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Saridogan T, Akcakanat A, Zhao M, Evans KW, Yuca E, Scott S, Kirby BP, Zheng X, Ha MJ, Chen H, Ng PKS, DiPeri TP, Mills GB, Rodon Ahnert J, Damodaran S, Meric-Bernstam F. Efficacy of futibatinib, an irreversible fibroblast growth factor receptor inhibitor, in FGFR-altered breast cancer. Sci Rep 2023; 13:20223. [PMID: 37980453 PMCID: PMC10657448 DOI: 10.1038/s41598-023-46586-y] [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: 06/08/2023] [Accepted: 11/02/2023] [Indexed: 11/20/2023] Open
Abstract
Several alterations in fibroblast growth factor receptor (FGFR) genes have been found in breast cancer; however, they have not been well characterized as therapeutic targets. Futibatinib (TAS-120; Taiho) is a novel, selective, pan-FGFR inhibitor that inhibits FGFR1-4 at nanomolar concentrations. We sought to determine futibatinib's efficacy in breast cancer models. Nine breast cancer patient-derived xenografts (PDXs) with various FGFR1-4 alterations and expression levels were treated with futibatinib. Antitumor efficacy was evaluated by change in tumor volume and time to tumor doubling. Alterations indicating sensitization to futibatinib in vivo were further characterized in vitro. FGFR gene expression between patient tumors and matching PDXs was significantly correlated; however, overall PDXs had higher FGFR3-4 expression. Futibatinib inhibited tumor growth in 3 of 9 PDXs, with tumor stabilization in an FGFR2-amplified model and prolonged regression (> 110 days) in an FGFR2 Y375C mutant/amplified model. FGFR2 overexpression and, to a greater extent, FGFR2 Y375C expression in MCF10A cells enhanced cell growth and sensitivity to futibatinib. Per institutional and public databases, FGFR2 mutations and amplifications had a population frequency of 1.1%-2.6% and 1.5%-2.5%, respectively, in breast cancer patients. FGFR2 alterations in breast cancer may represent infrequent but highly promising targets for futibatinib.
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Affiliation(s)
- Turcin Saridogan
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
- Department of Basic Oncology, Graduate School of Health Sciences, Hacettepe University, Ankara, 06100, Turkey
| | - Argun Akcakanat
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
| | - Ming Zhao
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
| | - Kurt W Evans
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
| | - Erkan Yuca
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
| | - Stephen Scott
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
| | - Bryce P Kirby
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
| | - Xiaofeng Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Min Jin Ha
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Biostatistics, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
| | - Huiqin Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Patrick K S Ng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Pediatrics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Timothy P DiPeri
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gordon B Mills
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA
- Precision Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Jordi Rodon Ahnert
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
- The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Senthil Damodaran
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, Unit 455, Houston, TX, 77030, USA.
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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202
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Flynn J, Ahmadi MM, McFarland CT, Kubal MD, Taylor MA, Cheng Z, Torchia EC, Edwards MG. Crowdsourcing temporal transcriptomic coronavirus host infection data: Resources, guide, and novel insights. Biol Methods Protoc 2023; 8:bpad033. [PMID: 38107402 PMCID: PMC10723038 DOI: 10.1093/biomethods/bpad033] [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: 08/09/2023] [Revised: 10/07/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
The emergence of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) reawakened the need to rapidly understand the molecular etiologies, pandemic potential, and prospective treatments of infectious agents. The lack of existing data on SARS-CoV-2 hampered early attempts to treat severe forms of coronavirus disease-2019 (COVID-19) during the pandemic. This study coupled existing transcriptomic data from severe acute respiratory syndrome-related coronavirus 1 (SARS-CoV-1) lung infection animal studies with crowdsourcing statistical approaches to derive temporal meta-signatures of host responses during early viral accumulation and subsequent clearance stages. Unsupervised and supervised machine learning approaches identified top dysregulated genes and potential biomarkers (e.g. CXCL10, BEX2, and ADM). Temporal meta-signatures revealed distinct gene expression programs with biological implications to a series of host responses underlying sustained Cxcl10 expression and Stat signaling. Cell cycle switched from G1/G0 phase genes, early in infection, to a G2/M gene signature during late infection that correlated with the enrichment of DNA damage response and repair genes. The SARS-CoV-1 meta-signatures were shown to closely emulate human SARS-CoV-2 host responses from emerging RNAseq, single cell, and proteomics data with early monocyte-macrophage activation followed by lymphocyte proliferation. The circulatory hormone adrenomedullin was observed as maximally elevated in elderly patients who died from COVID-19. Stage-specific correlations to compounds with potential to treat COVID-19 and future coronavirus infections were in part validated by a subset of twenty-four that are in clinical trials to treat COVID-19. This study represents a roadmap to leverage existing data in the public domain to derive novel molecular and biological insights and potential treatments to emerging human pathogens.
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Affiliation(s)
- James Flynn
- Illumina Corporation, San Diego, CA 92122, United States
| | - Mehdi M Ahmadi
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | | | | | - Mark A Taylor
- Bioinfo Solutions LLC, Parker, CO 80134, United States
| | - Zhang Cheng
- Illumina Corporation, San Diego, CA 92122, United States
| | - Enrique C Torchia
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
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203
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Wang H, Yan L, Liu L, Lu X, Chen Y, Zhang Q, Chen M, Cai L, Dai Z. A pyroptosis gene-based prognostic model for predicting survival in low-grade glioma. PeerJ 2023; 11:e16412. [PMID: 38025749 PMCID: PMC10652862 DOI: 10.7717/peerj.16412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/15/2023] [Indexed: 12/01/2023] Open
Abstract
Background Pyroptosis, a lytic form of programmed cell death initiated by inflammasomes, has been reported to be closely associated with tumor proliferation, invasion and metastasis. However, the roles of pyroptosis genes (PGs) in low-grade glioma (LGG) remain unclear. Methods We obtained information for 1,681 samples, including the mRNA expression profiles of LGGs and normal brain tissues and the relevant corresponding clinical information from two public datasets, TCGA and GTEx, and identified 45 differentially expressed pyroptosis genes (DEPGs). Among these DEPGs, nine hub pyroptosis genes (HPGs) were identified and used to construct a genetic risk scoring model. A total of 476 patients, selected as the training group, were divided into low-risk and high-risk groups according to the risk score. The area under the curve (AUC) values of the receiver operating characteristic (ROC) curves verified the accuracy of the model, and a nomogram combining the risk score and clinicopathological characteristics was used to predict the overall survival (OS) of LGG patients. In addition, a cohort from the Gene Expression Omnibus (GEO) database was selected as a validation group to verify the stability of the model. qRT-PCR was used to analyze the gene expression levels of nine HPGs in paracancerous and tumor tissues from 10 LGG patients. Results Survival analysis showed that, compared with patients in the low-risk group, patients in the high-risk group had a poorer prognosis. A risk score model combining PG expression levels with clinical features was considered an independent risk factor. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that immune-related genes were enriched among the DEPGs and that immune activity was increased in the high-risk group. Conclusion In summary, we successfully constructed a model to predict the prognosis of LGG patients, which will help to promote individualized treatment and provide potential new targets for immunotherapy.
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Affiliation(s)
- Hua Wang
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lin Yan
- Department of Breast Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lixiao Liu
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Xianghe Lu
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yingyu Chen
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qian Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Mengyu Chen
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lin Cai
- Department of Neurosurgery, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhang’an Dai
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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204
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Trivedi V, Noronha V, Sreekanthreddy P, Desai S, Poojary D, Varghese L, Gowda P, Butle A, Mishra R, Bal M, Mittal N, Rane S, Kane S, Basu S, Patil V, Menon N, Singh AK, Chaturvedi P, Chandrani P, Choughule A, Veldore V, Prabhash K, Dutt A. Association of Cutibacterium acnes with human thyroid cancer. Front Endocrinol (Lausanne) 2023; 14:1152514. [PMID: 38027096 PMCID: PMC10668118 DOI: 10.3389/fendo.2023.1152514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The diverse subtypes of thyroid carcinoma have distinct clinical outcomes despite a comparable spectrum of underlying genetic alterations. Beyond genetic alterations, sparse efforts have been made to characterize the microbes associated with thyroid cancer. In this study, we examine the microbial profile of thyroid cancer. Methods We sequenced the whole transcriptome of 70 thyroid cancers (40 papillary and 30 anaplastic). Using Infectious Pathogen Detector IPD 2.0, we analysed the relative abundance of 1060 microbes across 70 tumours from patients with thyroid cancer against 118 tumour samples from patients with breast, cervical, colorectal, and tongue cancer. Results Our analysis reveals a significant prevalence of Cutibacterium acnes in 58.6% thyroid cancer samples compared to other cancer types (p=0.00038). Immune cell fraction analysis between thyroid cancer samples with high and low Cutibacterium loads identify enrichment of immunosuppressive cells, including Tregs (p=0.015), and other anti-inflammatory cytokines in the tumour microenvironment, suggesting an immune evasion/immunosuppression milieu is associated with the infection. A higher burden of Cutibacterium acnes was also found to be associated with poor survival defining a distinct sub-group of thyroid cancer. Conclusion Cutibacterium acnes is associated with immune suppression and poor prognosis in a subpopulation of thyroid cancer. This study may help design novel therapeutic measures involving appropriate antibiotics to manage the disease better.
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Affiliation(s)
- Vaishakhi Trivedi
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Vanita Noronha
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | | | - Sanket Desai
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Disha Poojary
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Linu Varghese
- 4baseCare Oncosolutions Pvt ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Pooja Gowda
- 4baseCare Oncosolutions Pvt ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Munita Bal
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Neha Mittal
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Swapnil Rane
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Shubhada Kane
- Consultant Onco-pathologist, Jaslok Hospital, Mumbai, Maharashtra, India
| | - Sandip Basu
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Vijay Patil
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Nandini Menon
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Ajay Kumar Singh
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Pankaj Chaturvedi
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Department of Head and Neck Oncology, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Pratik Chandrani
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Medical oncology molecular laboratory, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Centre for Computational Biology, Bioinformatics and Crosstalk Lab, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Anuradha Choughule
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Vidya Veldore
- 4baseCare Oncosolutions Pvt ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Amit Dutt
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
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205
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Kourie HR, Zouein J, Succar B, Mardirossian A, Ahmadieh N, Chouery E, Mehawej C, Jalkh N, kattan J, Nemr E. Genetic Polymorphisms Involved in Bladder Cancer: A Global Review. Oncol Rev 2023; 17:10603. [PMID: 38025894 PMCID: PMC10657888 DOI: 10.3389/or.2023.10603] [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: 04/27/2022] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Bladder cancer (BC) has been associated with genetic susceptibility. Single peptide polymorphisms (SNPs) can modulate BC susceptibility. A literature search was performed covering the period between January 2000 and October 2020. Overall, 334 articles were selected, reporting 455 SNPs located in 244 genes. The selected 455 SNPs were further investigated. All SNPs that were associated with smoking and environmental exposure were excluded from this study. A total of 197 genes and 343 SNPs were found to be associated with BC, among which 177 genes and 291 SNPs had congruent results across all available studies. These genes and SNPs were classified into eight different categories according to their function.
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Affiliation(s)
- Hampig Raphael Kourie
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Joseph Zouein
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Bahaa Succar
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Avedis Mardirossian
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Nizar Ahmadieh
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Eliane Chouery
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
| | - Cybel Mehawej
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
| | - Nadine Jalkh
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Joseph kattan
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Elie Nemr
- Urology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
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206
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Zhu Y, Liu C, Xu Z, Zou Z, Xie T, Xing P, Wang L, Li J. Front-line therapy for brain metastases and non-brain metastases in advanced epidermal growth factor receptor-mutated non-small cell lung cancer: a network meta-analysis. Chin Med J (Engl) 2023; 136:2551-2561. [PMID: 37160733 PMCID: PMC10617931 DOI: 10.1097/cm9.0000000000002468] [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: 04/28/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND The brain is a common metastatic site in patients with non-small cell lung cancer (NSCLC), resulting in a relatively poor prognosis. Systemic therapy with epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) is recommended as the first-line treatment for EGFR -mutated, advanced NSCLC patients. However, intracranial activity varies in different drugs. Thus, brain metastasis (BM) should be considered when choosing the treatment regimens. We conducted this network meta-analysis to explore the optimal first-line therapeutic schedule for advanced EGFR -mutated NSCLC patients with different BM statuses. METHODS Randomized controlled trials focusing on EGFR-TKIs (alone or in combination) in advanced and EGFR -mutant NSCLC patients, who have not received systematic treatment, were systematically searched up to December 2021. We extracted and analyzed progression-free survival (PFS) and overall survival (OS). A network meta-analysis was performed with the Bayesian statistical model to determine the survival outcomes of all included therapy regimens using the R software. Hazard ratios (HRs) and 95% confidence intervals (CIs) were used to compare intervention measures, and overall rankings of therapies were estimated under the Bayesian framework. RESULTS This analysis included 17 RCTs with 5077 patients and 12 therapies, including osimertinib + bevacizumab, aumolertinib, osimertinib, afatinib, dacomitinib, standards of care (SoC, including gefitinib, erlotinib, or icotinib), SoC + apatinib, SoC + bevacizumab, SoC + ramucirumab, SoC + pemetrexed based chemotherapy (PbCT), PbCT, and pemetrexed free chemotherapy (PfCT). For patients with BM, SoC + PbCT improved PFS compared with SoC (HR = 0.40, 95% CI: 0.17-0.95), and osimertinib + bevacizumab was most likely to rank first in PFS, with a cumulative probability of 34.5%, followed by aumolertinib, with a cumulative probability of 28.3%. For patients without BM, osimertinib + bevacizumab, osimertinib, aumolertinib, SoC + PbCT, dacomitinib, SoC + ramucirumab, SoC + bevacizumab, and afatinib showed superior efficacy compared with SoC (HR = 0.43, 95% CI: 0.20-0.90; HR = 0.46, 95% CI: 0.31-0.68; HR = 0.51, 95% CI: 0.34-0.77; HR = 0.50, 95% CI: 0.38-0.66; HR = 0.62, 95% CI: 0.43-0.89; HR = 0.64, 95% CI: 0.44-0.94; HR = 0.61, 95% CI: 0.48-0.76; HR = 0.71, 95% CI: 0.50-1.00), PbCT (HR = 0.29, 95% CI: 0.11-0.74; HR = 0.31, 95% CI: 0.15-0.62; HR = 0.34, 95% CI: 0.17-0.69; HR = 0.34, 95% CI: 0.18-0.64; HR = 0.42, 95% CI: 0.21-0.82; HR = 0.43, 95% CI: 0.22-0.87; HR = 0.41, 95% CI: 0.22-0.74; HR = 0.48, 95% CI: 0.31-0.75), and PfCT (HR = 0.14, 95% CI: 0.06-0.32; HR = 0.15, 95% CI: 0.09-0.26; HR = 0.17, 95% CI: 0.09-0.29; HR = 0.16, 95% CI: 0.10-0.26; HR = 0.20, 95% CI: 0.12-0.35; HR = 0.21, 95% CI: 0.12-0.39; HR = 0.20, 95% CI: 0.12-0.31; HR = 0.23, 95% CI: 0.16-0.34) in terms of PFS. And, SoC + apatinib showed relatively superior PFS when compared with PbCT (HR = 0.44, 95% CI: 0.22-0.92) and PfCT (HR = 0.21, 95% CI: 0.12-0.39), but similar PFS to SoC (HR = 0.65, 95% CI: 0.42-1.03). No statistical differences were observed for PFS in patients without BM between PbCT and SoC (HR = 1.49, 95% CI: 0.84-2.64), but both showed favorable PFS when compared with PfCT (PfCT vs. SoC, HR = 3.09, 95% CI: 2.06-4.55; PbCT vs. PfCT, HR = 0.14, 95% CI: 0.06-0.32). For patients without BM, osimertinib + bevacizumab was most likely to rank the first, with cumulative probabilities of 47.1%. For OS, SoC + PbCT was most likely to rank first in patients with and without BM, with cumulative probabilities of 46.8%, and 37.3%, respectively. CONCLUSION Osimertinib + bevacizumab is most likely to rank first in PFS in advanced EGFR -mutated NSCLC patients with or without BM, and SoC + PbCT is most likely to rank first in OS.
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Affiliation(s)
- Yixiang Zhu
- Department of Medical 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
| | - Chengcheng Liu
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Ziyi Xu
- Department of Medical 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
| | - Zihua Zou
- Department of Medical 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
| | - Tongji Xie
- Department of Medical 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
| | - Puyuan Xing
- Department of Medical 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
| | - Le Wang
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junling Li
- Department of Medical 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
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Tian E, Zhou C, Quan S, Su C, Zhang G, Yu Q, Li J, Zhang J. RIPK2 inhibitors for disease therapy: Current status and perspectives. Eur J Med Chem 2023; 259:115683. [PMID: 37531744 DOI: 10.1016/j.ejmech.2023.115683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/11/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
Receptor-interacting protein kinase 2 (RIPK2) belongs to the receptor-interacting protein family (RIPs), which is mainly distributed in the cytoplasm. RIPK2 is widely expressed in human tissues, and its mRNA level is highly expressed in the spleen, leukocytes, placenta, testis, and heart. RIPK2 is a dual-specificity kinase with multiple domains, which can interact with tumor necrosis factor receptor (TNFR), and participate in the Toll-like receptor (TLR) and nucleotide-binding oligomerization domain (NOD) signaling pathways. It is considered as a vital adapter molecule involved in the innate immunity, adaptive immunity, and apoptosis. Functionally, RIPK2 and its targeted small molecules are of great significance in inflammatory responses, autoimmune diseases and tumors. The present study reviews the molecule structure and biological functions of RIPK2, and its correlation between human diseases. In addition, we focus on the structure-activity relationship of small molecule inhibitors of RIPK2 and their therapeutic potential in human diseases.
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Affiliation(s)
- Erkang Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Changhan Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Shuqi Quan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Chongying Su
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Guanning Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Quanwei Yu
- Joint Research Institution of Altitude Health, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Juan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Jifa Zhang
- Joint Research Institution of Altitude Health, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, 610041, China.
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208
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Saxena R, Chakrapani B, Sarath Krishnan MP, Gupta A, Gupta S, Das J, Gupta SC, Mirza AA, Rao S, Goyal B. Next generation sequencing uncovers multiple miRNAs associated molecular targets in gallbladder cancer patients. Sci Rep 2023; 13:19101. [PMID: 37925508 PMCID: PMC10625549 DOI: 10.1038/s41598-023-44767-3] [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: 05/13/2023] [Accepted: 10/12/2023] [Indexed: 11/06/2023] Open
Abstract
Gallbladder cancer (GBC) is a lethal disease with surgical resection as the only curative treatment. However, many patients are ineligible for surgery, and current adjuvant treatments exhibit limited effectiveness. Next-generation sequencing has improved our understanding of molecular pathways in cancer, sparking interest in microRNA-based gene regulation. The aim of the study is to identify dysregulated miRNAs in GBC and investigate their potential as therapeutic tools for effective and targeted treatment strategies. GBC and control tissue samples were sequenced for miRNA expression using the Illumina HiSeq platform. Biological processes and related pathways were determined using the Panther and Gene Ontology databases. 439 significantly differentially expressed miRNAs were identified; 19 of them were upregulated and 29 were downregulated. Key enriched biological processes included immune cell apoptosis, endoplasmic reticulum (ER) overload response, and negative regulation of the androgen receptor (AR) signaling pathway. Panther analysis revealed the insulin-like growth factor (IGF)-mitogen activated protein kinases (MAPK) cascade, p38 MAPK pathway, p53 pathway, and FAS (a subgroup of the tumor necrosis factor receptor) signaling pathway as highly enriched among dysregulated miRNAs. Kirsten rat sarcoma virus (KRAS), AR, and interferon gamma (IFN-γ) pathways were identified among the key pathways potentially amenable to targeted therapy. We concluded that a combination approach involving miRNA-based interventions could enhance therapeutic outcomes. Our research emphasizes the importance of precision medicine, targeting pathways using sense and anti-sense miRNAs as potential therapies in GBC.
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Affiliation(s)
- Rahul Saxena
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, 249203, India
| | - Baskar Chakrapani
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, 249203, India
| | - M P Sarath Krishnan
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, 249203, India
| | - Amit Gupta
- Department of General Surgery, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Sweety Gupta
- Department of Radiation Oncology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Jayanta Das
- Department of Biochemistry, All India Institute of Medical Sciences, Guwahati, Assam, India
| | - Subash C Gupta
- Department of Biochemistry, All India Institute of Medical Sciences, Guwahati, Assam, India
| | - Anissa A Mirza
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, 249203, India
| | - Shalinee Rao
- Department of Pathology and Laboratory Medicine, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Bela Goyal
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, 249203, India.
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209
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Brozos-Vázquez EM, Rodríguez-López C, Cortegoso-Mosquera A, López-Landrove S, Muinelo-Romay L, García-González J, López-López R, León-Mateos L. Immunotherapy in patients with brain metastasis: advances and challenges for the treatment and the application of circulating biomarkers. Front Immunol 2023; 14:1221113. [PMID: 38022574 PMCID: PMC10654987 DOI: 10.3389/fimmu.2023.1221113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The central nervous system (CNS) is one of the most frequent metastatic sites of various cancers, including lung cancer, breast cancer and melanoma. The development of brain metastases requires a specific therapeutic approach and is associated with high mortality and morbidity in cancer patients. Advances in precision medicine and the introduction in recent years of new drugs, such as immunotherapy, have made it possible to improve the prognosis of these patients by improving survival and quality of life. New diagnostic techniques such as liquid biopsy allow real-time monitoring of tumor evolution, providing molecular information on prognostic and predictive biomarkers of response to treatment in blood or other fluids. In this review, we perform an exhaustive update of the clinical trials that demonstrate the utility of immunotherapy in patients with brain metastases and the potential of circulating biomarkers to improving the results of efficacy and toxicity in this subgroup of patients.
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Affiliation(s)
- E M Brozos-Vázquez
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Medical Oncology Department, Complexo Hospitalario Universitario de A Coruña, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - C Rodríguez-López
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - A Cortegoso-Mosquera
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - S López-Landrove
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - L Muinelo-Romay
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - J García-González
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - R López-López
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - L León-Mateos
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
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210
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Javle M, King G, Spencer K, Borad MJ. Futibatinib, an Irreversible FGFR1-4 Inhibitor for the Treatment of FGFR-Aberrant Tumors. Oncologist 2023; 28:928-943. [PMID: 37390492 PMCID: PMC10628593 DOI: 10.1093/oncolo/oyad149] [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: 03/14/2023] [Accepted: 05/03/2023] [Indexed: 07/02/2023] Open
Abstract
Fibroblast growth factor receptors (FGFR) are emerging as an important therapeutic target for patients with advanced, refractory cancers. Most selective FGFR inhibitors under investigation show reversible binding, and their activity is limited by acquired drug resistance. This review summarizes the preclinical and clinical development of futibatinib, an irreversible FGFR1-4 inhibitor. Futibatinib stands out among FGFR inhibitors because of its covalent binding mechanism and low susceptibility to acquired resistance. Preclinical data indicated robust activity of futibatinib against acquired resistance mutations in the FGFR kinase domain. In early-phase studies, futibatinib showed activity in cholangiocarcinoma, and gastric, urothelial, breast, central nervous system, and head and neck cancers harboring various FGFR aberrations. Exploratory analyses indicated clinical benefit with futibatinib after prior FGFR inhibitor use. In a pivotal phase II trial, futibatinib demonstrated durable objective responses (42% objective response rate) and tolerability in previously treated patients with advanced intrahepatic cholangiocarcinoma harboring FGFR2 fusions or rearrangements. A manageable safety profile was observed across studies, and patient quality of life was maintained with futibatinib treatment in patients with cholangiocarcinoma. Hyperphosphatemia, the most common adverse event with futibatinib, was well managed and did not lead to treatment discontinuation. These data show clinically meaningful benefit with futibatinib in FGFR2-rearrangement-positive cholangiocarcinoma and provide support for further investigation of futibatinib across other indications. Future directions for this agent include elucidating mechanisms of resistance and exploration of combination therapy approaches.
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Affiliation(s)
- Milind Javle
- Department of Gastrointestinal Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gentry King
- Division of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Kristen Spencer
- Perlmutter Cancer Center of NYU Langone Health, New York, NY, USA
- NYU Grossman School of Medicine, New York University, New York, NY,USA
| | - Mitesh J Borad
- Department of Oncology, Mayo Clinic Cancer Center, Phoenix, AZ,USA
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211
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Hu G, Huang N, Zhang J, Zhang D, Wang S, Zhang Y, Wang L, Du Y, Kuang S, Ma K, Zhu H, Xu N, Liu M. LKB1 loss promotes colorectal cancer cell metastasis through regulating TNIK expression and actin cytoskeleton remodeling. Mol Carcinog 2023; 62:1659-1672. [PMID: 37449799 DOI: 10.1002/mc.23606] [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: 12/18/2022] [Revised: 05/19/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors. Approximately 5%-6% of CRC cases are associated with hereditary CRC syndromes, including the Peutz-Jeghers syndrome (PJS). Liver kinase B1 (LKB1), also known as STK11, is the major gene responsible for PJS. LKB1 heterozygotic deficiency is involved in intestinal polyps in mice, while the mechanism of LKB1 in CRC remains elusive. In this study, we generated LKB1 knockout (KO) CRC cell lines by using CRISPR-Cas9. LKB1 KO promoted CRC cell motility in vitro and tumor metastases in vivo. LKB1 attenuated expression of TRAF2 and NCK-interacting protein kinase (TNIK) as accessed by RNA-seq and western blots, and similar suppression was also detected in the tumor tissues of azoxymethane/dextran sodium sulfate-induced intestinal-specific LKB1-KO mice. LKB1 repressed TNIK expression through its kinase activity. Moreover, attenuating TNIK by shRNA inhibited cell migration and invasion of CRC cells. LKB1 loss-induced high metastatic potential of CRC cells was depended on TNIK upregulation. Furthermore, TNIK interacted with ARHGAP29 and further affected actin cytoskeleton remodeling. Taken together, LKB1 deficiency promoted CRC cell metastasis via TNIK upregulation and subsequently mediated cytoskeleton remodeling. These results suggest that LKB1-TNIK axis may play a crucial role in CRC progression.
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Affiliation(s)
- Guanghui Hu
- Laboratory of Cell and Molecular Biology & 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, China
| | - Ning Huang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Zhang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Die Zhang
- Laboratory of Cell and Molecular Biology & 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, China
| | - Shuren Wang
- Laboratory of Cell and Molecular Biology & 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, China
| | - Yuanyuan Zhang
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Panjiayuan, Chaoyang District, Beijing, People's Republic of China
| | - Liming Wang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yingxi Du
- Laboratory of Cell and Molecular Biology & 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, China
| | - Shuwen Kuang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Ma
- Laboratory of Cell and Molecular Biology & 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, China
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology & 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, China
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology & 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, China
| | - Mei Liu
- Laboratory of Cell and Molecular Biology & 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, China
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212
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Chougule A, Chandrani P, Noronha V, Pange P, Kale S, Nikam A, Nambiar K, Marchande D, Durve A, Gupta V, Jagtap V, Tiwrekar P, Menon N, Joshi A, Kaushal R, Pai T, Patil VM, Dutt A, Banavali SD, Prabhash K. Real-World Evidence of EGFR Targeted Therapy in NSCLC- A Brief Report of Decade Long Single Center Experience. JTO Clin Res Rep 2023; 4:100566. [PMID: 38033811 PMCID: PMC10682910 DOI: 10.1016/j.jtocrr.2023.100566] [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: 01/06/2023] [Revised: 08/10/2023] [Accepted: 08/20/2023] [Indexed: 12/02/2023] Open
Abstract
The significance of EGFR targeted therapy in the lung adenocarcinoma is paramount. Several controlled clinical trials have reported considerable survival of EGFR mutation positive patients on receiving the EGFR tyrosine kinase inhibitor (TKI). However, the real-world evidence of benefits of EGFR TKI would be further useful to understand how the designated therapeutic regimen benefits the patients. In this study, we report a decade long real-world evidence of EGFR molecular testing in lung cancer at Tata Memorial Hospital (Mumbai, India). Laboratory and hospital records containing basic demographic details, clinical characteristics, treatment regimen, survival outcome were collected retrospectively. Statistical association and survival analysis were performed using the R programming. The cohort includes 9,053 lung cancer patients tested for EGFR mutations during 2011 to 2019. Baseline T790M and compound mutations were the only mutations observed co-occurring while all other EGFR mutations were mutually exclusive. Furthermore, the baseline T790M were also observed to be associated with TTF1 positivity, smoking and local metastasis. Overall survival of the patients harboring co-occurring compound mutations was significantly lesser than the other EGFR positive patients. Overall, our study suggests that EGFR TKI may provide real-world benefit to the lung cancer patients harboring mutually exclusive EGFR mutations. On the other hand, further systematic study is essential to develop better therapeutic regimen for co-occurring baseline EGFR T790M and other compound mutations.
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Affiliation(s)
- Anuradha Chougule
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Pratik Chandrani
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Centre for Computational Biology, Bioinformatics and Crosstalk Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Vanita Noronha
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Priyanka Pange
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Shrutikaa Kale
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Ankita Nikam
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Kavya Nambiar
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Dipika Marchande
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Arpana Durve
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vinod Gupta
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vinita Jagtap
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Priyanka Tiwrekar
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Nandini Menon
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Amit Joshi
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Rajeev Kaushal
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Trupti Pai
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Vijay Maruti Patil
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Amit Dutt
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Shripad Dinanath Banavali
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Kumar Prabhash
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
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213
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Nadal E, Oré-Arce M, Remon J, Bernabé-Caro R, Covela-Rúa M, de Castro-Carpeño J, Massutí-Sureda B, Guillot-Morales M, Majem M, Maestu-Maiques I, Morilla-Ruíz I, Gironés R. Expert consensus to optimize the management of older adult patients with advanced EGFR-mutated non-small cell lung cancer. Clin Transl Oncol 2023; 25:3139-3151. [PMID: 37566345 PMCID: PMC10514135 DOI: 10.1007/s12094-023-03286-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/17/2023] [Indexed: 08/12/2023]
Abstract
Lung cancer (LC) is associated with ageing, with the average age of affected individuals being approximately 70 years. However, despite a higher incidence and prevalence among older people, the older adult population is underrepresented in clinical trials. For LC with Epidermal Growth Factor Receptor (EGFR) mutations, there is no clear association of this mutation with age. Geriatric assessments (GAs) and a multidisciplinary approach are essential for defining the optimal treatment. In this consensus, a group of experts selected from the Oncogeriatrics Section of the Spanish Society of Medical Oncology (Sección de Oncogeriatría de la Sociedad Española de Oncología Médica-SEOM), the Spanish Lung Cancer Group (Grupo Español de Cáncer de Pulmón-GECP) and the Association for Research on Lung Cancer in Women (Asociación para la Investigación del Cáncer de Pulmón en Mujeres-ICAPEM) evaluate the scientific evidence currently available and propose a series of recommendations to optimize the management of older adult patients with advanced LC with EGFR mutations.
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Affiliation(s)
- Ernest Nadal
- Department of Medical Oncology, Institut Català d’Oncologia (ICO), Institut d’Investigacions Biomèdiques de Bellvitge (IDIBELL), Duran i Reynals University Hospital, Barcelona, Spain
| | - Martín Oré-Arce
- Department of Medical Oncology, Marina Baixa de Villajoyosa Hospital, Alicante, Spain
| | - Jordi Remon
- Department of Medical Oncology, HM Nou Delfos Hospital, Barcelona, Spain
| | - Reyes Bernabé-Caro
- Department of Medical Oncology, Virgen del Rocío University Hospital, Sevilla University, Seville, Spain
| | - Marta Covela-Rúa
- Department of Medical Oncology, Lucus Augusti University Hospital, Lugo, Spain
| | | | | | | | - Margarita Majem
- Department of Medical Oncology, Santa Creu i Sant Pau Hospital, Barcelona, Spain
| | | | - Idoia Morilla-Ruíz
- Department of Medical Oncology, Navarra University Hospital-NavarraBioMed, IdisNa, Pamplona, Spain
| | - Regina Gironés
- Department of Medical Oncology, Polytechnic la Fe University Hospital, Avinguda de Fernando Abril Martorell, 106, 46026 Valencia, Valencia Spain
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214
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Malchers F, Nogova L, van Attekum MH, Maas L, Brägelmann J, Bartenhagen C, Girard L, Bosco G, Dahmen I, Michels S, Weeden CE, Scheel AH, Meder L, Golfmann K, Schuldt P, Siemanowski J, Rehker J, Merkelbach-Bruse S, Menon R, Gautschi O, Heuckmann JM, Brambilla E, Asselin-Labat ML, Persigehl T, Minna JD, Walczak H, Ullrich RT, Fischer M, Reinhardt HC, Wolf J, Büttner R, Peifer M, George J, Thomas RK. Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer. J Clin Invest 2023; 133:e170217. [PMID: 37606995 PMCID: PMC10617767 DOI: 10.1172/jci170217] [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: 03/07/2023] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
The discovery of frequent 8p11-p12 amplifications in squamous cell lung cancer (SQLC) has fueled hopes that FGFR1, located inside this amplicon, might be a therapeutic target. In a clinical trial, only 11% of patients with 8p11 amplification (detected by FISH) responded to FGFR kinase inhibitor treatment. To understand the mechanism of FGFR1 dependency, we performed deep genomic characterization of 52 SQLCs with 8p11-p12 amplification, including 10 tumors obtained from patients who had been treated with FGFR inhibitors. We discovered somatically altered variants of FGFR1 with deletion of exons 1-8 that resulted from intragenic tail-to-tail rearrangements. These ectodomain-deficient FGFR1 variants (ΔEC-FGFR1) were expressed in the affected tumors and were tumorigenic in both in vitro and in vivo models of lung cancer. Mechanistically, breakage-fusion-bridges were the source of 8p11-p12 amplification, resulting from frequent head-to-head and tail-to-tail rearrangements. Generally, tail-to-tail rearrangements within or in close proximity upstream of FGFR1 were associated with FGFR1 dependency. Thus, the genomic events shaping the architecture of the 8p11-p12 amplicon provide a mechanistic explanation for the emergence of FGFR1-driven SQLC. Specifically, we believe that FGFR1 ectodomain-deficient and FGFR1-centered amplifications caused by tail-to-tail rearrangements are a novel somatic genomic event that might be predictive of therapeutically relevant FGFR1 dependency.
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Affiliation(s)
- Florian Malchers
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Lucia Nogova
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Martijn H.A. van Attekum
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Lukas Maas
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Johannes Brägelmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Mildred Scheel School of Oncology, Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
| | - Luc Girard
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Graziella Bosco
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Ilona Dahmen
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Sebastian Michels
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Clare E. Weeden
- Personalized Oncology Division, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andreas H. Scheel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Lydia Meder
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Kristina Golfmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Philipp Schuldt
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Janna Siemanowski
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Jan Rehker
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Sabine Merkelbach-Bruse
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | | | - Oliver Gautschi
- University of Berne and Cantonal Hospital of Lucerne, Cantonal Hospital of Lucerne, Lucerne, Switzerland
| | | | | | - Marie-Liesse Asselin-Labat
- Personalized Oncology Division, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Thorsten Persigehl
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - John D. Minna
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Henning Walczak
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, United Kingdom
| | - Roland T. Ullrich
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jürgen Wolf
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Reinhard Büttner
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Martin Peifer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Julie George
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Department of Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Roman K. Thomas
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Luo Y, Wang H, Zhong J, Shi J, Zhang X, Yang Y, Wu R. Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma. Heliyon 2023; 9:e21336. [PMID: 37954334 PMCID: PMC10637964 DOI: 10.1016/j.heliyon.2023.e21336] [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: 07/19/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
Background APOBEC family play an important role in cancer mutagenesis and tumor development. The role of APOBEC family in lung adenocarcinoma (LUAD) has not been studied comprehensively. Materials and methods The expression data of pan-cancer as well as LUAD was obtained from public databases. The expression level of APOBEC family genes was analyzed in different normal and cancer tissues. APOBEC mutagenesis enrichment score (AMES) was utilized to evaluate the APOBEC-induced mutations and the relation of APOBEC with genomic instability. Gene set enrichment analysis was used to identify differentially enriched pathways. Univariate Cox regression and Lasso regression were applied to screen key prognostic genes. The immune cell infiltration was estimated by CIBERSORT. RT-qPCR assay, CCK-8 and Transwell assay were conducted to explore gene expression and lung cancer cell invasion. Results Cancer tissues had significantly altered expression of APOBEC family genes and the expression patterns of APOBEC family were different in different cancer types. APOBEC3B was the most aberrantly expressed in most cancer types. In LUAD, we observed a significantly positive correlation of AMES with intratumor heterogeneity (ITH), tumor neoantigen burden (TNB), and tumor mutation burden (TMB). High AMES group had high mutation counts of DNA damage repair pathways, and high enrichment of cell cycle and DNA repair pathways. We identified four prognostic genes (LYPD3, ANLN, MUC5B, and FOSL1) based on AMES, and constructed an AMES-related gene signature. The expressions of four genes were enhanced and accelerated the invasion ability and viability of lung cancer cells. Furthermore, we found that high group increased oxidative stress level. Conclusions APOBEC family was associated with genomic instability, DNA damage-related pathways, and cell cycle in LUAD. The AMES-related gene signature had a great potential to indicate the prognosis and guide immunotherapy/chemotherapy for patients suffering from LUAD.
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Affiliation(s)
- Yu Luo
- Gynecology Department of Jingmen Traditional Chinese Medicine Hospital, Jingmen, 448000, China
- Beijing University of Traditional Chinese Medicine Guoyitang Expert Clinic, National Medical Hall of Beijing University of Traditional Chinese Medicine, Jingmen Traditional Chinese Medicine Hospital, Jingmen, 448000, China
| | - Huiru Wang
- Clinical College of Traditional Chinese Medicine, Hubei University of Traditional Chinese Medicine, Wuhan, 430014, China
| | - Jian Zhong
- Department of Nephrology, Dongzhimen Hospital, Beijing University of Traditional Chinese Medicine, Beijing, 100105, China
| | - Jianrong Shi
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xianlin Zhang
- Department of Endocrinology, Wuhan Hospital of Traditional Chinese Medicine, Wuhan Traditional Chinese Medicine Hospital, Wuhan, 430014, China
| | - Yanni Yang
- Health Management Center of Jingmen Traditional Chinese Medicine Hospital, Jingmen, 448000, China
| | - Ruixin Wu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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216
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Manzano-Núñez F, Prates Tiago Aguilar L, Sempoux C, Lemaigre FP. Biliary Tract Cancer: Molecular Biology of Precursor Lesions. Semin Liver Dis 2023; 43:472-484. [PMID: 37944999 DOI: 10.1055/a-2207-9834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Biliary tract cancer is a devastating malignancy of the bile ducts and gallbladder with a dismal prognosis. The study of precancerous lesions has received considerable attention and led to a histopathological classification which, in some respects, remains an evolving field. Consequently, increasing efforts have been devoted to characterizing the molecular pathogenesis of the precursor lesions, with the aim of better understanding the mechanisms of tumor progression, and with the ultimate goal of meeting the challenges of early diagnosis and treatment. This review delves into the molecular mechanisms that initiate and promote the development of precursor lesions of intra- and extrahepatic cholangiocarcinoma and of gallbladder carcinoma. It addresses the genomic, epigenomic, and transcriptomic landscape of these precursors and provides an overview of animal and organoid models used to study them. In conclusion, this review summarizes the known molecular features of precancerous lesions in biliary tract cancer and highlights our fragmentary knowledge of the molecular pathogenesis of tumor initiation.
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Affiliation(s)
| | | | - Christine Sempoux
- Institute of Pathology, Lausanne University Hospital CHUV, University of Lausanne, Lausanne, Switzerland
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217
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Qian H, Hou C, Zhang Y, Ji S, Zhong C, Li J, Zhang Q, Huang J, Li C, ChengJi. Effects of concurrent TP53 mutations on the efficacy and prognosis of targeted therapy for advanced EGFR mutant lung adenocarcinoma. Cancer Genet 2023; 278-279:62-70. [PMID: 37672936 DOI: 10.1016/j.cancergen.2023.08.006] [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: 04/03/2023] [Revised: 07/08/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND How concurrent TP53 mutations affect targeted therapy of advanced Epidermal Growth Factor Receptor (EGFR) mutant lung adenocarcinoma remains controversial, particularly the deep classification of TP53 mutations. METHODS This study retrospectively analyzed the clinical data of advanced EGFR mutant lung adenocarcinoma patients treated with EGFR-tyrosine kinase inhibitors (TKIs) in the First Affiliated Hospital of Soochow University. The survival rates were compared using Log-rank tests. Potential prognostic factors were identified using multivariate Cox hazard regression models. RESULTS Total 156 advanced lung adenocarcinoma patients treated with EGFR-TKIs were included in this study. Multivariate analysis showed that male [hazard rate (HR): 1.537, 95% confidence interval (CI): 1.055-2.240, P = 0.025], brain metastasis (HR: 1.707, 95%CI: 1.086-2.682, P = 0.020) and concurrent TP53 mutations (HR: 1.569, 95%CI: 1.051-2.341, P = 0.028) were independent negative predictors of progression-free survival (PFS). EGFR L858R mutations (HR: 2.475, 95%CI: 1.443-4.248, p = 0.001), smoking history (HR: 2.530, 95%CI: 1.352-4.733, P = 0.004) and concurrent TP53 mutations (HR: 2.326, 95%CI: 1.283-4.218, P = 0.005) were associated with worse survival. Further analysis revealed that mutations in TP53 exons 4, 5 and 8 (P<0.05), missense mutations (P = 0.006) and nondisruptive mutations (P<0.001) were associated with shorter PFS, whereas mutations in TP53 exons 5 and 7 (P<0.05), missense mutations and non-missense mutations (P = 0.006; P = 0.007), disruptive mutations and nondisruptive mutations (P = 0.013; P = 0.013) were all associated with poorer survival times. In addition, the PFS and overall survival (OS) of nondisruptive mutations in exon 7 were worse than those in other exons (P = 0.041; P<0.001). CONCLUSIONS Concurrent TP53 mutations conferred worse EGFR-TKIs efficacy and prognosis in advanced EGFR mutant lung adenocarcinoma and the effects of different TP53 mutation types were heterogeneous.
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Affiliation(s)
- Huiwen Qian
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Chunqi Hou
- Department of Hemodialysis center, The First Affiliated Hospital of Soochow University, Suzhou 215000, China
| | - Yi Zhang
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Shundong Ji
- The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, MOH Key Laboratory of Thrombosis and Hemostasis, Collaborative Innovation Center of Hematology, Suzhou, China
| | - Chongke Zhong
- Department of Epidemiology, School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Juan Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China; Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Qianqian Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianan Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chong Li
- Department of Respiration, First People's Hospital of Changzhou, Third Affiliated Hospital of Soochow University, Changzhou, China.
| | - ChengJi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.
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218
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Chapadgaonkar SS, Bajpai SS, Godbole MS. Gut microbiome influences incidence and outcomes of breast cancer by regulating levels and activity of steroid hormones in women. Cancer Rep (Hoboken) 2023; 6:e1847. [PMID: 37311575 PMCID: PMC10644331 DOI: 10.1002/cnr2.1847] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/21/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Breast cancer, the leading cancer type in women worldwide, is affected by reproductive and nonreproductive factors. Estrogen and progesterone influence the incidence and progression of breast cancer. The microbiome of the gut, a complex organ that plays a vital role in digestion and homeostasis, enhances availability of estrogen and progesterone in the host. Thus, an altered gut microbiome may influence the hormone-induced breast cancer incidence. This review describes the current understanding of the roles of gut microbiome in influencing the incidence and progression of breast cancer, with an emphasis on the microbiome-induced metabolism of estrogen and progesterone. RECENT FINDINGS Microbiome has been recognized as a promising hallmark of cancer. Next-generation sequencing technologies have aided in rapid identification of components of the gut microbiome that are capable of metabolizing estrogen and progesterone. Moreover, studies have indicated a wider role of the gut microbiome in metabolizing chemotherapeutic and hormonal therapy agents and reducing their efficacy in patients with breast cancer, with a predominant effect in postmenopausal women. CONCLUSION The gut microbiome and variations in its composition significantly alter the incidence and therapy outcomes of patients with breast cancer. Thus, a healthy and diverse microbiome is required for better response to anticancer therapies. Finally, the review emphasizes the requirement of studies to elucidate mechanisms that may aid in improving the gut microbiome composition, and hence, survival outcomes of patients with breast cancer.
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Affiliation(s)
- Shilpa S. Chapadgaonkar
- Department of Biosciences and Technology, Faculty of Sciences and Health SciencesDr. Vishwanath Karad MIT World Peace UniversityPuneIndia
| | - Srashti S. Bajpai
- Department of Biosciences and Technology, Faculty of Sciences and Health SciencesDr. Vishwanath Karad MIT World Peace UniversityPuneIndia
| | - Mukul S. Godbole
- Department of Biosciences and Technology, Faculty of Sciences and Health SciencesDr. Vishwanath Karad MIT World Peace UniversityPuneIndia
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219
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Du Z, Chen X, Zhu P, Lv Q, Yong J, Gu J. Knocking down SOX2 overcomes the resistance of prostate cancer to castration via notch signaling. Mol Biol Rep 2023; 50:9007-9017. [PMID: 37716921 DOI: 10.1007/s11033-023-08757-y] [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: 03/07/2023] [Accepted: 08/16/2023] [Indexed: 09/18/2023]
Abstract
BACKGROUND Castration-resistant prostate cancer (CRPC) is a terminal type of advanced cancer resistant to androgen deprivation therapy (ADT). Due to the poor therapeutic response of CRPC, novel treatment strategies are urgently required. This study aimed to clarify the regulatory roles of the SOX2/Notch axis in CRPC. METHODS For the evaluation of the SOX2, Notch, and Hey1 expression in the prostate cancer (PCa) and CRPC tissues, we conducted immunohistochemistry (IHC) analyses. RT-PCR, Western blotting, and immunofluorescence were performed to evaluate SOX2 and Notch expression in enzalutamide-resistant LNCaP cells (Enza-R). CCK-8, Transwell, Wound healing, and Western blotting assays were used to assess the viability, invasion, migration, cell cycle, and drug-resistant in Enza-R cells. RESULTS Compared to the PCa tissues, CRPC tissues exhibited significantly elevated SOX2, Notch1, and Hey1 expression. SOX2-positive patients were more likely to develop bone metastases than SOX2-negative ones. Significant activation of the signaling associated with SOX2 and Notch was detected in Enza-R cells. The suppression of SOX2 clearly inactivated the Notch signaling and inhibited malignant behaviors, including proliferation, invasion, migration, and drug resistance in Enza-R cells. Theγsecretase inhibitor, GSI-IX, abrogated the enzalutamide resistance by inhibiting Notch signaling in vitro in vitro. Also, GSI-IX alone had a significant anti-tumor effect in Enza-R cells. CONCLUSION We demonstrated that SOX2/Notch signaling was responsible for Enzalutamide resistance in CRPC. Targeting SOX2/Notch signaling might represent a new choice for the treatment and therapy of CRPC.
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Affiliation(s)
- Zhongbo Du
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, China.
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.
| | - Xiaobin Chen
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, China
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Pingyu Zhu
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, China
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Qi Lv
- Department of Operation, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jun Yong
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Junqing Gu
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.
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220
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Desai S. Influence of pathogens on host genome and epigenome in development of head and neck cancer. Cancer Rep (Hoboken) 2023; 6:e1846. [PMID: 37322598 PMCID: PMC10644332 DOI: 10.1002/cnr2.1846] [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: 04/01/2023] [Revised: 05/11/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Head and neck cancer (HNSCC) is a heterogeneous group of cancers, affecting multiple regions such as oral cavity, pharynx, larynx, and nasal region, each showing a distinct molecular profile. HNSCC accounts for more than 6 million cases worldwide, soaring mainly in the developing countries. RECENT FINDINGS The aetiology of HNSCC is complex and multifactorial, involving both genetic and environmental factors. The critical role of microbiome, which includes bacteria, viruses, and fungi, is under spotlight due to the recent reports on their contribution in the development and progression of HNSCC. This review focuses on the effect of opportunistic pathogens on the host genome and epigenome, which contributes to the disease progression. Drawing parallels from the host-pathogen interactions observed in other tumour types arising from the epithelial tissue such as colorectal cancer, the review also calls attention to the potential explorations of the role of pathogens in HNSCC biology and discusses the clinical implications of microbiome research in detection and treatment of HNSCC. CONCLUSION Our understanding of the genomic effects of the microbes on the disease progression and the mechanistic insights of the host-pathogen interaction will pave way to novel treatment and preventive approaches in HNSCC.
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221
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Zheng Y, Shen G, Zhang C, Huo X, Xin Y, Fang Q, Guan Y, Zhao F, Ren D, Liu Z, Wang M, Zhao J. Efficacy of anti-HER2 drugs in the treatment of patients with HER2-mutated cancers: a systematic review and meta-analysis. Clin Exp Med 2023; 23:3205-3216. [PMID: 37120775 DOI: 10.1007/s10238-023-01072-7] [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: 12/08/2022] [Accepted: 04/06/2023] [Indexed: 05/01/2023]
Abstract
Anti-human epidermal growth factor receptor-2 (anti-HER2) therapy has shown excellent efficacy in patients with HER2 overexpression and amplification. Although HER2 mutations are rarely expressed in several cancers, when they occur, they can activate the HER2 signaling pathway. In recent years, studies have shown that anti-HER2 drugs have promising efficacy in patients with HER2 mutations. Based on keywords, we searched databases, such as PubMed, Embase, and Cochrane Library, and the main conference abstracts. We extracted data on objective response rate (ORR), clinical benefit rate (CBR), duration of response (DOR), progression-free survival (PFS), and overall survival (OS) from studies on the efficacy of anti-HER2 therapies in patients with HER2-mutated cancers, and analyzed grade 3 or higher adverse events (AEs). We included 19 single-arm clinical studies and 3 randomized controlled trials (RCTs), containing a total of 1017 patients with HER2 mutations, involving seven drugs and nine cancers, and 18 studies enrolled a high proportion of heavily pretreated patients who had received multiple lines of therapy. Our results showed pooled ORR and CBR of 25.0% (range, 3.8-72.7%; 95% CI, 18-32%) and 36.0% (range, 8.3-63.0%; 95% CI, 31-42%) for anti-HER2 therapy in HER2-mutated cancers. The pooled median PFS, OS, DOR were 4.89 (95% CI, 4.16-5.62), 12.78 (95% CI, 10.24-15.32), and 8.12 (95% CI, 6.48-9.75) months, respectively. In a subgroup analysis, we analyzed the ORR for different cancers, showing 27.0, 25.0, 23.0, and 16.0% for breast, lung, cervical, and biliary tract cancers, respectively. ORR analyses were performed for different drugs as monotherapy or in combination, showing 60.0% for trastuzumab deruxtecan (T-DXd), 31.0% for pyrotinib, 26.0% for neratinib combined with trastuzumab, 25.0% for neratinib combined with fulvestrant, 19.0% for trastuzumab combined with pertuzumab, and 16.0% for neratinib. In addition, we found that diarrhoea, neutropenia, and thrombocytopenia were the most common grade ≥ 3 AEs associated with anti-HER2 therapeutic agents. In this meta-analysis of heavily pretreated patients with HER2 mutations, anti-HER2 therapies, DS-8201 and trastuzumab emtansine, showed promising efficacy and activity. Anti-HER2 therapies showed different efficacies in different or the same cancer settings and all had a tolerable safety profile.
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Affiliation(s)
- Yonghui Zheng
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Guoshuang Shen
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Chengrong Zhang
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Xingfa Huo
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Yuanfang Xin
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Qianqian Fang
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Yumei Guan
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Fuxing Zhao
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Dengfeng Ren
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Zhen Liu
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Miaozhou Wang
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Jiuda Zhao
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital, Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China.
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Cotton JL, Estrada Diez J, Sagar V, Chen J, Piquet M, Alford J, Song Y, Li X, Riester M, DiMare MT, Schumacher K, Boulay G, Sprouffske K, Fan L, Burks T, Mansur L, Wagner J, Bhang HEC, Iartchouk O, Reece-Hoyes J, Morris EJ, Hammerman PS, Ruddy DA, Korn JM, Engelman JA, Niederst MJ. Expressed Barcoding Enables High-Resolution Tracking of the Evolution of Drug Tolerance. Cancer Res 2023; 83:3611-3623. [PMID: 37603596 DOI: 10.1158/0008-5472.can-23-0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/11/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
For a majority of patients with non-small cell lung cancer with EGFR mutations, treatment with EGFR inhibitors (EGFRi) induces a clinical response. Despite this initial reduction in tumor size, residual disease persists that leads to disease relapse. Elucidating the preexisting biological differences between sensitive cells and surviving drug-tolerant persister cells and deciphering how drug-tolerant cells evolve in response to treatment could help identify strategies to improve the efficacy of EGFRi. In this study, we tracked the origins and clonal evolution of drug-tolerant cells at a high resolution by using an expressed barcoding system coupled with single-cell RNA sequencing. This platform enabled longitudinal profiling of gene expression and drug sensitivity in response to EGFRi across a large number of clones. Drug-tolerant cells had higher expression of key survival pathways such as YAP and EMT at baseline and could also differentially adapt their gene expression following EGFRi treatment compared with sensitive cells. In addition, drug combinations targeting common downstream components (MAPK) or orthogonal factors (chemotherapy) showed greater efficacy than EGFRi alone, which is attributable to broader targeting of the heterogeneous EGFRi-tolerance mechanisms present in tumors. Overall, this approach facilitates thorough examination of clonal evolution in response to therapy that could inform the development of improved diagnostic approaches and treatment strategies for targeting drug-tolerant cells. SIGNIFICANCE The evolution and heterogeneity of EGFR inhibitor tolerance are identified in a large number of clones at enhanced cellular and temporal resolution using an expressed barcode technology coupled with single-cell RNA sequencing.
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Affiliation(s)
- Jennifer L Cotton
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Javier Estrada Diez
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Vivek Sagar
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Julie Chen
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Michelle Piquet
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Alford
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Youngchul Song
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Xiaoyan Li
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Markus Riester
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew T DiMare
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Katja Schumacher
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Gaylor Boulay
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Kathleen Sprouffske
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Lin Fan
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Tyler Burks
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Leandra Mansur
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joel Wagner
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Hyo-Eun C Bhang
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Oleg Iartchouk
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Reece-Hoyes
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Erick J Morris
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Peter S Hammerman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - David A Ruddy
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joshua M Korn
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jeffrey A Engelman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew J Niederst
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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Tsuchihashi K, Ito M, Arita S, Kusaba H, Kusano W, Matsumura T, Kitazono T, Ueno S, Taguchi R, Yoshihiro T, Doi Y, Arimizu K, Ohmura H, Kajitani T, Nio K, Nakano M, Oshima K, Tamura S, Shirakawa T, Shimokawa H, Uchino K, Hanamura F, Okumura Y, Komoda M, Isobe T, Ariyama H, Esaki T, Hashimoto K, Komune N, Matsuo M, Matsumoto K, Asai K, Yoshitake T, Yamamoto H, Oda Y, Akashi K, Baba E. Survival outcomes including salvage therapy of adult head and neck para-meningeal rhabdomyosarcoma: a multicenter retrospective study from Japan. BMC Cancer 2023; 23:1046. [PMID: 37904096 PMCID: PMC10617040 DOI: 10.1186/s12885-023-11528-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Rhabdomyosarcoma is the most common soft tissue sarcoma in children, but rare in adults. Para-meningeal rhabdomyosarcoma in head and neck (PM-HNRMS) is less applicable for surgery due to the anatomic reason. PM-HNRMS has a poor prognosis in children. However, its clinical outcomes remain unclear in adults due to the rarity. Further, there is almost no detailed data about salvage therapy. METHODS We retrospectively examined the adult patients with PM-HNRMS treated at institutions belonging to the Kyushu Medical Oncology Group from 2009 to 2022. We evaluated the overall survival (OS) and progression-free survival (PFS) of the patients who received a first-line therapy. We also reviewed the clinical outcomes of patients who progressed against a first-line therapy and received salvage therapy. RESULTS Total 11 patients of PM-HNRMS received a first-line therapy. The characteristics were as follows: median age: 38 years (range 25 - 63 years), histology (alveolar/spindle): 10/1, and risk group (intermediate/high): 7/4. As a first-line therapy, VAC and ARST0431-based regimen was performed in 10 and 1 patients, respectively. During a first-line therapy, definitive radiation for all lesions were performed in seven patients. The median PFS was 14.2 months (95%CI: 6.0 - 25.8 months): 17.1 months (95%CI: 6.0 - not reached (NR)) for patients with stage I-III and 8.5 months (95%CI: 5.2 - 25.8 months) for patients with stage IV. The 1-year and 3-year PFS rates were 54.5% and 11.3% for all patients. Median OS in all patients was 40.8 months (95%CI: 12.1 months-NR): 40.8 months (95%CI: 12.1 - NR) for patients with stage I-III and NR for patients with stage IV. The 5-year OS rate was 48.5% for all patients. Among seven patients who received salvage therapy, three are still alive, two of whom remain disease-free for over 4 years after completion of the last therapy. Those two patients received multi-modal therapy including local therapy for all detected lesions. CONCLUSION The cure rate of adult PM-HNRMS is low in spite of a first-line therapy in this study. Salvage therapy might prolong the survival in patients who received the multi-modal therapy including local therapy for all detected lesions.
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Affiliation(s)
- Kenji Tsuchihashi
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Mamoru Ito
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Shuji Arita
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Hitoshi Kusaba
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
- Department of Medical Oncology Organization, Hamanomachi Hospital, Fukuoka, Japan
| | - Wataru Kusano
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Takashi Matsumura
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Takafumi Kitazono
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Shohei Ueno
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryosuke Taguchi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoyasu Yoshihiro
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Yasuhiro Doi
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Kohei Arimizu
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Hirofumi Ohmura
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Tatsuhiro Kajitani
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Kenta Nio
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
- Department of Medical Oncology Organization, Hamanomachi Hospital, Fukuoka, Japan
| | - Michitaka Nakano
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Kotoe Oshima
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Shingo Tamura
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
- Department of Medical Oncology, Clinical Research Institute, National Hospital Organization Kyushu Medical Center, Fukuoka, Japan
| | - Tsuyoshi Shirakawa
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Hozumi Shimokawa
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
- Department of Hematology and Oncology, Japan Community Health care Organization Kyushu Hospital, Fukuoka, Japan
| | - Keita Uchino
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Fumiyasu Hanamura
- Department of Gastrointestinal and Medical Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
- Department of Internal Medicine, Kyushu University Beppu Hospital, Oita, Japan
| | - Yuta Okumura
- Department of Gastrointestinal and Medical Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Masato Komoda
- Department of Gastrointestinal and Medical Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Taichi Isobe
- Department of Oncology and Social Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Higashi-ku, 812-8582, Japan
| | - Hiroshi Ariyama
- Department of Hematology, Oncology and Cardiovascular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Taito Esaki
- Department of Gastrointestinal and Medical Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Kazuki Hashimoto
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Noritaka Komune
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mioko Matsuo
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiji Matsumoto
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kaori Asai
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of radiation therapy, Hamanomachi Hospital, Fukuoka, Japan
| | - Tadamasa Yoshitake
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hidetaka Yamamoto
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eishi Baba
- Department of Oncology and Social Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Higashi-ku, 812-8582, Japan.
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Chen Y, Zhang K, Zhang R, Wang Z, Yang L, Zhao T, Zhang S, Lin Y, Zhao H, Liu Y, Wei Y, Zhou Y, Zhang J, Ye X, Zhao J, Li X, Que J, Shi S, Liu K. Targeting the SOX2/CDP protein complex with a peptide suppresses the malignant progression of esophageal squamous cell carcinoma. Cell Death Discov 2023; 9:399. [PMID: 37891174 PMCID: PMC10611744 DOI: 10.1038/s41420-023-01693-7] [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: 05/31/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Emerging evidence indicates that SOX2 is an oncogene for esophageal squamous cell carcinoma (ESCC). However, direct targeting of SOX2 is not feasible given that this transcription factor plays important roles in the maintenance of tissues such as the brain. Here, we identified CDP (Homeobox protein cut-like 1 or CASP) as a unique SOX2 binding partner enriched in ESCC with Duolink proximity ligation assay, bimolecular fluorescence complementation (BiFc) and immunoprecipitation. We then screened a peptide aptamer library using BiFc and immunoprecipitation and identified several peptide aptamers, including P58, that blocked the CDP/SOX2 interaction, leading to the inhibition of ESCC progress in vitro and in vivo. Upon administration, synthetic peptide P58, containing the YGRKKRRQRRR cell-penetrating peptide and the fluorophore TAMRA, also blocked the growth and metastasis of ESCC in both mice and zebrafish. Therefore, targeting the SOX2 binding partner CDP with peptide P58 offers an alternative avenue to treat ESCC with increased SOX2 levels.
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Affiliation(s)
- Yunyun Chen
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Kun Zhang
- Department of General Surgery, Fuzhou First General Hospital affiliated with Fujian Medical University, Fuzhou, Fujian, 350009, P. R. China
| | - Rui Zhang
- Department of Laboratory Medicine, The Second Hospital of Fuzhou, Fuzhou, Fujian, 350007, P. R. China
| | - Zhuo Wang
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Liang Yang
- Westlake University, Hangzhou, Zhejiang, 310024, P. R. China
| | - Tingting Zhao
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Shihui Zhang
- Centre for Translational Stem Cell Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, 999077, P. R. China
| | - Yong Lin
- Science and Technology Service Center, Fujian Health College, Fuzhou, Fujian, 350101, P. R. China
| | - Hongzhou Zhao
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Yongpan Liu
- School of Life Science, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Yuxuan Wei
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Yijian Zhou
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Jiaying Zhang
- School of Life Science, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Xianzong Ye
- Department of Pathology, 900 Hospital of the Joint Logistics Team (Dongfang Hospital, Xiamen University), Fuzhou, Fujian, 350025, P. R. China
| | - Jing Zhao
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Xinxin Li
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Jianwen Que
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Songlin Shi
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China.
| | - Kuancan Liu
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China.
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China.
- School of Life Science, Nanchang Normal University, Nanchang, Jiangxi, 330032, P. R. China.
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225
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Abatti LE, Lado-Fernández P, Huynh L, Collado M, Hoffman M, Mitchell J. Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma. Nucleic Acids Res 2023; 51:10109-10131. [PMID: 37738673 PMCID: PMC10602899 DOI: 10.1093/nar/gkad734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023] Open
Abstract
Enhancer reprogramming has been proposed as a key source of transcriptional dysregulation during tumorigenesis, but the molecular mechanisms underlying this process remain unclear. Here, we identify an enhancer cluster required for normal development that is aberrantly activated in breast and lung adenocarcinoma. Deletion of the SRR124-134 cluster disrupts expression of the SOX2 oncogene, dysregulates genome-wide transcription and chromatin accessibility and reduces the ability of cancer cells to form colonies in vitro. Analysis of primary tumors reveals a correlation between chromatin accessibility at this cluster and SOX2 overexpression in breast and lung cancer patients. We demonstrate that FOXA1 is an activator and NFIB is a repressor of SRR124-134 activity and SOX2 transcription in cancer cells, revealing a co-opting of the regulatory mechanisms involved in early development. Notably, we show that the conserved SRR124 and SRR134 regions are essential during mouse development, where homozygous deletion results in the lethal failure of esophageal-tracheal separation. These findings provide insights into how developmental enhancers can be reprogrammed during tumorigenesis and underscore the importance of understanding enhancer dynamics during development and disease.
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Affiliation(s)
- Luis E Abatti
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Lado-Fernández
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
- Department of Physiology and Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Linh Huynh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Manuel Collado
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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226
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Pezzotti G, Ohgitani E, Imamura H, Ikegami S, Shin-Ya M, Adachi T, Adachi K, Yamamoto T, Kanamura N, Marin E, Zhu W, Higasa K, Yasukochi Y, Okuma K, Mazda O. Raman Multi-Omic Snapshot and Statistical Validation of Structural Differences between Herpes Simplex Type I and Epstein-Barr Viruses. Int J Mol Sci 2023; 24:15567. [PMID: 37958551 PMCID: PMC10647490 DOI: 10.3390/ijms242115567] [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: 09/05/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Raman spectroscopy was applied to study the structural differences between herpes simplex virus Type I (HSV-1) and Epstein-Barr virus (EBV). Raman spectra were first collected with statistical validity on clusters of the respective virions and analyzed according to principal component analysis (PCA). Then, average spectra were computed and a machine-learning approach applied to deconvolute them into sub-band components in order to perform comparative analyses. The Raman results revealed marked structural differences between the two viral strains, which could mainly be traced back to the massive presence of carbohydrates in the glycoproteins of EBV virions. Clear differences could also be recorded for selected tyrosine and tryptophan Raman bands sensitive to pH at the virion/environment interface. According to the observed spectral differences, Raman signatures of known biomolecules were interpreted to link structural differences with the viral functions of the two strains. The present study confirms the unique ability of Raman spectroscopy for answering structural questions at the molecular level in virology and, despite the structural complexity of viral structures, its capacity to readily and reliably differentiate between different virus types and strains.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-Machi, Hirakata 573-1010, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-Ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Saki Ikegami
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
| | - Masaharu Shin-Ya
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan;
| | - Keiji Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
| | - Koichiro Higasa
- Genome Analysis, Institute of Biomedical Science, Kansai Medical University, 2-3-1 Shinmachi, Hirakata 573-1191, Japan; (K.H.); (Y.Y.)
| | - Yoshiki Yasukochi
- Genome Analysis, Institute of Biomedical Science, Kansai Medical University, 2-3-1 Shinmachi, Hirakata 573-1191, Japan; (K.H.); (Y.Y.)
| | - Kazu Okuma
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan;
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
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227
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Zeng Z, Fu M, Hu Y, Wei Y, Wei X, Luo M. Regulation and signaling pathways in cancer stem cells: implications for targeted therapy for cancer. Mol Cancer 2023; 22:172. [PMID: 37853437 PMCID: PMC10583419 DOI: 10.1186/s12943-023-01877-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
Cancer stem cells (CSCs), initially identified in leukemia in 1994, constitute a distinct subset of tumor cells characterized by surface markers such as CD133, CD44, and ALDH. Their behavior is regulated through a complex interplay of networks, including transcriptional, post-transcriptional, epigenetic, tumor microenvironment (TME), and epithelial-mesenchymal transition (EMT) factors. Numerous signaling pathways were found to be involved in the regulatory network of CSCs. The maintenance of CSC characteristics plays a pivotal role in driving CSC-associated tumor metastasis and conferring resistance to therapy. Consequently, CSCs have emerged as promising targets in cancer treatment. To date, researchers have developed several anticancer agents tailored to specifically target CSCs, with some of these treatment strategies currently undergoing preclinical or clinical trials. In this review, we outline the origin and biological characteristics of CSCs, explore the regulatory networks governing CSCs, discuss the signaling pathways implicated in these networks, and investigate the influential factors contributing to therapy resistance in CSCs. Finally, we offer insights into preclinical and clinical agents designed to eliminate CSCs.
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Affiliation(s)
- Zhen Zeng
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Minyang Fu
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuan Hu
- Department of Pediatric Nephrology Nursing, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Min Luo
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China.
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228
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Lau HC, Yuan X, Huang H, Zhang M, Hsueh CY, Gong H. Fusobacterium nucleatum facilitates proliferation and autophagy by activating miR-361-3p/NUDT1 axis through oxidative stress in hypopharyngeal squamous cell carcinoma. BMC Cancer 2023; 23:990. [PMID: 37848855 PMCID: PMC10580517 DOI: 10.1186/s12885-023-11439-4] [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: 07/26/2023] [Accepted: 09/24/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND To investigate how Fusobacterium nucleatum (Fn) promotes oxidative stress and mediates proliferation and autophagy in hypopharyngeal squamous cell carcinoma (HPSCC). METHODS The prognosis for 82 HPSCC cases was retrospectively analyzed. HPSCC cell line FaDu was co-cultured with Fn. Knockdown of NUDT1 (shNUDT1 group) was done after observing DNA damage response. CCK8 and tumorigenesis assays for proliferation observation, mitochondria ROS (MitoROS) measurement to examine intracellular oxidative stress, and ELISA to analyze concentration of 8-oxo-2'-deoxyguanosine (8-oxo-dG) in cells. Dual-luciferase reporter assays clarified miR-361-3p connection with NUDT1. Autophagy flow was observed using electron microscopy and related proteins. RESULTS Fn was highly associated with NUDT1. The shNUDT1 group experienced lower proliferation compared with normal FaDu (NC group) in vivo and in vitro. The shNUDT1 group showed 8-oxo-dG and γH2AX to be elevated. Intracellular ROS decreased in shNUDT1Fn group when compared to Fn group. Upregulating miR-361-3p could suppress NUDT1 expression and downstream proliferation and autophagy. Fn modulated miR-361-3p via OH-, which could be proven by H2O2 assay and N-acetylcysteine. CONCLUSIONS Higher Fn in HPSCC patients suggests poorer prognosis. NUDT1 might affect cell proliferation and autophagy and modulate DNA damage response. The oxidative stress induced miR-361-3p/NUDT1 axis is first introduced in microbiome-carcinoma research.
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Affiliation(s)
- Hui-Ching Lau
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR China
| | - Xiaohui Yuan
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR China
| | - Huiying Huang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR China
| | - Ming Zhang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR China
| | - Chi-Yao Hsueh
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR China
| | - Hongli Gong
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China.
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR China.
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Macaya I, Roman M, Welch C, Entrialgo-Cadierno R, Salmon M, Santos A, Feliu I, Kovalski J, Lopez I, Rodriguez-Remirez M, Palomino-Echeverria S, Lonfgren SM, Ferrero M, Calabuig S, Ludwig IA, Lara-Astiaso D, Jantus-Lewintre E, Guruceaga E, Narayanan S, Ponz-Sarvise M, Pineda-Lucena A, Lecanda F, Ruggero D, Khatri P, Santamaria E, Fernandez-Irigoyen J, Ferrer I, Paz-Ares L, Drosten M, Barbacid M, Gil-Bazo I, Vicent S. Signature-driven repurposing of Midostaurin for combination with MEK1/2 and KRASG12C inhibitors in lung cancer. Nat Commun 2023; 14:6332. [PMID: 37816716 PMCID: PMC10564741 DOI: 10.1038/s41467-023-41828-z] [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: 12/13/2022] [Accepted: 09/20/2023] [Indexed: 10/12/2023] Open
Abstract
Drug combinations are key to circumvent resistance mechanisms compromising response to single anti-cancer targeted therapies. The implementation of combinatorial approaches involving MEK1/2 or KRASG12C inhibitors in the context of KRAS-mutated lung cancers focuses fundamentally on targeting KRAS proximal activators or effectors. However, the antitumor effect is highly determined by compensatory mechanisms arising in defined cell types or tumor subgroups. A potential strategy to find drug combinations targeting a larger fraction of KRAS-mutated lung cancers may capitalize on the common, distal gene expression output elicited by oncogenic KRAS. By integrating a signature-driven drug repurposing approach with a pairwise pharmacological screen, here we show synergistic drug combinations consisting of multi-tyrosine kinase PKC inhibitors together with MEK1/2 or KRASG12C inhibitors. Such combinations elicit a cytotoxic response in both in vitro and in vivo models, which in part involves inhibition of the PKC inhibitor target AURKB. Proteome profiling links dysregulation of MYC expression to the effect of both PKC inhibitor-based drug combinations. Furthermore, MYC overexpression appears as a resistance mechanism to MEK1/2 and KRASG12C inhibitors. Our study provides a rational framework for selecting drugs entering combinatorial strategies and unveils MEK1/2- and KRASG12C-based therapies for lung cancer.
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Affiliation(s)
- Irati Macaya
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
| | - Marta Roman
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Connor Welch
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
| | | | - Marina Salmon
- Experimental Oncology Group, Molecular Oncology Program, Spanish National Cancer Center (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Alba Santos
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- H12O-CNIO Lung Cancer Clinical Research Unit, Instituto de Investigación Hospital 12 de Octubre & Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Iker Feliu
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
| | - Joanna Kovalski
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Ines Lopez
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
| | - Maria Rodriguez-Remirez
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
| | - Sara Palomino-Echeverria
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra, Pamplona, Spain
| | - Shane M Lonfgren
- Stanford Institute for Immunity, Transplantation and Infection, Stanford, CA, USA
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Macarena Ferrero
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario de Valencia, Valencia, Spain
- Mixed Unit TRIAL (Principe Felipe Research Centre & Fundación para la Investigación del Hospital General Universitario de Valencia), Valencia, Spain
| | - Silvia Calabuig
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario de Valencia, Valencia, Spain
- Mixed Unit TRIAL (Principe Felipe Research Centre & Fundación para la Investigación del Hospital General Universitario de Valencia), Valencia, Spain
- Department of Pathology, Universitat de Valencia, Valencia, Spain
| | - Iziar A Ludwig
- University of Navarra, Center for Applied Medical Research, Molecular Therapies Program, Pamplona, Spain
| | - David Lara-Astiaso
- University of Navarra, Center for Applied Medical Research, Genomics Platform, Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario de Valencia, Valencia, Spain
- Mixed Unit TRIAL (Principe Felipe Research Centre & Fundación para la Investigación del Hospital General Universitario de Valencia), Valencia, Spain
- Department of Pathology, Universitat de Valencia, Valencia, Spain
| | - Elizabeth Guruceaga
- University of Navarra, Center for Applied Medical Research, Bioinformatics Platform, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- ProteoRed-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Shruthi Narayanan
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- Clinica Universidad de Navarra, Department of Medical Oncology, Pamplona, Spain
| | - Mariano Ponz-Sarvise
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Clinica Universidad de Navarra, Department of Medical Oncology, Pamplona, Spain
| | - Antonio Pineda-Lucena
- University of Navarra, Center for Applied Medical Research, Molecular Therapies Program, Pamplona, Spain
| | - Fernando Lecanda
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- University of Navarra, Department of Pathology, Anatomy and Physiology, Pamplona, Spain
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Purvesh Khatri
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra, Pamplona, Spain
| | - Enrique Santamaria
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- ProteoRed-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Joaquin Fernandez-Irigoyen
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- ProteoRed-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Irene Ferrer
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- H12O-CNIO Lung Cancer Clinical Research Unit, Instituto de Investigación Hospital 12 de Octubre & Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Luis Paz-Ares
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- H12O-CNIO Lung Cancer Clinical Research Unit, Instituto de Investigación Hospital 12 de Octubre & Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
- Medical School, Universidad Complutense, Madrid, Spain
| | - Matthias Drosten
- Experimental Oncology Group, Molecular Oncology Program, Spanish National Cancer Center (CNIO), Madrid, Spain
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain
| | - Mariano Barbacid
- Experimental Oncology Group, Molecular Oncology Program, Spanish National Cancer Center (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ignacio Gil-Bazo
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Clinica Universidad de Navarra, Department of Medical Oncology, Pamplona, Spain
- Department of Oncology, Fundación Instituto Valenciano de Oncología, Valencia, Spain
| | - Silve Vicent
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
- University of Navarra, Department of Pathology, Anatomy and Physiology, Pamplona, Spain.
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Han Y, Rovella V, Smirnov A, Buonomo OC, Mauriello A, Perretta T, Shi Y, Woodmsith J, Bischof J, Melino G, Candi E, Bernassola F. A BRCA2 germline mutation and high expression of immune checkpoints in a TNBC patient. Cell Death Discov 2023; 9:370. [PMID: 37813891 PMCID: PMC10562433 DOI: 10.1038/s41420-023-01651-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/23/2023] [Accepted: 09/13/2023] [Indexed: 10/11/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of mammary carcinoma. Here, we describe a case of an 81-year-old female diagnosed with ductal triple negative breast cancer with a germline pathogenic variant in BReast CAncer gene2 (BRCA2). Genetic testing also revealed the presence of four somatic mutations in the ephrin type-A receptor 3 (EphA3), TP53, BRCA1-associated protein (BAP1), and MYB genes. The BRCA2, TP53, and BAP1 gene mutations are highly predictive of a defective homologous recombination repair system and subsequent chromosomal instability in this patient. Coherently, the patient displayed a strong homologous recombination deficiency signature and high tumor mutational burden status, which are generally associated with increased probability of immune neoantigens formation and presentation, and with tumor immunogenicity. Analysis of immune checkpoint revealed high expression of programmed cell death ligand 1 (PD-L1), programmed cell death ligand 2 (PD-L2), programmed death 1 (PD1), and cytotoxic T-lymphocyte-associated protein 4 (CTLA 4), suggesting that the patient might likely benefit from immunotherapies. Altogether, these findings support an unveiled link between BRCA2 inactivation, HR deficiency and increased expression of immune checkpoints in TNBC. This clinical case highlights the importance of screening TNBC patients for genetic mutations and TMB biomarkers in order to predict the potential efficacy of immunotherapy.
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Affiliation(s)
- Yuyi Han
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
- Department of Ophthalmology, The Affiliated Hospital of Jiangnan University, 214000, Wuxi, China
| | - Valentina Rovella
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Artem Smirnov
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00100, Rome, Italy
| | - Oreste Claudio Buonomo
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Alessandro Mauriello
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Tommaso Perretta
- Department of Diagnostic Imaging and Interventional Radiology, Policlinico Tor Vergata University, Rome, 00133, Italy
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University, Institutes for Translational Medicine, Soochow University, Suzhou, 215000, China
| | | | - Julia Bischof
- Indivumed GmbH, Falkenried, 88 Building D, 20251, Hamburg, Germany
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
| | - Eleonora Candi
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00100, Rome, Italy.
| | - Francesca Bernassola
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
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Zhu L, Zhou D, Chen Y, Guo T, Chen W, Pan X. Correlation Analysis of the TP53 Mutation With Clinical Characteristics in the Prognosis of Non-Small Cell Lung Cancer. Clin Med Insights Oncol 2023; 17:11795549231184918. [PMID: 37823008 PMCID: PMC10563498 DOI: 10.1177/11795549231184918] [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: 12/13/2022] [Accepted: 06/12/2023] [Indexed: 10/13/2023] Open
Abstract
Background Non-small cell lung cancer (NSCLC) with TP53 mutations has a worse prognosis. It was generally more resistant to chemotherapy and radiation. Our aim was to investigate the correlation between the TP53 co-mutated gene and clinical features, and prognostic value in patients with NSCLC. Methods Seventy-three patients with a diagnosis of NSCLC at our hospital were recruited. They were divided into the TP53 mutation status (minor) (TP53 MU) and TP53 wild-type (major) (TP53 WT) groups according to their clinical characteristics after their mutation data and clinical information were collected. Serum markers were compared between groups using Mann-Whitney U test. Other clinical factors were compared between groups using χ2 test and Fisher exact test. The log-rank test was used to compare survival curves. Results Of the 73 patients with NSCLC, 37 (50.68%) were found to carry TP53 mutation. TP53 MU and TP53 WT groups (n = 36) showed a significant difference in the number of smokers, incidence of squamous cell carcinoma, EGFR mutation, and number of advanced patients (P < .05), while gender, age, lymph node metastasis, and KRAS mutation did not differ significantly between the 2 groups. The survival curves in the TP53/KRAS and the TP53/EGFR co-mutation groups suggest that patients with NSCLC may have a shorter progression-free survival (PFS) if they carry one of the 2 types of co-mutation. Conclusions TP53 gene mutations are more common in patients with NSCLC and squamous cell carcinoma. New predictive markers for NSCLC prognosis may be TP53/KRAS and TP53/EGFR co-mutations.
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Affiliation(s)
- Lihuan Zhu
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
| | - Dongsheng Zhou
- Department of Radiology, Fujian Provincial Hospital and Provincial Clinical College, Fujian Medical University, Fuzhou, China
| | - Yiyong Chen
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
| | - Tianxing Guo
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
| | - Wenshu Chen
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
| | - Xiaojie Pan
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
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232
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Hon JX, Wahab NA, Karim AKA, Mokhtar NM, Mokhtar MH. MicroRNAs in Endometriosis: Insights into Inflammation and Progesterone Resistance. Int J Mol Sci 2023; 24:15001. [PMID: 37834449 PMCID: PMC10573326 DOI: 10.3390/ijms241915001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Endometriosis, a non-malignant gynecological disorder influenced by estrogen, involves the growth of endometrial tissue outside the uterus. Its development includes processes such as inflammation, progesterone resistance, angiogenesis, and cell proliferation. Epigenetic factors, particularly the dysregulation of microRNAs (miRNAs), have emerged as key factors in these mechanisms in endometriosis. This review aims to unveil the intricate molecular processes that control inflammation, progesterone resistance, and miRNA functions in endometriosis. In addition, it provides a comprehensive overview of the current understanding regarding the involvement of miRNAs in the inflammatory aspects of this condition. This synthesis encompasses research investigating the molecular underpinnings of inflammation, along with the biogenesis and roles of miRNAs in endometriosis. Furthermore, it examines human studies and functional analyses to establish the intricate connection between miRNAs, inflammation, and progesterone resistance in the context of endometriosis. The results highlight the significant impact of dysregulated miRNAs on the inflammatory pathways and hormonal imbalances characteristic of endometriosis. Consequently, miRNAs hold promise as potential non-invasive biomarkers and targeted therapeutic agents aimed at addressing inflammation and enhancing the response to progesterone treatment in individuals with endometriosis.
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Affiliation(s)
- Jing-Xian Hon
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Norhazlina Abdul Wahab
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Abdul Kadir Abdul Karim
- Department of Obstetrics & Gynecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Mohd Helmy Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
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233
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Kiss Z, Gálffy G, Müller V, Moldvay J, Sárosi V, Pápai-Székely Z, Csada E, Kerpel-Fronius A, Király Z, Szász Z, Hódi G, Polányi Z, Kovács K, Karamousouli E, Knollmajer K, Szabó TG, Berta A, Vokó Z, Rokszin G, Abonyi-Tóth Z, Barcza Z, Tamási L, Bogos K. Significant changes in advanced lung cancer survival during the past decade in Hungary: impact of modern immunotherapy and the COVID-19 pandemic. Front Oncol 2023; 13:1207295. [PMID: 37860193 PMCID: PMC10584310 DOI: 10.3389/fonc.2023.1207295] [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: 04/17/2023] [Accepted: 09/14/2023] [Indexed: 10/21/2023] Open
Abstract
Objective The approval of immunotherapy (I-O) for the treatment of late-stage non-small cell lung cancer (NSCLC) opened new perspectives in improving survival outcomes. However, survival data have not yet been provided from the period of the Covid-19 pandemic. The aims of our study were to assess and compare survival outcomes of patients with advanced LC receiving systemic anticancer treatment (SACT) before and after the approval of immunotherapy in Hungary, and to examine the impact of pandemic on survival outcomes using data from the Hungarian National Health Insurance Fund (NHIF) database. Methods This retrospective, longitudinal study included patients aged ≥20 years who were diagnosed with advanced stage lung cancer (LC) (ICD-10 C34) between 1 January 2011 and 31 December 2021 and received SACT treatment without LC-related surgery. Survival rates were evaluated by year of diagnosis, sex, age, and LC histology. Results In total, 35,416 patients were newly diagnosed with advanced LC and received SACT during the study period (mean age at diagnosis: 62.1-66.3 years). In patients with non-squamous cell carcinoma, 3-year survival was significantly higher among those diagnosed in 2019 vs. 2011-2012 (28.7% [95% CI: 26.4%-30.9%] vs. 14.45% [95% CI: 13.21%-15.69%], respectively). In patients with squamous cell carcinoma, 3-year survival rates were 22.3% (95% CI: 19.4%-25.2%) and 13.37% (95% CI: 11.8%-15.0%) in 2019 and 2011-2012, respectively, the change was statistically significant. Compared to 2011-2012, the hazard ratio of survival change for non-squamous cell carcinoma patients was 0.91, 0.82, and 0.62 in 2015-2016, 2017-2018, and 2019, respectively (p<0.001 for all cases). In the squamous cell carcinoma group, corresponding hazard ratios were 0.93, 0.87, and 0.78, respectively (p<0.001 for all cases). Survival improvements remained significant in both patient populations during the Covid-19 pandemic (2020-2021). No significant improvements were found in the survival of patients with small cell carcinoma. Platinum-based chemotherapy was the most common first-line treatment in all diagnostic periods, however, the proportion of patients receiving first- or second-line immunotherapy significantly increased during the study period. Conclusion 3-year survival rates of NSCLC almost doubled among patients with non-squamous cell carcinoma and significantly improved at squamous cell carcinoma over the past decade in Hungary. Improvements could potentially be attributable by the introduction of immunotherapy and were not offset by the Covid-19 pandemic.
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Affiliation(s)
- Zoltán Kiss
- MSD Pharma Hungary Ltd, Budapest, Hungary
- Second Department of Medicine and Nephrology-Diabetes Center, University of Pécs Medical School, Pécs, Hungary
| | - Gabriella Gálffy
- Pulmonology Hospital Törökbálint, Department of Pulmonology, Törökbálin, Hungary
| | - Veronika Müller
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Judit Moldvay
- 1st Department of Pulmonology, National Korányi Institute of Pulmonology, Budapest, Hungary
- 2nd Department of Pathology, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | | | - Zsolt Pápai-Székely
- Fejér County Szent György, University Teaching Hospital, Székesfehérvár, Hungary
| | - Edit Csada
- Csongrád-Csanád County Hospital for Chest Diseases, Deszk, Hungary
| | - Anna Kerpel-Fronius
- National Korányi Institute of Pulmonology, Department of Radiology, Budapest, Hungary
| | - Zsolt Király
- Veszprém County Pulmonary Hospital, Farkasgyepű, Hungary
| | - Zoltán Szász
- Department of Pulmonology, Petz Aladár University Teaching Hospital, Győr, Hungary
| | - Gábor Hódi
- MSD Pharma Hungary Ltd, Budapest, Hungary
| | | | | | | | | | | | | | - Zoltán Vokó
- Center for Health Technology Assessment, Semmelweis University, Budapest, Hungary
- Syreon Research Institute, Budapest, Hungary
| | | | - Zsolt Abonyi-Tóth
- RxTarget Ltd., Szolnok, Hungary
- Department of Biostatistics, University of Veterinary Medicine, Budapest, Hungary
| | | | - Lilla Tamási
- Pulmonology Hospital Törökbálint, Department of Pulmonology, Törökbálin, Hungary
| | - Krisztina Bogos
- National Korányi Institute of Pulmonology, Budapest, Hungary
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Dehner CA, Broski SM, Meis JM, Murugan P, Chrisinger JSA, Sosa C, Petersen M, Halling KC, Gupta S, Folpe AL. Fusion-driven Spindle Cell Rhabdomyosarcomas of Bone and Soft Tissue: A Clinicopathologic and Molecular Genetic Study of 25 Cases. Mod Pathol 2023; 36:100271. [PMID: 37422156 DOI: 10.1016/j.modpat.2023.100271] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/10/2023]
Abstract
The evolving classification of rhabdomyosarcoma (RMS) now includes spindle cell RMS (SRMS). Bone/soft tissue SRMS often harbor TFCP2, or less often MEIS1 rearrangements. We studied 25 fusion-driven SRMS involving bone (n = 19) and soft tissue (n = 6). Osseous SRMS occurred in 13 women and 6 men (median age: 41 years) and involved the pelvis (5), sacrum (2), spine (4), maxilla (4), mandible (1), skull (1), and femur (2). Follow-up (median: 5 months) demonstrated local recurrence in 2/16 and distant metastases in 8/17 patients (median time to metastasis: 1 month). Eight patients died of disease; 9 were alive with disease. Soft tissue SRMS occurred in 4 men and 2 women (median: 50 years). Follow-up (median: 10 months) revealed distant metastasis at diagnosis (1), alive with unresected tumor (1), and no evidence of disease (4). Next-generation sequencing demonstrated FUS::TFCP2 (12), EWSR1::TFCP2 (3) and MEIS1::NCOA2 (2); FISH identified EWSR1 (2) rearrangements. Most TFCP2-rearranged SRMS (13/17) showed spindled/epithelioid morphology, rarely with rhabdomyoblasts. The bone tumors were diffusely desmin and MyoD1 positive with limited myogenin; 10/13 were ALK -positive and 6/15 were keratin positive. Soft tissue SRMS harbored EWSR1::TFCP2, MEIS1::NCOA2, ZFP64::NCOA2, MEIS1::FOXO1, TCF12::VGLL3 and DCTN1::ALK, and displayed spindled/epithelioid, leiomyomatous, and myxofibrosarcoma-like morphologies. Immunohistochemistry (IHC) was positive for MyoD1 (6/6), focal desmin (5/6), myogenin (3/6), and keratin (1/6). We conclude that TFCP2-rearranged SRMS of bone and soft tissue show consistent morphologic and IHC features, likely representing a distinct subset of RMS. Non-TFCP2 fusion-positive SRMS could represent a single RMS subset, multiple subtypes of RMS, or "fusion-defined" sarcomas with rhabdomyoblastic differentiation.
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Affiliation(s)
- Carina A Dehner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Jeanne M Meis
- Department of Pathology and Laboratory Medicine, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Paari Murugan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - John S A Chrisinger
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Carlos Sosa
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew Petersen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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Advani R, Luzzi S, Scott E, Dalgliesh C, Weischenfeldt J, Munkley J, Elliott DJ. Epithelial specific splicing regulator proteins as emerging oncogenes in aggressive prostate cancer. Oncogene 2023; 42:3161-3168. [PMID: 37752235 PMCID: PMC10589096 DOI: 10.1038/s41388-023-02838-9] [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: 07/07/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
Prostate cancer progression is connected to the activity of conventional oncogenes and tumour suppressors and driven by circulating steroid hormones. A key issue has been how to identify and care for aggressively developing prostate tumours. Here we discuss how expression of the splicing regulators ESRP1 and ESRP2, and how their role as "masterminds" of epithelial splicing patterns, have been identified as markers of aggressively proliferating prostate primary tumours. We suggest that the origin of prostate cancer within epithelial cells, and the subsequent association of ESRP1 and ESRP2 expression with more aggressive disease progression, identify ESRP1 and ESRP2 as lineage survival oncogenes. To move this field on in the future it will be important to identify the gene expression targets controlled by ESRP1/2 that regulate prostate cancer proliferation. Potential future therapies could be designed to target ESRP1 and ESRP2 protein activity or their regulated splice isoforms in aggressive prostate tumours. Design of these therapies is potentially complicated by the risk of producing a more mesenchymal splicing environment that might promote tumour metastasis.
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Affiliation(s)
- Rahul Advani
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Sara Luzzi
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Emma Scott
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Caroline Dalgliesh
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer Munkley
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - David J Elliott
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom.
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236
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Ning J, Luo Y, Chen L, Xiao G, Tanzhu G, Zhou R. CircRNAs and lung cancer: Insight into their roles in metastasis. Biomed Pharmacother 2023; 166:115260. [PMID: 37633056 DOI: 10.1016/j.biopha.2023.115260] [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: 06/04/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. A major contributing factor to the poor survival rates in lung cancer is the high prevalence of metastasis at the time of diagnosis. To address this critical issue, it is imperative to investigate the mechanisms underlying lung cancer metastasis. Circular RNAs (circRNAs), a distinct type of ribonucleic acid characterized by their unique circular structure, have been implicated in the progression of various diseases. Recent studies have highlighted the close association between circRNAs and the occurrence and development of lung cancer, particularly in relation to metastasis. In this review, we provide a concise overview of the expression patterns and prognostic significance of circRNAs in lung cancer. Additionally, we summarized the current understanding of the clinical relevance of circRNAs in lung cancer metastasis. Furthermore, we systematically focused on the roles of circRNAs in each step of lung cancer metastasis, reflecting the sequential progression of this process. Notably, circRNAs exhibit dual functionality in lung cancer metastasis, acting both as facilitators and inhibitors of metastatic processes. Given their potential, circRNAs hold promise as novel biomarkers and therapeutic targets for lung cancer metastasis, warranting further investigation.
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Affiliation(s)
- Jiaoyang Ning
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yi Luo
- Department of Geriatric Medicine, Center of Coronary Circulation, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
| | - Liu Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Gang Xiao
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Guilong Tanzhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China.
| | - Rongrong Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China.
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Kendall Bártů M, Němejcová K, Michálková R, Stružinská I, Hájková N, Hojný J, Krkavcová E, Laco J, Matěj R, Drozenová J, Méhes G, Fabian P, Hausnerová J, Švajdler M, Škapa P, Cibula D, Zima T, Dundr P. HER2 status as a potential predictive biomarker for ovarian clear cell carcinoma. Virchows Arch 2023; 483:497-507. [PMID: 37676270 DOI: 10.1007/s00428-023-03640-4] [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: 06/05/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Ovarian clear cell carcinoma (OCCC) is a subtype of ovarian carcinoma characterized by unique biological features and highly malignant characteristics including low chemosensitivity. Therefore, new therapeutic targets are needed. These could include the downstream pathways of receptor tyrosine kinases, especially the human epidermal growth factor receptor 2 (HER2). Our main objective was to characterize the HER2 status using immunohistochemistry (IHC) and FISH on 118 OCCCs, also considering the novel paradigm of HER2-zero and HER2-low status. Other aims included determination of the association between HER2 status and survival, HER2 gene DNA and RNA NGS analysis, HER2 gene expression analysis, and correlation between IHC and gene expression in HER2-zero and HER2-low cases. Cases with HER2 overexpression/amplification accounted for 5.1% (6/118), with additional 3% harbouring HER2 gene mutation. The remaining 112 (94.9%) cases were HER2-negative. Of these, 75% were classified as HER2-zero and 25% as HER2-low. This percentage of HER2 aberrations is significant concerning their possible therapeutic influence. Cases from the HER2-zero group showed significantly better survival. Although this relationship lost statistical significance in multivariate analysis, the results have potential therapeutic significance. HER2 gene expression analysis showed a significant correlation with HER2 IHC status in the entire cohort (HER2-positive vs. HER2-negative), while in the cohort of only HER2-negative cases, the results did not reach statistical significance, suggesting that gene expression analysis would not be suitable to confirm the subdivision into HER2-low and HER2-zero. Our results also emphasize the need for standardized HER2 testing in OCCC to determine the best predictor of clinical response.
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Affiliation(s)
- Michaela Kendall Bártů
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800 Prague 2, Prague, Czech Republic.
| | - Kristýna Němejcová
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800 Prague 2, Prague, Czech Republic
| | - Romana Michálková
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800 Prague 2, Prague, Czech Republic
| | - Ivana Stružinská
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800 Prague 2, Prague, Czech Republic
| | - Nikola Hájková
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800 Prague 2, Prague, Czech Republic
| | - Jan Hojný
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800 Prague 2, Prague, Czech Republic
| | - Eva Krkavcová
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800 Prague 2, Prague, Czech Republic
| | - Jan Laco
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Radoslav Matěj
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800 Prague 2, Prague, Czech Republic
- Department of Pathology, 3rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady, 10034, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, Third Faculty of Medicine, Charles University, Thomayer University Hospital, Prague, Czech Republic
| | - Jana Drozenová
- Department of Pathology, 3rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady, 10034, Prague, Czech Republic
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary
| | - Pavel Fabian
- Department of Oncological Pathology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Jitka Hausnerová
- Department of Pathology, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Marián Švajdler
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Petr Škapa
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - David Cibula
- Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Tomáš Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavel Dundr
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800 Prague 2, Prague, Czech Republic
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Liu X, Tian F, Cui J, Gong L, Xiang L, Fan B, Liu S, Zhan J, Zhou Y, Jiang B, Wang M, Sun G, Gong Y, Zou Y. CUL4B functions as a tumor suppressor in KRAS-driven lung tumors by inhibiting the recruitment of myeloid-derived suppressor cells. Oncogene 2023; 42:3113-3126. [PMID: 37653114 DOI: 10.1038/s41388-023-02824-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023]
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. KRAS mutations are the most common oncogenic alterations found in lung cancer. Unfortunately, treating KRAS-mutant lung adenocarcinoma (ADC) remains a major oncotherapeutic challenge. Here, we used both autochthonous and transplantable KRAS-mutant tumor models to investigate the role of tumor-derived CUL4B in KRAS-driven lung cancers. We showed that knockout or knockdown of CUL4B promotes lung ADC growth and progression in both models. Mechanistically, CUL4B directly binds to the promoter of Cxcl2 and epigenetically represses its transcription. CUL4B deletion increases the expression of CXCL2, which binds to CXCR2 on myeloid-derived suppressor cells (MDSCs) and promotes their migration to the tumor microenvironment. Targeting of MDSCs significantly delayed the growth of CUL4B knockdown KRAS-mutant tumors. Collectively, our study provides mechanistic insights into the novel tumor suppressor-like functions of CUL4B in regulating KRAS-driven lung tumor development.
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Affiliation(s)
- Xiaochen Liu
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Clinical Laboratory, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fei Tian
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jianfeng Cui
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Li Gong
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Lu Xiang
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Bowen Fan
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shuangteng Liu
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jiafeng Zhan
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yadi Zhou
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Baichun Jiang
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Molin Wang
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Gongping Sun
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yaoqin Gong
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
| | - Yongxin Zou
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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239
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Paturu R, Lingaiah R, Kumari N, Singh S, Krishnani N, Srivastava S, Siddiqui SH, Nath A. Non-Small Cell Lung Cancer: Targetable Variants in Concurrent Tissue and Liquid Biopsy Testing in a North Indian Cohort. Asian Pac J Cancer Prev 2023; 24:3467-3475. [PMID: 37898852 PMCID: PMC10770664 DOI: 10.31557/apjcp.2023.24.10.3467] [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: 04/16/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
OBJECTIVES Testing for EGFR, ALK, ROS1 and MET alterations in paired tissue and plasma samples of treatment-naïve patients of NSCLC and correlating their status with overall survival. MATERIALS AND METHODS One hundred treatment-naïve patients were recruited after obtaining informed consent. Ten ml of blood was collected within a period of two weeks from histological diagnosis, prior to the start of any treatment. DNA & RNA extraction was done from formalin-fixed paraffin embedded (FFPE) tissue and total cell-free nucleic acid extraction was done from plasma samples. EGFR mutation, ALK, ROS1 and MET rearrangements were tested by ARMS (Amplification Refractory Mutation System) PCR. All statistical analyses were conducted in R version 4.1.1. RESULTS A total of 61 cases showed molecular alterations in tissue samples which included EGFR mutations (47), ALK rearrangements (12), ROS1 fusion (2). MET alteration was not detected. Forty-three cases showed EGFR mutations in plasma, 26 of which were concurrently positive in tissue. Concordance observed was 62%. ALK-EML4 rearrangement, ROS1 fusion and MET were not detected in plasma samples. Sensitivity and specificity for detection of EGFR mutation in plasma were 55.3% and 67.9% respectively. Univariate Cox regression analysis showed a positive association between EGFR mutation in tissue and overall survival (HR = 0.4; 95% CI: 0.2-0.7; p = 0.003) and improved overall survival in those who received targeted therapy (HR = 0.29; 95% CI: 0.1-0.8; p = 0.02). CONCLUSION Concurrent testing in tissue and liquid biopsy in NSCLC increased the detection of EGFR mutations (47% to 64%). This has substantial implications in deciding treatment and administration targeted therapy and the consequent overall survival.
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Affiliation(s)
- Radha Paturu
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Raghavendra Lingaiah
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Niraj Kumari
- Department of Pathology & Lab Medicine, AIIMS Raebareli, Raebareli, Uttar Pradesh, India.
| | - Shalini Singh
- Department of Radiotherapy, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Narendra Krishnani
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Shreya Srivastava
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Saima Haleem Siddiqui
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Alok Nath
- Department of Pulmonary Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
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240
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Liang X, Guan R, Zhu J, Meng Y, Zhu J, Yang Y, Cui Y, Dai J, Mao W, Lv L, Shen D, Guo R. A clinical decision support system to predict the efficacy for EGFR-TKIs based on artificial neural network. J Cancer Res Clin Oncol 2023; 149:12265-12274. [PMID: 37434091 DOI: 10.1007/s00432-023-05104-3] [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: 05/18/2023] [Accepted: 06/30/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND The efficacy of epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI) was affected by numerous factors. In the study, we developed and validated an artificial neural network (ANN) system based on clinical characteristics and next-generation sequencing (NGS) to support clinical decisions. METHODS A multicenter retrospective non-interventional study was conducted. 240 patients from three hospitals with advanced non-small cell lung cancer (NSCLC) and EGFR mutation were tested by NGS before the first treatment. All patients received formal EGFR-TKIs treatment. Five different models were individually trained to predict the efficacy of EGFR-TKIs based on one medical center with 188 patients. Two independent cohorts from other medical centers were collected for external validation. RESULTS Compared with logistic regression, four machine learning methods showed better predicting abilities for EGFR-TKIs. The inclusion of NGS tests improved the predictive power of models. ANN performed best on the dataset with mutations TP53, RB1, PIK3CA, EGFR mutation sites, and tumor mutation burden (TMB). The prediction accuracy, recall and AUC were 0.82, 0.82, and 0.82, respectively in our final model. In the external validation set, ANN still showed good performance and differentiated patients with poor outcomes. Finally, a clinical decision support software based on ANN was developed and provided a visualization interface for clinicians. CONCLUSION This study provides an approach to assess the efficacy of NSCLC patients with first-line EGFR-TKI treatment. Software is developed to support clinical decisions.
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Affiliation(s)
- Xiao Liang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Oncology, Jiangyin People's Hospital, Jiangyin, China
| | - Runwei Guan
- School of Electronics and Computer Science, University of Southampton, Southampton, UK
| | - Jiamin Zhu
- Department of Oncology, Jiangyin People's Hospital, Jiangyin, China
| | - Yue Meng
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, China
| | - Jing Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Oncology, The Affiliated Jiangning Hospital With Nanjing Medical University, Nanjing, China
| | - Yuxiang Yang
- School of Computer Science and Engineering, Northeastern University, Shenyang, China
| | - Yanan Cui
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiali Dai
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Weidong Mao
- Department of Oncology, Jiangyin People's Hospital, Jiangyin, China
| | - Liting Lv
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, China.
| | - Dong Shen
- Department of Oncology, Jiangyin People's Hospital, Jiangyin, China.
| | - Renhua Guo
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Ho H, Yu SL, Chen HY, Yuan SS, Su KY, Hsu YC, Hsu CP, Chuang CY, Chang YH, Li YC, Cheng CL, Chang GC, Yang PC, Li KC. Whole exome sequencing and MicroRNA profiling of lung adenocarcinoma identified risk prediction features for tumors at stage I and its substages. Lung Cancer 2023; 184:107352. [PMID: 37657238 DOI: 10.1016/j.lungcan.2023.107352] [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: 05/02/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023]
Abstract
OBJECTIVES About 20% of stage I lung adenocarcinoma (LUAD) patients suffer a relapse after surgical resection. While finer substages have been defined and refined in the AJCC staging system, clinical investigations on the tumor molecular landscape are lacking. MATERIALS AND METHODS We performed whole exome sequencing, DNA copy number and microRNA profiling on paired tumor-normal samples from a cohort of 113 treatment-naïve stage I Taiwanese LUAD patients. We searched for molecular features associated with relapse-free survival (RFS) of stage I or its substages and validated the findings with an independent Caucasian LUAD cohort. RESULTS We found sixteen nonsynonymous mutations harbored at EGFR, KRAS, TP53, CTNNB1 and six other genes associated with poor RFS in a dose-dependent manner via variant allele fraction (VAF). An index, maxVAF, was constructed to quantify the overall mutation load from genes other than EGFR. High maxVAF scores discriminated a small group of high-risk LUAD at stage I (median RFS: 4.5 versus 69.5 months; HR = 10.5, 95% CI = 4.22-26.12, P < 0.001). At the substage level, higher risk was found for patients with high maxVAF or high miR-31; IA (median RFS: 32.1 versus 122.8 months, P = 0.005) and IB (median RFS: 7.1 versus 26.2, P = 0.049). MicroRNAs, miR-182, miR-183 and miR-196a were found correlated with EGFR mutation and poor RFS in stage IB patients. CONCLUSION Distinctive features of somatic gene mutation and microRNA expression of stage I LUAD are characterized to complement the survival prognosis by substaging. The findings open up more options for precision management of stage I LUAD patients.
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Affiliation(s)
- Hao Ho
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan; Institute of Medical Device and Imaging, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Shin-Sheng Yuan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Chiung Hsu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Chung-Ping Hsu
- Division of Thoracic Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Cheng-Yen Chuang
- Division of Thoracic Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ya-Hsuan Chang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yu-Cheng Li
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chiou-Ling Cheng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Gee-Chen Chang
- Division of Pulmonary Medicine, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan; Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; School of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.
| | - Pan-Chyr Yang
- Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Ker-Chau Li
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan; Department of Statistics, University of California Los Angeles, Los Angeles, CA.
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Shill MC, Biswas B, Kamal S, Islam M, Rima SS, Ferdausi FA, Chowdhury Q, Reza HM, Bepari AK. Screening of plasma IL-6 and IL-17 in Bangladeshi lung cancer patients. Heliyon 2023; 9:e20471. [PMID: 37810816 PMCID: PMC10556768 DOI: 10.1016/j.heliyon.2023.e20471] [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: 06/23/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/10/2023] Open
Abstract
Lung cancer is responsible for causing one of the highest numbers of cancer deaths. In Bangladesh, both men and women are affected by lung cancer, and environmental contaminants are believed to be one of the main risk factors apart from smoking. The diagnosis of lung cancer is difficult due to the delicate structure and complexity of the lungs. Diagnosis in later stages results in a poor prognosis of the disease. Tissue biopsy is the most reliable way of identifying lung cancer, but it is invasive and requires identification of the primary neoplasm within the lungs. As inflammation is involved in carcinogenesis, circulating levels of cytokines might be elevated in patients during the early stages of cancer. Increased IL-6 levels have been associated with the promotion of tumor growth, and IL-17 is believed to aid metastasis of lung cancer. In this study, the use of IL-6 and IL-17 was investigated as diagnostic markers for lung cancer. IL-6 and IL-17 levels were compared between 35 lung cancer patients and 19 healthy individuals. IL-6 levels were markedly elevated (7.417 pg/mL) in lung cancer cases compared to the controls (0.970 pg/mL), indicating a positive correlation (p < 0.05). IL-17 levels were only slightly higher in lung cancer patients (9.400 pg/mL) compared to healthy individuals (8.922 pg/mL). Both IL-6 and IL-17 levels were higher in patients with adenocarcinoma compared with other subtypes of lung cancer. Treatment with chemotherapy and radiotherapy did not significantly affect IL-6 levels. However, IL-17 levels were reduced due to cancer treatment. Further studies with larger sample sizes assessing the IL-6 and IL-17 in lung cancer patients are needed to establish the diagnostic role of the two cytokines.
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Affiliation(s)
- Manik Chandra Shill
- Department of Pharmaceutical Sciences, North South University, Dhaka, 1229, Bangladesh
| | - Bisshojit Biswas
- Department of Pharmaceutical Sciences, North South University, Dhaka, 1229, Bangladesh
| | - Sadia Kamal
- Department of Pharmaceutical Sciences, North South University, Dhaka, 1229, Bangladesh
| | - Moriam Islam
- Department of Pharmaceutical Sciences, North South University, Dhaka, 1229, Bangladesh
| | - Sharmin Sultana Rima
- Department of Pharmaceutical Sciences, North South University, Dhaka, 1229, Bangladesh
| | | | | | - Hasan Mahmud Reza
- Department of Pharmaceutical Sciences, North South University, Dhaka, 1229, Bangladesh
| | - Asim Kumar Bepari
- Department of Pharmaceutical Sciences, North South University, Dhaka, 1229, Bangladesh
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Wu R, Ma R, Duan X, Zhang J, Li K, Yu L, Zhang M, Liu P, Wang C. Identification of specific prognostic markers for lung squamous cell carcinoma based on tumor progression, immune infiltration, and stem index. Front Immunol 2023; 14:1236444. [PMID: 37841237 PMCID: PMC10570622 DOI: 10.3389/fimmu.2023.1236444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Lung squamous cell carcinoma (LUSC) is a unique subform of nonsmall cell lung cancer (NSCLC). The lack of specific driver genes as therapeutic targets leads to worse prognoses in patients with LUSC, even with chemotherapy, radiotherapy, or immune checkpoint inhibitors. Furthermore, research on the LUSC-specific prognosis genes is lacking. This study aimed to develop a comprehensive LUSC-specific differentially expressed genes (DEGs) signature for prognosis correlated with tumor progression, immune infiltration,and stem index. Methods RNA sequencing data for LUSC and lung adenocarcinoma (LUAD) were extracted from The Cancer Genome Atlas (TCGA) data portal, and DEGs analyses were conducted in TCGA-LUSC and TCGA-LUAD cohorts to identify specific DEGs associated with LUSC. Functional analysis and protein-protein interaction network were performed to annotate the roles of LUSC-specific DEGs and select the top 100 LUSC-specific DEGs. Univariate Cox regression and least absolute shrinkage and selection operator regression analyses were performed to select prognosis-related DEGs. Results Overall, 1,604 LUSC-specific DEGs were obtained, and a validated seven-gene signature was constructed comprising FGG, C3, FGA, JUN, CST3, CPSF4, and HIST1H2BH. FGG, C3, FGA, JUN, and CST3 were correlated with poor LUSC prognosis, whereas CPSF4 and HIST1H2BH were potential positive prognosis markers in patients with LUSC. Receiver operating characteristic analysis further confirmed that the genetic profile could accurately estimate the overall survival of LUSC patients. Analysis of immune infiltration demonstrated that the high risk (HR) LUSC patients exhibited accelerated tumor infiltration, relative to low risk (LR) LUSC patients. Molecular expressions of immune checkpoint genes differed significantly between the HR and LR cohorts. A ceRNA network containing 19 lncRNAs, 50 miRNAs, and 7 prognostic DEGs was constructed to demonstrate the prognostic value of novel biomarkers of LUSC-specific DEGs based on tumor progression, stemindex, and immune infiltration. In vitro experimental models confirmed that LUSC-specific DEG FGG expression was significantly higher in tumor cells and correlated with immune tumor progression, immune infiltration, and stem index. In vitro experimental models confirmed that LUSC-specific DEG FGG expression was significantly higher in tumor cells and correlated with immune tumor progression, immune infiltration, and stem index. Conclusion Our study demonstrated the potential clinical implication of the 7- DEGs signature for prognosis prediction of LUSC patients based on tumor progression, immune infiltration, and stem index. And the FGG could be an independent prognostic biomarker of LUSC promoting cell proliferation, migration, invasion, THP-1 cell infiltration, and stem cell maintenance.
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Affiliation(s)
- Rihan Wu
- School of Life Science, Inner Mongolia University, Hohhot, China
- The Department of Oncology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Ru Ma
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Xiaojun Duan
- School of Life Science, Inner Mongolia University, Hohhot, China
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Jiandong Zhang
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Kexin Li
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Lei Yu
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Mingyang Zhang
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Pengxia Liu
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Changshan Wang
- School of Life Science, Inner Mongolia University, Hohhot, China
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Wang Z, Wang Y, Li Z, Xue W, Hu S, Kong X. Lipid metabolism as a target for cancer drug resistance: progress and prospects. Front Pharmacol 2023; 14:1274335. [PMID: 37841917 PMCID: PMC10571713 DOI: 10.3389/fphar.2023.1274335] [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: 08/08/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023] Open
Abstract
Cancer is the world's leading cause of human death today, and the treatment process of cancer is highly complex. Chemotherapy and targeted therapy are commonly used in cancer treatment, and the emergence of drug resistance is a significant problem in cancer treatment. Therefore, the mechanism of drug resistance during cancer treatment has become a hot issue in current research. A series of studies have found that lipid metabolism is closely related to cancer drug resistance. This paper details the changes of lipid metabolism in drug resistance and how lipid metabolism affects drug resistance. More importantly, most studies have reported that combination therapy may lead to changes in lipid-related metabolic pathways, which may reverse the development of cancer drug resistance and enhance or rescue the sensitivity to therapeutic drugs. This paper summarizes the progress of drug design targeting lipid metabolism in improving drug resistance, and providing new ideas and strategies for future tumor treatment. Therefore, this paper reviews the issues of combining medications with lipid metabolism and drug resistance.
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Affiliation(s)
- Zi’an Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Yueqin Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Zeyun Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Wenhua Xue
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Shousen Hu
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangzhen Kong
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
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Luna HGC, Imasa MS, Juat N, Hernandez KV, Sayo TM, Cristal-Luna G, Asur-Galang SM, Bellengan M, Duga KJ, Buenaobra BB, De los Santos MI, Medina D, Samo J, Literal VM, Bascos NA, Sy-Naval S. The differential prognostic implications of PD-L1 expression in the outcomes of Filipinos with EGFR-mutant NSCLC treated with tyrosine kinase inhibitors. Transl Lung Cancer Res 2023; 12:1896-1911. [PMID: 37854154 PMCID: PMC10579834 DOI: 10.21037/tlcr-23-118] [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: 02/19/2023] [Accepted: 07/20/2023] [Indexed: 10/20/2023]
Abstract
Background The tumor immune microenvironment influences tumor evolution in non-small cell lung cancer (NSCLC). Yet, the prognostic value of programmed death-ligand 1 (PD-L1) in epidermal growth factor receptor (EGFR)-mutant NSCLC remains controversial. Additionally, prognostic studies in Filipinos with EGFR-mutant NSCLC remain unexplored to this day. Methods We prospectively studied the outcomes of EGFR-mutant NSCLC in Filipino cohort, and retrospectively verified the survival trend using The Cancer Genome Atlas (TCGA) cohort. Kaplan-Meier method and generalized linear regression were used to assess survival. Expression and DNA methylation of cluster of differentiation 274 (CD274, gene that codes for PD-L1) were examined from TCGA tumor profiles. Pearson's correlation was used to correlate PD-L1 expression with outcomes associated with occurrence of EGFR mutations, tyrosine kinase inhibitor (TKI) types, and programmed cell death protein 1 (PD-1) expression. Proteome network analysis was used to examine the correlation between drug resistance and PD-L1. Results PD-L1 positivity was associated with significantly longer progression-free survival (PFS; P=0.0096) but had a significantly contrasting influence in the overall survival (OS; P=0.0011). PD-L1 positivity (in both protein and RNA) was associated with longer median OS (mOS) in exon21 L858R, whereas, negativity was associated with longer mOS in exon19 deletion (exon19del). Stratification (high, low, negative) of PD-L1 expression lacked significant prognostic value (all P>0.05). PD-L1/CD274 expression (P<0.05) and DNA methylation (P<0.001) vary significantly among NSCLC subtypes and in different disease stages. Erlotinib treatment produced the longest median progression-free survival (mPFS; 874 days) relative to other EGFR-TKIs (137-311 days). PD-L1 lacked a significant correlation with EGFR-TKIs. Consistent with the immune-regulation activities of PD-1, higher expression leads to relatively shorter mOS. PD-1 correlated positively with PD-L1 expression and occurrence of exon21 L858R. Conclusions PD-L1 differentially influenced the outcomes of Filipinos with EGFR-mutant NSCLC. NSCLC subtypes, disease stage, and PD-1 expression may impact the collective outcomes associated with PD-L1 and EGFR-sensitizing mutations.
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Affiliation(s)
- Herdee Gloriane C. Luna
- Lung Center of the Philippines, Quezon City, Philippines
- National Kidney and Transplant Institute, Quezon City, Philippines
| | | | - Necy Juat
- National Kidney and Transplant Institute, Quezon City, Philippines
| | | | - Treah May Sayo
- Lung Center of the Philippines, Quezon City, Philippines
| | | | - Sheena Marie Asur-Galang
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Mirasol Bellengan
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Kent John Duga
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Bien Brian Buenaobra
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Marvin I. De los Santos
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Daniel Medina
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Jamirah Samo
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Venus Minerva Literal
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Neil Andrew Bascos
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City, Philippines
- Protein, Proteomics and Metabolomics Facility, Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
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Zou F, Chen W, Song T, Xing J, Zhang Y, Chen K, Hu W, Li L, Ning J, Li C, Yu W, Cheng F. SQLE Knockdown inhibits bladder cancer progression by regulating the PTEN/AKT/GSK3β signaling pathway through P53. Cancer Cell Int 2023; 23:221. [PMID: 37770925 PMCID: PMC10540347 DOI: 10.1186/s12935-023-02997-5] [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: 03/14/2023] [Accepted: 07/19/2023] [Indexed: 09/30/2023] Open
Abstract
Bladder cancer (BCa) is one of the most common malignancies worldwide. However, the lack of accurate and effective targeted drugs has become a major problem in current clinical treatment of BCa. Studies have demonstrated that squalene epoxidase (SQLE), as a key rate-limiting enzyme in cholesterol biosynthesis, is involved in cancer development. In this study, our analysis of The Cancer Genome Atlas, The Genotype-Tissue Expression, and Gene Expression Omnibus databases showed that SQLE expression was significantly higher in cancer tissues than it was in adjacent normal tissues, and BCa tissues with a high SQLE expression displayed a poor prognosis. We then confirmed this result in qRT-PCR and immunohistochemical staining experiments, and our vitro studies demonstrated that SQLE knockdown inhibited tumor cell proliferation and metastasis through the PTEN/AKT/GSK3β signaling pathway. By means of rescue experiments, we proved that that P53 is a key molecule in SQLE-mediated regulation of the PTEN/AKT/GSK3β signaling pathway. Simultaneously, we verified the above findings through a tumorigenesis experiment in nude mice. In conclusion, our study shows that SQLE promotes BCa growth through the P53/PTEN/AKT/GSK3β axis, which may serve as a therapeutic biological target for BCa.
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Affiliation(s)
- Fan Zou
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China
| | - Wu Chen
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China
| | - Tianbao Song
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China
| | - Ji Xing
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China
| | - Yunlong Zhang
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China
| | - Kang Chen
- Department of Urology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Weimin Hu
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China
| | - Linzhi Li
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China
| | - Jinzhuo Ning
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China
| | - Chenglong Li
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China
| | - Weimin Yu
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China.
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, 99 ziyang road, Wuhan, 430060, Hubei Province, China.
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Chiang CY, Fan S, Zheng H, Guo W, Zheng Z, Sun Y, Zhong C, Zeng J, Li S, Zhang M, Xiao T, Zheng D. Methylation of KRAS by SETD7 promotes KRAS degradation in non-small cell lung cancer. Cell Rep 2023; 42:113003. [PMID: 37682707 DOI: 10.1016/j.celrep.2023.113003] [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: 07/19/2021] [Revised: 06/18/2023] [Accepted: 08/02/2023] [Indexed: 09/10/2023] Open
Abstract
Oncogenic KRAS mutations are a key driver for initiation and progression in non-small cell lung cancer (NSCLC). However, how post-translational modifications (PTMs) of KRAS, especially methylation, modify KRAS activity remain largely unclear. Here, we show that SET domain containing histone lysine methyltransferase 7 (SETD7) interacts with KRAS and methylates KRAS at lysines 182 and 184. SETD7-mediated methylation of KRAS leads to degradation of KRAS and attenuation of the RAS/MEK/ERK signaling cascade, endowing SETD7 with a potent tumor-suppressive role in NSCLC, both in vitro and in vivo. Mechanistically, RABGEF1, a ubiquitin E3 ligase of KRAS, is recruited and promotes KRAS degradation in a K182/K184 methylation-dependent manner. Notably, SETD7 is inversely correlated with KRAS at the protein level in clinical NSCLC tissues. Low SETD7 or RABGEF1 expression is associated with poor prognosis in lung adenocarcinoma patients. Altogether, our results define a tumor-suppressive function of SETD7 that operates via modulating KRAS methylation and degradation.
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Affiliation(s)
- Cheng-Yao Chiang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School, Thoracic Surgery Department of the First Affiliated Hospital, Shenzhen University, Shenzhen 518055, China
| | - Songqing Fan
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hongmei Zheng
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Wenjun Guo
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School, Thoracic Surgery Department of the First Affiliated Hospital, Shenzhen University, Shenzhen 518055, China
| | - Zehan Zheng
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School, Thoracic Surgery Department of the First Affiliated Hospital, Shenzhen University, Shenzhen 518055, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Chuanqi Zhong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Juan Zeng
- School of Biomedical Engineering, Guangdong Medical University, Dongguan, Guangdong 523808, China
| | - Shuaihu Li
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School, Thoracic Surgery Department of the First Affiliated Hospital, Shenzhen University, Shenzhen 518055, China
| | - Min Zhang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School, Thoracic Surgery Department of the First Affiliated Hospital, Shenzhen University, Shenzhen 518055, China
| | - Tian Xiao
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School, Thoracic Surgery Department of the First Affiliated Hospital, Shenzhen University, Shenzhen 518055, China.
| | - Duo Zheng
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School, Thoracic Surgery Department of the First Affiliated Hospital, Shenzhen University, Shenzhen 518055, China.
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Sahu P, Donovan C, Paudel KR, Pickles S, Chimankar V, Kim RY, Horvart JC, Dua K, Ieni A, Nucera F, Bielefeldt-Ohmann H, Mazilli S, Caramori G, Lyons JG, Hansbro PM. Pre-clinical lung squamous cell carcinoma mouse models to identify novel biomarkers and therapeutic interventions. Front Oncol 2023; 13:1260411. [PMID: 37817767 PMCID: PMC10560855 DOI: 10.3389/fonc.2023.1260411] [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: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 10/12/2023] Open
Abstract
Primary lung carcinoma or lung cancer (LC) is classified into small-cell or non-small-cell (NSCLC) lung carcinoma. Lung squamous cell carcinoma (LSCC) is the second most common subtype of NSCLC responsible for 30% of all LCs, and its survival remains low with only 24% of patients living for five years or longer post-diagnosis primarily due to the advanced stage of tumors at the time of diagnosis. The pathogenesis of LSCC is still poorly understood and has hampered the development of effective diagnostics and therapies. This review highlights the known risk factors, genetic and epigenetic alterations, miRNA biomarkers linked to the development and diagnosis of LSCC and the lack of therapeutic strategies to target specifically LSCC. We will also discuss existing animal models of LSCC including carcinogen induced, transgenic and xenograft mouse models, and their advantages and limitations along with the chemopreventive studies and molecular studies conducted using them. The importance of developing new and improved mouse models will also be discussed that will provide further insights into the initiation and progression of LSCC, and enable the identification of new biomarkers and therapeutic targets.
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Affiliation(s)
- Priyanka Sahu
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
| | - Chantal Donovan
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Sophie Pickles
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Vrushali Chimankar
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Richard Y. Kim
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Jay C. Horvart
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Antonio Ieni
- Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi”, Section of Anatomic Pathology, University of Messina, Messina, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy
| | - Helle Bielefeldt-Ohmann
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Sarah Mazilli
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy
| | - J. Guy Lyons
- Department of Dermatology, The University of Sydney at Royal Prince Alfred Hospital, Sydney, Australia, and Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Philip M. Hansbro
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
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Wakuda K, Kenmotsu H, Sato Y, Nakamura A, Akamatsu H, Tachihara M, Miura S, Yokoyama T, Mori K, Nakagawa K, Yamamoto N. Randomized, open-label phase II study of brigatinib and carboplatin plus pemetrexed and brigatinib alone for chemotherapy-naive patients with ALK-rearranged non-squamous non-small cell lung cancer: treatment rationale and protocol design of the B-DASH study (WJOG 14720 L). BMC Cancer 2023; 23:902. [PMID: 37749521 PMCID: PMC10519075 DOI: 10.1186/s12885-023-11417-w] [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: 02/04/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND The ALTA-1L study compared brigatinib with crizotinib in untreated ALK-rearranged non-small cell lung cancer (NSCLC) patients, demonstrating the efficacy of brigatinib. Although the median progression-free survival (PFS) of brigatinib group was 24.0 months, the one-year PFS rate was 70%. In the NEJ009 study, patients with EGFR mutations showed improved outcomes with gefitinib plus chemotherapy compared with gefitinib monotherapy. To evaluate the efficacy of the combination of brigatinib with chemotherapy for patients with ALK-rearranged NSCLC, we designed B-DASH study (WJOG 14720L). METHODS B-DASH study is a multicenter, two-arm, phase II study. Eligible patients have untreated stage IIIB, stage IIIC, stage IV, or postoperative relapse ALK-rearranged nonsquamous NSCLC. Patients will be randomized in a 1:1 ratio to receive brigatinib (180 mg once daily with a 7-day lead-in period at 90 mg) monotherapy or carboplatin (area under the curve = 5 on day 1) plus pemetrexed (500 mg/m2 on day 1) and brigatinib in a 3-week cycle for up to four cycles, followed by pemetrexed and brigatinib as maintenance therapy. The target hazard ratio of 0.62 is set based on the NEJ009 study. With one-sided alpha = 0.20 and power = 0.8, the sample size for the B-DASH study was calculated to be 110, considering the possibility of patients dropping out. The primary endpoint is PFS. The key secondary endpoints are the overall response rate and overall survival. We will evaluate tumor-derived DNA from plasma specimens before treatment, 42 days after administering the study drug, and on the day of progressive disease. Recruitment began in November 2021 and is ongoing. DISCUSSION The efficacy of combination therapy with tyrosine kinase inhibitors and cytotoxic chemotherapy was demonstrated in patients with EGFR mutations but remains unclear in patients with ALK-rearranged NSCLC. The B-DASH study is the only trial of brigatinib combined with chemotherapy in patients with untreated ALK-rearranged NSCLC. TRIAL REGISTRATION jRCT identifier: jRCTs041210103.
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Affiliation(s)
- Kazushige Wakuda
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo Nagaizumi-Cho Suntou-Gun, Shizuoka, 411-8777 Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo Nagaizumi-Cho Suntou-Gun, Shizuoka, 411-8777 Japan
| | - Yuki Sato
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, 2-1-1 Minatojimaminami-Machi Chuo-Ku Kobe, Hyogo, 650-0047 Japan
| | - Atsushi Nakamura
- Department of Pulmonary Medicine, Sendai Kousei Hospital, 4-15 Hirose-Cho Aoba-Ku Sendai, Miyagi, 980-0873 Japan
| | - Hiroaki Akamatsu
- Internal Medicine III, Wakayama Medical University, 811-1, Kimiidera, Wakayama, 641-8509 Japan
| | - Motoko Tachihara
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe, Hyogo 650-0017 Japan
| | - Satoru Miura
- Department of Internal Medicine, Niigata Cancer Center Hospital, 2-15-3 Kawagishi-Cho, Chuo-Ku, Niigata, 951-8566 Japan
| | - Toshihide Yokoyama
- Department of Respiratory Medicine, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki, Okayama 710-8602 Japan
| | - Keita Mori
- Dividion of Cliniccal Research Center, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo Nagaizumi-Cho Suntou-Gun, Shizuoka, 411-8777 Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka, 589-8511 Japan
| | - Nobuyuki Yamamoto
- Internal Medicine III, Wakayama Medical University, 811-1, Kimiidera, Wakayama, 641-8509 Japan
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Cui Y, Wang Z, Wang X, Zhang Y, Zhang Y, Pan T, Zhang Z, Li S, Guo Y, Akutsu T, Song J. SMG: self-supervised masked graph learning for cancer gene identification. Brief Bioinform 2023; 24:bbad406. [PMID: 37950905 PMCID: PMC10639095 DOI: 10.1093/bib/bbad406] [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: 06/13/2023] [Revised: 09/26/2023] [Accepted: 10/24/2023] [Indexed: 11/13/2023] Open
Abstract
Cancer genomics is dedicated to elucidating the genes and pathways that contribute to cancer progression and development. Identifying cancer genes (CGs) associated with the initiation and progression of cancer is critical for characterization of molecular-level mechanism in cancer research. In recent years, the growing availability of high-throughput molecular data and advancements in deep learning technologies has enabled the modelling of complex interactions and topological information within genomic data. Nevertheless, because of the limited labelled data, pinpointing CGs from a multitude of potential mutations remains an exceptionally challenging task. To address this, we propose a novel deep learning framework, termed self-supervised masked graph learning (SMG), which comprises SMG reconstruction (pretext task) and task-specific fine-tuning (downstream task). In the pretext task, the nodes of multi-omic featured protein-protein interaction (PPI) networks are randomly substituted with a defined mask token. The PPI networks are then reconstructed using the graph neural network (GNN)-based autoencoder, which explores the node correlations in a self-prediction manner. In the downstream tasks, the pre-trained GNN encoder embeds the input networks into feature graphs, whereas a task-specific layer proceeds with the final prediction. To assess the performance of the proposed SMG method, benchmarking experiments are performed on three node-level tasks (identification of CGs, essential genes and healthy driver genes) and one graph-level task (identification of disease subnetwork) across eight PPI networks. Benchmarking experiments and performance comparison with existing state-of-the-art methods demonstrate the superiority of SMG on multi-omic feature engineering.
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Affiliation(s)
- Yan Cui
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Zhikang Wang
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Xiaoyu Wang
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Yiwen Zhang
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Ying Zhang
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Tong Pan
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | | | - Shanshan Li
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Yuming Guo
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Jiangning Song
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
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