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Yen H, Chen P, Huang RY, Jeng J, Lai I. Clinicopathological features and cancer transcriptomic profiling of poorly cohesive gastric carcinoma subtypes. J Pathol Clin Res 2024; 10:e12387. [PMID: 38860888 PMCID: PMC11165978 DOI: 10.1002/2056-4538.12387] [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: 03/18/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/12/2024]
Abstract
Gastric poorly cohesive carcinoma (PCC) manifests with a diffuse pattern and diverse tumor cell morphologies, often indicating a more unfavorable prognosis. Recent consensus has reclassified PCC based on the proportion of signet-ring cells (SRCs) in tumors for research purposes. The two most distinct subtypes, poorly cohesive carcinoma not otherwise specified (PCC-NOS) and signet-ring cell carcinoma (SRCC), are characterized by less than 10% and more than 90% SRCs, respectively. However, research comparing the clinicopathological and transcriptomic differences between these subtypes remains limited. In this study, we conducted a comparative analysis of clinicopathological features in 55 advanced-stage PCCs, consisting of 43 PCC-NOS and 12 SRCC cases. Subsequently, 12 PCC-NOS and 5 SRCC cases were randomly selected for initial cancer-related gene expression profiling and pathway enrichment analysis using the GeoMx digital spatial profiler, followed by validation in a separate validation group comprising 16 PCC-NOS and 6 SRCC cases. These transcriptomic findings were then correlated with tumor morphology and clinicopathological data. PCC-NOS cases exhibited larger tumor size, a higher prevalence of pathological N3 disease, and a worse 1-year progression-free survival rate compared to SRCC cases. Clustering of PCC-NOS and SRCC was successfully achieved using the GeoMx Cancer Transcriptome Atlas. Among all studied genes, only MMP7 showed differential expression, with its overexpression significantly associated with the PCC-NOS subtype, increased perineural invasion, and earlier disease progression. Pathway analysis revealed significantly enriched pathways in PCC-NOS related to vesicle-mediated transport, adaptive immune systems, oncogenic signaling, and extracellular matrix organization, while SRCC displayed significant enrichment in pathways associated with respiratory electron transport and the cell cycle. In conclusion, this study compares and correlates clinicopathological features and transcriptomic data between PCC-NOS and SRCC at advanced stages, employing the latest consensus classification and a novel platform for analysis.
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Affiliation(s)
- Hung‐Hsuan Yen
- Department of SurgeryNational Taiwan University Hospital Hsin‐Chu BranchHsinchuTaiwan
- Department of SurgeryNational Taiwan University HospitalTaipeiTaiwan
| | - Pin‐Yu Chen
- Graduate Institute of Anatomy and Cell Biology, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Ruby Yun‐Ju Huang
- School of Medicine, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Jung‐Ming Jeng
- Department of PathologyNational Taiwan University HospitalTaipeiTaiwan
| | - I‐Rue Lai
- Department of SurgeryNational Taiwan University HospitalTaipeiTaiwan
- Graduate Institute of Anatomy and Cell Biology, College of MedicineNational Taiwan UniversityTaipeiTaiwan
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Hong W, Hu Q, Tan Y, Duan Q, Zhang Q, Chen D, Qi C, Wang D. Gastrointestinal signet ring cell malignancy: current advancement and future prospects. Invest New Drugs 2023; 41:861-869. [PMID: 37864727 DOI: 10.1007/s10637-023-01403-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Globally, gastrointestinal cancer is the most widespread neoplastic disease and the primary contributor to cancer-associated fatalities. Gastrointestinal signet ring cell carcinoma (SRCC) exhibits unique distinguishing features in several aspects when compared to adenocarcinomas (ACs). The scarcity of signet ring cell carcinoma has resulted in a heightened significance of related clinical and molecular investigations. However, a comprehensive and systematic review of the clinical, molecular, therapeutic, and research aspects of this disease is currently absent. This review provides an overview of the latest developments in our understanding of the clinical and molecular features of gastrointestinal signet ring cell carcinoma (SRCC). Additionally, we have compiled a list of potential therapeutic targets or biomarkers, as well as an examination of the current treatment options and the possible mechanisms of formation.
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Affiliation(s)
- Weiping Hong
- Department of Oncology, Guangdong Sanjiu Brain Hospital, 578 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province, China
| | - Qingjun Hu
- Department of Oncology, Guangdong Sanjiu Brain Hospital, 578 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province, China
| | - Yuan Tan
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Qianqian Duan
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Qin Zhang
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Dongsheng Chen
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Chuang Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Da Wang
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Rd., Hangzhou, China.
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Miao J, Yang Z, Guo W, Liu L, Song P, Ding C, Guan W. Integrative analysis of the proteome and transcriptome in gastric cancer identified LRP1B as a potential biomarker. Biomark Med 2022; 16:1101-1111. [PMID: 36606427 DOI: 10.2217/bmm-2022-0288] [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: 01/07/2023] Open
Abstract
Background: The aim of this study was to discover unique membrane proteins associated with gastric cancer (GC) in proteomics analysis. Methods: Using a data-independent acquisition strategy, we compared the relative expression levels of membrane proteins in GC. Results: A total of 2774 differentially expressed membrane proteins were identified between GC and normal cell lines. Conjoint analysis of transcriptomes and proteomes provided 11 potential biomarkers (GPRC5A, PSAT1, NUDCD1, RCC2, IPO4, FAM91A1, KANK2, PRADC1, NME4, METTL7A and LRP1B) for further exploration. Downregulation of LRP1B in GC was validated by immunohistochemistry. Moreover, LRP1B demonstrated an area under the receiver operating characteristic curve of 0.917 in differentiating GC from normal tissues. Conclusion: LRP1B was identified as a meaningful indicator assisting in GC detection and labeling of tumor boundaries.
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Affiliation(s)
- Ji Miao
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Zhi Yang
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Wen Guo
- Department of Pathology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, China
| | - Lixiang Liu
- Department of General Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, China
| | - Peng Song
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Chao Ding
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Wenxian Guan
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
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Mani DR, Krug K, Zhang B, Satpathy S, Clauser KR, Ding L, Ellis M, Gillette MA, Carr SA. Cancer proteogenomics: current impact and future prospects. Nat Rev Cancer 2022; 22:298-313. [PMID: 35236940 DOI: 10.1038/s41568-022-00446-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the functions of the vast majority of somatic mutations and copy number variants in tumours remain unknown, and the causes of resistance to targeted therapies and methods to overcome them are poorly defined. Recent improvements in mass spectrometry-based proteomics now enable direct examination of the consequences of genomic aberrations, providing deep and quantitative characterization of tumour tissues. Integration of proteins and their post-translational modifications with genomic, epigenomic and transcriptomic data constitutes the new field of proteogenomics, and is already leading to new biological and diagnostic knowledge with the potential to improve our understanding of malignant transformation and therapeutic outcomes. In this Review we describe recent developments in proteogenomics and key findings from the proteogenomic analysis of a wide range of cancers. Considerations relevant to the selection and use of samples for proteogenomics and the current technologies used to generate, analyse and integrate proteomic with genomic data are described. Applications of proteogenomics in translational studies and immuno-oncology are rapidly emerging, and the prospect for their full integration into therapeutic trials and clinical care seems bright.
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Affiliation(s)
- D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
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Zaragoza-Huesca D, Garrido-Rodríguez P, Jiménez-Fonseca P, Martínez de Castro E, Sánchez-Cánovas M, Visa L, Custodio A, Fernández-Montes A, Peñas-Martínez J, Morales del Burgo P, Gallego J, Luengo-Gil G, Vicente V, Martínez-Martínez I, Carmona-Bayonas A. Identification of Thrombosis-Related Genes in Patients with Advanced Gastric Cancer: Data from AGAMENON-SEOM Registry. Biomedicines 2022; 10:biomedicines10010148. [PMID: 35052827 PMCID: PMC8773420 DOI: 10.3390/biomedicines10010148] [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: 12/15/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 02/01/2023] Open
Abstract
Advanced gastric cancer is one of the most thrombogenic neoplasms. However, genetic mechanisms underlying this complication remain obscure, and the molecular and histological heterogeneity of this neoplasm hinder the identification of thrombotic biomarkers. Therefore, our main objective was to identify genes related to thrombosis regardless of Lauren subtypes. Furthermore, in a secondary exploratory study, we seek to discover thrombosis-associated genes that were specific to each TCGA molecular subtype. We designed a nested case-control study using the cohort of the AGAMENON national advanced gastric cancer registry. Ninety-seven patients were selected—48 with and 49 without venous thromboembolism (using propensity score matching to adjust for confounding factors)—and a differential gene expression array stratified by Lauren histopathological subtypes was carried out in primary tumor samples. For the secondary objective, the aforementioned differential expression analysis was conducted for each TCGA group. Fifteen genes were determined to be associated with thrombosis with the same expression trend in both the intestinal and diffuse subtypes. In thrombotic subjects, CRELD1, KCNH8, CRYGN, MAGEB16, SAA1, ARL11, CCDC169, TRMT61A, RIPPLY3 and PLA2G6 were underexpressed (adjusted-p < 0.05), while PRKD3, MIR5683, SDCBP, EPS8 and CDC45 were overexpressed (adjusted-p < 0.05), and correlated, by logistic regression, with lower or higher thrombotic risk, respectively, in the overall cohort. In each TCGA molecular subtype, we identified a series of genes differentially expressed in thrombosis that appear to be subtype-specific. We have identified several genes associated with venous thromboembolism in advanced gastric cancer that are common to Lauren intestinal and diffuse subtypes. Should these genetic factors be validated in the future, they could be complemented with existing clinical models to bolster the ability to predict thrombotic risk in individuals with advanced gastric adenocarcinoma.
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Affiliation(s)
- David Zaragoza-Huesca
- Centro Regional de Hemodonación, Department of Haematology and Medical Oncology, Hospital General Universitario Morales Meseguer, University of Murcia, IMIB-Arrixaca, 30003 Murcia, Spain; (D.Z.-H.); (P.G.-R.); (M.S.-C.); (J.P.-M.); (G.L.-G.); (V.V.); (A.C.-B.)
| | - Pedro Garrido-Rodríguez
- Centro Regional de Hemodonación, Department of Haematology and Medical Oncology, Hospital General Universitario Morales Meseguer, University of Murcia, IMIB-Arrixaca, 30003 Murcia, Spain; (D.Z.-H.); (P.G.-R.); (M.S.-C.); (J.P.-M.); (G.L.-G.); (V.V.); (A.C.-B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, U-765-CIBERER, Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Paula Jiménez-Fonseca
- Department of Medical Oncology, Instituto de Investigación Sanitaria del Principado de Asturias—ISPA, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - Eva Martínez de Castro
- Department of Medical Oncology, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain;
| | - Manuel Sánchez-Cánovas
- Centro Regional de Hemodonación, Department of Haematology and Medical Oncology, Hospital General Universitario Morales Meseguer, University of Murcia, IMIB-Arrixaca, 30003 Murcia, Spain; (D.Z.-H.); (P.G.-R.); (M.S.-C.); (J.P.-M.); (G.L.-G.); (V.V.); (A.C.-B.)
| | - Laura Visa
- Department of Medical Oncology, Hospital del Mar, 08003 Barcelona, Spain;
| | - Ana Custodio
- Department of Medical Oncology, Hospital Universitario La Paz, CIBERONC CB16/12/00398, 28046 Madrid, Spain;
| | - Ana Fernández-Montes
- Department of Medical Oncology, Complejo Hospitalario Universitario de Ourense, 32005 Ourense, Spain;
| | - Julia Peñas-Martínez
- Centro Regional de Hemodonación, Department of Haematology and Medical Oncology, Hospital General Universitario Morales Meseguer, University of Murcia, IMIB-Arrixaca, 30003 Murcia, Spain; (D.Z.-H.); (P.G.-R.); (M.S.-C.); (J.P.-M.); (G.L.-G.); (V.V.); (A.C.-B.)
| | | | - Javier Gallego
- Department of Medical Oncology, Hospital General Universitario de Elche, 03203 Elche, Spain;
| | - Ginés Luengo-Gil
- Centro Regional de Hemodonación, Department of Haematology and Medical Oncology, Hospital General Universitario Morales Meseguer, University of Murcia, IMIB-Arrixaca, 30003 Murcia, Spain; (D.Z.-H.); (P.G.-R.); (M.S.-C.); (J.P.-M.); (G.L.-G.); (V.V.); (A.C.-B.)
| | - Vicente Vicente
- Centro Regional de Hemodonación, Department of Haematology and Medical Oncology, Hospital General Universitario Morales Meseguer, University of Murcia, IMIB-Arrixaca, 30003 Murcia, Spain; (D.Z.-H.); (P.G.-R.); (M.S.-C.); (J.P.-M.); (G.L.-G.); (V.V.); (A.C.-B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, U-765-CIBERER, Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Irene Martínez-Martínez
- Centro Regional de Hemodonación, Department of Haematology and Medical Oncology, Hospital General Universitario Morales Meseguer, University of Murcia, IMIB-Arrixaca, 30003 Murcia, Spain; (D.Z.-H.); (P.G.-R.); (M.S.-C.); (J.P.-M.); (G.L.-G.); (V.V.); (A.C.-B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, U-765-CIBERER, Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-968-341-990
| | - Alberto Carmona-Bayonas
- Centro Regional de Hemodonación, Department of Haematology and Medical Oncology, Hospital General Universitario Morales Meseguer, University of Murcia, IMIB-Arrixaca, 30003 Murcia, Spain; (D.Z.-H.); (P.G.-R.); (M.S.-C.); (J.P.-M.); (G.L.-G.); (V.V.); (A.C.-B.)
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