1
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Bao C, Tourdot RW, Brunette GJ, Stewart C, Sun L, Baba H, Watanabe M, Agoston AT, Jajoo K, Davison JM, Nason KS, Getz G, Wang KK, Imamura Y, Odze R, Bass AJ, Stachler MD, Zhang CZ. Genomic signatures of past and present chromosomal instability in Barrett's esophagus and early esophageal adenocarcinoma. Nat Commun 2023; 14:6203. [PMID: 37794034 PMCID: PMC10550953 DOI: 10.1038/s41467-023-41805-6] [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: 08/01/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.
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Affiliation(s)
- Chunyang Bao
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Richard W Tourdot
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Gregory J Brunette
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Chip Stewart
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Lili Sun
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 2 Chome-40-1 Kurokami, Chuo Ward, Kumamoto, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Agoston T Agoston
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kunal Jajoo
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Jon M Davison
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Katie S Nason
- Department of Surgery, Baystate Medical Center, University of Massachusetts Medical School, 759 Chestnut St, Springfield, MA, 01107, USA
| | - Gad Getz
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kenneth K Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Yu Imamura
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Robert Odze
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Department of Pathology and Lab Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
| | - Matthew D Stachler
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Department of Pathology, University of California, San Francisco. 513 Parnassus Ave, San Francisco, CA, 94143, USA.
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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2
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Corver WE, Ter Haar NT. High-Resolution Multiparameter DNA Flow Cytometry for Accurate Ploidy Assessment and the Detection and Sorting of Tumor and Stromal Subpopulations from Paraffin-Embedded Tissues. Curr Protoc 2023; 3:e825. [PMID: 37428889 DOI: 10.1002/cpz1.825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
This article contains detailed protocols for the simultaneous flow cytometric identification of tumor cells and stromal cells and measurement of DNA content of formalin-fixed, paraffin-embedded (FFPE) tissues. The vimentin-positive stromal cell fraction can be used as an internal reference for accurate DNA content assessments of FFPE carcinoma tissues. This allows clear detection of keratin-positive tumor cells with a DNA index lower than 1.0 (near-haploidy) and of keratin-positive tumor cells with a DNA index close to 1.0 in overall DNA aneuploid samples, thus improving DNA ploidy assessment in FFPE carcinomas. Furthermore, the protocol is useful for studying molecular genetic alterations and intratumor heterogeneity in archival FFPE samples. Keratin-positive tumor cell fractions can be sorted for further molecular genetic analysis, while DNA from the sorted vimentin-positive stromal cells can serve as a reference when normal tissue of the patient is not available. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Multiparameter DNA content analysis of FFPE carcinomas Alternate Protocol 1: Immunocytochemistry for keratin and vimentin, and DNA labeling for blue and red excitation Alternate Protocol 2: Immunocytochemistry for keratin and vimentin, and DNA labeling for blue excitation Support Protocol: Sorting cell population from FFPE carcinomas.
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3
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Karlsson K, Przybilla MJ, Kotler E, Khan A, Xu H, Karagyozova K, Sockell A, Wong WH, Liu K, Mah A, Lo YH, Lu B, Houlahan KE, Ma Z, Suarez CJ, Barnes CP, Kuo CJ, Curtis C. Deterministic evolution and stringent selection during preneoplasia. Nature 2023; 618:383-393. [PMID: 37258665 PMCID: PMC10247377 DOI: 10.1038/s41586-023-06102-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/19/2023] [Indexed: 06/02/2023]
Abstract
The earliest events during human tumour initiation, although poorly characterized, may hold clues to malignancy detection and prevention1. Here we model occult preneoplasia by biallelic inactivation of TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over 2 years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single-cell sequencing of TP53-deficient gastric organoids similarly indicates progression towards malignant transcriptional programmes. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programmes repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference and a marked degree of phenotypic convergence in premalignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and show evolutionary constraints and barriers to malignant transformation, with implications for earlier detection and interception of aggressive, genome-instable tumours.
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Affiliation(s)
- Kasper Karlsson
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Science for Life Laboratory and Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Moritz J Przybilla
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Wellcome Sanger Institute & University of Cambridge, Hinxton, UK
| | - Eran Kotler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Aziz Khan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hang Xu
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kremena Karagyozova
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra Sockell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Wing H Wong
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine Liu
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Amanda Mah
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuan-Hung Lo
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Bingxin Lu
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Kathleen E Houlahan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhicheng Ma
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Calvin J Kuo
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christina Curtis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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4
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Ballout F, Lu H, Chen Z, Hu T, Chen L, Washington MK, El-Rifai W, Peng D. Targeting NRF2 Sensitizes Esophageal Adenocarcinoma Cells to Cisplatin through Induction of Ferroptosis and Apoptosis. Antioxidants (Basel) 2022; 11:1859. [PMID: 36290582 PMCID: PMC9598457 DOI: 10.3390/antiox11101859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 08/10/2023] Open
Abstract
Esophageal adenocarcinoma (EAC), the predominant type of esophageal cancer in the United States, develops through Barrett's esophagus (BE)-dysplasia-carcinoma cascade. Gastroesophageal reflux disease, where acidic bile salts refluxate into the esophagus, is the main risk factor for the development of BE and its progression to EAC. The NFE2-related factor 2 (NRF2) is the master cellular antioxidant regulator. We detected high NRF2 protein levels in the EAC cell lines and primary tissues. Knockdown of NRF2 significantly enhanced acidic bile salt-induced oxidative stress, DNA damage, and inhibited EAC cell growth. Brusatol, an NRF2 inhibitor, significantly inhibited NRF2 transcriptional activity and downregulated the NRF2 target genes. We discovered that in addition to inducing apoptosis, Brusatol alone or in combination with cisplatin (CDDP) induced significant lipid peroxidation and ferroptosis, as evidenced by reduced xCT and GPX4 expression, two known ferroptosis markers. The combination of Brusatol and CDDP significantly inhibited EAC tumor xenograft growth in vivo and confirmed the in vitro data showing ferroptosis as an important mechanism in the tumors treated with Brusatol or Brusatol and CDDP combination. Our data support the role of NRF2 in protecting against stress-induced apoptosis and ferroptosis in EACs. Targeting NRF2 in combination with platinum therapy can be an effective strategy for eliminating cancer cells in EAC.
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Affiliation(s)
- Farah Ballout
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Heng Lu
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Zheng Chen
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Tianling Hu
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lei Chen
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Mary Kay Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wael El-Rifai
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Veterans Affairs, Miami Healthcare System, Miami, FL 33136, USA
| | - Dunfa Peng
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Veterans Affairs, Miami Healthcare System, Miami, FL 33136, USA
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5
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Ma SZ, Chen HX, Liang ZD, Qi XS. Risk factors for Barrett's esophagus: Recent advances. Shijie Huaren Xiaohua Zazhi 2022; 30:605-613. [DOI: 10.11569/wcjd.v30.i14.605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) is the most common malignant tumor of the esophagus in the West. During the past few decades, its morbidity has been increasing in China. Barrett's esophagus (BE) is defined as the replacement of normal squamous epithelium in the lower esophagus by metaplasia of columnar epithelium. BE is closely related to the occurrence of EAC. Knowledge regarding the risk factors for the occurrence and development of BE is of great significance for early screening and diagnosis of BE and prevention of EAC. In this paper, we review the clinical, demographics-related, lifestyle-related, and medications-related risk factors for BE to provide more valuable scientific evidence for the prevention and treatment of BE.
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Affiliation(s)
- Shao-Ze Ma
- Department of Gastroenterology, General Hospital of Northern Theater Command, Shenyang 110840, Liaoning Province, China,Graduate School of Dalian Medical University, Dalian 116044, Liaoning Province, China
| | - Hong-Xin Chen
- Department of Gastroenterology, General Hospital of Northern Theater Command, Shenyang 110840, Liaoning Province, China,Graduate School of Liaoning University of Traditional Chinese Medicine, Shenyang 110031, Liaoning Province, China
| | - Zhen-Dong Liang
- Department of Gastroenterology, General Hospital of Northern Theater Command, Shenyang 110840, Liaoning Province, China
| | - Xing-Shun Qi
- Department of Gastroenterology, General Hospital of Northern Theater Command, Shenyang 110840, Liaoning Province, China
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6
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Paulson TG, Galipeau PC, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Hadi K, Shah M, Arora K, Shelton J, Johnson M, Corvelo A, Maley CC, Yao X, Sanghvi R, Venturini E, Emde AK, Hubert B, Imielinski M, Robine N, Reid BJ, Li X. Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression. Nat Commun 2022; 13:2300. [PMID: 35484108 PMCID: PMC9050715 DOI: 10.1038/s41467-022-29767-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
While the genomes of normal tissues undergo dynamic changes over time, little is understood about the temporal-spatial dynamics of genomes in premalignant tissues that progress to cancer compared to those that remain cancer-free. Here we use whole genome sequencing to contrast genomic alterations in 427 longitudinal samples from 40 patients with stable Barrett’s esophagus compared to 40 Barrett’s patients who progressed to esophageal adenocarcinoma (ESAD). We show the same somatic mutational processes are active in Barrett’s tissue regardless of outcome, with high levels of mutation, ESAD gene and focal chromosomal alterations, and similar mutational signatures. The critical distinction between stable Barrett’s versus those who progress to cancer is acquisition and expansion of TP53−/− cell populations having complex structural variants and high-level amplifications, which are detectable up to six years prior to a cancer diagnosis. These findings reveal the timing of common somatic genome dynamics in stable Barrett’s esophagus and define key genomic features specific to progression to esophageal adenocarcinoma, both of which are critical for cancer prevention and early detection strategies. Barrett’s esophagus is a pre-malignant condition that can progress to esophageal cancer. Here, the authors carry out whole genome sequencing of samples from patients who did or did not progress to cancer and find that mutations in many genes occur regardless of progression status, but also find features associated with progressive disease.
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Affiliation(s)
- Thomas G Paulson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.
| | - Patricia C Galipeau
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Kenji M Oman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Carissa A Sanchez
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Mary K Kuhner
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195-5065, USA
| | - Lucian P Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA
| | - Kevin Hadi
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Minita Shah
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Kanika Arora
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | | | - Molly Johnson
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Andre Corvelo
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | - Xiaotong Yao
- New York Genome Center (NYGC), New York, NY, 10013, USA
| | | | | | | | | | - Marcin Imielinski
- New York Genome Center (NYGC), New York, NY, 10013, USA.,Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine and Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10065, USA
| | | | - Brian J Reid
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195-5065, USA.,Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Xiaohong Li
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.
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7
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Zhang CZ, Pellman D. Cancer Genomic Rearrangements and Copy Number Alterations from Errors in Cell Division. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070620-094029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Analysis of cancer genomes has shown that a large fraction of chromosomal changes originate from catastrophic events including whole-genome duplication, chromothripsis, breakage-fusion-bridge cycles, and chromoplexy. Through sophisticated computational analysis of cancer genomes and experimental recapitulation of these catastrophic alterations, we have gained significant insights into the origin, mechanism, and evolutionary dynamics of cancer genome complexity. In this review, we summarize this progress and survey the major unresolved questions, with particular emphasis on the relative contributions of chromosome fragmentation and DNA replication errors to complex chromosomal alterations.
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Affiliation(s)
- Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - David Pellman
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts, USA
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8
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Yalchin M, Baker AM, Graham TA, Hart A. Predicting Colorectal Cancer Occurrence in IBD. Cancers (Basel) 2021; 13:2908. [PMID: 34200768 PMCID: PMC8230430 DOI: 10.3390/cancers13122908] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
Patients with colonic inflammatory bowel disease (IBD) are at an increased risk of developing colorectal cancer (CRC), and are therefore enrolled into a surveillance programme aimed at detecting dysplasia or early cancer. Current surveillance programmes are guided by clinical, endoscopic or histological predictors of colitis-associated CRC (CA-CRC). We have seen great progress in our understanding of these predictors of disease progression, and advances in endoscopic technique and management, along with improved medical care, has been mirrored by the falling incidence of CA-CRC over the last 50 years. However, more could be done to improve our molecular understanding of CA-CRC progression and enable better risk stratification for patients with IBD. This review summarises the known risk factors associated with CA-CRC and explores the molecular landscape that has the potential to complement and optimise the existing IBD surveillance programme.
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Affiliation(s)
- Mehmet Yalchin
- Inflammatory Bowel Disease Department, St. Mark’s Hospital, Watford R.d., Harrow HA1 3UJ, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Ann-Marie Baker
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Trevor A. Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Ailsa Hart
- Inflammatory Bowel Disease Department, St. Mark’s Hospital, Watford R.d., Harrow HA1 3UJ, UK
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9
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Bajpai M, Panda A, Birudaraju K, Van Gurp J, Chak A, Das KM, Javidian P, Aviv H. Recurring Translocations in Barrett's Esophageal Adenocarcinoma. Front Genet 2021; 12:674741. [PMID: 34178034 PMCID: PMC8220202 DOI: 10.3389/fgene.2021.674741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Barrett's esophagus (BE) is a premalignant metaplasia in patients with chronic gastroesophageal reflux disease (GERD). BE can progress to esophageal adenocarcinoma (EA) with less than 15% 5-year survival. Chromosomal aneuploidy, deletions, and duplication are early events in BE progression to EA, but reliable diagnostic assays to detect chromosomal markers in premalignant stages of EA arising from BE are lacking. Previously, we investigated chromosomal changes in an in vitro model of acid and bile exposure-induced Barrett's epithelial carcinogenesis (BEC). In addition to detecting changes already known to occur in BE and EA, we also reported a novel recurring chromosomal translocation t(10:16) in the BE cells at an earlier time point before they undergo malignant transformation. In this study, we refine the chromosomal event with the help of fluorescence microscopy techniques as a three-way translocation between chromosomes 2, 10, and 16, t(2:10;16) (p22;q22;q22). We also designed an exclusive fluorescent in situ hybridization for esophageal adenocarcinoma (FISH-EA) assay that detects these chromosomal breakpoints and fusions. We validate the feasibility of the FISH-EA assay to objectively detect these chromosome events in primary tissues by confirming the presence of one of the fusions in paraffin-embedded formalin-fixed human EA tumors. Clinical validation in a larger cohort of BE progressors and non-progressors will confirm the specificity and sensitivity of the FISH-EA assay in identifying malignant potential in the early stages of EA.
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Affiliation(s)
- Manisha Bajpai
- Department of Medicine-Gastroenterology and Hepatology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Anshuman Panda
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Kristen Birudaraju
- Cytogenetics Laboratory, Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
| | - James Van Gurp
- Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
| | - Amitabh Chak
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Kiron M Das
- Department of Medicine-Gastroenterology and Hepatology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Parisa Javidian
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States.,Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
| | - Hana Aviv
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States.,Cytogenetics Laboratory, Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
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10
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Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity. Sci Rep 2021; 11:10571. [PMID: 34011996 PMCID: PMC8134446 DOI: 10.1038/s41598-021-90170-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 11/08/2022] Open
Abstract
Breast cancers exhibit intratumoral heterogeneity associated with disease progression and therapeutic resistance. To define the sources and the extent of heterogeneity, we performed an in-depth analysis of the genomic architecture of three chemoradiation-naïve breast cancers with well-defined clinical features including variable ER, PR, ERBB2 receptor expression and two distinct pathogenic BRCA2mut genotypes. The latter included a germ line carrier and a patient with a somatic variant. In each case we combined DNA content-based flow cytometry with whole exome sequencing and genome wide copy number variant (CNV) analysis of distinct populations sorted from multiple (4–18) mapped biopsies within the tumors and involved lymph nodes. Interrogating flow-sorted tumor populations from each biopsy provided an objective method to distinguish fixed and variable genomic lesions in each tumor. Notably we show that tumors exploit CNVs to fix mutations and deletions in distinct populations throughout each tumor. The identification of fixed genomic lesions that are shared or unique within each tumor, has broad implications for the study of tumor heterogeneity including the presence of tumor markers and therapeutic targets, and of candidate neoepitopes in breast and other solid tumors that can advance more effective treatment and clinical management of patients with disease.
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11
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Persistent or recurrent Barrett's neoplasia after an endoscopic therapy session is associated with DNA content abnormality and can be detected by DNA flow cytometric analysis of paraffin-embedded tissue. Mod Pathol 2021; 34:1889-1900. [PMID: 34108638 PMCID: PMC8443444 DOI: 10.1038/s41379-021-00832-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/16/2022]
Abstract
Endoscopic therapy is currently the standard of care for the treatment of high-grade dysplasia (HGD) or intramucosal adenocarcinoma (IMC) in patients with Barrett's esophagus (BE). Visible lesions are treated with endoscopic mucosal resection (EMR), which is often coupled with radiofrequency ablation (RFA). However, endoscopic therapy may require multiple sessions (one session every 2-3 months) and does not always assure complete eradication of neoplasia. Furthermore, despite complete eradication, recurrences are not uncommon. This study assesses which potential risk factors can predict a poor response after endoscopic sessions. Forty-five BE patients who underwent at least one endoscopic session (EMR alone or ablation with or without preceding EMR) for the treatment of HGD/IMC, low-grade dysplasia (LGD), or indefinite for dysplasia (IND) were analyzed. DNA flow cytometry was performed on 82 formalin-fixed paraffin-embedded samples from the 45 patients, including 78 HGD/IMC, 2 LGD, and 2 IND. Eight non-dysplastic BE samples were used as controls. Three to four 60-micron thick sections were cut from each tissue block, and the area of HGD/IMC, LGD, or IND was manually dissected. Potential associations between clinicopathologic risk factors and persistent/recurrent HGD/IMC following each endoscopic session were examined using univariate and multivariate Cox models with frailty terms. Sixty (73%) of the 82 specimens showed abnormal DNA content (aneuploidy or elevated 4N fraction). These were all specimens with HGD/IMC (representing 77% of that group). Of these 60 HGD/IMC samples with abnormal DNA content, 42 (70%) were associated with subsequent development of persistent/recurrent HGD/IMC (n = 41) or esophageal adenocarcinoma (EAC; n = 1) within a mean follow-up time of 16 months (range: 1 month to 9.4 years). In contrast, only 6 (27%, all HGD/IMC) of the 22 remaining samples (all with normal DNA content) were associated with persistent/recurrent HGD/IMC. For outcome analysis per patient, 11 (24%) of the 45 patients developed persistent/recurrent HGD/IMC or EAC, despite multiple endoscopic sessions (mean: 3.6, range: 1-11). In a univariate Cox model, the presence of abnormal DNA content (hazard ratio [HR] = 3.8, p = 0.007), long BE segment ≥ 3 cm (HR = 3.4, p = 0.002), endoscopic nodularity (HR = 2.5, p = 0.042), and treatment with EMR alone (HR = 2.9, p = 0.006) were significantly associated with an increased risk for persistent/recurrent HGD/IMC or EAC. However, only abnormal DNA content (HR = 6.0, p = 0.003) and treatment with EMR alone (HR = 2.7, p = 0.047) remained as significant risk factors in a multivariate analysis. Age ≥ 60 years, gender, ethnicity, body mass index (BMI) ≥ 30 kg/m2, presence of hiatal hernia, and positive EMR lateral margin for neoplasia were not significant risk factors for persistent/recurrent HGD/IMC or EAC (p > 0.05). Three-month, 6-month, 1-year, 3-year, and 6-year adjusted probabilities of persistent/recurrent HGD/IMC or EAC in the setting of abnormal DNA content were 31%, 56%, 67%, 79%, and 83%, respectively. The corresponding probabilities in the setting of normal DNA content were 10%, 21%, 28%, 38%, and 43%, respectively. In conclusion, in BE patients with baseline HGD/IMC, both DNA content abnormality and treatment with EMR alone were significantly associated with persistent/recurrent HGD/IMC or EAC following each endoscopic session. DNA content abnormality as detected by DNA flow cytometry identifies HGD/IMC patients at highest risk for persistent/recurrent HGD/IMC or EAC, and it also serves as a diagnostic marker of HGD/IMC with an estimated sensitivity of 77%. The diagnosis of HGD/IMC in the setting of abnormal DNA content may warrant alternative treatment strategies as well as long-term follow-up with shorter surveillance intervals.
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12
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Maitra I, Date RS, Martin FL. Towards screening Barrett's oesophagus: current guidelines, imaging modalities and future developments. Clin J Gastroenterol 2020; 13:635-649. [PMID: 32495144 PMCID: PMC7519897 DOI: 10.1007/s12328-020-01135-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
Barrett's oesophagus is the only known precursor to oesophageal adenocarcinoma (OAC). Although guidelines on the screening and surveillance exist in Barrett's oesophagus, the current strategies are inadequate. Oesophagogastroduodenoscopy (OGD) is the gold standard method in screening for Barrett's oesophagus. This invasive method is expensive with associated risks negating its use as a current screening tool for Barrett's oesophagus. This review explores current definitions, epidemiology, biomarkers, surveillance, and screening in Barrett's oesophagus. Imaging modalities applicable to this condition are discussed, in addition to future developments. There is an urgent need for an alternative non-invasive method of screening and/or surveillance which could be highly beneficial towards reducing waiting times, alleviating patient fears and reducing future costs in current healthcare services. Vibrational spectroscopy has been shown to be promising in categorising Barrett's oesophagus through to high-grade dysplasia (HGD) and OAC. These techniques need further validation through multicentre trials.
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Affiliation(s)
- Ishaan Maitra
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE UK
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13
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Lenkiewicz E, Malasi S, Hogenson TL, Flores LF, Barham W, Phillips WJ, Roesler AS, Chambers KR, Rajbhandari N, Hayashi A, Antal CE, Downes M, Grandgenett PM, Hollingsworth MA, Cridebring D, Xiong Y, Lee JH, Ye Z, Yan H, Hernandez MC, Leiting JL, Evans RM, Ordog T, Truty MJ, Borad MJ, Reya T, Von Hoff DD, Fernandez-Zapico ME, Barrett MT. Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas. Cancer Res 2020; 80:4324-4334. [PMID: 32928922 DOI: 10.1158/0008-5472.can-20-0078] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/07/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
Adenosquamous cancer of the pancreas (ASCP) is a subtype of pancreatic cancer that has a worse prognosis and greater metastatic potential than the more common pancreatic ductal adenocarcinoma (PDAC) subtype. To distinguish the genomic landscape of ASCP and identify actionable targets for this lethal cancer, we applied DNA content flow cytometry to a series of 15 tumor samples including five patient-derived xenografts (PDX). We interrogated purified sorted tumor fractions from these samples with whole-genome copy-number variant (CNV), whole-exome sequencing, and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analyses. These identified a variety of somatic genomic lesions targeting chromatin regulators in ASCP genomes that were superimposed on well-characterized genomic lesions including mutations in TP53 (87%) and KRAS (73%), amplification of MYC (47%), and homozygous deletion of CDKN2A (40%) that are common in PDACs. Furthermore, a comparison of ATAC-seq profiles of three ASCP and three PDAC genomes using flow-sorted PDX models identified genes with accessible chromatin unique to the ASCP genomes, including the lysine methyltransferase SMYD2 and the pancreatic cancer stem cell regulator RORC in all three ASCPs, and a FGFR1-ERLIN2 fusion associated with focal CNVs in both genes in a single ASCP. Finally, we demonstrate significant activity of a pan FGFR inhibitor against organoids derived from the FGFR1-ERLIN2 fusion-positive ASCP PDX model. Our results suggest that the genomic and epigenomic landscape of ASCP provide new strategies for targeting this aggressive subtype of pancreatic cancer. SIGNIFICANCE: These data provide a unique description of the ASCP genomic and epigenomic landscape and identify candidate therapeutic targets for this dismal cancer.
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Affiliation(s)
- Elizabeth Lenkiewicz
- Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Smriti Malasi
- Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Tara L Hogenson
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, Minnesota
| | - Luis F Flores
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, Minnesota
| | - Whitney Barham
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, Minnesota
| | - William J Phillips
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, Minnesota
| | - Alexander S Roesler
- Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Kendall R Chambers
- Department of Pharmacology, University of California, San Diego School of Medicine, La Jolla, California
| | - Nirakar Rajbhandari
- Department of Pharmacology, University of California, San Diego School of Medicine, La Jolla, California
| | - Akimasa Hayashi
- The David M. Rubenstein Center for Pancreatic Cancer Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Corina E Antal
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Paul M Grandgenett
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Michael A Hollingsworth
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Yuning Xiong
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota.,Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jeong-Heon Lee
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota.,Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Zhenqing Ye
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota.,Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Huihuang Yan
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota.,Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | | | | | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota.,Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mark J Truty
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Mitesh J Borad
- Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Scottsdale, Arizona.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota.,Mayo Clinic Cancer Center, Mayo Clinic, Phoenix, Arizona
| | - Tannishtha Reya
- Department of Pharmacology, University of California, San Diego School of Medicine, La Jolla, California
| | - Daniel D Von Hoff
- Translational Genomics Research Institute, Phoenix, Arizona.,Virginia G Piper Cancer Center at HonorHealth, Scottsdale, Arizona
| | - Martin E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, Minnesota
| | - Michael T Barrett
- Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Scottsdale, Arizona.
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Abstract
Diffuse gliomas inevitably progress, but our understanding of the molecular events associated with recurrence is limited. Recent work from the Glioma Longitudinal Analysis (GLASS) consortium (Barthel et al., 2019) reports temporal DNA sequencing on a large cohort of primary and recurrent glioma pairs, establishing the evolutionary molecular characteristics of adult diffuse gliomas.
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Affiliation(s)
- Ashwin Narayanan
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Sevin Turcan
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany.
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15
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The cyclical hit model: how paligenosis might establish the mutational landscape in Barrett's esophagus and esophageal adenocarcinoma. Curr Opin Gastroenterol 2019; 35:363-370. [PMID: 31021922 DOI: 10.1097/mog.0000000000000540] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW In this review, we explore a paligenosis-based model to explain Barrett's esophagus development and progression: 'the cyclical hit model.' RECENT FINDINGS Genomic analyses have highlighted the high mutational burden of esophageal adenocarcinoma, Barrett's esophagus, and even normal esophageal epithelium. Somatic mutations in key genes including TP53 occur early in the neoplastic progression sequence of Barrett's esophagus, whereas chromosomal amplification resulting in oncogene activation occurs as a critical late event. Paligenosis is a shared injury response mechanism characterized by activation of autophagy, expression of progenitor markers, and increased mTORC signaling-induced cell-cycle reentry. In the setting of chronic injury/inflammation, cycles of paligenosis may allow accumulation of mutations until eventually the mutational burden, in concert perhaps with mutations in key driver oncogenes, finally alters the cell's ability to redifferentiate, leading to the emergence of a potential neoplastic clone. SUMMARY Under conditions of chronic gastroesophageal refluxate exposure, the normal esophageal squamous epithelium might undergo multiple cycles of paligenosis, allowing initially silent mutations to accumulate until key events impart mutant clones with an oncogenic survival advantage.
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Genomic landscape of allelic imbalance in premalignant atypical adenomatous hyperplasias of the lung. EBioMedicine 2019; 42:296-303. [PMID: 30905849 PMCID: PMC6491940 DOI: 10.1016/j.ebiom.2019.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 02/08/2023] Open
Abstract
Background Genomic investigation of atypical adenomatous hyperplasia (AAH), the only known precursor lesion to lung adenocarcinomas (LUAD), presents challenges due to the low mutant cell fractions. This necessitates sensitive methods for detection of chromosomal aberrations to better study the role of critical alterations in early lung cancer pathogenesis and the progression from AAH to LUAD. Methods We applied a sensitive haplotype-based statistical technique to detect chromosomal alterations leading to allelic imbalance (AI) from genotype array profiling of 48 matched normal lung parenchyma, AAH and tumor tissues from 16 stage-I LUAD patients. To gain insights into shared developmental trajectories among tissues, we performed phylogenetic analyses and integrated our results with point mutation data, highlighting significantly-mutated driver genes in LUAD pathogenesis. Findings AI was detected in nine AAHs (56%). Six cases exhibited recurrent loss of 17p. AI and the enrichment of 17p events were predominantly identified in patients with smoking history. Among the nine AAH tissues with detected AI, seven exhibited evidence for shared chromosomal aberrations with matched LUAD specimens, including losses harboring tumor suppressors on 17p, 8p, 9p, 9q, 19p, and gains encompassing oncogenes on 8q, 12p and 1q. Interpretation Chromosomal aberrations, particularly 17p loss, appear to play critical roles early in AAH pathogenesis. Genomic instability in AAH, as well as truncal chromosomal aberrations shared with LUAD, provide evidence for mutation accumulation and are suggestive of a cancerized field contributing to the clonal selection and expansion of these premalignant lesions. Fund Supported in part by Cancer Prevention and Research Institute of Texas (CPRIT) grant RP150079 (PS and HK), NIH grant R01HG005859 (PS) and The University of Texas MD Anderson Cancer Center Core Support Grant.
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17
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Complex structural rearrangements are present in high-grade dysplastic Barrett's oesophagus samples. BMC Med Genomics 2019; 12:31. [PMID: 30717762 PMCID: PMC6360790 DOI: 10.1186/s12920-019-0476-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
Background Oesophageal adenocarcinoma (EAC) incidence is increasing and has a poor survival rate. Barrett’s oesophagus (BE) is a precursor condition that is associated with EAC and often occurs in conjunction with chronic gastro-oesophageal reflux, however many individuals diagnosed with BE never progress to cancer. An understanding of the genomic features of BE and EAC may help with the early identification of at-risk individuals. Methods In this study, we assessed the genomic features of 16 BE samples using whole-genome sequencing. These included non-dysplastic samples collected at two time-points from two BE patients who had not progressed to EAC over several years. Seven other non-dysplastic samples and five dysplastic BE samples with high-grade dysplasia were also examined. We compared the genome profiles of these 16 BE samples with 22 EAC samples. Results We observed that samples from the two non-progressor individuals had low numbers of somatic single nucleotide variants, indels and structural variation events compared to dysplastic and the remaining non-dysplastic BE. EAC had the highest level of somatic genomic variations. Mutational signature 17, which is common in EAC, was also present in non-dysplastic and dysplastic BE, but was not present in the non-progressors. Many dysplastic samples had mutations in genes previously reported in EAC, whereas only mutations in CDKN2A or in the fragile site genes appeared common in non-dysplastic samples. Rearrangement signatures were used to identify a signature associated with localised complex events such as chromothripsis and breakage fusion-bridge that are characteristic of EACs. Two dysplastic BE samples had a high contribution of this signature and contained evidence of localised rearrangements. Two other dysplastic samples also had regions of localised structural rearrangements. There was no evidence for complex events in non-dysplastic samples. Conclusions The presence of complex localised rearrangements in dysplastic samples indicates a need for further investigations into the role such events play in the progression from BE to EAC. Electronic supplementary material The online version of this article (10.1186/s12920-019-0476-9) contains supplementary material, which is available to authorized users.
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18
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Abstract
Esophageal adenocarcinoma (EAC) develops from Barrett's esophagus (BE), a condition where the normal squamous epithelia is replaced by specialized intestinal metaplasia in response to chronic gastroesophageal acid reflux. In a minority of individuals, BE can progress to low- and high-grade dysplasia and eventually to intra-mucosal and then invasive carcinoma. BE provides researchers with a unique model to characterize the process by which a carcinoma arises from its precursor lesion. Molecular studies of BE have demonstrated that it is not simply a metaplastic tissue, but rather it harbors frequent alterations that are also present in dysplastic BE and in EAC. Both BE and EAC are characterized by loss of heterozygosity, aneuploidy, specific genetic mutations, and clonal diversity. Epigenetic abnormalities, primary alterations in DNA methylation, are also frequently seen in BE and EAC. Candidate gene and array-based approaches have demonstrated that numerous tumor suppressor genes exhibit aberrant promoter methylation, and some of these altered genes are associated with the neoplastic progression of BE. It has also been shown that the BE and EAC epigenomes are characterized by hypomethylation of intragenic and non-coding regions Recent studies have also provided new insight into the evolutionary forces underlying the molecular alterations seen in BE and EAC and into the molecular pathogenesis of EAC.
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Affiliation(s)
- William M. Grady
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA,University of Washington School of Medicine, Department of Internal Medicine, Seattle, WA
| | - Ming Yu
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA
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19
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Vedeld HM, Goel A, Lind GE. Epigenetic biomarkers in gastrointestinal cancers: The current state and clinical perspectives. Semin Cancer Biol 2018; 51:36-49. [PMID: 29253542 PMCID: PMC7286571 DOI: 10.1016/j.semcancer.2017.12.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/17/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023]
Abstract
Each year, almost 4.1 million people are diagnosed with gastrointestinal (GI) cancers. Due to late detection of this disease, the mortality is high, causing approximately 3 million cancer-related deaths annually, worldwide. Although the incidence and survival differs according to organ site, earlier detection and improved prognostication have the potential to reduce overall mortality burden from these cancers. Epigenetic changes, including aberrant promoter DNA methylation, are common events in both cancer initiation and progression. Furthermore, such changes may be identified non-invasively with the use of PCR based methods, in bodily fluids of cancer patients. These features make aberrant DNA methylation a promising substrate for the development of disease biomarkers for early detection, prognosis and for predicting response to therapy. In this article, we will provide an update and current clinical perspectives for DNA methylation alterations in patients with colorectal, gastric, pancreatic, liver and esophageal cancers, and discuss their potential role as cancer biomarkers.
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Affiliation(s)
- Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Ajay Goel
- Center for Gastrointestinal Research, and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA.
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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20
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Abstract
The incidence of esophageal adenocarcinoma (EAC) and its precursor lesion Barrett's esophagus (BE) has been increasing steadily in the western world in recent decades. Understanding the cellular origins of BE and the conditions responsible for their malignant transformation would greatly facilitate risk assessment and identification of patients at risk of progression, but this topic remains a source of debate. Here, we review recent findings that have provided support for the gastroesophageal junction (GEJ) as the main source of stem cells that give rise to BE and EAC. These include both gastric cardia cells and transitional basal cells. Furthermore, we discuss the role of chronic injury and inflammation in a tumor microenvironment as a major factor in promoting stem cell expansion and proliferation as well as transformation of the GEJ-derived stem cells and progression to EAC. We conclude that there exists a large amount of empirical support for the GEJ as the likely source of BE stem cells. While BE seems to resemble a successful adaptation to esophageal damage, carcinogenesis appears as a consequence of natural selection at the level of GEJ stem cells, and later glands, that expand into the esophagus wherein the local ecology creates the selective landscape for cancer progression.
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21
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Nieto T, Tomlinson CL, Dretzke J, Bayliss S, Price MJ, Dilworth M, Beggs AD, Tucker O. A systematic review of epigenetic biomarkers in progression from non-dysplastic Barrett's oesophagus to oesophageal adenocarcinoma. BMJ Open 2018; 8:e020427. [PMID: 29961009 PMCID: PMC6042533 DOI: 10.1136/bmjopen-2017-020427] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/16/2018] [Accepted: 05/03/2018] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES The objective of this systematic review is to identify and summarise studies which examine epigenetic biomarkers in patients with Barrett's oesophagus (BO) and their association with progression to oesophageal adenocarcinoma (OADC). BO is a precursor lesion for OADC. There is no clinical test to predict patients who are likely to progress to OADC. An epigenetic biomarker could predict patients who are at high risk of progression from BO to OADC which could facilitate earlier diagnosis and spare those unlikely to develop cancer from regular invasive surveillance endoscopy. SETTING A systematic search was conducted of the following databases: MEDLINE, MEDLINE in Process, EMBASE, Cochrane Central, ISI Conference Proceedings Citation Index and the British Library's ZETOC. Studies were conducted in secondary and tertiary care settings. PARTICIPANTS All studies measuring epigenetic change in patients over 18 years old who progressed from non-dysplastic BO to OADC were included. Genetic, in vitro and studies which did not measure progression in the same patient cohort were excluded. Study inclusion and risk of bias of individual eligible studies were assessed in duplicate by two reviewers using a modified Quality in Prognostic Studies tool. RESULTS 14 studies met the inclusion criteria. 42 epigenetic markers were identified, and 5 studies developed models aiming to predict progression to OADC. CONCLUSIONS The evidence from this systematic review is suggestive of a role for p16 as an epigenetic biomarker for the progression of BO to OADC. PROSPERO NUMBER CRD42016038654.
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Affiliation(s)
- Tom Nieto
- Department of Surgery, University of Birmingham, Birmingham, UK
| | - Claire L Tomlinson
- Birmingham Clinical Trials Unit, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Janine Dretzke
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Susan Bayliss
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Malcolm James Price
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Mark Dilworth
- Department of Surgery, Heart of England Foundation Trust and Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Andrew D Beggs
- Department of Surgery, University of Birmingham, Birmingham, UK
| | - Olga Tucker
- Department of Surgery, University of Birmingham, Birmingham, UK
- Department of Surgery, Heart of England Foundation Trust and Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
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22
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Wangsa D, Quintanilla I, Torabi K, Vila-Casadesús M, Ercilla A, Klus G, Yuce Z, Galofré C, Cuatrecasas M, Lozano JJ, Agell N, Cimini D, Castells A, Ried T, Camps J. Near-tetraploid cancer cells show chromosome instability triggered by replication stress and exhibit enhanced invasiveness. FASEB J 2018; 32:3502-3517. [PMID: 29452566 DOI: 10.1096/fj.201700247rr] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A considerable proportion of tumors exhibit aneuploid karyotypes, likely resulting from the progressive loss of chromosomes after whole-genome duplication. Here, by using isogenic diploid and near-tetraploid (4N) single-cell-derived clones from the same parental cell lines, we aimed at exploring how polyploidization affects cellular functions and how tetraploidy generates chromosome instability. Gene expression profiling in 4N clones revealed a significant enrichment of transcripts involved in cell cycle and DNA replication. Increased levels of replication stress in 4N cells resulted in DNA damage, impaired proliferation caused by a cell cycle delay during S phase, and higher sensitivity to S phase checkpoint inhibitors. In fact, increased levels of replication stress were also observed in nontransformed, proliferative posttetraploid RPE1 cells. Additionally, replication stress promoted higher levels of intercellular genomic heterogeneity and ongoing genomic instability, which could be explained by high rates of mitotic defects, and was alleviated by the supplementation of exogenous nucleosides. Finally, our data found that 4N cancer cells displayed increased migratory and invasive capacity, both in vitro and in primary colorectal tumors, indicating that tetraploidy can promote aggressive cancer cell behavior.-Wangsa, D., Quintanilla, I., Torabi, K., Vila-Casadesús, M., Ercilla, A., Klus, G., Yuce, Z., Galofré, C., Cuatrecasas, M., Lozano, J. J., Agell, N., Cimini, D., Castells, A., Ried, T., Camps, J. Near-tetraploid cancer cells show chromosome instability triggered by replication stress and exhibit enhanced invasiveness.
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Affiliation(s)
- Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Isabel Quintanilla
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Keyvan Torabi
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Maria Vila-Casadesús
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain.,Bioinformatics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Amaia Ercilla
- Departament de Biologia Cel·lular, Immunologia i Neurociències, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Gregory Klus
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zeynep Yuce
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Department of Medical Biology and Genetics, School of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Claudia Galofré
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Department of Pathology-Centro de Diagnóstico Biomédico (CDB), Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Juan José Lozano
- Bioinformatics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Neus Agell
- Departament de Biologia Cel·lular, Immunologia i Neurociències, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Daniela Cimini
- Department of Biological Sciences, Biocomplexity Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Antoni Castells
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Rasool S, Ganai BA, Sameer AS, Masood A. Esophageal Cancer: Associated Factors with Special Reference to the Kashmir Valley. TUMORI JOURNAL 2018; 98:191-203. [DOI: 10.1177/030089161209800203] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Esophageal cancer is one of the most common cancers worldwide. It is a multifactorial disease, and no single agent has been identified so far as the sole cause of the cancer. Many factors like smoking, the consumption of alcohol, fungal-contaminated, spicy and various nitrosamine-containing food stuffs and hot beverages, nutritional deficiency of some vitamins like β-carotene, vitamin A, C and E and minerals like zinc, selenium and molybdenum, the use of opium, HPV infection and various genetic factors have been found associated with the occurrence of the disease worldwide. Wide geographic differences and substantial changes in the incidence of esophageal cancer occurring over time have been suggested. Among the risk factors in India, betel quid chewing carries a relatively high risk. High incidences in Kashmir have been associated with the consumption of hot salted tea, sun-dried, smoked foods, tobacco in the form of hukka and various genetic factors. The exact cause of esophageal squamous cell carcinoma is unknown. Much work has been carried out on the role of various environmental factors, gene mutations, and polymorphisms worldwide, including Kashmir. Although the Kashmir valley is present on the border of the ‘high risk esophageal cancer belt’ and esophageal squamous cell carcinoma represents the most commonly occurring malignancy in Kashmir, the amount of information available on various associated factors is still very little as there is a paucity of various epidemiological and molecular studies being carried out in this field.
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Affiliation(s)
- Sabha Rasool
- Department of Biochemistry, University of Kashmir, Hazratbal, Srinagar, Kashmir
| | - Bashir A Ganai
- Department of Biochemistry, University of Kashmir, Hazratbal, Srinagar, Kashmir
| | - A Syed Sameer
- Department of Biochemistry, Medical College, Sher-I-Kashmir Institute of Medical Sciences, Bemina, Srinagar, Kashmir, India
| | - Akbar Masood
- Department of Biochemistry, University of Kashmir, Hazratbal, Srinagar, Kashmir
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24
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Abstract
Where does cancer come from? Although the cell-of-origin is difficult to pinpoint, cancer clones harbor information about their clonal ancestries. In an effort to find cells before they evolve into a life-threatening cancer, physicians currently diagnose premalignant diseases at frequencies that substantially exceed those of clinical cancers. Cancer risk prediction relies on our ability to distinguish between which premalignant features will lead to cancer mortality and which are characteristic of inconsequential disease. Here, we review the evolution of cancer from premalignant disease, and discuss the concept that even phenotypically normal cell progenies inherently gain more malignant potential with age. We describe the hurdles of prognosticating cancer risk in premalignant disease by making reference to the underlying continuous and multivariate natures of genotypes and phenotypes and the particular challenge inherent in defining a cell lineage as "cancerized."
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Affiliation(s)
- Kit Curtius
- Centre for Tumor Biology, Barts Cancer Institute, EC1M 6BQ London, United Kingdom
| | - Nicholas A Wright
- Centre for Tumor Biology, Barts Cancer Institute, EC1M 6BQ London, United Kingdom
| | - Trevor A Graham
- Centre for Tumor Biology, Barts Cancer Institute, EC1M 6BQ London, United Kingdom
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25
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Yang L, Lin PC. Mechanisms that drive inflammatory tumor microenvironment, tumor heterogeneity, and metastatic progression. Semin Cancer Biol 2017; 47:185-195. [PMID: 28782608 PMCID: PMC5698110 DOI: 10.1016/j.semcancer.2017.08.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/26/2017] [Accepted: 08/01/2017] [Indexed: 12/12/2022]
Abstract
Treatment of cancer metastasis has been largely ineffective. It is paramount to understand the mechanisms underlying the metastatic process, of which the tumor microenvironment is an indispensable participant. What are the critical cellular and molecular players at the primary tumor site where metastatic cascade initiates? How is tumor-associated inflammation regulated? How do altered vasculatures contribute to metastasis? What is the dynamic nature or heterogeneity of primary tumors and what are the challenges to catch a moving target? This review summarizes recent progress, mechanistic understanding, and options for metastasis-targeted therapy.
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Affiliation(s)
- Li Yang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA.
| | - P Charles Lin
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA.
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26
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Clonal Evolution in Multiple Myeloma. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2017; 16 Suppl:S130-4. [PMID: 27521309 DOI: 10.1016/j.clml.2016.02.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 02/09/2016] [Indexed: 01/03/2023]
Abstract
Multiple myeloma (MM) is the second most common hematologic malignancy encountered among patients in the United States. The last decade has seen incremental improvements in the survival of patients with MM. These advances are, to a large extent, attributable to the addition of proteasome inhibitors and immunomodulatory drugs to the armamentarium of treatment options. The adoption of these drug classes was the result of an empiric research paradigm. However, with the application of next generation sequencing technologies, we are now starting to unravel the genomic landscape of MM. It is hoped that this will allow us to better disentangle the biology of the disease and allow for identification of new therapeutic targets. In this article, we review what we have learned to date about the mutational profile, clonal architecture, and evolution of the disease, and discuss the potential clinical implications of these findings.
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27
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Contino G, Vaughan TL, Whiteman D, Fitzgerald RC. The Evolving Genomic Landscape of Barrett's Esophagus and Esophageal Adenocarcinoma. Gastroenterology 2017; 153:657-673.e1. [PMID: 28716721 PMCID: PMC6025803 DOI: 10.1053/j.gastro.2017.07.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 06/21/2017] [Accepted: 07/11/2017] [Indexed: 12/13/2022]
Abstract
We have recently gained unprecedented insight into genetic factors that determine risk for Barrett's esophagus (BE) and progression to esophageal adenocarcinoma (EA). Next-generation sequencing technologies have allowed us to identify somatic mutations that initiate BE and track genetic changes during development of tumors and invasive cancer. These technologies led to identification of mechanisms of tumorigenesis that challenge the current multistep model of progression to EA. Newer, cost-effective technologies create opportunities to rapidly translate the analysis of DNA into tools that can identify patients with BE at high risk for cancer, detect dysplastic lesions more reliably, and uncover mechanisms of carcinogenesis.
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Affiliation(s)
- Gianmarco Contino
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK.
| | - Thomas L Vaughan
- Cancer Epidemiology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - David Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
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28
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Goel R, Subramaniam RM, Wachsmann JW. PET/Computed Tomography Scanning and Precision Medicine: Esophageal Cancer. PET Clin 2017; 12:373-391. [PMID: 28867110 DOI: 10.1016/j.cpet.2017.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Esophageal cancer commonly has a poor prognosis, which requires an accurate diagnosis and early treatment to improve outcome. Other modalities for staging, such as endoscopic ultrasound imaging and computed tomography (CT) scans, have a role in diagnosis and staging. However, PET with fluorine-18 fluoro-2-deoxy-d-glucose/CT (FDG PET/CT) scanning allows for improved detection of distant metastatic disease and can help to prevent unnecessary interventions that would increase morbidity. FDG PET/CT scanning is valuable in the neoadjuvant chemotherapy assessment and predicting survival outcomes subsequent to surgery. FDG PET/CT scanning detects recurrent disease and metastases in follow-up.
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Affiliation(s)
- Reema Goel
- Department of Radiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8896, USA
| | - Rathan M Subramaniam
- Department of Radiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8896, USA; Department of Clinical Sciences, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8896, USA; Department of Biomedical Engineering, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8896, USA; Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8896, USA; Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8896, USA
| | - Jason W Wachsmann
- Department of Radiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8896, USA.
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Disseminated tumour cells with highly aberrant genomes are linked to poor prognosis in operable oesophageal adenocarcinoma. Br J Cancer 2017; 117:725-733. [PMID: 28728164 PMCID: PMC5572184 DOI: 10.1038/bjc.2017.233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 06/13/2017] [Accepted: 06/23/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Chromosomal instability (CIN) has repeatedly been identified as a prognostic marker. Here we evaluated the percentage of aberrant genome per cell (PAG) as a measure of CIN in single disseminated tumour cells (DTC) isolated from patients with operable oesophageal adenocarcinoma (EAC), to assess the impact of CINhigh DTCs on prognosis. METHODS We isolated CK18positive DTCs from bone marrow (BM) or lymph node (LN) preparations of operable EAC patients. After whole-genome amplification, single DTCs were analysed for chromosomal gains and losses using metaphase-based comparative genomic hybridisation (mCGH). We calculated the PAG for each DTC and determined the critical threshold value that identifies high-risk patients by STEPP (Subpopulation Treatment Effect Pattern Plot) analysis in two independent EAC patient cohorts (cohort #1, n=44; cohort #2; n=29). RESULTS The most common chromosomal alterations observed among the DTCs were typical for EAC, but the DTCs showed a varying PAG between individual patients. Generally, LNDTCs displayed a significantly higher PAG than BMDTCs. STEPP analysis revealed an increasing PAG of DTCs to be correlated with an increased risk for short survival in two independent EAC cohorts as well as in the corresponding pooled analysis. In all three data sets (cohort #1, cohort #2 and pooled cohort), PAGhigh DTCs conferred an independent risk for a significantly decreased survival. CONCLUSIONS The analysis of PAG/CIN in solitary marker-positive DTCs identifies operable EAC patients with poor prognosis, indicating a more aggressive minimal residual disease.
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30
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Altaf K, Xiong JJ, la Iglesia DD, Hickey L, Kaul A. Meta-analysis of biomarkers predicting risk of malignant progression in Barrett's oesophagus. Br J Surg 2017; 104:493-502. [PMID: 28295252 DOI: 10.1002/bjs.10484] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/18/2016] [Accepted: 12/08/2016] [Indexed: 02/05/2023]
Abstract
BACKGROUND Barrett's oesophagus is a precursor to the development of oesophageal adenocarcinoma. This study sought to clarify the role of genetic, chromosomal and proliferation biomarkers that have been the subjects of multiple studies through meta-analysis. METHODS MEDLINE, Embase, PubMed and the Cochrane Library were searched for clinical studies assessing the value of p53, p16, Ki-67 and DNA content abnormalities in Barrett's oesophagus. The main outcome measure was the risk of development of high-grade dysplasia (HGD) or oesophageal adenocarcinoma. RESULTS Some 102 studies, with 12 353 samples, were identified. Mutation (diagnostic odds ratio (DOR) 10·91, sensitivity 47 per cent, specificity 92 per cent, positive likelihood ratio (PLR) 4·71, negative likelihood ratio (NLR) 0·65, area under the curve (AUC) 0·792) and loss (DOR 16·16, sensitivity 31 per cent, specificity 98 per cent, PLR 6·66, NLR 0·41, AUC 0·923) of p53 were found to be superior to the other p53 abnormalities (loss of heterozygosity (LOH) and overexpression). Ki-67 had high sensitivity in identifying high-risk patients (DOR 5·54, sensitivity 82 per cent, specificity 48 per cent, PLR 1·59, NLR 0·42, AUC 0·761). Aneuploidy (DOR 12·08, sensitivity 53 per cent, specificity 87 per cent, PLR 4·26, NLR 0·42, AUC 0·846), tetraploidy (DOR 5·87, sensitivity 46 per cent, specificity 85 per cent, PLR 3·47, NLR 0·65, AUC 0·793) and loss of Y chromosome (DOR 9·23, sensitivity 68 per cent, specificity 80 per cent, PLR 2·67, NLR 0·49, AUC 0·807) also predicted malignant development, but p16 aberrations (hypermethylation, LOH, mutation and loss) failed to demonstrate any advantage over the other biomarkers studied. CONCLUSION Loss and mutation of p53, and raised level of Ki-67 predicted malignant progression in Barrett's oesophagus.
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Affiliation(s)
- K Altaf
- Department of Surgery, Whiston Hospital, St Helen's and Knowsley Hospitals NHS Foundation Trust, Liverpool, UK
| | - J-J Xiong
- Department of Hepato-Biliary-Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - D De la Iglesia
- Department of Gastroenterology and Hepatology, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - L Hickey
- Department of Surgery, Whiston Hospital, St Helen's and Knowsley Hospitals NHS Foundation Trust, Liverpool, UK
| | - A Kaul
- Department of Surgery, Whiston Hospital, St Helen's and Knowsley Hospitals NHS Foundation Trust, Liverpool, UK
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31
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van Nistelrooij AMJ, van Marion R, Koppert LB, Biermann K, Spaander MCW, Tilanus HW, van Lanschot JJB, Wijnhoven BPL, Dinjens WNM. Molecular clonality analysis of esophageal adenocarcinoma by multiregion sequencing of tumor samples. BMC Res Notes 2017; 10:144. [PMID: 28376920 PMCID: PMC5379534 DOI: 10.1186/s13104-017-2456-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 03/17/2017] [Indexed: 01/10/2023] Open
Abstract
Background Intratumor heterogeneity has been demonstrated in several cancer types, following a model of branched evolution. It is unknown to which extent intratumor heterogeneity is applicable to esophageal adenocarcinoma. Therefore the aim of this study was to characterise intratumor heterogeneity in esophageal adenocarcinoma. Methods Multiregional targeted sequencing of four commonly altered genes was performed on 19 tumor regions collected from five esophageal adenocarcinomas. Alterations were classified as homogeneous or heterogeneous based on mutational and loss of heterozygosity analysis. Results Identical TP53 mutations and homogeneously loss of heterozygosity of the TP53 locus were identified in all separated tumor regions in each of five adenocarcinomas, and in the corresponding Barrett’s esophagus and tumor positive lymph node of one primary tumor. Loss of heterozygosity of the P16 locus was homogeneous among all tumor regions in four adenocarcinomas, and an identical pattern of loss of heterozygosity was present in the Barrett’s esophagus. Loss of heterozygosity of the SMAD4 and APC loci was observed in a heterogeneous pattern. Conclusions Known driver alterations, such as TP53 and P16 are homogeneously present within each adenocarcinoma, and therefore occur early during carcinogenesis and subsequently clonally expand throughout the entire tumor. However, loss of heterozygosity of the SMAD4 and APC loci shows a heterogeneous pattern, indicating intratumor heterogeneity of esophageal adenocarcinoma.
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Affiliation(s)
- Anna M J van Nistelrooij
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Linetta B Koppert
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Katharina Biermann
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Manon C W Spaander
- Department of Gastroenterology & Hepatology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Hugo W Tilanus
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - J Jan B van Lanschot
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Bas P L Wijnhoven
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
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Abbosh C, Venkatesan S, Janes SM, Fitzgerald RC, Swanton C. Evolutionary dynamics in pre-invasive neoplasia. CURRENT OPINION IN SYSTEMS BIOLOGY 2017; 2:1-8. [PMID: 30603736 PMCID: PMC6312179 DOI: 10.1016/j.coisb.2017.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mutational processes occur in normal tissues from conception throughout life. Field cancerization describes the preconditioning of an area of epithelium to tumor growth. Pre-invasive lesions may arise in these fields, however only a minority of pre-invasive neoplasia progresses to overt malignancy. Within this review we discuss recent advances in our understanding of genomic instability processes in normal tissue, describe evolutionary dynamics in pre-invasive disease and highlight current evidence describing how increasing genomic instability may drive the transition from pre-invasive to invasive disease. Appreciation of the evolutionary rulebooks that operate in pre-invasive neoplasia may facilitate screening strategies, risk-stratification of pre-invasive lesions and precipitate novel preventative treatments in at-risk patient populations.
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Affiliation(s)
- Christopher Abbosh
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley St., London WC1E 6DD, UK
| | - Subramanian Venkatesan
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley St., London WC1E 6DD, UK
- Translational Cancer Therapeutics Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT
| | - Samuel M Janes
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, Rayne Building, University College London, London, UK
| | - Rebecca C Fitzgerald
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Charles Swanton
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley St., London WC1E 6DD, UK
- Translational Cancer Therapeutics Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT
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33
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Letsolo BT, Jones RE, Rowson J, Grimstead JW, Keith WN, Jenkins GJS, Baird DM. Extensive telomere erosion is consistent with localised clonal expansions in Barrett's metaplasia. PLoS One 2017; 12:e0174833. [PMID: 28362812 PMCID: PMC5375150 DOI: 10.1371/journal.pone.0174833] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/15/2017] [Indexed: 12/24/2022] Open
Abstract
Barrett's oesophagus is a premalignant metaplastic condition that predisposes patients to the development of oesophageal adenocarcinoma. However, only a minor fraction of Barrett's oesophagus patients progress to adenocarcinoma and it is thus essential to determine bio-molecular markers that can predict the progression of this condition. Telomere dysfunction is considered to drive clonal evolution in several tumour types and telomere length analysis provides clinically relevant prognostic and predictive information. The aim of this work was to use high-resolution telomere analysis to examine telomere dynamics in Barrett's oesophagus. Telomere length analysis of XpYp, 17p, 11q and 9p, chromosome arms that contain key cancer related genes that are known to be subjected to copy number changes in Barrett's metaplasia, revealed similar profiles at each chromosome end, indicating that no one specific telomere is likely to suffer preferential telomere erosion. Analysis of patient matched tissues (233 samples from 32 patients) sampled from normal squamous oesophagus, Z-line, and 2 cm intervals within Barrett's metaplasia, plus oesophago-gastric junction, gastric body and antrum, revealed extensive telomere erosion in Barrett's metaplasia to within the length ranges at which telomere fusion is detected in other tumour types. Telomere erosion was not uniform, with distinct zones displaying more extensive erosion and more homogenous telomere length profiles. These data are consistent with an extensive proliferative history of cells within Barrett's metaplasia and are indicative of localised clonal growth. The extent of telomere erosion highlights the potential of telomere dysfunction to drive genome instability and clonal evolution in Barrett's metaplasia.
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Affiliation(s)
- Boitelo T. Letsolo
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Rhiannon E. Jones
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Jan Rowson
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Julia W. Grimstead
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - W. Nicol Keith
- Institute of Cancer Sciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gareth J. S. Jenkins
- GI Cancer Group, School of Medicine, Swansea University, Swansea, United Kingdom
| | - Duncan M. Baird
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
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Abstract
In The Cancer Genome Atlas the goals were to define how to treat advanced cancers with targeted therapy. However, the challenges facing cancer interception for early detection and prevention include length bias in which current screening and surveillance approaches frequently miss rapidly progressing cancers that then present at advanced stages in the clinic with symptoms (underdiagnosis). In contrast, many early detection strategies detect benign conditions that may never progress to cancer during a lifetime, and the patient dies of unrelated causes (overdiagnosis). This challenge to cancer interception is believed to be due to the speed at which the neoplasm evolves, called length bias sampling; rapidly progressing cancers are missed by current early detection strategies. In contrast, slowly or non-progressing cancers or their precursors are selectively detected. This has led to the concept of cancer interception, which can be defined as active interception of a biological process that drives cancer development before the patient presents in the clinic with an advanced, symptomatic cancer. The solutions needed to advance strategies for cancer interception require assessing the rate at which the cancer evolves over time and space. This is an essential challenge that needs to be addressed by robust study designs including normal and non-progressing controls when known to be appropriate.
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Affiliation(s)
- Brian J. Reid
- Correspondence Address correspondence to: Brian J. Reid, MD, PhD, 1100 Fairview Avenue N, C1-157, PO Box 19024, Seattle, Washington 98109-1024. fax: (206) 667-6192.1100 Fairview Avenue N, C1-157, PO Box 19024SeattleWashington 98109-1024
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35
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Abstract
Chromosomal aberrations during cell division represent one of the first recognized features of human cancer cells, and modern detection methods have revealed the pervasiveness of aneuploidy in cancer. The ongoing karyotypic changes brought about by chromosomal instability (CIN) contribute to tumor heterogeneity, drug resistance, and treatment failure. Whole-chromosome and segmental aneuploidies resulting from CIN have been proposed to allow "macroevolutionary" leaps that may contribute to profound phenotypic change. In this review, we will outline evidence indicating that aneuploidy and CIN contribute to cancer evolution.
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Affiliation(s)
- Laurent Sansregret
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, United Kingdom
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, United Kingdom
- CRUK Lung Cancer Centre of Excellence/UCL Cancer Institute, London WC1E 6BT, United Kingdom
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Timmer MR, Martinez P, Lau CT, Westra WM, Calpe S, Rygiel AM, Rosmolen WD, Meijer SL, ten Kate FJ, Dijkgraaf MG, Mallant-Hent RC, Naber AH, van Oijen AH, Baak LC, Scholten P, Böhmer CJ, Fockens P, Maley CC, Graham TA, Bergman JJ, Krishnadath KK. Derivation of genetic biomarkers for cancer risk stratification in Barrett's oesophagus: a prospective cohort study. Gut 2016; 65:1602-10. [PMID: 26104750 PMCID: PMC4988941 DOI: 10.1136/gutjnl-2015-309642] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/06/2015] [Indexed: 01/10/2023]
Abstract
OBJECTIVE The risk of developing adenocarcinoma in non-dysplastic Barrett's oesophagus is low and difficult to predict. Accurate tools for risk stratification are needed to increase the efficiency of surveillance. We aimed to develop a prediction model for progression using clinical variables and genetic markers. METHODS In a prospective cohort of patients with non-dysplastic Barrett's oesophagus, we evaluated six molecular markers: p16, p53, Her-2/neu, 20q, MYC and aneusomy by DNA fluorescence in situ hybridisation on brush cytology specimens. Primary study outcomes were the development of high-grade dysplasia or oesophageal adenocarcinoma. The most predictive clinical variables and markers were determined using Cox proportional-hazards models, receiver operating characteristic curves and a leave-one-out analysis. RESULTS A total of 428 patients participated (345 men; median age 60 years) with a cumulative follow-up of 2019 patient-years (median 45 months per patient). Of these patients, 22 progressed; nine developed high-grade dysplasia and 13 oesophageal adenocarcinoma. The clinical variables, age and circumferential Barrett's length, and the markers, p16 loss, MYC gain and aneusomy, were significantly associated with progression on univariate analysis. We defined an 'Abnormal Marker Count' that counted abnormalities in p16, MYC and aneusomy, which significantly improved risk prediction beyond using just age and Barrett's length. In multivariate analysis, these three factors identified a high-risk group with an 8.7-fold (95% CI 2.6 to 29.8) increased HR when compared with the low-risk group, with an area under the curve of 0.76 (95% CI 0.66 to 0.86). CONCLUSIONS A prediction model based on age, Barrett's length and the markers p16, MYC and aneusomy determines progression risk in non-dysplastic Barrett's oesophagus.
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Affiliation(s)
- Margriet R. Timmer
- Department of Gastroenterology and Hepatology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Pierre Martinez
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, EC1M 6BQ, United Kingdom
| | - Chiu T. Lau
- Department of Gastroenterology and Hepatology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Wytske M. Westra
- Department of Gastroenterology and Hepatology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Silvia Calpe
- Department of Gastroenterology and Hepatology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Agnieszka M. Rygiel
- Department of Gastroenterology and Hepatology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Wilda D. Rosmolen
- Department of Gastroenterology and Hepatology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Sybren L. Meijer
- Department of Pathology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Fiebo J.W. ten Kate
- Department of Pathology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Marcel G.W. Dijkgraaf
- Clinical Research Unit, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | | | - Anton H.J. Naber
- Department of Gastroenterology, Tergooiziekenhuizen, 1213 XZ, Hilversum, The Netherlands
| | | | - Lubbertus C. Baak
- Department of Gastroenterology, Onze Lieve Vrouwe Gasthuis, 1091 AC, Amsterdam, The Netherlands
| | - Pieter Scholten
- Department of Gastroenterology, Sint Lucas Andreas Ziekenhuis, 1061 AE, Amsterdam, The Netherlands
| | - Clarisse J.M. Böhmer
- Department of Gastroenterology, Spaarne Ziekenhuis, 2134 TM, Hoofddorp, The Netherlands
| | - Paul Fockens
- Department of Gastroenterology and Hepatology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Carlo C. Maley
- Centre for Evolution and Cancer, University of California at San Francisco, CA 94143-0128, USA
| | - Trevor A. Graham
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, EC1M 6BQ, United Kingdom
| | - Jacques J.G.H.M. Bergman
- Department of Gastroenterology and Hepatology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
| | - Kausilia K. Krishnadath
- Department of Gastroenterology and Hepatology, Academic Medical Centre – University of Amsterdam, 1011 AZ, Amsterdam, The Netherlands
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Bhardwaj V, Horvat A, Korolkova O, Washington MK, El-Rifai W, Dikalov SI, Zaika AI. Prevention of DNA damage in Barrett's esophageal cells exposed to acidic bile salts. Carcinogenesis 2016; 37:1161-1169. [PMID: 27655834 DOI: 10.1093/carcin/bgw100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 09/01/2016] [Accepted: 09/20/2016] [Indexed: 12/15/2022] Open
Abstract
Esophageal adenocarcinoma (EA) is one of the fastest rising tumors in the USA. The major risk factor for EA is gastroesophageal reflux disease (GERD). During GERD, esophageal cells are exposed to refluxate which contains gastric acid frequently mixed with duodenal bile. This may lead to mucosal injury and Barrett's metaplasia (BE) that are important factors contributing to development of EA. In this study, we investigated DNA damage in BE cells exposed to acidic bile salts and explored for potential protective strategies. Exposure of BE cells to acidic bile salts led to significant DNA damage, which in turn, was due to generation of reactive oxygen species (ROS). We found that acidic bile salts induce a rapid increase in superoxide radicals and hydrogen peroxide, which were determined using electron paramagnetic resonance spectroscopy and Amplex Red assay. Analyzing a panel of natural antioxidants, we identified apocynin to be the most effective in protecting esophageal cells from DNA damage induced by acidic bile salts. Mechanistic analyses showed that apocynin inhibited ROS generation and increases the DNA repair capacity of BE cells. We identified BRCA1 and p73 proteins as apocynin targets. Downregulation of p73 inhibited the protective effect of apocynin. Taken together, our results suggest potential application of natural compounds such as apocynin for prevention of reflux-induced DNA damage and GERD-associated tumorigenesis.
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Affiliation(s)
- Vikas Bhardwaj
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA.,Department of Surgery
| | | | | | | | - Wael El-Rifai
- Department of Surgery.,Department of Cancer Biology and
| | - Sergey I Dikalov
- Division of Clinical Pharmacology, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Alexander I Zaika
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA, .,Department of Surgery.,Department of Cancer Biology and
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Levine AJ, Puzio-Kuter AM, Chan CS, Hainaut P. The Role of the p53 Protein in Stem-Cell Biology and Epigenetic Regulation. Cold Spring Harb Perspect Med 2016; 6:a026153. [PMID: 27352800 PMCID: PMC5008064 DOI: 10.1101/cshperspect.a026153] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The p53 protein plays a passive and an active role in stem cells. The transcriptional activities of p53 for cell-cycle arrest and DNA repair are largely turned off in stem cells, but there is some indication that long-term stem-cell viability may require other p53-regulated functions. When p53 is activated in stem cells, it stops cell division and promotes the commitment to a differentiation pathway and the formation of progenitor cells. In the absence of any p53 activity, stem-cell replication continues and mistakes in the normal epigenetic pathway occur at a higher probability. In the presence of a functionally active p53 protein, epigenetic stability is enforced and stem-cell replication is regulated by commitment to differentiation. Over a lifetime of an organism, stem-cell clones compete in a tissue niche for Darwinian replicative advantages and in doing so accumulate mutations that permit stem-cell replication. Mutations in the p53 gene give stem cells this advantage, increase the clonal stem-cell population, and lower the age at which cancers can occur. Li-Fraumeni patients that inherit p53 mutations develop tumors in a tissue-type-specific fashion at younger ages. Throughout the life of a Li-Fraumeni patient, the tumor types that arise occur in tissues where stem cells are active and cell division is most rapid. Thus, p53 mutations that are inherited or occur during developmental life act in stem cells of the mesenchymal and epithelial lineages, whereas p53 mutations that occur in progenitor or differentiated (somatic) cells later in life function in tissues of endodermal origins, indicating that p53 may function differently in different developmental lineages.
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Affiliation(s)
- Arnold J Levine
- Institute for Advanced Study, Princeton, New Jersey 08340 Cancer Institute of New Jersey of Rutgers Medical School, New Brunswick, New Jersey 08903
| | - Anna M Puzio-Kuter
- Institute for Advanced Study, Princeton, New Jersey 08340 Cancer Institute of New Jersey of Rutgers Medical School, New Brunswick, New Jersey 08903
| | - Chang S Chan
- Institute for Advanced Study, Princeton, New Jersey 08340 Cancer Institute of New Jersey of Rutgers Medical School, New Brunswick, New Jersey 08903
| | - Pierre Hainaut
- Grenoble Institute for Research on Cancer, Grenoble, France
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Martinez P, Timmer MR, Lau CT, Calpe S, Sancho-Serra MDC, Straub D, Baker AM, Meijer SL, Kate FJWT, Mallant-Hent RC, Naber AHJ, van Oijen AHAM, Baak LC, Scholten P, Böhmer CJM, Fockens P, Bergman JJGHM, Maley CC, Graham TA, Krishnadath KK. Dynamic clonal equilibrium and predetermined cancer risk in Barrett's oesophagus. Nat Commun 2016; 7:12158. [PMID: 27538785 PMCID: PMC4992167 DOI: 10.1038/ncomms12158] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/06/2016] [Indexed: 12/24/2022] Open
Abstract
Surveillance of Barrett's oesophagus allows us to study the evolutionary dynamics of a human neoplasm over time. Here we use multicolour fluorescence in situ hybridization on brush cytology specimens, from two time points with a median interval of 37 months in 195 non-dysplastic Barrett's patients, and a third time point in a subset of 90 patients at a median interval of 36 months, to study clonal evolution at single-cell resolution. Baseline genetic diversity predicts progression and remains in a stable dynamic equilibrium over time. Clonal expansions are rare, being detected once every 36.8 patient years, and growing at an average rate of 1.58 cm(2) (95% CI: 0.09-4.06) per year, often involving the p16 locus. This suggests a lack of strong clonal selection in Barrett's and that the malignant potential of 'benign' Barrett's lesions is predetermined, with important implications for surveillance programs.
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Affiliation(s)
- Pierre Martinez
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Margriet R. Timmer
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Chiu T. Lau
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Silvia Calpe
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Maria del Carmen Sancho-Serra
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Danielle Straub
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Sybren L. Meijer
- Department of Pathology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Fiebo J. W. ten Kate
- Department of Pathology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Rosalie C. Mallant-Hent
- Department of Gastroenterology and Hepatology, Flevoziekenhuis, 1300 EG Almere, The Netherlands
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
| | - Anton H. J. Naber
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Tergooiziekenhuizen, 1201 DA Hilversum, The Netherlands
| | - Arnoud H. A. M. van Oijen
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Medisch Centrum, 1800 AM Alkmaar, The Netherlands
| | - Lubbertus C. Baak
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Onze Lieve Vrouwe Gasthuis, 1091 AC Amsterdam, The Netherlands
| | - Pieter Scholten
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Sint Lucas Andreas Ziekenhuis, 1006 AE Amsterdam, The Netherlands
| | - Clarisse J. M. Böhmer
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Spaarne Ziekenhuis, 2134 TM Hoofddorp, The Netherlands
| | - Paul Fockens
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Jacques J. G. H. M. Bergman
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
| | - Carlo C. Maley
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, Arizona 85281, USA
| | - Trevor A. Graham
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Kausilia K Krishnadath
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
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Brandtner AK, Quante M. Risk prediction in Barrett's esophagus - aspects of a combination of molecular and epidemiologic biomarkers reflecting alterations of the microenvironment. Scand J Clin Lab Invest 2016; 245:S63-S69. [PMID: 27467504 DOI: 10.1080/00365513.2016.1210327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Barrett's esophagus (BE) is a chronic, metaplastic lesion of the esophagus and the only known precursor of esophageal adenocarcinoma. The identification of risk factors to assess the risk for BE and their correspondence with hallmarks of malignant progression for early stratification purposes is critically needed. Data legitimate the assumption that aside of reflux symptoms and related conditions, also demographic and environmental factors are thought to be associated with the risk for BE and its progression to esophageal adenocarcinoma. Molecular biomarkers and inflammatory mechanisms are subjects of intensive research and dispone of promising features regarding risk assessment especially for progressive BE. The amount of investigated epidemiologic factors, as well as discovered biomarkers gets confusingly large. Despite the recognized potential relevance of environmental and molecular factors, the efforts to date have resulted in moderately applicable risk estimates. More prospective data is needed to allow an imputation of the mostly retrospectively assessed factors to reappraise their meaningfulness in risk prediction approaches.
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Affiliation(s)
- Anna K Brandtner
- a II. Medizinische Klinik, Klinikum Rechts der Isar , Technische Universität München , Munich , Germany
- b Inflammation Research Unit, Department of Internal Medicine I , Medical University of Innsbruck , Innsbruck , Austria
| | - Michael Quante
- a II. Medizinische Klinik, Klinikum Rechts der Isar , Technische Universität München , Munich , Germany
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Genomic amplification of 9p24.1 targeting JAK2, PD-L1, and PD-L2 is enriched in high-risk triple negative breast cancer. Oncotarget 2016; 6:26483-93. [PMID: 26317899 PMCID: PMC4694916 DOI: 10.18632/oncotarget.4494] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/22/2015] [Indexed: 12/16/2022] Open
Abstract
We used DNA content flow cytometry followed by oligonucleotide array based comparative genomic hybridization to survey the genomes of 326 tumors, including 41 untreated surgically resected triple negative breast cancers (TNBC). A high level (log2ratio ≥ 1) 9p24 amplicon was found in TNBC (12/41), glioblastomas (2/44), and colon carcinomas (2/68). The shortest region of overlap for the amplicon targets 9p24.1 and includes the loci for PD-L1, PD-L2, and JAK2 (PDJ amplicon). In contrast this amplicon was absent in ER+ (0/8) and HER2+ (0/15) breast tumors, and in pancreatic ductal adenocarcinomas (0/150). The PDJ amplicon in TNBCs was correlated with clinical outcomes in group comparisons by two-sample t-tests for continuous variables and chi-squared tests for categorical variables. TNBC patients with the PDJ amplicon had a worse outcome with worse disease-free and overall survival. Quantitative RT-PCR confirmed that the PDJ amplicon in TNBC is associated with elevated expression of JAK2 and of the PD-1 ligands. These initial findings demonstrate that the PDJ amplicon is enriched in TNBC, targets signaling pathways that activate the PD-1 mediated immune checkpoint, and identifies patients with a poor prognosis.
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Abstract
The article by Banerjee and colleagues published in this issue of the journal involving a randomized control prevention trial of ursodeoxycholic acid (UDCA) in Barrett esophagus reported a null outcome despite being well designed and executed. Possible reasons for this null outcome are discussed focusing on use of surrogate endpoints in the trial. The trial is especially topical because it comes at a time when there are calls for a Pre-Cancer Genome Atlas (PCGA) for "understanding the earliest molecular and cellular events associated with cancer initiation…" This commentary discusses current concepts in prevention research including branched evolution that leads to therapeutic resistance. Length bias sampling postulates underdiagnosis is due to rapidly progressing disease that is difficult to detect by screening because it progresses to cancer too rapidly and that overdiagnosis is the result of very slowly or nonprogressing disease that is easy to detect by screening because it persists for a lifetime and the patient dies of unrelated causes. Finally, it also explores study designs, including surrogate endpoints in Barrett esophagus trials, and opportunities and pitfalls for a PCGA in the context of high levels of over and underdiagnosis of Barrett esophagus as well as many other cancers and their precursors. Cancer Prev Res; 9(7); 512-7. ©2016 AACRSee related article by Banerjee, et al., p. 528.
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Affiliation(s)
- Brian J Reid
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington.
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43
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Cell autonomous and microenvironmental regulation of tumor progression in precursor states of multiple myeloma. Curr Opin Hematol 2016; 23:426-33. [DOI: 10.1097/moh.0000000000000259] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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The Complex, Clonal, and Controversial Nature of Barrett's Esophagus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 908:27-40. [PMID: 27573766 DOI: 10.1007/978-3-319-41388-4_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Barrett's esophagus (BO) is a preneoplastic condition described as the replacement of the stratified squamous epithelium of the distal esophagus with one that histologically presents as a diverse mixture of metaplastic glands resembling gastric or intestinal-type columnar epithelium. The clonal origins of BO are still unclear. More recently, we have begun to investigate the relationship between the various metaplastic gland phenotypes observed in BO, how they evolve, and the cancer risk they bestow. Studies have revealed that glands along the BO segment are clonal units containing a single stem cell clone that can give rise to all the differentiated epithelial cell types in glands. Clonal lineage tracing analysis has revealed that Barrett's glands are capable of bifurcation and this facilitates clonal expansion and competition. In fact, BO in some patients appears to consist of multiple, independently initiated clones that compete with each other for space and possibly resources. This chapter discusses the concepts of clonal competition and expansion in BO and sets out to query what we know about the role of gland diversity and phenotypic evolution within this complex columnar metaplasia.
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Paulson TG. Studying Cancer Evolution in Barrett’s Esophagus and Esophageal Adenocarcinoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 908:213-36. [DOI: 10.1007/978-3-319-41388-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Abstract
Beginning in the 1980s, an alarming rise in the incidence of esophageal adenocarcinoma (EA) led to screening of patients with reflux to detect Barrett's esophagus (BE) and surveillance of BE to detect early EA. This strategy, based on linear progression disease models, resulted in selective detection of BE that does not progress to EA over a lifetime (overdiagnosis) and missed BE that rapidly progresses to EA (underdiagnosis). Here we review the historical thought processes that resulted in this undesired outcome and the transformation in our understanding of genetic and evolutionary principles governing neoplastic progression that has come from application of modern genomic technologies to cancers and their precursors. This new synthesis provides improved strategies for prevention and early detection of EA by addressing the environmental and mutational processes that can determine "windows of opportunity" in time to detect rapidly progressing BE and distinguish it from slowly or nonprogressing BE.
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Affiliation(s)
- Brian J. Reid
- Division of Human Biology, FredHutch, Seattle WA,Division of Public Health Sciences, FredHutch, Seattle WA,Department of Genome Sciences, University of Washington,Department of Medicine, University of Washington,Corresponding author Brian J. Reid, M.D., Ph.D. 1100 Fairview Ave N., C1-157 P.O. Box 19024 Seattle, WA 98109-1024 206-667-4073 (phone) 206-667-6192 (FAX)
| | | | - Xiaohong Li
- Division of Human Biology, FredHutch, Seattle WA
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Abstract
There has been a substantial increase in the incidence of esophageal adenocarcinoma over the past 40 years. Meta-analyses of large prospective cohorts and population-based case-control studies demonstrate consistent associations between obesity and the development of adenocarcinoma of the esophagus and esophago-gastric junction, with an approximate doubling of risk of esophageal adenocarcinoma among patients who are obese, and an almost five-fold increased risk among those with BMI >40 kg/m2. The pathologic precursor, specialized intestinal metaplasia in Barrett's esophagus, is also associated with increased adiposity. Epidemiologic evidence suggests that this cancer risk is not solely due to increased gastro-esophageal reflux, and that adipose tissue itself, in particular visceral adipose, may fuel carcinogenesis through the production of adipokines, cytokines, growth factors, and increased inflammation. The robust epidemiologic evidence linking obesity with esophageal adenocarcinoma makes it an exemplar model for investigating the molecular mechanisms underpinning obesity-associated malignant progression, which are discussed in this review.
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Affiliation(s)
- Jessie A Elliott
- a 1 Department of Surgery, Trinity Centre for Health Sciences, Trinity College Dublin & St. James' Hospital, Dublin 8, Ireland
- b 2 Diabetes Complications Research Centre, Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin 4, Ireland
| | - Claire L Donohoe
- a 1 Department of Surgery, Trinity Centre for Health Sciences, Trinity College Dublin & St. James' Hospital, Dublin 8, Ireland
| | - John V Reynolds
- a 1 Department of Surgery, Trinity Centre for Health Sciences, Trinity College Dublin & St. James' Hospital, Dublin 8, Ireland
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Matsumoto T, Shimizu T, Takai A, Marusawa H. Exploring the Mechanisms of Gastrointestinal Cancer Development Using Deep Sequencing Analysis. Cancers (Basel) 2015; 7:1037-51. [PMID: 26083936 PMCID: PMC4491698 DOI: 10.3390/cancers7020823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/08/2015] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized cancer genomics due to their high throughput sequencing capacity. Reports of the gene mutation profiles of various cancers by many researchers, including international cancer genome research consortia, have increased over recent years. In addition to detecting somatic mutations in tumor cells, NGS technologies enable us to approach the subject of carcinogenic mechanisms from new perspectives. Deep sequencing, a method of optimizing the high throughput capacity of NGS technologies, allows for the detection of genetic aberrations in small subsets of premalignant and/or tumor cells in noncancerous chronically inflamed tissues. Genome-wide NGS data also make it possible to clarify the mutational signatures of each cancer tissue by identifying the precise pattern of nucleotide alterations in the cancer genome, providing new information regarding the mechanisms of tumorigenesis. In this review, we highlight these new methods taking advantage of NGS technologies, and discuss our current understanding of carcinogenic mechanisms elucidated from such approaches.
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Affiliation(s)
- Tomonori Matsumoto
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Takahiro Shimizu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Hiroyuki Marusawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
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Zeb MH, Baruah A, Kossak SK, Buttar NS. Chemoprevention in Barrett's Esophagus: Current Status. Gastroenterol Clin North Am 2015; 44:391-413. [PMID: 26021201 DOI: 10.1016/j.gtc.2015.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemoprevention in Barrett's esophagus is currently applied only in research settings. Identifying pathways that can be targeted by safe, pharmaceutical or natural compounds is key to expanding the scope of chemoprevention. Defining meaningful surrogate markers of cancer progression is critical to test the efficacy of chemopreventive approaches. Combinatorial chemoprevention that targets multiple components of the same pathway or parallel pathways could reduce the risk and improve the efficacy of chemoprevention. Here we discuss the role of chemoprevention as an independent or an adjuvant management option in BE-associated esophageal adenocarcinoma.
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Affiliation(s)
- Muhammad H Zeb
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Anushka Baruah
- Department of Internal Medicine, John H. Stroger, Jr. Hospital of Cook County, 1901 W. Harrison Street, Chicago, IL 60612, USA
| | - Sarah K Kossak
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Navtej S Buttar
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA.
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Kaz AM, Grady WM, Stachler MD, Bass AJ. Genetic and Epigenetic Alterations in Barrett's Esophagus and Esophageal Adenocarcinoma. Gastroenterol Clin North Am 2015; 44:473-89. [PMID: 26021206 PMCID: PMC4449457 DOI: 10.1016/j.gtc.2015.02.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Esophageal adenocarcinoma (EAC) develops from Barrett's esophagus (BE), wherein normal squamous epithelia is replaced by specialized intestinal metaplasia in response to chronic gastroesophageal acid reflux. BE can progress to low- and high-grade dysplasia, intramucosal, and invasive carcinoma. Both BE and EAC are characterized by loss of heterozygosity, aneuploidy, specific genetic mutations, and clonal diversity. Given the limitations of histopathology, genomic and epigenomic analyses may improve the precision of risk stratification. Assays to detect molecular alterations associated with neoplastic progression could be used to improve the pathologic assessment of BE/EAC and to select high-risk patients for more intensive surveillance.
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Affiliation(s)
- Andrew M. Kaz
- VA Puget Sound Health Care System, R&D Department, Seattle, WA,Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA,University of Washington School of Medicine, Department of Internal Medicine, Seattle, WA
| | - William M. Grady
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA,University of Washington School of Medicine, Department of Internal Medicine, Seattle, WA
| | - Matthew D. Stachler
- Department of Pathology, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA
| | - Adam J. Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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