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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Moreau M, Alouani E, Flecchia C, Falcoz A, Gallois C, Auclin E, André T, Cohen R, Hollebecque A, Turpin A, Pernot S, Masson T, Di Fiore F, Dutherge M, Mazard T, Hautefeuille V, Van Laethem JL, De la Fouchardière C, Perkins G, Ben-Abdelghani M, Sclafani F, Aparicio T, Kim S, Vernerey D, Taieb J, Guimbaud R, Tougeron D. A multicenter study evaluating efficacy of immune checkpoint inhibitors in advanced non-colorectal digestive cancers with microsatellite instability. Eur J Cancer 2024; 202:114033. [PMID: 38537314 DOI: 10.1016/j.ejca.2024.114033] [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: 11/18/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND One randomized phase III trial comparing chemotherapy (CT) with immune checkpoint inhibitors (ICI) has demonstrated significant efficacy of ICI in deficient DNA mismatch repair system/microsatellite instability-high (dMMR/MSI-H) metastatic colorectal cancer. However, few studies have compared ICI with CT in other advanced dMMR/MSI-H digestive tumors. METHODS In this multicenter study, we included patients with advanced dMMR/MSI-H non-colorectal digestive tumors treated with chemotherapy and/or ICIs. Patients were divided retrospectively into two groups, a CT group and an immunotherapy (IO) group. The primary endpoint was progression-free survival (PFS). A propensity score approach using the inverse probability of treatment weighting (IPTW) method was applied to deal with potential differences between the two groups. RESULTS 133 patients (45.1/27.1/27.8% with gastric/small bowel/other carcinomas) were included. The majority of patients received ICI in 1st (29.1%) or 2nd line (44.4%). The 24-month PFS rates were 7.9% in the CT group and 71.2% in the IO group. Using the IPTW method, IO treatment was associated with better PFS (HR=0.227; 95% CI 0.147-0.351; p < 0.0001). The overall response rate was 26.3% in the CT group versus 60.7% in the IO group (p < 0.001) with prolonged duration of disease control in the IO group (p < 0.001). In multivariable analysis, predictive factors of PFS for patients treated with IO were good performance status, absence of liver metastasis and prior primary tumor resection, whereas no association was found for the site of the primary tumor. CONCLUSIONS In the absence of randomized trials, our study highlights the superior efficacy of ICI compared with standard-of-care therapy in patients with unresectable or metastatic dMMR/MSI-H non-colorectal digestive cancer, regardless of tumor type, with acceptable toxicity.
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Affiliation(s)
- Mathilde Moreau
- Hepato-Gastroenterology Department, Poitiers University Hospital, Poitiers 86000, France
| | - Emily Alouani
- Digestive Oncology Department, Toulouse University Hospital, IUCT Rangueil-Larrey, 31059 Toulouse, France
| | - Clémence Flecchia
- Department of Digestive Oncology, Georges-Pompidou European Hospital, Paris 75015, France
| | - Antoine Falcoz
- Methodological and Quality of Life in Oncology Unit, University Hospital of Besançon, Besançon, France; INSERM, Etablissement Français du Sang Bourgogne Franche-Comté, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Claire Gallois
- Department of Digestive Oncology, Georges-Pompidou European Hospital, Paris 75015, France
| | - Edouard Auclin
- Department of Digestive Oncology, Georges-Pompidou European Hospital, Paris 75015, France
| | - Thierry André
- Sorbonne University, Department of Medical Oncology, Hôpital Saint-Antoine, AP-HP, and INSERM UMRS 938, Équipe Instabilité des Microsatellites et Cancer, Équipe Labellisée par la Ligue Nationale Contre le Cancer, SIRIC CURAMUS, Centre de Recherche Saint Antoine, Paris, France
| | - Romain Cohen
- Sorbonne University, Department of Medical Oncology, Hôpital Saint-Antoine, AP-HP, and INSERM UMRS 938, Équipe Instabilité des Microsatellites et Cancer, Équipe Labellisée par la Ligue Nationale Contre le Cancer, SIRIC CURAMUS, Centre de Recherche Saint Antoine, Paris, France
| | - Antoine Hollebecque
- Department of Medical Oncology, Gustave Roussy Institute, Villejuif 94805, France
| | - Anthony Turpin
- Medical Oncology Department, CHU Lille, University of Lille, Lille, France
| | - Simon Pernot
- Medical Oncology Department, Bergonié Institute, Bordeaux 33076, France
| | - Thérèse Masson
- Medical Oncology Department, La Rochelle Hospital, La Rochelle 17019, France
| | - Frederic Di Fiore
- Department of Medical Oncology, Rouen University Hospital, Rouen 76000, France
| | - Marie Dutherge
- Department of Medical Oncology, Rouen University Hospital, Rouen 76000, France
| | - Thibault Mazard
- Department of Medical Oncology, IRCM, INSERM, University of Montpellier, ICM, Montpellier, France
| | - Vincent Hautefeuille
- Department of Hepato-Gastroenterology and Digestive Oncology, Amiens University Hospital, Amiens, France
| | - Jean-Luc Van Laethem
- Digestive Oncology Department, Erasme Hospital, The Brussels University Hospital, Anderlecht 1070, Belgium
| | | | - Géraldine Perkins
- Department of Medical Oncology, Rennes University Hospital, Ponchaillou, Rennes 35000, France
| | - Meher Ben-Abdelghani
- Department of Medical Oncology, European Oncology Institute of Strasbourg, Strasbourg 67200, France
| | - Francesco Sclafani
- Digestive Oncology Department, Institut Jules Bordet, The Brussels University Hospital, Anderlecht 1070, Belgium
| | - Thomas Aparicio
- Gastroenterology Department, Saint-Louis Hospital, Paris 75010, France
| | - Stefano Kim
- Department of Medical Oncology, Besançon University Hospital, Besançon 25000, France
| | - Dewi Vernerey
- Methodological and Quality of Life in Oncology Unit, University Hospital of Besançon, Besançon, France; INSERM, Etablissement Français du Sang Bourgogne Franche-Comté, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Julien Taieb
- Department of Digestive Oncology, Georges-Pompidou European Hospital, Paris 75015, France
| | - Rosine Guimbaud
- Digestive Oncology Department, Toulouse University Hospital, IUCT Rangueil-Larrey, 31059 Toulouse, France
| | - David Tougeron
- Hepato-Gastroenterology Department, Poitiers University Hospital, Poitiers 86000, France.
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Cui Z, Zou F, Wang R, Wang L, Cheng F, Wang L, Pan R, Guan X, Zheng N, Wang W. Integrative bioinformatics analysis of WDHD1: a potential biomarker for pan-cancer prognosis, diagnosis, and immunotherapy. World J Surg Oncol 2023; 21:309. [PMID: 37759234 PMCID: PMC10523704 DOI: 10.1186/s12957-023-03187-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Although WD repeat and high-mobility group box DNA binding protein 1 (WDHD1) played an essential role in DNA replication, chromosome stability, and DNA damage repair, the panoramic picture of WDHD1 in human tumors remains unclear. Hence, this study aims to comprehensively characterize WDHD1 across 33 human cancers. METHODS Based on publicly available databases such as TCGA, GTEx, and HPA, we used a bioinformatics approach to systematically explore the genomic features and biological functions of WDHD1 in pan-cancer. RESULTS WDHD1 mRNA levels were significantly increased in more than 20 types of tumor tissues. Elevated WDHD1 expression was associated with significantly shorter overall survival (OS) in 10 tumors. Furthermore, in uterine corpus endometrial carcinoma (UCEC) and liver hepatocellular carcinoma (LIHC), WDHD1 expression was significantly associated with higher histological grades and pathological stages. In addition, WDHD1 had a high diagnostic value among 16 tumors (area under the ROC curve [AUC] > 0.9). Functional enrichment analyses suggested that WDHD1 probably participated in many oncogenic pathways such as E2F and MYC targets (false discovery rate [FDR] < 0.05), and it was involved in the processes of DNA replication and DNA damage repair (p.adjust < 0.05). WDHD1 expression also correlated with the half-maximal inhibitory concentrations (IC50) of rapamycin (4 out of 10 cancers) and paclitaxel (10 out of 10 cancers). Overall, WDHD1 was negatively associated with immune cell infiltration and might promote tumor immune escape. Our analysis of genomic alterations suggested that WDHD1 was altered in 1.5% of pan-cancer cohorts and the "mutation" was the predominant type of alteration. Finally, through correlation analysis, we found that WDHD1 might be closely associated with tumor heterogeneity, tumor stemness, mismatch repair (MMR), and RNA methylation modification, which were all processes associated with the tumor progression. CONCLUSIONS Our pan-cancer analysis of WDHD1 provides valuable insights into the genomic characterization and biological functions of WDHD1 in human cancers and offers some theoretical support for the future use of WDHD1-targeted therapies, immunotherapies, and chemotherapeutic combinations for the management of tumors.
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Affiliation(s)
- Zhiwei Cui
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Fan Zou
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Rongli Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lijun Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Feiyan Cheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lihui Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rumeng Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xin Guan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Nini Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wei Wang
- Department of Anesthesiology, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, 710061, Shaanxi, China.
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Conte M, Di Mauro A, Capasso L, Montella L, De Simone M, Nebbioso A, Altucci L. Targeting HDAC2-Mediated Immune Regulation to Overcome Therapeutic Resistance in Mutant Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15071960. [PMID: 37046620 PMCID: PMC10093005 DOI: 10.3390/cancers15071960] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/08/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
A large body of clinical and experimental evidence indicates that colorectal cancer is one of the most common multifactorial diseases. Although some useful prognostic biomarkers for clinical therapy have already been identified, it is still difficult to characterize a therapeutic signature that is able to define the most appropriate treatment. Gene expression levels of the epigenetic regulator histone deacetylase 2 (HDAC2) are deregulated in colorectal cancer, and this deregulation is tightly associated with immune dysfunction. By interrogating bioinformatic databases, we identified patients who presented simultaneous alterations in HDAC2, class II major histocompatibility complex transactivator (CIITA), and beta-2 microglobulin (B2M) genes based on mutation levels, structural variants, and RNA expression levels. We found that B2M plays an important role in these alterations and that mutations in this gene are potentially oncogenic. The dysregulated mRNA expression levels of HDAC2 were reported in about 5% of the profiled patients, while other specific alterations were described for CIITA. By analyzing immune infiltrates, we then identified correlations among these three genes in colorectal cancer patients and differential infiltration levels of genetic variants, suggesting that HDAC2 may have an indirect immune-related role in specific subgroups of immune infiltrates. Using this approach to carry out extensive immunological signature studies could provide further clinical information that is relevant to more resistant forms of colorectal cancer.
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Affiliation(s)
- Mariarosaria Conte
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
- Correspondence: ; Tel.: +39-081-5667564
| | - Annabella Di Mauro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Lucia Capasso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
| | - Liliana Montella
- ASL NA2 NORD, Oncology Operative Unit, “Santa Maria delle Grazie” Hospital, 80078 Pozzuoli, Italy;
| | - Mariacarla De Simone
- Stem Cell Transplantation Unit, Division of Hematology, Cardarelli Hospital, 80131 Naples, Italy;
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
- BIOGEM, Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy
- IEOS, Institute for Endocrinology and Experimental Oncology, CNRs, 80131 Napoli, Italy
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Hu Z, Liu Z, Zheng J, Peng Y, Lu X, Li J, Tan K, Cui H. Microsatellite instability-related prognostic risk score (MSI-pRS) defines a subset of lung squamous cell carcinoma (LUSC) patients with genomic instability and poor clinical outcome. Front Genet 2023; 14:1061002. [PMID: 36873930 PMCID: PMC9981642 DOI: 10.3389/fgene.2023.1061002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
Background: Lung squamous cell carcinoma (LUSC) shares less typical onco-drivers and target resistance, but a high overall mutation rate and marked genomic complexity. Mismatch repair (MMR) deficiency leads to microsatellite instability (MSI) and genomic instability. MSI is not an ideal option for prognosis of LUSC, whereas its function deserves exploration. Method: MSI status was classified by MMR proteins using unsupervised clustering in the TCGA-LUSC dataset. The MSI score of each sample was determined by gene set variation analysis. Intersections of the differential expression genes and differential methylation probes were classified into functional modules by weighted gene co-expression network analysis. Least absolute shrinkage and selection operator regression and stepwise gene selection were performed for model downscaling. Results: Compared with the MSI-low (MSI-L) phenotype, MSI-high (MSI-H) displayed higher genomic instability. The MSI score was decreased from MSI-H to normal samples (MSI-H > MSI-L > normal). A total of 843 genes activated by hypomethylation and 430 genes silenced by hypermethylation in MSI-H tumors were classified into six functional modules. CCDC68, LYSMD1, RPS7, and CDK20 were used to construct MSI-related prognostic risk score (MSI-pRS). Low MSI-pRS was a protective prognostic factor in all cohorts (HR = 0.46, 0.47, 0.37; p-value = 7.57e-06, 0.009, 0.021). The model contains tumor stage, age, and MSI-pRS that showed good discrimination and calibration. Decision curve analyses indicated that microsatellite instability-related prognostic risk score added extra value to the prognosis. A low MSI-pRS was negatively correlated with genomic instability. LUSC with low MSI-pRS was associated with increased genomic instability and cold immunophenotype. Conclusion: MSI-pRS is a promising prognostic biomarker in LUSC as the substitute of MSI. Moreover, we first declared that LYSMD1 contributed to genomic instability of LUSC. Our findings provided new insights in the biomarker finder of LUSC.
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Affiliation(s)
- Zixin Hu
- Beijing University of Chinese Medicine, Beijing, China.,Department of Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Zhening Liu
- Beijing University of Chinese Medicine, Beijing, China.,Department of Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Jiabin Zheng
- Department of Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Yanmei Peng
- Department of Oncology, Fangshan Hospital, Beijing, China
| | - Xingyu Lu
- Beijing University of Chinese Medicine, Beijing, China.,Department of Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Jia Li
- Beijing University of Chinese Medicine, Beijing, China.,Department of Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Kexin Tan
- Beijing University of Chinese Medicine, Beijing, China.,Department of Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Huijuan Cui
- Department of Oncology, China-Japan Friendship Hospital, Beijing, China
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Optimizing the Choice for Adjuvant Chemotherapy in Gastric Cancer. Cancers (Basel) 2022; 14:cancers14194670. [PMID: 36230592 PMCID: PMC9563297 DOI: 10.3390/cancers14194670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Gastric cancer is the fourth largest cause of tumor-related death worldwide. Despite advances in the management of resectable cancer and improvements in early diagnosis, especially in east Asia where screening campaigns are actively performed, many patients experience recurrence and die because of the disease. Adjuvant systemic chemotherapy is administered after radical surgery in order to reduce the risk of recurrence and death. The modality of administration and regimens of chemotherapy in this setting are different between Eastern and Western countries. In Asia, adjuvant chemotherapy is traditionally given after surgery, while in Europe it is commonly scheduled after preoperative chemotherapy and surgery (perioperative chemotherapy), and in Northern America it is usually combined with radiotherapy (chemoradiotherapy). All these approaches are sustained by well-designed phase III clinical studies, and none may be considered superior to the others in the absence of head-to-head comparisons. The identification of predictive and/or prognostic factors could help to select patients at higher risk of recurrence and those more likely to receive a benefit from the adjuvant treatment. This would allow clinicians to avoid the administration of undue toxicity to non-responder patients and even to reduce the cost of unnecessary treatment. Abstract Advances in the management of gastric cancer have improved patient survival in the last decade. Nonetheless, the number of patients relapsing and dying after a diagnosis of localized gastric cancer is still too high, even in early stages (10% in stage I). Adjuvant systemic chemotherapy has been proven to significantly improve outcomes. In the present article we have critically reviewed the clinical trials that guide the current clinical practice in the adjuvant treatment of patients affected by resectable gastric cancer, focusing on the different approaches worldwide, i.e., adjuvant chemotherapy, adjuvant chemoradiotherapy, and perioperative chemotherapy. We also delineate the clinical–pathological characteristics that are commonly taken into account to identify patients at a higher risk of recurrence and requiring adjuvant chemotherapy, and also describe novel biomarkers and therapeutic agents that might allow personalization of the treatment.
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