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Chen H, Jing C, Shang L, Zhu X, Zhang R, Liu Y, Wang M, Xu K, Ma T, Jing H, Wang Z, Li X, Chong W, Li L. Molecular characterization and clinical relevance of metabolic signature subtypes in gastric cancer. Cell Rep 2024; 43:114424. [PMID: 38959111 DOI: 10.1016/j.celrep.2024.114424] [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: 12/04/2023] [Revised: 05/06/2024] [Accepted: 06/14/2024] [Indexed: 07/05/2024] Open
Abstract
Metabolic reprogramming dictates tumor molecular attributes and therapeutic potentials. However, the comprehensive metabolic characteristics in gastric cancer (GC) remain obscure. Here, metabolic signature-based clustering analysis identifies three subtypes with distinct molecular and clinical features: MSC1 showed better prognosis and upregulation of the tricarboxylic acid (TCA) cycle and lipid metabolism, combined with frequent TP53 and RHOA mutation; MSC2 had moderate prognosis and elevated nucleotide and amino acid metabolism, enriched by intestinal histology and mismatch repair deficient (dMMR); and MSC3 exhibited poor prognosis and enhanced glycan and energy metabolism, accompanied by diffuse histology and frequent CDH1 mutation. The Shandong Provincial Hospital (SDPH) in-house dataset with matched transcriptomic, metabolomic, and spatial-metabolomic analysis also validated these findings. Further, we constructed the metabolic subtype-related prognosis gene (MSPG) scoring model to quantify the activity of individual tumors and found a positive correlation with cuproptosis signaling. In conclusion, comprehensive recognition of the metabolite signature can enhance the understanding of diversity and heterogeneity in GC.
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Affiliation(s)
- Hao Chen
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China.
| | - Changqing Jing
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Xingyu Zhu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Ronghua Zhang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Yuan Liu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Mingfei Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Kang Xu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Tianrong Ma
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Haiyan Jing
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Ze Wang
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Xin Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Wei Chong
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China.
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China.
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Chong W, Ren H, Chen H, Xu K, Zhu X, Liu Y, Sang Y, Li H, Liu J, Ye C, Shang L, Jing C, Li L. Clinical features and molecular landscape of cuproptosis signature-related molecular subtype in gastric cancer. IMETA 2024; 3:e190. [PMID: 38898987 PMCID: PMC11183172 DOI: 10.1002/imt2.190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/07/2024] [Accepted: 03/14/2024] [Indexed: 06/21/2024]
Abstract
Recent studies have highlighted the biological significance of cuproptosis in disease occurrence and development. However, it remains unclear whether cuproptosis signaling also has potential impacts on tumor initiation and prognosis of gastric cancer (GC). In this study, 16 cuproptosis-related genes (CRGs) transcriptional profiles were harnessed to perform the regularized latent variable model-based clustering in GC. A cuproptosis signature risk scoring (CSRS) scheme, based on a weighted sum of principle components of the CRGs, was used to evaluate the prognosis and risk of individual tumors of GC. Four distinct cuproptosis signature-based clusters, characterized by differential expression patterns of CRGs, were identified among 1136 GC samples across three independent databases. The four clusters were also associated with different clinical outcomes and tumor immune contexture. Based on the CSRS, GC patients can be divided into CSRS-High and CSRS-Low subtypes. We found that DBT, MTF1, and ATP7A were significantly elevated in the CSRS-High subtype, while SLC31A1, GCSH, LIAS, DLAT, FDX1, DLD, and PDHA1 were increased in the CSRS-Low subtype. Patients with CSRS-Low score were characterized by prolonged survival time. Further analysis indicated that CSRS-Low score also correlated with greater tumor mutation burden (TMB) and higher mutation rates of significantly mutated genes (SMG) in GC. In addition, the CSRS-High subtype harbored more significantly amplified focal regions related to tumorigenesis (3q27.1, 12p12.1, 11q13.3, etc.) than the CSRS-Low tumors. Drug sensitivity analyses revealed the potential compounds for the treatment of gastric cancer with CSRS-High score, which were experimentally validated using GC cells. This study highlights that cuproptosis signature-based subtyping is significantly associated with different clinical features and molecular landscape of GC. Quantitative evaluation of the CSRS of individual tumors will strengthen our understanding of the occurrence and development of cuproptosis and the treatment progress of GC.
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Affiliation(s)
- Wei Chong
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Huicheng Ren
- Department of Gastrointestinal SurgeryZibo Central HospitalZiboChina
| | - Hao Chen
- Clinical Research Center of Shandong University, Clinical Epidemiology UnitQilu Hospital of Shandong UniversityJinanChina
| | - Kang Xu
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Xingyu Zhu
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Yuan Liu
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Yaodong Sang
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Han Li
- Department of Gastroenterological SurgeryThe First Affiliated Hospital of Shandong First Medical UniversityJinanChina
| | - Jin Liu
- Department of GastroenterologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Chunshui Ye
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Liang Shang
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Changqing Jing
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Leping Li
- Department of Gastrointestinal SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
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Pang LL, Zhou HQ, Zhang YX, Zhuang WT, Pang F, Chen LJ, Liao J, Huang YH, Mao TQ, Mai ZH, Zhang L, Fang WF. SWI/SNF family mutations in advanced NSCLC: genetic characteristics and immune checkpoint inhibitors' therapeutic implication. ESMO Open 2024; 9:103472. [PMID: 38833972 PMCID: PMC11179082 DOI: 10.1016/j.esmoop.2024.103472] [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: 08/27/2023] [Revised: 03/21/2024] [Accepted: 04/21/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND SWItch/Sucrose NonFermentable (SWI/SNF) mutations have garnered increasing attention because of their association with unfavorable prognosis. However, the genetic landscape of SWI/SNF family mutations in Chinese non-small-cell lung cancer (NSCLC) is poorly understood. In addition, the optimal treatment strategy has not yet been determined. PATIENTS AND METHODS We collected sequencing data on 2027 lung tumor samples from multiple centers in China to comprehensively analyze the genomic characteristics of the SWI/SNF family within the Chinese NSCLC population. Meanwhile, 519 patients with NSCLC from Sun Yat-sen University Cancer Center were enrolled to investigate the potential implications of immunotherapy on patients with SWI/SNF mutations and to identify beneficial subpopulations. We also validated our findings in multiple publicly available cohorts. RESULTS Approximately 15% of Chinese patients with lung cancer harbored mutations in the SWI/SNF chromatin remodeling complex, which were mutually exclusive to the EGFR mutations. Patients with SWI/SNFmut NSCLC who received first-line chemoimmunotherapy had better survival outcomes than those who received chemotherapy alone (median progression-free survival: 8.70 versus 6.93 months; P = 0.028). This finding was also confirmed by external validation using the POPLAR/OAK cohort. SWI/SNFmut NSCLC is frequently characterized by high tumor mutational burden and concurrent TP53 or STK11/KEAP mutations. Further analysis indicated that TP53 and STK11/KEAP1 mutations could be stratifying factors in facilitating personalized immunotherapy and guiding patient selection. CONCLUSIONS This study provides a step forward in understanding the genetic and immunological characterization of SWI/SNF genetic alterations. Moreover, our study reveals substantial benefits of immunotherapy over chemotherapy for SWI/SNF-mutant patients, especially the SWI/SNFmut and TP53mut subgroups.
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Affiliation(s)
- L-L Pang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - H-Q Zhou
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - Y-X Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - W-T Zhuang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - F Pang
- Shanghai OrigiMed Co., Ltd, Shanghai
| | - L-J Chen
- Shanghai OrigiMed Co., Ltd, Shanghai
| | - J Liao
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - Y-H Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - T-Q Mao
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - Z-H Mai
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - L Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou.
| | - W-F Fang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou.
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Ma H, Zhang J, Shi Y, Wang Z, Nie W, Cai J, Huang Y, Liu B, Wang X, Lian C. PBK correlates with prognosis, immune escape and drug response in LUAD. Sci Rep 2023; 13:20452. [PMID: 37993518 PMCID: PMC10665404 DOI: 10.1038/s41598-023-47781-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023] Open
Abstract
PBK (PDZ-binding kinase) is a protein-coding gene that encodes a serine/threonine protein kinase associated with the dual-specific mitogen-activated protein kinase (MAPKK) family. Overexpression of this gene is closely linked to tumor development. In this study, we aimed to investigate the role of PBK in lung adenocarcinoma (LUAD) progression, prognosis, and immune evasion. We conducted a pan-cancer analysis of PBK to examine its expression and prognostic value. In the LUAD cohort, we analyzed PBK expression, prognosis, mutational features, and immune infiltration in groups with different PBK expression levels. We constructed a PBK-associated genomic model, integrated it into a nomogram, and compared high and low-risk subgroups. In our pan-cancer analysis, PBK was significantly upregulated, particularly in LUAD patients, and displayed poor prognosis. The high PBK expression group had many deletion mutations but still showed gene upregulation. Immune infiltration analysis indicated that PBK-triggered immune escape in the high expression group might relate to antigen presentation, dendritic cell, and CD8+ T cell infiltration. We constructed a 5-gene prognostic model and a nomogram to quantify individual survival probabilities. The PBK-associated gene prognostic model reliably predicted patient prognosis and drug response. Our findings offer new insights into PBK-induced immune escape and targeted therapy during LUAD development, providing valuable suggestions for clinical treatment approaches.
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Affiliation(s)
- Hongyu Ma
- Department of Clinical Medicine, Bengbu Medical College, Bengbu, 233000, China
- Department of Pulmonary and Critical Care Medicine, Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, China
| | - Jing Zhang
- Department of Genetics, School of Life Sciences, Bengbu Medical College, Bengbu, 233000, China
| | - Yan Shi
- Department of Pulmonary and Critical Care Medicine, Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, China
| | - Ziqiang Wang
- Research Center of Clinical Laboratory Science, Bengbu Medical College, Bengbu, 233000, China
| | - Wenhu Nie
- Department of Clinical Medicine, Bengbu Medical College, Bengbu, 233000, China
| | - Jingjing Cai
- Department of Clinical Medicine, Bengbu Medical College, Bengbu, 233000, China
| | - Yinglong Huang
- Department of Genetics, School of Life Sciences, Bengbu Medical College, Bengbu, 233000, China
| | - Bin Liu
- Department of Respiratory and Critical Care Medicine, Fuyang People's Hospital, Fuyang, 236000, China
| | - Xiaojing Wang
- Department of Pulmonary and Critical Care Medicine, Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, China.
| | - Chaoqun Lian
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical College, Bengbu, 233000, China.
- Research Center of Clinical Laboratory Science, Bengbu Medical College, Bengbu, 233000, China.
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Brambilla M, Beninato T, Piemontese A, Mazzeo L, Pircher CC, Manglaviti S, Ambrosini P, Signorelli D, Lorenzini D, Prelaj A, Ferrara R, Proto C, Lo Russo G, Pizzutilo EG, Ganzinelli M, Grande I, Capone I, Di Mauro RM, Conca E, Dumitrascu AD, Zanella C, Leporati R, Rota S, Garassino MC, Marchetti P, de Braud FM, Occhipinti M. Exploring the Role of Immunotherapy-Based Treatments for Advanced Non-Small-Cell Lung Cancer With Novel Driver Alterations. Clin Lung Cancer 2023; 24:631-640.e2. [PMID: 37775370 DOI: 10.1016/j.cllc.2023.08.004] [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: 04/25/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 10/01/2023]
Abstract
BACKGROUND Immunotherapy (IO) single agent or combined with chemotherapy (CT-IO) is the standard treatment for advanced non-small-cell lung cancer (aNSCLC) without driver alterations. IO efficacy in patients with novel driver alterations is not well reported. MATERIALS AND METHODS Data of aNSCLC patients treated with IO or CT-IO in any line from January 2016 to September 2022 were retrospectively collected. Patients harboring novel driver alterations (m-cohort), including MET exon 14 skipping, BRAF (V600E or atypical), RET rearrangements, HER2 point mutations/exon 20 insertions or uncommon EGFR mutations/EGFR exon 20 insertions, and wild type patients (wt-cohort) were eligible. Clinico-pathological data were extracted from Institutional databases and compared through chi square or Fisher's exact test. Survivals were estimated through Kaplan-Meier method and compared by log-rank test. RESULTS m-cohort and wt-cohort included 84 and 444 patients, respectively. Progression free survival (PFS) was 5.53 vs. 4.57 months (P= .846) and overall survival (OS) was 25.1 vs. 9.37 months, (P < .0001) for m-cohort compared to wt-cohort. Within the m-cohort, BRAF atypical mutations had the better outcomes (Overall Response Rate [ORR], PFS), targeted agents timing did not affect response to IO and CT-IO had better ORR and disease control rate (DCR) compared to IO single agent (P = .0160 and P = .0152). In the PD-L1≥50% group, first line IO single agent resulted in inferior ORR (P = .027) and PFS (P = .022) in m-cohort compared to wt-cohort. CONCLUSION IO based treatments seem not detrimental for patients harboring novel driver alteration. Adding CT could improve modest responses to IO alone. Confirmation on larger datasets is required.
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Affiliation(s)
- Marta Brambilla
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Teresa Beninato
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| | - Anna Piemontese
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Laura Mazzeo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Electronics, Information and Bioengineering, Polytechnic University of Milan, Milan, Italy
| | | | - Sara Manglaviti
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Ambrosini
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Diego Signorelli
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Daniele Lorenzini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Arsela Prelaj
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Electronics, Information and Bioengineering, Polytechnic University of Milan, Milan, Italy
| | - Roberto Ferrara
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Università Vita-Salute San Raffaele, Milan, Italy
| | - Claudia Proto
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giuseppe Lo Russo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elio Gregory Pizzutilo
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Monica Ganzinelli
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ilaria Grande
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Iolanda Capone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rosa Maria Di Mauro
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Conca
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andra Diana Dumitrascu
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Caterina Zanella
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rita Leporati
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Simone Rota
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marina Chiara Garassino
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Medicine, University of Chicago, Chicago, IL
| | | | - Filippo Maria de Braud
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Department of Oncology and Hemato-Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mario Occhipinti
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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SMARCA4: Current status and future perspectives in non-small-cell lung cancer. Cancer Lett 2023; 554:216022. [PMID: 36450331 DOI: 10.1016/j.canlet.2022.216022] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
SMARCA4, also known as transcription activator, is an ATP-dependent catalytic subunit of SWI/SNF (SWItch/Sucrose NonFermentable) chromatin-remodeling complexes that participates in the regulation of chromatin structure and gene expression by supplying energy. As a tumor suppressor that has aberrant expression in ∼10% of non-small-cell lung cancers (NSCLCs), SMARCA4 possesses many biological functions, including regulating gene expression, differentiation and transcription. Furthermore, NSCLC patients with SMARCA4 alterations have a weak response to conventional chemotherapy and poor prognosis. Therefore, the mechanisms of SMARCA4 in NSCLC development urgently need to be explored to identify novel biomarkers and precise therapeutic strategies for this subtype. This review systematically describes the biological functions of SMARCA4 and its role in NSCLC development, metastasis, functional epigenetics and potential therapeutic approaches for NSCLCs with SMARCA4 alterations. Additionally, this paper explores the relationship and regulatory mechanisms shared by SMARCA4 and its mutually exclusive catalytic subunit SMARCA2. We aim to provide innovative treatment strategies and improve clinical outcomes for NSCLC patients with SMARCA4 alterations.
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7
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Chong W, Zhu X, Ren H, Ye C, Xu K, Wang Z, Jia S, Shang L, Li L, Chen H. Integrated multi-omics characterization of KRAS mutant colorectal cancer. Am J Cancer Res 2022; 12:5138-5154. [PMID: 35836817 PMCID: PMC9274732 DOI: 10.7150/thno.73089] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/15/2022] [Indexed: 01/12/2023] Open
Abstract
KRAS mutation is the most frequent oncogenic aberration in colorectal cancer (CRC). The molecular mechanism and clinical implications of KRAS mutation in CRC remain unclear and show high heterogeneity within these tumors. Methods: We harnessed the multi-omics data (genomic, transcriptomic, proteomic, and phosphoproteomic etc.) of KRAS-mutant CRC tumors and performed unsupervised clustering to identify proteomics-based subgroups and molecular characterization. Results: In-depth analysis of the tumor microenvironment by single-cell transcriptomic revealed the cellular landscape of KRAS-mutant CRC tumors and identified the specific cell subsets with KRAS mutation. Integrated multi-omics analyses separated the KRAS-mutant tumors into two distinct molecular subtypes, termed KRAS-M1 (KM1) and KRAS-M2 (KM2). The two subtypes had a similar distribution of mutated residues in KRAS (G12D/V/C etc.) but were characterized by distinct features in terms of prognosis, genetic alterations, microenvironment dysregulation, biological phenotype, and potential therapeutic approaches. Proteogenomic analyses revealed that the EMT, TGF-β and angiogenesis pathways were enriched in the KM2 subtype and that the KM2 subtype was associated with the mesenchymal phenotype-related CMS4 subtype, which indicated stromal invasion and worse prognosis. The KM1 subtype was characterized predominantly by activation of the cell cycle, E2F and RNA transcription and was associated with the chromosomal instability (CIN)-related ProS-E proteomic subtype, which suggested cyclin-dependent features and better survival outcomes. Moreover, drug sensitivity analyses based on three compound databases revealed subgroup-specific agents for KM1 and KM2 tumors. Conclusions: This study clarifies the molecular heterogeneity of KRAS-mutant CRC and reveals new biological subtypes and therapeutic possibilities for these tumors.
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Affiliation(s)
- Wei Chong
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xingyu Zhu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Huicheng Ren
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Chunshui Ye
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Kang Xu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zhe Wang
- Department of Tumor Cell Biology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Shengtao Jia
- Department of Tumor Cell Biology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.,✉ Corresponding authors: Dr. Hao Chen, Ph.D, Clinical Research Center of Shandong University, Unit of Clinical Epidemiology, Qilu Hospital of Shandong University, Jinan, Shandong 250021, P.R. China. E-mail: , . Prof. Leping Li, Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China. E-mail:
| | - Hao Chen
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong, 250021, China.,✉ Corresponding authors: Dr. Hao Chen, Ph.D, Clinical Research Center of Shandong University, Unit of Clinical Epidemiology, Qilu Hospital of Shandong University, Jinan, Shandong 250021, P.R. China. E-mail: , . Prof. Leping Li, Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China. E-mail:
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