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Zhou Y, Mo S, Cui H, Sun R, Zhang W, Zhuang X, Xu E, Li H, Cheng Y, Meng Y, Liu M, Yan T, Liu H, Zhang L, Yang B, Xi Y, Wang S, Cheng X, Li S, Liu Z, Zhan Q, Hu Z, Cui Y. Immune-tumor interaction dictates spatially directed evolution of esophageal squamous cell carcinoma. Natl Sci Rev 2024; 11:nwae150. [PMID: 38803565 PMCID: PMC11129594 DOI: 10.1093/nsr/nwae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/14/2024] [Accepted: 04/08/2024] [Indexed: 05/29/2024] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a poor-prognostic cancer type with extensive intra- and inter-patient heterogeneity in both genomic variations and tumor microenvironment (TME). However, the patterns and drivers of spatial genomic and microenvironmental heterogeneity of ESCC remain largely unknown. Here, we generated a spatial multi-omic atlas by whole-exome, transcriptome, and methylome sequencing of 507 tumor samples from 103 patients. We identified a novel tumor suppressor PREX2, accounting for 22% of ESCCs with frequent somatic mutations or hyper-methylation, which promoted migration and invasion of ESCC cells in vitro. Analysis of the TME and quantification of subclonal expansion indicated that ESCCs undergo spatially directed evolution, where subclones mostly originated from the tumor center but had a biased clonal expansion to the upper direction of the esophagus. Interestingly, we found upper regions of ESCCs often underwent stronger immunoediting with increased selective fitness, suggesting more stringent immune selection. In addition, distinct TMEs were associated with variable genomic and clinical outcomes. Among them, hot TME was associated with high immune evasion and subclonal heterogeneity. We also found that immunoediting, instead of CD8+ T cell abundance, acts as an independent prognostic factor of ESCCs. Importantly, we found significant heterogeneity in previously considered potential therapeutic targets, as well as BRCAness characteristics in a subset of patients, emphasizing the importance of focusing on heterogeneity in ESCC targeted therapy. Collectively, these findings provide novel insights into the mechanisms of the spatial evolution of ESCC and inform precision therapeutic strategies.
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Affiliation(s)
- Yong Zhou
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen 518000, China
| | - Shanlan Mo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China
| | - Heyang Cui
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Ruifang Sun
- Department of Tumor Biobank, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Weimin Zhang
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaofei Zhuang
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Enwei Xu
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Hongyi Li
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - Yikun Cheng
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- College of Letters & Science, University of California Berkeley, Berkeley, CA 94704, USA
| | - Yongsheng Meng
- Department of Tumor Biobank, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Meilin Liu
- Department of Tumor Biobank, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Ting Yan
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - Huijuan Liu
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - Ling Zhang
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - Bin Yang
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Yanfeng Xi
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Shubin Wang
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xiaolong Cheng
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - ShuaiCheng Li
- City University of Hong Kong Shenzhen Research Institute, Shenzhen 518000, China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qimin Zhan
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
| | - Zheng Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China
| | - Yongping Cui
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
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2
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Lim H, Gingras MC, Zhao J, Byun J, Castro PD, Tsavachidis S, Hu J, Doddapaneni H, Han Y, Muzny DM, Gibbs RA, Amos CI, Thrift AP. Somatic mutations of esophageal adenocarcinoma: a comparison between Black and White patients. Sci Rep 2024; 14:8988. [PMID: 38637560 PMCID: PMC11026501 DOI: 10.1038/s41598-024-59257-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Esophageal adenocarcinoma is the most common histological subtype of esophageal cancer in Western countries and shows poor prognosis with rapid growth. EAC is characterized by a strong male predominance and racial disparity. EAC is up to fivefold more common among Whites than Blacks, yet Black patients with EAC have poorer survival rates. The racial disparity remains largely unknown, and there is limited knowledge of mutations in EAC regarding racial disparities. We used whole-exome sequencing to show somatic mutation profiles derived from tumor samples from 18 EAC male patients. We identified three molecular subgroups based on the pre-defined esophageal cancer-specific mutational signatures. Group 1 is associated with age and NTHL1 deficiency-related signatures. Group 2 occurs primarily in Black patients and is associated with signatures related to DNA damage from oxidative stress and NTHL1 deficiency-related signatures. Group 3 is associated with defective homologous recombination-based DNA often caused by BRCA mutation in White patients. We observed significantly mutated race related genes (LCE2B in Black, SDR39U1 in White) were (q-value < 0.1). Our findings underscore the possibility of distinct molecular mutation patterns in EAC among different races. Further studies are needed to validate our findings, which could contribute to precision medicine in EAC.
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Affiliation(s)
- Hyeyeun Lim
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jing Zhao
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Patricia D Castro
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Spiridon Tsavachidis
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, MS: BCM451, Suite 100D, Houston, TX, 77030, USA.
| | - Aaron P Thrift
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, MS: BCM307, Room 621D, Houston, TX, 77030, USA.
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3
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O'Neill JR, Yébenes Mayordomo M, Mitulović G, Al Shboul S, Bedran G, Faktor J, Hernychova L, Uhrik L, Gomez-Herranz M, Kocikowski M, Save V, Vojtěšek B, Arends M, Hupp T, Alfaro J. Multi-omic analysis of Esophageal Adenocarcinoma uncovers candidate therapeutic targets and cancer-selective post-transcriptional regulation. Mol Cell Proteomics 2024:100764. [PMID: 38604503 DOI: 10.1016/j.mcpro.2024.100764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 03/08/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND Efforts to address the poor prognosis associated with esophageal adenocarcinoma (EAC) have been hampered by a lack of biomarkers to identify early disease and therapeutic targets. Despite extensive efforts to understand the somatic mutations associated with EAC over the past decade, a gap remains in understanding how the atlas of genomic aberrations in this cancer impacts the proteome and which somatic variants are of importance for the disease phenotype. METHODS We performed a quantitative proteomic analysis of 23 EACs and matched adjacent normal esophageal and gastric tissues. We explored the correlation of transcript and protein abundance using tissue-matched RNA-seq and proteomic data from 7 patients and further integrated these data with a cohort of EAC RNA-seq data (n=264 patients), EAC whole-genome sequencing (n=454 patients) and external published datasets. CENTRAL FINDINGS We quantified protein expression from 5879 genes in EAC and patient-matched normal tissues. Several biomarker candidates with EAC-selective expression were identified including the transmembrane protein GPA33. We further verified the EAC-enriched expression of GPA33 in an external cohort of 115 patients and confirm this as an attractive diagnostic and therapeutic target. To further extend the insights gained from our proteomic data, an integrated analysis of protein and RNA expression in EAC and normal tissues revealed several genes with poorly correlated Protein and RNA abundance, suggesting post-transcriptional regulation of protein expression. These outlier genes including SLC25A30, TAOK2, and AGMAT, only rarely demonstrated somatic mutation suggesting post-transcriptional drivers for this EAC-specific phenotype. AGMAT was demonstrated to be over-expressed at the protein level in EAC compared to adjacent normal tissues with an EAC-selective, post-transcriptional mechanism of regulation of protein abundance proposed. CONCLUSIONS By quantitative proteomic analysis we have identified GPA33 as an EAC-selective biomarker. Integrated analysis of proteome, transcriptome, and genome in EAC has revealed several genes with tumor-selective, post-transcriptional regulation of protein expression which may be an exploitable vulnerability.
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Affiliation(s)
- J Robert O'Neill
- Cambridge Oesophagogastric Centre, Addenbrooke's Hospital, Hills Rd, Cambridge CB2 0QQ
| | - Marcos Yébenes Mayordomo
- International Center for Cancer Vaccine Science (ICCVS), University of Gdansk, Gdansk, Poland; Institute of Genetics and Cancer (IGC), University of Edinburgh, Edinburgh, Scotland
| | - Goran Mitulović
- Clinical Department of Laboratory Medicine Proteomics Core Facility, Medical University Vienna, 1090 Vienna, Austria
| | - Sofian Al Shboul
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan
| | - Georges Bedran
- International Center for Cancer Vaccine Science (ICCVS), University of Gdansk, Gdansk, Poland
| | - Jakub Faktor
- International Center for Cancer Vaccine Science (ICCVS), University of Gdansk, Gdansk, Poland
| | | | - Lukas Uhrik
- Masaryk Memorial Cancer Institute: Brno, Czech Republic
| | - Maria Gomez-Herranz
- International Center for Cancer Vaccine Science (ICCVS), University of Gdansk, Gdansk, Poland
| | - Mikołaj Kocikowski
- International Center for Cancer Vaccine Science (ICCVS), University of Gdansk, Gdansk, Poland
| | - Vicki Save
- Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | | | - Mark Arends
- Edinburgh Pathology, Institute of Genetics and Cancer (IGC), University of Edinburgh, Edinburgh, Scotland
| | - Ted Hupp
- International Center for Cancer Vaccine Science (ICCVS), University of Gdansk, Gdansk, Poland; Institute of Genetics and Cancer (IGC), University of Edinburgh, Edinburgh, Scotland
| | - Javier Alfaro
- International Center for Cancer Vaccine Science (ICCVS), University of Gdansk, Gdansk, Poland
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4
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Zhang Y, Weh KM, Tripp BA, Clarke JL, Howard CL, Sunilkumar S, Howell AB, Kresty LA. Cranberry Proanthocyanidins Mitigate Reflux-Induced Transporter Dysregulation in an Esophageal Adenocarcinoma Model. Pharmaceuticals (Basel) 2023; 16:1697. [PMID: 38139823 PMCID: PMC10747310 DOI: 10.3390/ph16121697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
We recently reported that cranberry proanthocyanidins (C-PACs) inhibit esophageal adenocarcinoma (EAC) by 83% through reversing reflux-induced bacterial, inflammatory and immune-implicated proteins and genes as well as reducing esophageal bile acids, which drive EAC progression. This study investigated whether C-PACs' mitigation of bile reflux-induced transporter dysregulation mechanistically contributes to EAC prevention. RNA was isolated from water-, C-PAC- and reflux-exposed rat esophagi with and without C-PAC treatment. Differential gene expression was determined by means of RNA sequencing and RT-PCR, followed by protein assessments. The literature, coupled with the publicly available Gene Expression Omnibus dataset GSE26886, was used to assess transporter expression levels in normal and EAC patient biopsies for translational relevance. Significant changes in ATP-binding cassette (ABC) transporters implicated in therapeutic resistance in humans (i.e., Abcb1, Abcb4, Abcc1, Abcc3, Abcc4, Abcc6 and Abcc10) and the transport of drugs, xenobiotics, lipids, and bile were altered in the reflux model with C-PACs' mitigating changes. Additionally, C-PACs restored reflux-induced changes in solute carrier (SLC), aquaporin, proton and cation transporters (i.e., Slc2a1, Slc7a11, Slc9a1, Slco2a1 and Atp6v0c). This research supports the suggestion that transporters merit investigation not only for their roles in metabolism and therapeutic resistance, but as targets for cancer prevention and targeting preventive agents in combination with chemotherapeutics.
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Affiliation(s)
- Yun Zhang
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
| | - Katherine M. Weh
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
| | - Bridget A. Tripp
- Bioinformatics Core Research Facility, Center for Biotechnology, University of Nebraska—Lincoln, N300 Beadle Center, Lincoln, NE 68588, USA;
| | - Jennifer L. Clarke
- Department of Statistics and Department of Food Science Technology, Quantitative Life Sciences Initiative, University of Nebraska—Lincoln, 253 Food Innovation Center, Lincoln, NE 68583, USA;
| | - Connor L. Howard
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
| | - Shruthi Sunilkumar
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
| | - Amy B. Howell
- Marucci Center for Blueberry and Cranberry Research, Rutgers University, 125A Lake Oswego Road, Chatsworth, NJ 08019, USA;
| | - Laura A. Kresty
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA; (Y.Z.); (K.M.W.); (C.L.H.); (S.S.)
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5
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M Naeini M, Newell F, Aoude LG, Bonazzi VF, Patel K, Lampe G, Koufariotis LT, Lakis V, Addala V, Kondrashova O, Johnston RL, Sharma S, Brosda S, Holmes O, Leonard C, Wood S, Xu Q, Thomas J, Walpole E, Tao Mai G, Ackland SP, Martin J, Burge M, Finch R, Karapetis CS, Shannon J, Nott L, Bohmer R, Wilson K, Barnes E, Zalcberg JR, Mark Smithers B, Simes J, Price T, Gebski V, Nones K, Watson DI, Pearson JV, Barbour AP, Waddell N. Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy. Nat Commun 2023; 14:3155. [PMID: 37258531 DOI: 10.1038/s41467-023-38891-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Oesophageal adenocarcinoma is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigate whole genome, transcriptomic and methylation data from 115 oesophageal adenocarcinoma patients mostly from the DOCTOR phase II clinical trial (Australian New Zealand Clinical Trials Registry-ACTRN12609000665235), with exploratory analysis pre-specified in the study protocol of the trial. We report genomic features associated with poorer overall survival, such as the APOBEC mutational and RS3-like rearrangement signatures. We also show that positron emission tomography non-responders have more sub-clonal genomic copy number alterations. Transcriptomic analysis categorises patients into four immune clusters correlated with survival. The immune suppressed cluster is associated with worse survival, enriched with myeloid-derived cells, and an epithelial-mesenchymal transition signature. The immune hot cluster is associated with better survival, enriched with lymphocytes, myeloid-derived cells, and an immune signature including CCL5, CD8A, and NKG7. The immune clusters highlight patients who may respond to immunotherapy and thus may guide future clinical trials.
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Affiliation(s)
- Marjan M Naeini
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Lauren G Aoude
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Vanessa F Bonazzi
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Kalpana Patel
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Guy Lampe
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | | | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Venkateswar Addala
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Rebecca L Johnston
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Sowmya Sharma
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, 4006, Australia
- Anatomical Pathology, Australian Clinical Labs, 2153, Sydney, Australia
| | - Sandra Brosda
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Janine Thomas
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
- Mater Research Institute, Mater Misericordiae, South Brisbane, QLD, 4101, Australia
| | - Euan Walpole
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | - G Tao Mai
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | - Stephen P Ackland
- Department of Medical Oncology, Calvary Mater Newcastle, Waratah, NSW, 2298, Australia
| | - Jarad Martin
- Department of Radiation Oncology, Calvary Mater Newcastle, Waratah, NSW, 2298, Australia
| | - Matthew Burge
- Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - Robert Finch
- Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - Christos S Karapetis
- Flinders University Department of Medical Oncology, Flinders Medical Centre, Adelaide, SA, 5042, Australia
| | - Jenny Shannon
- Nepean Cancer Care Centre, Nepean Hospital, Sydney, NSW, 2747, Australia
| | - Louise Nott
- Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Robert Bohmer
- Department of General Surgery, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Kate Wilson
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Elizabeth Barnes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - John R Zalcberg
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - B Mark Smithers
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, 4006, Australia
| | - John Simes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Timothy Price
- Medical Oncology Unit, The Queen Elizabeth Hospital and University of Adelaide, Adelaide, SA, 5011, Australia
| | - Val Gebski
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - David I Watson
- Flinders University Discipline of Surgery, Flinders Medical Centre, Adelaide, SA, 5042, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Andrew P Barbour
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia.
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia.
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
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Impact of the Tumor Microenvironment for Esophageal Tumor Development—An Opportunity for Prevention? Cancers (Basel) 2022; 14:cancers14092246. [PMID: 35565378 PMCID: PMC9100503 DOI: 10.3390/cancers14092246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Researchers increasingly appreciate the tumor microenvironment (TME) for its role in the development and therapy resistance of cancers like esophageal adenocarcinoma. A better understanding of the TME fueling carcinogenesis is necessary for tailored prevention and therapies. Here, we highlight recent insights into tumor initiation, interactions with the immune system and possible novel preventative measures. Abstract Despite therapeutical advancements, and in contrast to other malignancies, esophageal adenocarcinoma (EAC) prognosis remains dismal while the incidence has markedly increased worldwide over the past decades. EAC is a malignancy of the distal esophageal squamous epithelium at the squamocolumnar junction with gastric cells expanding into the esophagus. Most EAC patients have a history of Barret’s esophagus (BE), a metaplastic adaption to chronic reflux, initially causing an inflammatory microenvironment. Thus, the immune system is highly involved early on in disease development and progression. Normally, anti-tumor immunity could prevent carcinogenesis but in rare cases BE still progresses over a dysplastic intermediate state to EAC. The inflammatory milieu during the initial esophagitis phase changes to a tolerogenic immune environment in BE, and back to pro-inflammatory conditions in dysplasia and finally to an immune-suppressive tumor microenvironment in EAC. Consequently, there is a huge interest in understanding the underpinnings that lead to the inflammation driven stepwise progression of the disease. Since knowledge about the constellations of the various involved cells and signaling molecules is currently fragmentary, a comprehensive description of these changes is needed, allowing better preventative measures, diagnosis, and novel therapeutic targets.
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7
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Zou B, Guo D, Kong P, Wang Y, Cheng X, Cui Y. Integrative Genomic Analyses of 1,145 Patient Samples Reveal New Biomarkers in Esophageal Squamous Cell Carcinoma. Front Mol Biosci 2022; 8:792779. [PMID: 35127817 PMCID: PMC8814608 DOI: 10.3389/fmolb.2021.792779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
Due to the lack of effective diagnostic markers and therapeutic targets, esophageal squamous cell carcinoma (ESCC) shows a poor 5 years survival rate of less than 30%. To explore the potential therapeutic targets of ESCC, we integrated and reanalyzed the mutation data of WGS (whole genome sequencing) or WES (whole exome sequencing) from a total of 1,145 samples in 7 large ESCC cohorts, including 270 ESCC gene expression data. Two new mutation signatures and 20 driver genes were identified in our study. Among them, AP3S1, MUC16, and RPS15 were reported for the first time. We also discovered that the KMT2D was associated with the multiple clinical characteristics of ESCC, and KMT2D knockdown cells showed enhanced cell migration and cell invasion. Furthermore, a few neoantigens were shared between ESCC patients. For ESCC, compared to TMB, neoantigen might be treated as a better immunotherapy biomarker. Our research expands the understanding of ESCC mutations and helps the identification of ESCC biomarkers, especially for immunotherapy biomarkers.
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Affiliation(s)
- Binbin Zou
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Dinghe Guo
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Pengzhou Kong
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Yanqiang Wang
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Xiaolong Cheng
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
- *Correspondence: Xiaolong Cheng, ; Yongping Cui,
| | - Yongping Cui
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
- Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Peking University Shenzhen Hospital, Shenzhen, China
- *Correspondence: Xiaolong Cheng, ; Yongping Cui,
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Lonie JM, Barbour AP, Dolcetti R. Understanding the immuno-biology of oesophageal adenocarcinoma: Towards improved therapeutic approaches. Cancer Treat Rev 2021; 98:102219. [PMID: 33993033 DOI: 10.1016/j.ctrv.2021.102219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/12/2022]
Abstract
With an incidence that is constantly rising, oesophageal adenocarcinoma (OAC) is becoming an increasing health burden worldwide. Although significant advances in treatment regimens have improved patient outcomes, survival rates for this deadly cancer remain unsatisfactory. This highlights the need to improve current therapeutic approaches and develop novel therapeutic strategies for treating OAC patients. The advent of immunotherapy has revolutionised treatment across a range of malignancies, however outcomes in OAC show modest results. The inherent resistance of OAC to treatment reflects the complex genomic landscape of this cancer, which displays a lack of ubiquitous driver mutations and large-scale genomic alterations along with high tumour and immune heterogeneity. Research into the immune landscape of OAC is limited, and elucidation of the mechanisms surrounding the immune responses to this complex cancer will result in improved therapeutic approaches. This review explores what is known about the immuno-biology of OAC and explores promising therapeutic avenues that may improve responses to immunotherapeutic regimens.
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Affiliation(s)
- James M Lonie
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.
| | - Andrew P Barbour
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia; Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Riccardo Dolcetti
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia; Sir Peter MacCallum Cancer Centre, The University of Melbourne, Melbourne, Victoria, Australia
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Fatehi Hassanabad A, Chehade R, Breadner D, Raphael J. Esophageal carcinoma: Towards targeted therapies. Cell Oncol (Dordr) 2019; 43:195-209. [PMID: 31848929 DOI: 10.1007/s13402-019-00488-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Patients with esophageal cancer are confronted with high mortality rates. Whether it is esophageal squamous cell carcinoma (ESCC) or esophageal adenocarcinoma (EAC), patients usually present at advanced stages, with treatment options traditionally involving chemotherapy in metastatic settings. With the comprehensive genomic characterization of esophageal cancers, targeted therapies are gaining interest and agents such as ramucirumab, trastuzumab and pembrolizumab are already being used for the treatment of EAC. CONCLUSIONS Pembrolizumab has recently been FDA-approved for PD-L1 positive, locally advanced or metastatic ESCC. Despite comprehensive molecular characterization, however, available targed therapies for ESCC are still lagging behind. Herein, we discuss current trends towards more targeted therapies in esophageal cancers, taking into consideration unique features of ESCCs and EACs. Patients progressing on standard therapies should be subjected to genomic profiling and considered for clinical trials aimed at testing targeted therapies. Future targeted therapies may include CDK4/6 inhibitors, PARP inhibitors and inhibitors targeting the NRF2 and Wnt signaling pathways. Ultimately, optimized biomarker assays and next generation sequencing platforms may allow for the identification of subcategories of ESCC and EAC patients that will benefit from selective targeted therapies and/or combinations thereof.
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Affiliation(s)
| | - Rania Chehade
- Department of Medicine, Schulich School of Medicine and Dentistry, Schulich School of Medicine and Dentistry at Western University, London, ON, Canada
| | - Daniel Breadner
- Department of Oncology, Division of Medical Oncology, London Regional Cancer Program, Schulich School of Medicine and Dentistry at Western University, London, ON, Canada
| | - Jacques Raphael
- Department of Oncology, Division of Medical Oncology, London Regional Cancer Program, Schulich School of Medicine and Dentistry at Western University, London, ON, Canada
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