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Asada K, Kaneko S, Takasawa K, Shiraishi K, Shinkai N, Shimada Y, Takahashi S, Machino H, Kobayashi K, Bolatkan A, Komatsu M, Yamada M, Miyake M, Watanabe H, Tateishi A, Mizuno T, Okubo Y, Mukai M, Yoshida T, Yoshida Y, Horinouchi H, Watanabe SI, Ohe Y, Yatabe Y, Kohno T, Hamamoto R. Multi-omics and clustering analyses reveal the mechanisms underlying unmet needs for patients with lung adenocarcinoma and identify potential therapeutic targets. Mol Cancer 2024; 23:182. [PMID: 39218851 PMCID: PMC11367768 DOI: 10.1186/s12943-024-02093-w] [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: 04/28/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The cancer genome contains several driver mutations. However, in some cases, no known drivers have been identified; these remaining areas of unmet needs, leading to limited progress in cancer therapy. Whole-genome sequencing (WGS) can identify non-coding alterations associated with the disease. Consequently, exploration of non-coding regions using WGS and other omics data such as ChIP-sequencing (ChIP-seq) to discern novel alterations and mechanisms related to tumorigenesis have been attractive these days. METHODS Integrated multi-omics analyses, including WGS, ChIP-seq, DNA methylation, and RNA-sequencing (RNA-seq), were conducted on samples from patients with non-clinically actionable genetic alterations (non-CAGAs) in lung adenocarcinoma (LUAD). Second-level cluster analysis was performed to reinforce the correlations associated with patient survival, as identified by RNA-seq. Subsequent differential gene expression analysis was performed to identify potential druggable targets. RESULTS Differences in H3K27ac marks in non-CAGAs LUAD were found and confirmed by analyzing RNA-seq data, in which mastermind-like transcriptional coactivator 2 (MAML2) was suppressed. The down-regulated genes whose expression was correlated to MAML2 expression were associated with patient prognosis. WGS analysis revealed somatic mutations associated with the H3K27ac marks in the MAML2 region and high levels of DNA methylation in MAML2 were observed in tumor samples. The second-level cluster analysis enabled patient stratification and subsequent analyses identified potential therapeutic target genes and treatment options. CONCLUSIONS We overcome the persistent challenges of identifying alterations or driver mutations in coding regions related to tumorigenesis through a novel approach combining multi-omics data with clinical information to reveal the molecular mechanisms underlying non-CAGAs LUAD, stratify patients to improve patient prognosis, and identify potential therapeutic targets. This approach may be applicable to studies of other cancers with unmet needs.
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Affiliation(s)
- Ken Asada
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan.
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan.
| | - Syuzo Kaneko
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Ken Takasawa
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Norio Shinkai
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Yoko Shimada
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Satoshi Takahashi
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Hidenori Machino
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Kazuma Kobayashi
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Amina Bolatkan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Masaaki Komatsu
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Masayoshi Yamada
- Department of Endoscopy, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Mototaka Miyake
- Department of Diagnostic Radiology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Hirokazu Watanabe
- Department of Diagnostic Radiology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Akiko Tateishi
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Takaaki Mizuno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yu Okubo
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Masami Mukai
- Division of Medical Informatics, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Tatsuya Yoshida
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yukihiro Yoshida
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Hidehito Horinouchi
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, 104-0045, Japan.
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan.
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan.
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2
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Demetriou AN, Chow F, Craig DW, Webb MG, Ormond DR, Battiste J, Chakravarti A, Colman H, Villano JL, Schneider BP, Liu JKC, Churchman ML, Zada G. Profiling the molecular and clinical landscape of glioblastoma utilizing the Oncology Research Information Exchange Network brain cancer database. Neurooncol Adv 2024; 6:vdae046. [PMID: 38665799 PMCID: PMC11044707 DOI: 10.1093/noajnl/vdae046] [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] [Indexed: 04/28/2024] Open
Abstract
Background Glioblastoma exhibits aggressive growth and poor outcomes despite treatment, and its marked variability renders therapeutic design and prognostication challenging. The Oncology Research Information Exchange Network (ORIEN) database contains complementary clinical, genomic, and transcriptomic profiling of 206 glioblastoma patients, providing opportunities to identify novel associations between molecular features and clinical outcomes. Methods Survival analyses were performed using the Logrank test, and clinical features were evaluated using Wilcoxon and chi-squared tests with q-values derived via Benjamini-Hochberg correction. Mutational analyses utilized sample-level enrichments from whole exome sequencing data, and statistical tests were performed using the one-sided Fisher Exact test with Benjamini-Hochberg correction. Transcriptomic analyses utilized a student's t-test with Benjamini-Hochberg correction. Expression fold changes were processed with Ingenuity Pathway Analysis to determine pathway-level alterations between groups. Results Key findings include an association of MUC17, SYNE1, and TENM1 mutations with prolonged overall survival (OS); decreased OS associated with higher epithelial growth factor receptor (EGFR) mRNA expression, but not with EGFR amplification or mutation; a 14-transcript signature associated with OS > 2 years; and 2 transcripts associated with OS < 1 year. Conclusions Herein, we report the first clinical, genomic, and transcriptomic analysis of ORIEN glioblastoma cases, incorporating sample reclassification under updated 2021 diagnostic criteria. These findings create multiple avenues for further investigation and reinforce the value of multi-institutional consortia such as ORIEN in deepening our knowledge of intractable diseases such as glioblastoma.
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Affiliation(s)
- Alexandra N Demetriou
- Keck School of Medicine, University of Southern California (USC), Los Angeles, California, USA
| | - Frances Chow
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - David W Craig
- Department of Integrative Translational Sciences, City of Hope, Duarte, California, USA
| | - Michelle G Webb
- Department of Integrative Translational Sciences, City of Hope, Duarte, California, USA
| | - D Ryan Ormond
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - James Battiste
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, College of Medicine at The Ohio State University, Columbus, Ohio, USA
| | - Howard Colman
- Huntsman Cancer Institute and Department of Neurosurgery, University of Utah, Salt Lake City, Utah, USA
| | - John L Villano
- Department of Internal Medicine, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Bryan P Schneider
- Department of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - James K C Liu
- Department of Neuro-Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | | | - Gabriel Zada
- Department of Neurological Surgery, Keck School of Medicine of USC, Los Angeles, California, USA
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Machado GC, Ferrer VP. MUC17 mutations and methylation are associated with poor prognosis in adult-type diffuse glioma patients. J Neurol Sci 2023; 452:120762. [PMID: 37562166 DOI: 10.1016/j.jns.2023.120762] [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: 02/10/2023] [Revised: 07/03/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Diffuse gliomas are tumors that arise from glial or glial progenitor cells. They are currently classified as astrocytoma isocitrate dehydrogenase (IDH)-mutant or oligodendroglioma IDH-mutant, and 1p/19q-codeleted, both slower-growing tumors, or glioblastoma (GBM), a more aggressive tumor. Despite advances in the diagnosis and treatment of gliomas, the median survival time after diagnosis of GBM remains low, approximately 15 months, with a 5-year overall survival rate of only 6.8%. Therefore, new biomarkers that could support the earlier diagnosis and prognosis of these tumors would be of great value. MUC17, a membrane-bound mucin, has been identified as a potential biomarker for several tumors. However, the role of this mucin in adult gliomas has not yet been explored. Here, we show for the first time, in a retrospective study and by in silico analysis that MUC17 is one of the relevant mutant genes in adult gliomas. Moreover, that an increase in MUC17 methylation correlates with an increase in glioma malignancy grade. Patients with MUC17 mutations had a poorer prognosis than their wild-type counterparts in both GBM and non-GBM glioma cohorts. We also analyzed mutational profiles that correlated strongly with poor survival. Therefore, in this study, we present a new potential biomarker for further investigation, especially for the prognosis of adult diffuse gliomas.
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Affiliation(s)
- Gabriel Cardoso Machado
- Laboratory of Cell and Molecular Biology of Tumors, Department of Cell and Molecular Biology, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil; Graduate Program in Pathological Anatomy, Faculty of Medicine, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Laboratory of Cell and Molecular Biology of Tumors, Department of Cell and Molecular Biology, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil; Graduate Program in Pathological Anatomy, Faculty of Medicine, Rio de Janeiro Federal University, Rio de Janeiro, Brazil.
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Gene Expression Analysis Reveals Prognostic Biomarkers of the Tyrosine Metabolism Reprogramming Pathway for Prostate Cancer. JOURNAL OF ONCOLOGY 2022; 2022:5504173. [PMID: 35847355 PMCID: PMC9279037 DOI: 10.1155/2022/5504173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
Background Tyrosine metabolism pathway-related genes were related to prostate cancer progression, which may be used as potential prognostic markers. Aims To dissect the dysregulation of tyrosine metabolism in prostate cancer and build a prognostic signature based on tyrosine metabolism-related genes for prostate cancer. Materials and Method. Cross-platform gene expression data of prostate cancer cohorts were collected from both The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Based on the expression of tyrosine metabolism-related enzymes (TMREs), an unsupervised consensus clustering method was used to classify prostate cancer patients into different molecular subtypes. We employed the least absolute shrinkage and selection operator (LASSO) Cox regression analysis to evaluate prognostic characteristics based on TMREs to obtain a prognostic effect. The nomogram model was established and used to synthesize molecular subtypes, prognostic characteristics, and clinicopathological features. Kaplan–Meier plots and logrank analysis were used to clarify survival differences between subtypes. Results Based on the hierarchical clustering method and the expression profiles of TMREs, prostate cancer samples were assigned into two subgroups (S1, subgroup 1; S2, subgroup 2), and the Kaplan–Meier plot and logrank analysis showed distinct survival outcomes between S1 and S2 subgroups. We further established a four-gene-based prognostic signature, and both in-group testing dataset and out-group testing dataset indicated the robustness of this model. By combining the four gene-based signatures and clinicopathological features, the nomogram model achieved better survival outcomes than any single classifier. Interestingly, we found that immune-related pathways were significantly concentrated on S1-upregulated genes, and the abundance of memory B cells, CD4+ resting memory T cells, M0 macrophages, resting dendritic cells, and resting mast cells were significantly different between S1 and S2 subgroups. Conclusions Our results indicate the prognostic value of genes related to tyrosine metabolism in prostate cancer and provide inspiration for treatment and prevention strategies.
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X-Box Binding Protein 1 (XBP1): A Potential Role in Chemotherapy Response, Clinical Pathologic Features, Non-Inflamed Tumour Microenvironment for Breast Cancer. Biosci Rep 2022; 42:231292. [PMID: 35543228 PMCID: PMC9202509 DOI: 10.1042/bsr20220225] [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: 01/28/2022] [Revised: 03/17/2022] [Accepted: 04/04/2022] [Indexed: 12/09/2022] Open
Abstract
X-box binding protein 1 (XBP1) is mainly expressed in breast cancer (BC) in human cancers. Its tumorigenesis and favourable prognosis are contradictory, and its essential role in chemotherapeutic response and immunosuppression is unknown in BC. The study firstly identified XBP1 who received neoadjuvant chemotherapy (NAC) from GSE25055 and GSE24460. Associations between XBP1 expression and clinicopathological characteristics was investigated using Oncomine, TCGA, UALCAN and bc-GenExMiner. The prognostic value of XBP1 was assessed using the Kaplan–Meier Plotter, bc-GenExMiner, GSE25055, and GSE25056. Furthermore, we systematically correlated XBP1 and immunological characteristics in the BC tumour microenvironment (TME) using TISIDB, TIMER, GSE25055, GSE25056 and TCGA dataset. Finally, an essential role of XBP1 in chemotherapy response was evaluated based on GSE25055, GSE25065, GSE24460, GSE5846, ROC Plotter and CELL databases. Furthermore, XBP1 mRNA expression levels were obviously highest in BC among human cancers and were significantly related to a good prognosis. In addition, XBP1 mRNA and protein levels were higher in the luminal subtype than in normal tissues and basal-like subtype, which might be attributed to membrane transport-related processes. Apart from BC, negative immunological correlations of XBP1 were not observed in other malignancies. XBP1 might shape the non-inflamed TME in BC. Finally, XBP1 expression was higher in chemo-resistive than chemo-sensitive cases, it had a predictive value and could independently predict chemotherapy response in BC patients receiving NAC. Our study suggests that the essential role of XBP1 in clinical pathologic features, non-inflamed TME, chemotherapy response in BC.
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Dong M, Shan B, Han X, Zhao X, Wang F, Zhu L, Ou Q, Ma X, Pan Y. Baseline Mutations and Up-Regulation of PI3K-AKT Pathway Serve as Potential Indicators of Lack of Response to Neoadjuvant Chemotherapy in Stage II/III Breast Cancer. Front Oncol 2022; 11:784985. [PMID: 35480699 PMCID: PMC9036956 DOI: 10.3389/fonc.2021.784985] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/28/2021] [Indexed: 12/19/2022] Open
Abstract
Background Neoadjuvant chemotherapy (NAC) has been expanded to hormone receptor (HR) positive breast cancer (BC) patients with operable disease, to increase the likelihood of breast-conserving surgery. Genomic profiling at baseline would reveal NAC response relevant genomic features and signaling pathways, guiding clinical NAC utilization based on patients’ genomic characteristics. Methods We prospectively studied stage II/III BC patients who were eligible for breast-conserving surgery. Patients received epirubicin and cyclophosphamide for 4 cycles, followed by another 4-cycle docetaxel, and human epidermal growth factor receptor (HER2) positive patients were additionally treated with herceptin when using docetaxel (EC-T(H)). NAC responses were evaluated as pathologic complete response (pCR) or non-pathologic complete response (non-pCR). Genomic features related to NAC responses were identified by profiling baseline tumor tissues sampled one day before NAC, using whole-exome sequencing. Differentially expressed genes and up-/down-regulated pathways were investigated by performing RNA-sequencing. Results A total of 25 stage II/III BC patients were enrolled, including 5 patients ultimately evaluated as pCR and 20 patients evaluated as non-pCR. PIK3CA (48%) and TP53 (40%) mutations were enriched in patients not achieving pCR. Mutated phosphatidylinositol-3-kinase-AKT (PI3K-AKT) pathway and homologous recombinational repair pathway were also more frequently observed in patients evaluated as non-pCR. Significant arm-level amplifications (8q24.23 and 17q12) and deletions (1p32.2, 4p14, 7q11.23, 10q21.3, 11q23.3, etc.) were identified among patients not achieving pCR, while patients achieving pCR displayed no significant copy number alterations. Significantly up-regulated expression of PI3K-AKT pathway genes was also detected among patients failed to achieve pCR, compared to patients achieving pCR. Conclusion Compared to BC patients achieving pCR to NAC, aberrant activation of PI3K-AKT pathway genes were more frequently observed in patients not achieving pCR, consistent with the significant up-regulation of PI3K-AKT pathway gene expression in the non-pCR subgroup. Together, these findings indicate that upregulated PI3K-AKT pathway serves as a potential indicator of lack of response to NAC in stage II/III BC patients, and other effective therapeutic options are urgently needed for those resistant patients.
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Affiliation(s)
- Menghao Dong
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Benjie Shan
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xinghua Han
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaotian Zhao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Fufeng Wang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Liuqing Zhu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Qiuxiang Ou
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xiaopeng Ma
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yueyin Pan
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Baxter DE, Allinson LM, Al Amri WS, Poulter JA, Pramanik A, Thorne JL, Verghese ET, Hughes TA. MiR-195 and Its Target SEMA6D Regulate Chemoresponse in Breast Cancer. Cancers (Basel) 2021; 13:cancers13235979. [PMID: 34885090 PMCID: PMC8656586 DOI: 10.3390/cancers13235979] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND poor prognosis primary breast cancers are typically treated with cytotoxic chemotherapy. However, recurrences remain relatively common even after this aggressive therapy. Comparison of matched tumours pre- and post-chemotherapy can allow identification of molecular characteristics of therapy resistance and thereby potentially aid discovery of novel predictive markers or targets for chemosensitisation. Through this comparison, we aimed to identify microRNAs associated with chemoresistance, define microRNA target genes, and assess targets as predictors of chemotherapy response. METHODS cancer cells were laser microdissected from matched breast cancer tissues pre- and post-chemotherapy from estrogen receptor positive/HER2 negative breast cancers showing partial responses to epirubicin/cyclophosphamide chemotherapy (n = 5). MicroRNA expression was profiled using qPCR arrays. MicroRNA/mRNA expression was manipulated in estrogen receptor positive/HER2 negative breast cancer cell lines (MCF7 and MDA-MB-175 cells) with mimics, inhibitors or siRNAs, and chemoresponse was assessed using MTT and colony forming survival assays. MicroRNA targets were identified by RNA-sequencing of microRNA mimic pull-downs, and comparison of these with mRNAs containing predicted microRNA binding sites. Survival correlations were tested using the METABRIC expression dataset (n = 1979). RESULTS miR-195 and miR-26b were consistently up-regulated after therapy, and changes in their expression in cell lines caused significant differences in chemotherapy sensitivity, in accordance with up-regulation driving resistance. SEMA6D was defined and confirmed as a target of the microRNAs. Reduced SEMA6D expression was significantly associated with chemoresistance, in accordance with SEMA6D being a down-stream effector of the microRNAs. Finally, low SEMA6D expression in breast cancers was significantly associated with poor survival after chemotherapy, but not after other therapies. CONCLUSIONS microRNAs and their targets influence chemoresponse, allowing the identification of SEMA6D as a predictive marker for chemotherapy response that could be used to direct therapy or as a target in chemosensitisation strategies.
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Affiliation(s)
- Diana E. Baxter
- School of Medicine, University of Leeds, Leeds LS9 7TF, UK; (D.E.B.); (J.A.P.); (A.P.)
- Cancer Research UK Manchester Institute, University of Manchester, Manchester SK10 4TG, UK
| | - Lisa M. Allinson
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AD, UK;
| | - Waleed S. Al Amri
- Department of Histopathology and Cytopathology, The Royal Hospital, Muscat, Oman;
| | - James A. Poulter
- School of Medicine, University of Leeds, Leeds LS9 7TF, UK; (D.E.B.); (J.A.P.); (A.P.)
| | - Arindam Pramanik
- School of Medicine, University of Leeds, Leeds LS9 7TF, UK; (D.E.B.); (J.A.P.); (A.P.)
| | - James L. Thorne
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK;
| | - Eldo T. Verghese
- Department of Histopathology, St. James’s University Hospital, Leeds LS9 7JX, UK;
| | - Thomas A. Hughes
- School of Medicine, University of Leeds, Leeds LS9 7TF, UK; (D.E.B.); (J.A.P.); (A.P.)
- Correspondence:
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Gwili N, Jones SJ, Amri WA, Carr IM, Harris S, Hogan BV, Hughes WE, Kim B, Langlands FE, Millican-Slater RA, Pramanik A, Thorne JL, Verghese ET, Wells G, Hamza M, Younis L, El Deeb NMF, Hughes TA. Transcriptome profiles of stem-like cells from primary breast cancers allow identification of ITGA7 as a predictive marker of chemotherapy response. Br J Cancer 2021; 125:983-993. [PMID: 34253873 PMCID: PMC8476506 DOI: 10.1038/s41416-021-01484-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/07/2021] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Breast cancer stem cells (BCSCs) are drivers of therapy-resistance, therefore are responsible for poor survival. Molecular signatures of BCSCs from primary cancers remain undefined. Here, we identify the consistent transcriptome of primary BCSCs shared across breast cancer subtypes, and we examine the clinical relevance of ITGA7, one of the genes differentially expressed in BCSCs. METHODS Primary BCSCs were assessed using immunohistochemistry and fluorescently labelled using Aldefluor (n = 17). Transcriptomes of fluorescently sorted BCSCs and matched non-stem cancer cells were determined using RNA-seq (n = 6). ITGA7 expression was examined in breast cancers using immunohistochemistry (n = 305), and its functional role was tested using siRNA in breast cancer cells. RESULTS Proportions of BCSCs varied from 0 to 9.4%. 38 genes were significantly differentially expressed in BCSCs; genes were enriched for functions in vessel morphogenesis, motility, and metabolism. ITGA7 was found to be significantly downregulated in BCSCs, and low expression significantly correlated with reduced survival in patients treated with chemotherapy, and with chemoresistance in breast cancer cells in vitro. CONCLUSIONS This study is the first to define the molecular profile of BCSCs from a range of primary breast cancers. ITGA7 acts as a predictive marker for chemotherapy response, in accordance with its downregulation in BCSCs.
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Affiliation(s)
- Noha Gwili
- grid.9909.90000 0004 1936 8403School of Medicine, University of Leeds, Leeds, UK ,grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Stacey J. Jones
- grid.9909.90000 0004 1936 8403School of Medicine, University of Leeds, Leeds, UK ,grid.415967.80000 0000 9965 1030Department of Breast Surgery, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Waleed Al Amri
- grid.416132.30000 0004 1772 5665Department of Histopathology and Cytopathology, The Royal Hospital, Muscat, Oman
| | - Ian M. Carr
- grid.9909.90000 0004 1936 8403School of Medicine, University of Leeds, Leeds, UK
| | - Sarah Harris
- grid.9909.90000 0004 1936 8403School of Physics and Astronomy, University of Leeds, Leeds, UK
| | - Brian V. Hogan
- grid.415967.80000 0000 9965 1030Department of Breast Surgery, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - William E. Hughes
- grid.414235.50000 0004 0619 2154Children’s Medical Research Institute, Westmead, NSW Australia ,grid.1005.40000 0004 4902 0432St. Vincent’s Clinical School, University of New South Wales, Sydney, Australia
| | - Baek Kim
- grid.415967.80000 0000 9965 1030Department of Breast Surgery, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Fiona E. Langlands
- Department of Breast Surgery, Bradford Teaching Hospitals NHS Trust, Bradford, UK
| | | | - Arindam Pramanik
- grid.9909.90000 0004 1936 8403School of Medicine, University of Leeds, Leeds, UK
| | - James L. Thorne
- grid.9909.90000 0004 1936 8403School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Eldo T. Verghese
- grid.443984.6Department of Histopathology, St. James’s University Hospital, Leeds, UK
| | - Geoff Wells
- grid.83440.3b0000000121901201School of Pharmacy, University College London, London, UK
| | - Mervat Hamza
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Layla Younis
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Nevine M. F. El Deeb
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Thomas A. Hughes
- grid.9909.90000 0004 1936 8403School of Medicine, University of Leeds, Leeds, UK
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Almasmoum H. The Roles of Transmembrane Mucins Located on Chromosome 7q22.1 in Colorectal Cancer. Cancer Manag Res 2021; 13:3271-3280. [PMID: 33883940 PMCID: PMC8053700 DOI: 10.2147/cmar.s299089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/16/2021] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common types of cancers. It is associated with a poor prognosis and high mortality. The role of mucins (MUCs) in colon tumorigenesis is unclear, but it might be significant in the progression of malignancy. Some mucins, such as MUC1 and MUC13, act as oncogenes, whereas others, such as MUC2 and MUC6, are tumor suppressors. However, there are still mucins with unidentified roles in CRC. In this review, we discuss the reported roles of mucins in CRC. Moreover, we review the capability of the mucin family to serve as a sensitive and specific histopathological marker for the early diagnosis of CRC. Lastly, the role of mucin genes clustered on chromosome 7q22 in CRC and other cancers is also discussed.
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Affiliation(s)
- Hussain Almasmoum
- Laboratory Medicine Department, Faculty of Applied Medical Science, Umm Al-Qura University, Makkah, 7607, Saudi Arabia
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Inhibition of interferon-signalling halts cancer-associated fibroblast-dependent protection of breast cancer cells from chemotherapy. Br J Cancer 2021; 124:1110-1120. [PMID: 33398063 PMCID: PMC7960738 DOI: 10.1038/s41416-020-01226-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Triple negative breast cancers (TNBC) have poor prognoses despite aggressive treatment with cytotoxic chemotherapy. Cancer-associated fibroblasts (CAFs) are prominent in tumour stroma. Our hypothesis was that CAFs modulate chemotherapy sensitivity. METHODS TNBC cells and breast fibroblasts were cultured; survival after chemotherapeutics was assessed using luciferase or clonogenic assays. Signalling was investigated using transcriptomics, reporters, recombinant proteins and blocking antibodies. Clinical relevance was investigated using immunohistochemistry. RESULTS Breast CAFs dose-dependently protected TNBC cell lines MDA-MB-231 and MDA-MB-157, but not MDA-MB-468s, from chemotherapy. CAF-induced protection was associated with interferon (IFN) activation. CAFs were induced to express IFNβ1 by chemotherapy and TNBC co-culture, leading to paracrine activation in cancer cells. Recombinant IFNs were sufficient to protect MDA-MB-231 and MDA-MB-157 but not MDA-MB-468 cells. In TNBC patients, IFNβ1 expression in CAFs correlated with cancer cell expression of MX1, a marker of activated IFN signalling. High expression of IFNβ1 (CAFs) or MX1 (tumour cells) correlated with reduced survival after chemotherapy, especially in claudin-low tumours (which MDA-MB-231 and MDA-MB-157 cells represent). Antibodies that block IFN receptors reduced CAF-dependent chemoprotection. CONCLUSIONS CAF-induced activation of IFN signalling in claudin-low TNBCs results in chemoresistance. Inhibition of this pathway represents a novel method to improve breast cancer outcomes.
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The Unique Biology behind the Early Onset of Breast Cancer. Genes (Basel) 2021; 12:genes12030372. [PMID: 33807872 PMCID: PMC8000244 DOI: 10.3390/genes12030372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 01/19/2023] Open
Abstract
Breast cancer commonly affects women of older age; however, in developing countries, up to 20% of breast cancer cases present in young women (younger than 40 years as defined by oncology literature). Breast cancer in young women is often defined to be aggressive in nature, usually of high histological grade at the time of diagnosis and negative for endocrine receptors with poor overall survival rate. Several researchers have attributed this aggressive nature to a hidden unique biology. However, findings in this aspect remain controversial. Thus, in this article, we aimed to review published work addressing somatic mutations, chromosome copy number variants, single nucleotide polymorphisms, differential gene expression, microRNAs and gene methylation profile of early-onset breast cancer, as well as its altered pathways resulting from those aberrations. Distinct biology behind early-onset of breast cancer was clear among estrogen receptor-positive and sporadic cases. However, further research is needed to determine and validate specific novel markers, which may help in customizing therapy for this group of patients.
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12
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Identification of candidate mediators of chemoresponse in breast cancer through therapy-driven selection of somatic variants. Breast Cancer Res Treat 2020; 183:607-616. [PMID: 32734521 PMCID: PMC7497675 DOI: 10.1007/s10549-020-05836-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022]
Abstract
Purpose More than a third of primary breast cancer patients are treated with cytotoxic chemotherapy, typically without guidance from predictive markers. Increased use of neoadjuvant chemotherapy provides opportunities for identification of molecules associated with treatment response, by comparing matched tumour samples before and after therapy. Our hypothesis was that somatic variants of increased prevalence after therapy promote resistance, while variants with reduced prevalence cause sensitivity. Methods We performed systematic analyses of matched pairs of cancer exomes from primary oestrogen receptor-positive/HER2-negative breast cancers (n = 6) treated with neoadjuvant epirubicin/cyclophosphamide. We identified candidate genes as mediators of chemotherapy response by consistent subclonal changes in somatic variant prevalence through therapy, predicted variant impact on gene function, and enrichment of specific functional pathways. Influence of candidate genes on breast cancer outcome was tested using publicly available breast cancer expression data (n = 1903). Results We identified 14 genes as the strongest candidate mediators of chemoresponse: TCHH, MUC17, ARAP2, FLG2, ABL1, CENPF, COL6A3, DMBT1, ITGA7, PLXNA1, S100PBP, SYNE1, ZFHX4, and CACNA1C. Genes contained somatic variants showing prevalence changes in up to 4 patients, with up to 3 being predicted as damaging. Genes coding for extra-cellular matrix components or related signalling pathways were significantly over-represented among variants showing prevalence changes. Expression of 5 genes (TCHH, ABL1, CENPF, S100PBP, and ZFHX4) was significantly associated with patient survival. Conclusions Genomic analysis of paired pre- and post-therapy samples resulting from neoadjuvant therapy provides a powerful method for identification of mediators of response. Genes we identified should be assessed as predictive markers or targets in chemo-sensitization. Electronic supplementary material The online version of this article (10.1007/s10549-020-05836-7) contains supplementary material, which is available to authorized users.
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