Ta
- Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Angela Cheng
- Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Anthony Karnezis
- Pathology and Laboratory Medicine, UC Davis Medical Center, California
| | - Jutta Huvila
- Department of Pathology, University of Turku, Turku University Hospital, Turku, Finland
| | - Jessica N McAlpine
- Gynecologic Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blake Gilks
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada; Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada
| | - Amy Jamieson
- Gynecologic Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lynn N Hoang
- Pathology and Laboratory Medicine, University of British Columbia and Vancouver General Hospital, British Columbia, Canada; Genetic Pathology Evaluation Center (GPEC) and Molecular and Advanced Pathology Core (MAPcore), British Columbia, Canada.
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31
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M Naeini M, Newell F, Aoude LG, Bonazzi VF, Patel K, Lampe G, Koufariotis LT, Lakis V, Addala V, Kondrashova O, Johnston RL, Sharma S, Brosda S, Holmes O, Leonard C, Wood S, Xu Q, Thomas J, Walpole E, Tao Mai G, Ackland SP, Martin J, Burge M, Finch R, Karapetis CS, Shannon J, Nott L, Bohmer R, Wilson K, Barnes E, Zalcberg JR, Mark Smithers B, Simes J, Price T, Gebski V, Nones K, Watson DI, Pearson JV, Barbour AP, Waddell N. Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy. Nat Commun 2023; 14:3155. [PMID: 37258531 PMCID: PMC10232490 DOI: 10.1038/s41467-023-38891-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Oesophageal adenocarcinoma is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigate whole genome, transcriptomic and methylation data from 115 oesophageal adenocarcinoma patients mostly from the DOCTOR phase II clinical trial (Australian New Zealand Clinical Trials Registry-ACTRN12609000665235), with exploratory analysis pre-specified in the study protocol of the trial. We report genomic features associated with poorer overall survival, such as the APOBEC mutational and RS3-like rearrangement signatures. We also show that positron emission tomography non-responders have more sub-clonal genomic copy number alterations. Transcriptomic analysis categorises patients into four immune clusters correlated with survival. The immune suppressed cluster is associated with worse survival, enriched with myeloid-derived cells, and an epithelial-mesenchymal transition signature. The immune hot cluster is associated with better survival, enriched with lymphocytes, myeloid-derived cells, and an immune signature including CCL5, CD8A, and NKG7. The immune clusters highlight patients who may respond to immunotherapy and thus may guide future clinical trials.
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Affiliation(s)
- Marjan M Naeini
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Lauren G Aoude
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Vanessa F Bonazzi
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Kalpana Patel
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Guy Lampe
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | | | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Venkateswar Addala
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Rebecca L Johnston
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Sowmya Sharma
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, 4006, Australia
- Anatomical Pathology, Australian Clinical Labs, 2153, Sydney, Australia
| | - Sandra Brosda
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Janine Thomas
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
- Mater Research Institute, Mater Misericordiae, South Brisbane, QLD, 4101, Australia
| | - Euan Walpole
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | - G Tao Mai
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | - Stephen P Ackland
- Department of Medical Oncology, Calvary Mater Newcastle, Waratah, NSW, 2298, Australia
| | - Jarad Martin
- Department of Radiation Oncology, Calvary Mater Newcastle, Waratah, NSW, 2298, Australia
| | - Matthew Burge
- Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - Robert Finch
- Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - Christos S Karapetis
- Flinders University Department of Medical Oncology, Flinders Medical Centre, Adelaide, SA, 5042, Australia
| | - Jenny Shannon
- Nepean Cancer Care Centre, Nepean Hospital, Sydney, NSW, 2747, Australia
| | - Louise Nott
- Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Robert Bohmer
- Department of General Surgery, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Kate Wilson
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Elizabeth Barnes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - John R Zalcberg
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - B Mark Smithers
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, 4006, Australia
| | - John Simes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Timothy Price
- Medical Oncology Unit, The Queen Elizabeth Hospital and University of Adelaide, Adelaide, SA, 5011, Australia
| | - Val Gebski
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - David I Watson
- Flinders University Discipline of Surgery, Flinders Medical Centre, Adelaide, SA, 5042, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Andrew P Barbour
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia.
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia.
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
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Maslenkina K, Mikhaleva L, Naumenko M, Vandysheva R, Gushchin M, Atiakshin D, Buchwalow I, Tiemann M. Signaling Pathways in the Pathogenesis of Barrett's Esophagus and Esophageal Adenocarcinoma. Int J Mol Sci 2023; 24:ijms24119304. [PMID: 37298253 DOI: 10.3390/ijms24119304] [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: 04/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Barrett's esophagus (BE) is a premalignant lesion that can develop into esophageal adenocarcinoma (EAC). The development of Barrett's esophagus is caused by biliary reflux, which causes extensive mutagenesis in the stem cells of the epithelium in the distal esophagus and gastro-esophageal junction. Other possible cellular origins of BE include the stem cells of the mucosal esophageal glands and their ducts, the stem cells of the stomach, residual embryonic cells and circulating bone marrow stem cells. The classical concept of healing a caustic lesion has been replaced by the concept of a cytokine storm, which forms an inflammatory microenvironment eliciting a phenotypic shift toward intestinal metaplasia of the distal esophagus. This review describes the roles of the NOTCH, hedgehog, NF-κB and IL6/STAT3 molecular pathways in the pathogenesis of BE and EAC.
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Affiliation(s)
- Ksenia Maslenkina
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Liudmila Mikhaleva
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Maxim Naumenko
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Rositsa Vandysheva
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Michail Gushchin
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Dmitri Atiakshin
- Research and Educational Resource Centre for Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis Innovative Technologies, Peoples' Friendship University of Russia Named after Patrice Lumumba, 117198 Moscow, Russia
| | - Igor Buchwalow
- Research and Educational Resource Centre for Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis Innovative Technologies, Peoples' Friendship University of Russia Named after Patrice Lumumba, 117198 Moscow, Russia
- Institute for Hematopathology, Fangdieckstr. 75a, 22547 Hamburg, Germany
| | - Markus Tiemann
- Institute for Hematopathology, Fangdieckstr. 75a, 22547 Hamburg, Germany
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33
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Erasimus H, Kolnik V, Lacroix F, Sidhu S, D'Agostino S, Lemaitre O, Rohaut A, Sanchez I, Thill G, Didier M, Debussche L, Marcireau C. Genome-wide CRISPR Screen Reveals RAB10 as a Synthetic Lethal Gene in Colorectal and Pancreatic Cancers Carrying SMAD4 Loss. CANCER RESEARCH COMMUNICATIONS 2023; 3:780-792. [PMID: 37377893 PMCID: PMC10158796 DOI: 10.1158/2767-9764.crc-22-0301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 03/01/2023] [Accepted: 04/07/2023] [Indexed: 06/29/2023]
Abstract
The TGFβ signaling mediator SMAD4 is frequently mutated or deleted in colorectal and pancreatic cancers. SMAD4 acts as a tumor suppressor and its loss is associated with poorer patient outcomes. The purpose of this study was to find synthetic lethal interactions with SMAD4 deficiency to find novel therapeutic strategies for the treatment of patients with SMAD4-deficient colorectal or pancreatic cancers. Using pooled lentiviral single-guide RNA libraries, we conducted genome-wide loss-of-function screens in Cas9-expressing colorectal and pancreatic cancer cells harboring altered or wild-type SMAD4. The small GTPase protein RAB10 was identified and validated as a susceptibility gene in SMAD4-altered colorectal and pancreatic cancer cells. Rescue assays showed that RAB10 reintroduction reversed the antiproliferative effects of RAB10 knockout in SMAD4-negative cell lines. Further investigation is necessary to shed light on the mechanism by which RAB10 inhibition decreases cell proliferation of SMAD4-negative cells. Significance This study identified and validated RAB10 as new synthetic lethal gene with SMAD4. This was achieved by conducting a whole-genome CRISPR screens in different colorectal and pancreatic cell lines. A future RAB10 inhibitors could correspond to a new therapeutic solution for patients with cancer with SMAD4 deletion.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gilbert Thill
- Sanofi, Translational Sciences, Chilly-Mazarin, France
| | - Michel Didier
- Sanofi, Translational Sciences, Chilly-Mazarin, France
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34
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Cheng L, Zhang F, Zhao X, Wang L, Duan W, Guan J, Wang K, Liu Z, Wang X, Wang Z, Wu H, Chen Z, Teng L, Li Y, Xiao F, Fan T, Jian F. Mutational landscape of primary spinal cord astrocytoma. J Pathol 2023. [PMID: 37114614 DOI: 10.1002/path.6084] [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: 11/17/2022] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023]
Abstract
Primary spinal cord astrocytoma (SCA) is a rare disease. Knowledge about the molecular profiles of SCAs mostly comes from intracranial glioma; the pattern of genetic alterations of SCAs is not well understood. Herein, we describe genome-sequencing analyses of primary SCAs, aiming to characterize the mutational landscape of primary SCAs. We utilized whole exome sequencing (WES) to analyze somatic nucleotide variants (SNVs) and copy number variants (CNVs) among 51 primary SCAs. Driver genes were searched using four algorithms. GISTIC2 was used to detect significant CNVs. Additionally, recurrently mutated pathways were also summarized. A total of 12 driver genes were identified. Of those, H3F3A (47.1%), TP53 (29.4%), NF1 (19.6%), ATRX (17.6%), and PPM1D (17.6%) were the most frequently mutated genes. Furthermore, three novel driver genes seldom reported in glioma were identified: HNRNPC, SYNE1, and RBM10. Several germline mutations, including three variants (SLC16A8 rs2235573, LMF1 rs3751667, FAM20C rs774848096) that were associated with risk of brain glioma, were frequently observed in SCAs. Moreover, 12q14.1 (13.7%) encompassing the oncogene CDK4 was recurrently amplified and negatively affected patient prognosis. Besides frequently mutated RTK/RAS pathway and PI3K pathway, the cell cycle pathway controlling the phosphorylation of retinoblastoma protein (RB) was mutated in 39.2% of patients. Overall, a considerable degree of the somatic mutation landscape is shared between SCAs and brainstem glioma. Our work provides a key insight into the molecular profiling of primary SCAs, which might represent candidate drug targets and complement the molecular atlas of glioma. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Lei Cheng
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
| | - Fan Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, PR China
| | - Xingang Zhao
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, PR China
| | - Leiming Wang
- Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, PR China
| | - Wanru Duan
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
| | - Jian Guan
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
| | - Kai Wang
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
| | - Zhenlei Liu
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
| | - Xingwen Wang
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
| | - Zuowei Wang
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
| | - Hao Wu
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
| | - Zan Chen
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
| | - Lianghong Teng
- Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, PR China
| | - Yifei Li
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Fei Xiao
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Tao Fan
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, PR China
| | - Fengzeng Jian
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, PR China
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Kim JY, Jung J, Kim KM, Lee J, Im YH. TP53 mutations predict poor response to immunotherapy in patients with metastatic solid tumors. Cancer Med 2023. [PMID: 37081749 DOI: 10.1002/cam4.5953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/14/2023] [Accepted: 03/31/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND TP53 is the most commonly mutated gene across all cancer types. R175H mutation was considered structural mutation where the mutation causes misfolding of the protein and leads to a significant conformational alterations within p53's DNA binding domain. The aim of this study was to explain the reason why R175H worse the response to immunotherapy by analyzing tumor immune microenvironment through the expression of immune cells and PD-1. MATERIALS AND METHODS Patients diagnosed with metastatic carcinoma, including colorectal cancer (CRC), breast cancer (BRCA), gastric cancer (GC), non-small cell lung cancer (NSCLC), and 20 other cancer types, treated in a palliative setting at Samsung Medical Center between October 2019 and April 2021, were enrolled. Of these patients, those who underwent TDS analysis (TruSight™ Oncology 500 assay [TSO 500]) were finally analyzed. RESULTS Of 1770 patients, 1012 (57.2%) harbored genetic alterations in TP53. All mutations were single nucleotide variants (SNVs), and the most frequent SNV was R175H (n = 84, 7.5%) which was known as one of the most common hotspot TP53 mutation. The overall survival of patients with TP53 R175H mutations was significantly worse following chemotherapy (606 vs. 456 days, p < 0.001) or immunotherapy (822 vs. 350 days, p < 0.001) compared to those with TP53 mutation in other loci. RNA sequencing indicated that the immune response-related pathways were downregulated in tumors harboring TP53 R175H mutation. Moreover, the expression of CD8(+) T cells PD-1 were lowered in R175H mutation tumors. In the analysis of TP53 structural domain, compared to those having TP53 mutation in other domain, patients with mutations occurring in the nuclear exporter signal (NES) and E4F1-binding domains had significantly worse overall survival following chemotherapy (NES: 606 vs. 451 days, p = 0.043; E4F1: 606 vs. 469 days, p = 0.046) and immunotherapy (NES: 822 vs. 403 days, p < 0.001; E4F1: 822 vs. 413 days, p < 0.001). In addition, tumors with TP53 mutation and co-existing copy number amplification of CCND1, FGF4, and FGF19 in chromosome 11 conferred worse prognosis than those with only TP53 mutation (p < 0.050). DISCUSSION Each TP53 mutations indicated differential treatment outcomes following chemotherapy or immunotherapy in patients with metastatic cancer. Functional analysis including RNASeq suggested that TP53 mutation downregulated immune response. CONCLUSION Overall, we found each TP53 mutation to indicate different prognoses in patients with metastatic tumors undergoing chemotherapy and ICI treatment. Further validations, including a prospective cohort study or a functional study, would be particularly valuable in advancing the knowledge on this aspect and developing improved prognostic parameters.
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Affiliation(s)
- Ji-Yeon Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jaeyun Jung
- Innovative Institute for Precision Medicine, Samsung Medical Center, Seoul, South Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Innovative Institute for Precision Medicine, Samsung Medical Center, Seoul, South Korea
| | - Young-Hyuck Im
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Beydoun AS, Stabenau KA, Altman KW, Johnston N. Cancer Risk in Barrett's Esophagus: A Clinical Review. Int J Mol Sci 2023; 24:ijms24076018. [PMID: 37046992 PMCID: PMC10094310 DOI: 10.3390/ijms24076018] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) is rapidly increasing in incidence and is associated with a poor prognosis. Barrett's esophagus (BE) is a known precursor of esophageal adenocarcinoma. This review aims to explore Barrett's esophagus, esophageal adenocarcinoma, and the progression from the former to the latter. An overview of the definition, diagnosis, epidemiology, and risk factors for both entities are presented, with special attention being given to the areas of debate in the literature. The progression from Barrett's esophagus to esophageal adenocarcinoma is reviewed and the relevant molecular pathways are discussed. The definition of Barrett's esophagus remains debated and without international consensus. This, alongside other factors, has made establishing the true prevalence of Barrett's esophagus challenging. The degree of dysplasia can be a histological challenge, but is necessary to guide clinical management. The progression of BE to EAC is likely driven by inflammatory pathways, pepsin exposure, upregulation of growth factor pathways, and mitochondrial changes. Surveillance is maintained through serial endoscopic evaluation, with shorter intervals recommended for high-risk features.
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Affiliation(s)
- Ahmed Sam Beydoun
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kaleigh A Stabenau
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kenneth W Altman
- Department of Otolaryngology-Head & Neck Surgery, Geisinger Medical Center, Danville, PA 17822, USA
| | - Nikki Johnston
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Li J, Li L, You P, Wei Y, Xu B. Towards artificial intelligence to multi-omics characterization of tumor heterogeneity in esophageal cancer. Semin Cancer Biol 2023; 91:35-49. [PMID: 36868394 DOI: 10.1016/j.semcancer.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023]
Abstract
Esophageal cancer is a unique and complex heterogeneous malignancy, with substantial tumor heterogeneity: at the cellular levels, tumors are composed of tumor and stromal cellular components; at the genetic levels, they comprise genetically distinct tumor clones; at the phenotypic levels, cells in distinct microenvironmental niches acquire diverse phenotypic features. This heterogeneity affects almost every process of esophageal cancer progression from onset to metastases and recurrence, etc. Intertumoral and intratumoral heterogeneity are major obstacles in the treatment of esophageal cancer, but also offer the potential to manipulate the heterogeneity themselves as a new therapeutic strategy. The high-dimensional, multi-faceted characterization of genomics, epigenomics, transcriptomics, proteomics, metabonomics, etc. of esophageal cancer has opened novel horizons for dissecting tumor heterogeneity. Artificial intelligence especially machine learning and deep learning algorithms, are able to make decisive interpretations of data from multi-omics layers. To date, artificial intelligence has emerged as a promising computational tool for analyzing and dissecting esophageal patient-specific multi-omics data. This review provides a comprehensive review of tumor heterogeneity from a multi-omics perspective. Especially, we discuss the novel techniques single-cell sequencing and spatial transcriptomics, which have revolutionized our understanding of the cell compositions of esophageal cancer and allowed us to determine novel cell types. We focus on the latest advances in artificial intelligence in integrating multi-omics data of esophageal cancer. Artificial intelligence-based multi-omics data integration computational tools exert a key role in tumor heterogeneity assessment, which will potentially boost the development of precision oncology in esophageal cancer.
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Affiliation(s)
- Junyu Li
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China; Jiangxi Health Committee Key (JHCK) Laboratory of Tumor Metastasis, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China
| | - Lin Li
- Department of Thoracic Oncology, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China
| | - Peimeng You
- Nanchang University, Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China
| | - Yiping Wei
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China.
| | - Bin Xu
- Jiangxi Health Committee Key (JHCK) Laboratory of Tumor Metastasis, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China.
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Holzapfel N, Zhang A, Choi WJ, Denroche R, Jang G, Dodd A, Bucur R, Wilson J, Sapisochin G, Notta F, Grant RC, Gallinger S, Knox JJ, O'Kane GM. Whole-genome sequencing of 20 cholangiocarcinoma cases reveals unique profiles in patients with cirrhosis and primary sclerosing cholangitis. J Gastrointest Oncol 2023; 14:379-389. [PMID: 36915452 PMCID: PMC10007933 DOI: 10.21037/jgo-22-676] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/21/2022] [Indexed: 02/07/2023] Open
Abstract
Background Cholangiocarcinoma (CCA) is a molecularly heterogenous disease that is often fatal. Whole genome sequencing (WGS) can provide additional knowledge of mutational spectra compared with panel sequencing. We describe the molecular landscape of CCA using whole-genome sequencing and compare the mutational landscape between short-term and long-term survivors. Methods We explored molecular differences between short-term and long-term survivors by performing WGS on 20 patient samples from our biliary tract cancer database. Short-term survivors were enriched for cases with underlying primary sclerosing cholangitis (PSC) and patients with cirrhosis. All samples underwent tumour epithelial enrichment using laser capture microdissection (LCM). Results Dominant single base substitution (SBS) signatures across the cohort included SBS1 and SBS5, with the latter more prevalent in long-term survivors. SBS17 was evident in 3 cases, all of whom had underlying ulcerative colitis (UC) with PSC. Additional rare signatures included SBS3 in a patient treated for prior mantle cell lymphoma and SBS26/SBS6 in a patient with a tumor mutational burden of 33 mutations/Mb and a pathogenic MLH1 germline mutation. Somatic TP53 inactivating mutations were present in 8/10 (80%) short-term survivors and in none of the long-term survivors. Additional mutations occurred in KRAS, SMAD4, CDKN2A, and chromatin remodelling genes. The long-term survivor group harboured predicted fusions in FGFR (n=2) and pathogenic mutations in BRAF and IDH1 (n=2). Conclusions TP53 alterations are associated with poor outcomes in patients with CCA. Patients with underlying inflammatory/autoimmune conditions may be enriched for unique tumour mutational signatures.
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Affiliation(s)
- Nicholas Holzapfel
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Amy Zhang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Woo-Jin Choi
- Department of Surgery, University of Toronto, Ontario, Canada
| | - Robert Denroche
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gunho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anna Dodd
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Roxana Bucur
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Julie Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Robert C Grant
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Surgery, University of Toronto, Ontario, Canada
| | - Jennifer J Knox
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Grainne M O'Kane
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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Orsini A, Mastracci L, Bozzarelli I, Ferrari A, Isidori F, Fiocca R, Lugaresi M, D’Errico A, Malvi D, Cataldi-Stagetti E, Spaggiari P, Tomezzoli A, Albarello L, Ristimäki A, Bottiglieri L, Krishnadath KK, Rosati R, Fumagalli Romario U, De Manzoni G, Räsänen J, Martinelli G, Mattioli S, Bonora E. Correlations between Molecular Alterations, Histopathological Characteristics, and Poor Prognosis in Esophageal Adenocarcinoma. Cancers (Basel) 2023; 15:cancers15051408. [PMID: 36900206 PMCID: PMC10000513 DOI: 10.3390/cancers15051408] [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: 01/14/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) is a severe malignancy with increasing incidence, poorly understood pathogenesis, and low survival rates. We sequenced 164 EAC samples of naïve patients (without chemo-radiotherapy) with high coverage using next-generation sequencing technologies. A total of 337 variants were identified across the whole cohort, with TP53 as the most frequently altered gene (67.27%). Missense mutations in TP53 correlated with worse cancer-specific survival (log-rank p = 0.001). In seven cases, we found disruptive mutations in HNF1alpha associated with other gene alterations. Moreover, we detected gene fusions through massive parallel sequencing of RNA, indicating that it is not a rare event in EAC. In conclusion, we report that a specific type of TP53 mutation (missense changes) negatively affected cancer-specific survival in EAC. HNF1alpha was identified as a new EAC-mutated gene.
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Affiliation(s)
- Arianna Orsini
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Luca Mastracci
- Unit of Anatomic Pathology, Ospedale Policlinico San Martino IRCCS, 16125 Genova, Italy
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genova, 16125 Genova, Italy
| | - Isotta Bozzarelli
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Anna Ferrari
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Federica Isidori
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Roberto Fiocca
- Unit of Anatomic Pathology, Ospedale Policlinico San Martino IRCCS, 16125 Genova, Italy
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genova, 16125 Genova, Italy
| | - Marialuisa Lugaresi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
- Division of Thoracic Surgery, Maria Cecilia Hospital, GVM Care & Research Group, Cotignola, 48022 Ravenna, Italy
| | - Antonietta D’Errico
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Deborah Malvi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Erica Cataldi-Stagetti
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Paola Spaggiari
- Unit of Anatomic Pathology, Humanitas University, 20089 Milan, Italy
| | - Anna Tomezzoli
- Unit of Anatomic Pathology, Azienda Ospedaliera di Verona, 37122 Verona, Italy
| | - Luca Albarello
- Pathology Unit, San Raffaele Scientific Institute, 20135 Milan, Italy
| | - Ari Ristimäki
- Department of Pathology, HUSLAB and HUS Diagnostic Center, University of Helsinki, 00170 Helsinki, Finland
- Helsinki University Hospital, 00170 Helsinki, Finland
| | - Luca Bottiglieri
- Unit of Anatomic Pathology, Istituto Europeo di Oncologia, 20122 Milan, Italy
| | - Kausilia K. Krishnadath
- Laboratory of Experimental Medicine and Pediatrics (LEMP), Department of Gastroenterology and Hepatology, University Hospital Antwerp, 2650 Antwerp, Belgium
| | - Riccardo Rosati
- Department of Gastrointestinal Surgery, San Raffaele Hospital, Vita-Salute San Raffaele University, 20135 Milan, Italy
| | | | - Giovanni De Manzoni
- Department of Surgery, General and Upper G.I. Surgery Division, University of Verona, 37126 Verona, Italy
| | - Jari Räsänen
- Department of General Thoracic and Esophageal Surgery, Helsinki University Hospital, 00170 Helsinki, Finland
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Sandro Mattioli
- Division of Thoracic Surgery, Maria Cecilia Hospital, GVM Care & Research Group, Cotignola, 48022 Ravenna, Italy
| | - Elena Bonora
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
- Correspondence: ; Tel.: +39-0512094761
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Identification of potential biomarkers in Barrett's esophagus derived esophageal adenocarcinoma. Sci Rep 2023; 13:2345. [PMID: 36759514 PMCID: PMC9910260 DOI: 10.1038/s41598-022-17107-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/20/2022] [Indexed: 02/11/2023] Open
Abstract
Almost 50% of esophageal adenocarcinoma (EAC) patients progressed from Barrett's esophagus (BE). EAC is often diagnosed at late stages and is related to dismal prognosis. However, there are still no effective methods for stratification and therapy in BE and EAC. Two public datasets (GSE26886 and GSE37200) were analyzed to identify differentially expressed genes (DEGs) between BE and EAC. Then, a series of bioinformatics analyses were performed to explore potential biomarkers associated with BE-EAC. 27 up- and 104 down-regulated genes were observed between GSE26886 and GSE37200. The GO and KEGG enrichment analysis indicated that the DEGs were highly involved in tumorigenesis. Subsequently, Weighted Gene Co-Expression Network Analysis (WGCNA) were performed to explore the potential genes related to BE-EAC, which were validated in The Cancer Genome Atlas (TCGA) database, and 5 up-regulated genes (MYO1A, ACE2, COL1A1, LGALS4, and ADRA2A) and 3 down-regulated genes (AADAC, RAB27A, and P2RY14) were found in EAC. Meanwhile, ADRA2A and AADAC could contribute to EAC pathogenesis and progression. MYO1A, ACE2, COL1A1, LGALS4, ADRA2A, AADAC, RAB27A, and P2RY14 could be potential novel diagnostic and prognostic biomarkers in BE-EAC.
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Gier RA, Hueros RAR, Rong J, DeMarshall M, Karakasheva TA, Muir AB, Falk GW, Zhang NR, Shaffer SM. Clonal cell states link Barrett's esophagus and esophageal adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525564. [PMID: 36747708 PMCID: PMC9900873 DOI: 10.1101/2023.01.26.525564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Barrett's esophagus is a common type of metaplasia and a precursor of esophageal adenocarcinoma. However, the cell states and lineage connections underlying the origin, maintenance, and progression of Barrett's esophagus have not been resolved in humans. To address this, we performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue. Our analysis revealed discrete lineages in Barrett's esophagus, normal esophagus, and gastric cardia. Transitional basal progenitor cells of the gastroesophageal junction were unexpectedly related to both esophagus and gastric cardia cells. Barrett's esophagus was polyclonal, with lineages that contained all progenitor and differentiated cell types. In contrast, precancerous dysplastic foci were initiated by the expansion of a single molecularly aberrant Barrett's esophagus clone. Together, these findings provide a comprehensive view of the cell dynamics of Barrett's esophagus, linking cell states along the full disease trajectory, from its origin to cancer.
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Affiliation(s)
- Rodrigo A. Gier
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Raúl A. Reyes Hueros
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiazhen Rong
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maureen DeMarshall
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tatiana A. Karakasheva
- Gastrointestinal Epithelium Modeling Program, Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amanda B. Muir
- Gastrointestinal Epithelium Modeling Program, Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gary W. Falk
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy R. Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney M. Shaffer
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Li L, Sun J, Liu N, Yu R, Zhang J, Pang J, Ou Q, Yin Y, Cui J, Yao X, Zhao R, Shao Y, Yuan S, Yu J. Clinical Outcome-Related Cancer Pathways and Mutational Signatures in Patients With Unresectable Esophageal Squamous Cell Carcinoma Treated With Chemoradiotherapy. Int J Radiat Oncol Biol Phys 2023; 115:382-394. [PMID: 36167753 DOI: 10.1016/j.ijrobp.2022.07.1835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 01/11/2023]
Abstract
PURPOSE Definitive chemoradiotherapy (dCRT) is a standard-of-care for locally advanced unresectable esophageal squamous cell carcinoma (ESCC). However, even in individuals treated with the same dCRT regimen, differences in the local control rate and radiation-induced thoracic toxicity exist (radiation-induced esophagitis [RIE]). METHODS AND MATERIALS Here, we describe a comprehensive genomic evaluation of pretreatment tumor tissue samples from 183 patients with ESCC using targeted sequencing of 474 cancer-related genes. The association between endpoints (progression-free survival [PFS], overall survival, locoregional relapse-free survival, distant metastasis-free survival), toxicity (RIE) and genomic features, including altered pathways and the mutational signature, was analyzed. An independent cohort of 84 stage II-III patients with ESCC was used for validation. RESULTS Gene alterations in the cell cycle pathway were identified in 87% of cases. Other frequently altered pathways included PI3K-AKT (45.9%), NOTCH (38.3%), NRF2 (36.6%), RKT-RAS (28.4%), and homologous recombination repair (HRR; 20.2%). HRR pathway alterations correlated with shortened PFS (mutation vs wild-type: 9.00 vs 14.40 months, hazard ratio, 2.10; 95% confidence interval, 1.29-3.44), while altered RTK-RAS pathways were correlated with worse overall survival in patients with ESCC treated with chemoradiotherapy (mutation vs wild-type: 23.70 vs 33.50 months; hazard ratio, 1.65; 95% confidence interval, 1.01-2.69). Furthermore, enrichment of apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) signatures (signatures 2 and 13) was identified in ESCC tumors with altered HRR pathways. High APOBEC signatures and an altered HRR pathway were correlated with poor prognoses in dCRT-treated ESCC. Moreover, the APOBEC signature and/or the presence of HRR pathway alterations were associated with poor PFS and overall survival, which was validated in an independent whole exome sequence cohort. Notably, the altered HRR pathway was also associated with high-grade RIE toxicity in patients with ESCC. CONCLUSIONS Collectively, our results support the use of comprehensive genomic profiling to guide treatment and minimize RIE in patients with ESCC.
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Affiliation(s)
- Li Li
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jujie Sun
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Ning Liu
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ruoying Yu
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Junli Zhang
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Jiaohui Pang
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Qiuxiang Ou
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Ying Yin
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jinfeng Cui
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xuling Yao
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Ranran Zhao
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Shuanghu Yuan
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China; Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Jinming Yu
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China; Research Unit of Radiation Oncology, Chinese Academy of Medical Sciences, Jinan, Shandong, China.
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43
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Caspa Gokulan R, Paulrasu K, Azfar J, El-Rifai W, Que J, Boutaud OG, Ban Y, Gao Z, Buitrago MG, Dikalov SI, Zaika AI. Protein adduction causes non-mutational inhibition of p53 tumor suppressor. Cell Rep 2023; 42:112024. [PMID: 36848235 PMCID: PMC9989503 DOI: 10.1016/j.celrep.2023.112024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/04/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
p53 is a key tumor suppressor that is frequently mutated in human tumors. In this study, we investigated how p53 is regulated in precancerous lesions prior to mutations in the p53 gene. Analyzing esophageal cells in conditions of genotoxic stress that promotes development of esophageal adenocarcinoma, we find that p53 protein is adducted with reactive isolevuglandins (isoLGs), products of lipid peroxidation. Modification of p53 protein with isoLGs diminishes its acetylation and binding to the promoters of p53 target genes causing modulation of p53-dependent transcription. It also leads to accumulation of adducted p53 protein in intracellular amyloid-like aggregates that can be inhibited by isoLG scavenger 2-HOBA in vitro and in vivo. Taken together, our studies reveal a posttranslational modification of p53 protein that causes molecular aggregation of p53 protein and its non-mutational inactivation in conditions of DNA damage that may play an important role in human tumorigenesis.
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Affiliation(s)
| | | | - Jamal Azfar
- Department of Surgery, University of Miami, Miami, FL, USA
| | - Wael El-Rifai
- Department of Surgery, University of Miami, Miami, FL, USA
| | - Jianwen Que
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Olivier G Boutaud
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuguang Ban
- Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Zhen Gao
- Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | | | - Sergey I Dikalov
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexander I Zaika
- Department of Surgery, University of Miami, Miami, FL, USA; Department of Veterans Affairs, Miami VA Healthcare System, Miami, FL, USA.
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44
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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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45
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Cao B, Li J, Wang X, Ran Z, Tan J, Deng L, Hao Y. Mechanosensitive miR-99b mediates the regulatory effect of matrix stiffness on bone marrow mesenchymal stem cell fate both in vitro and in vivo. APL Bioeng 2023; 7:016106. [PMID: 36685676 PMCID: PMC9851713 DOI: 10.1063/5.0131125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023] Open
Abstract
Mechanical signals from extracellular matrix stiffness are important cues that regulate the proliferation and differentiation of bone marrow mesenchymal stem cells (BMSCs). However, the incorporation of BMSCs into soft hydrogels and the dominance of soft matrices for BMSC growth and differentiation limit the directed differentiation of BMSCs incorporated into hydrogels for tissue engineering, especially osteogenesis. Here, we found that the expression of miR-99b increased with increasing hydrogel stiffness and that miR-99b regulated the proliferation and differentiation of BMSCs seeded on the surface of substrates with different stiffnesses. Furthermore, miR-99b significantly promoted the migration of BMSCs in 3D hydrogels. Mechanistically, we demonstrated that matrix stiffness-sensitive miR-99b targets the mammalian target of the rapamycin signaling pathway to regulate the adipogenic and osteogenic differentiation of BMSCs. In addition, by modulating the expression of miR-99b, the osteogenic differentiation of BMSCs in soft 3D hydrogels was promoted. Consistently, the flexible BMSC-GelMA hydrogel transfected with miR-99b significantly promoted bone regeneration in the rat calvarial defect area. These results suggest that miR-99b plays a key role in the mechanotransduction and phenotypic transformation of BMSCs and may inspire new tissue engineering applications with MSCs as key components.
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Affiliation(s)
- Bojun Cao
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Jiaxin Li
- Department of Orthopedics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaowen Wang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zhaoyang Ran
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Jia Tan
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
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46
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Stawinski PM, Dziadkowiec KN, Kuo LA, Echavarria J, Saligram S. Barrett's Esophagus: An Updated Review. Diagnostics (Basel) 2023; 13:diagnostics13020321. [PMID: 36673131 PMCID: PMC9858189 DOI: 10.3390/diagnostics13020321] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 01/18/2023] Open
Abstract
Barrett’s esophagus (BE) is a change in the distal esophageal mucosal lining, whereby metaplastic columnar epithelium replaces squamous epithelium of the esophagus. This change represents a pre-malignant mucosal transformation which has a known association with the development of esophageal adenocarcinoma. Gastroesophageal reflux disease is a risk factor for BE, other risk factors include patients who are Caucasian, age > 50 years, central obesity, tobacco use, history of peptic stricture and erosive gastritis. Screening for BE remains selective based on risk factors, a screening program in the general population is not routinely recommended. Diagnosis of BE is established with a combination of endoscopic recognition, targeted biopsies, and histologic confirmation of columnar metaplasia. We aim to provide a comprehensive review of the epidemiology, pathogenesis, screening and advanced techniques of detecting and eradicating Barrett’s esophagus.
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47
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Ooki A, Osumi H, Chin K, Watanabe M, Yamaguchi K. Potent molecular-targeted therapies for advanced esophageal squamous cell carcinoma. Ther Adv Med Oncol 2023; 15:17588359221138377. [PMID: 36872946 PMCID: PMC9978325 DOI: 10.1177/17588359221138377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 10/21/2022] [Indexed: 01/15/2023] Open
Abstract
Esophageal cancer (EC) remains a public health concern with a high mortality and disease burden worldwide. Esophageal squamous cell carcinoma (ESCC) is a predominant histological subtype of EC that has unique etiology, molecular profiles, and clinicopathological features. Although systemic chemotherapy, including cytotoxic agents and immune checkpoint inhibitors, is the main therapeutic option for recurrent or metastatic ESCC patients, the clinical benefits are limited with poor prognosis. Personalized molecular-targeted therapies have been hampered due to the lack of robust treatment efficacy in clinical trials. Therefore, there is an urgent need to develop effective therapeutic strategies. In this review, we summarize the molecular profiles of ESCC based on the findings of pivotal comprehensive molecular analyses, highlighting potent therapeutic targets for establishing future precision medicine for ESCC patients, with the most recent results of clinical trials.
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Affiliation(s)
- Akira Ooki
- Department of Gastroenterological Chemotherapy,
Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31
Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Hiroki Osumi
- Department of Gastroenterological Chemotherapy,
Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo,
Japan
| | - Keisho Chin
- Department of Gastroenterological Chemotherapy,
Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo,
Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery,
Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo,
Japan
| | - Kensei Yamaguchi
- Department of Gastroenterological Chemotherapy,
Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo,
Japan
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48
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COOBoostR: An Extreme Gradient Boosting-Based Tool for Robust Tissue or Cell-of-Origin Prediction of Tumors. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010071. [PMID: 36676020 PMCID: PMC9865194 DOI: 10.3390/life13010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
We present here COOBoostR, a computational method designed for the putative prediction of the tissue- or cell-of-origin of various cancer types. COOBoostR leverages regional somatic mutation density information and chromatin mark features to be applied to an extreme gradient boosting-based machine-learning algorithm. COOBoostR ranks chromatin marks from various tissue and cell types, which best explain the somatic mutation density landscape of any sample of interest. A specific tissue or cell type matching the chromatin mark feature with highest explanatory power is designated as a potential tissue- or cell-of-origin. Through integrating either ChIP-seq based chromatin data, along with regional somatic mutation density data derived from normal cells/tissue, precancerous lesions, and cancer types, we show that COOBoostR outperforms existing random forest-based methods in prediction speed, with comparable or better tissue or cell-of-origin prediction performance (prediction accuracy-normal cells/tissue: 76.99%, precancerous lesions: 95.65%, cancer cells: 89.39%). In addition, our results suggest a dynamic somatic mutation accumulation at the normal tissue or cell stage which could be intertwined with the changes in open chromatin marks and enhancer sites. These results further represent chromatin marks shaping the somatic mutation landscape at the early stage of mutation accumulation, possibly even before the initiation of precancerous lesions or neoplasia.
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49
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Gupta S, Noona SW, Pambuccian SE, Robinson B, Martin LW, Williams E, Stelow EB, Raghavan SS. Malignant undifferentiated and rhabdoid tumors of the gastroesophageal junction and esophagus with SMARCA4 loss: a case series. Hum Pathol 2022; 134:56-65. [PMID: 36549598 DOI: 10.1016/j.humpath.2022.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Undifferentiated SMARCA4-deficient carcinoma of the esophagus and gastroesophageal junction is a rare, highly aggressive, and diagnostically challenging malignancy. Here we present a case series of high-grade undifferentiated malignant neoplasms of the esophagus and gastroesophageal junction that share SMARCA4 loss by immunohistochemistry and demonstrate a rhabdoid phenotype. Five cases are presented, including 4 men and 1 woman with an age range of 48-79 years. Interestingly, only one case showed intestinal metaplasia (Barrett's esophagus) and no cases demonstrated glandular dysplasia or glandular differentiation. In all, the lesional cells were immunoreactive with antibodies to keratins (3/5), CD34 (2/4), and CD138 (4/5). SMARCA4 expression was diffusely lost in all cases, whereas SMARCB1 expression was intact. OncoScan™ assay demonstrated loss of SMARCA4 in all cases analyzed. Additional OncoScan™ findings included abnormalities of CDKN2A in 2 of 3 cases, abnormalities of TP53 in 2 of 3 cases, and abnormalities of PTPRD in 2 of 3 cases, among other abnormalities.
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Affiliation(s)
- Srishti Gupta
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Sean W Noona
- Department of Surgery, University of Virginia, Charlottesville, VA 22908, USA
| | | | - Brian Robinson
- Department of Pathology, Emory University, Atlanta, GA 30322, USA
| | - Linda W Martin
- Department of Surgery, University of Virginia, Charlottesville, VA 22908, USA
| | - Eli Williams
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Edward B Stelow
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Shyam S Raghavan
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA.
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50
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Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
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