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Lin L, Deng J, Yu J, Bauden M, Andersson R, Shen X, Ansari D, Xue X. Anoikis-related genes linked with patient outcome in pancreatic cancer. Gene 2024; 930:148868. [PMID: 39154969 DOI: 10.1016/j.gene.2024.148868] [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: 02/06/2024] [Revised: 08/01/2024] [Accepted: 08/14/2024] [Indexed: 08/20/2024]
Abstract
Anoikis is programmed cell death occurring upon cell detachment from the extracellular matrix. Cancer cells need to evade anoikis to be able to metastasize to distant sites. However, the molecular features and prognostic value of anoikis-related genes (ARGs) in pancreatic cancer remain unclear. In this study, we utilized transcriptome data from the TCGA and GSE102238 databases to identify 64 ARGs significantly associated with prognosis. We used the "ConsensusClusterPlus" R package to stratify patients into high and low-risk prognostic subgroups. The KEGG and GSEA analyses revealed that the clusters with poor prognosis were enriched for the ECM receptor interaction pathway, the TP53 signaling pathway, and the galactose metabolism pathway, and that the cell cycle pathway was upregulated. A prognostic model consisting of seven ARGs (SERPINE1, EGF, E2F1, MSLN, RAB27B, ETV7, MST1) was constructed using LASSO regression and when combined with clinicopathological parameters using Cox regression, a prognostic Nomogram was created, which demonstrated high prognostic utility. Among the biomarker candidates, we report ETV7 as a novel, independent prognostic marker in pancreatic cancer. ETV7 was highly expressed in KRAS and TP53 co-occurrent mutant TCGA patients, indicating that it may be regulated by the two major driver genes of pancreatic cancer. Therefore, targeting ETV7 could be a potential focus for future therapeutic studies.
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Affiliation(s)
- Lizhi Lin
- Department of Surgery, Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden; Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jing Deng
- Department of Basic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jiaye Yu
- Department of Basic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Monika Bauden
- Department of Surgery, Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Roland Andersson
- Department of Surgery, Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Xian Shen
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Daniel Ansari
- Department of Surgery, Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden.
| | - Xiangyang Xue
- Department of Basic Medicine, Wenzhou Medical University, Wenzhou, China.
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Roy M, Hussain F. Mitigation of Breast Cancer Cells' Invasiveness via Down Regulation of ETV7, Hippo, and PI3K/mTOR Pathways by Vitamin D3 Gold-Nanoparticles. Int J Mol Sci 2024; 25:5348. [PMID: 38791386 PMCID: PMC11120902 DOI: 10.3390/ijms25105348] [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: 01/27/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Metastasis in breast cancer is the major cause of death in females (about 30%). Based on our earlier observation that Vitamin D3 downregulates mTOR, we hypothesized that Vitamin D3 conjugated to gold nanoparticles (VD3-GNPs) reduces breast cancer aggressiveness by downregulating the key cancer controller PI3K/AKT/mTOR. Western blots, migration/invasion assays, and other cell-based, biophysical, and bioinformatics studies are used to study breast cancer cell aggressiveness and nanoparticle characterization. Our VD3-GNP treatment of breast cancer cells (MCF-7 and MDA-MB-231) significantly reduces the aggressiveness (cancer cell migration and invasion rates > 45%) via the simultaneous downregulation of ETV7 and the Hippo pathway. Consistent with our hypothesis, we, indeed, found a downregulation of the PI3K/AKT/mTOR pathway. It is surprising that the extremely low dose of VD3 in the nano formulation (three orders of magnitude lower than in earlier studies) is quite effective in the alteration of cancer invasiveness and cell signaling pathways. Clearly, VD3-GNPs are a viable candidate for non-toxic, low-cost treatment for reducing breast cancer aggressiveness.
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Affiliation(s)
- Moumita Roy
- Mechanical Engineering Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Fazle Hussain
- Mechanical Engineering Department, Texas Tech University, Lubbock, TX 79409, USA
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3
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Turkarslan S, He Y, Hothi P, Murie C, Nicolas A, Kannan K, Park JH, Pan M, Awawda A, Cole ZD, Shapiro MA, Stuhlmiller TJ, Lee H, Patel AP, Cobbs C, Baliga NS. An atlas of causal and mechanistic drivers of interpatient heterogeneity in glioma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305380. [PMID: 38633778 PMCID: PMC11023657 DOI: 10.1101/2024.04.05.24305380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Grade IV glioma, formerly known as glioblastoma multiforme (GBM) is the most aggressive and lethal type of brain tumor, and its treatment remains challenging in part due to extensive interpatient heterogeneity in disease driving mechanisms and lack of prognostic and predictive biomarkers. Using mechanistic inference of node-edge relationship (MINER), we have analyzed multiomics profiles from 516 patients and constructed an atlas of causal and mechanistic drivers of interpatient heterogeneity in GBM (gbmMINER). The atlas has delineated how 30 driver mutations act in a combinatorial scheme to causally influence a network of regulators (306 transcription factors and 73 miRNAs) of 179 transcriptional "programs", influencing disease progression in patients across 23 disease states. Through extensive testing on independent patient cohorts, we share evidence that a machine learning model trained on activity profiles of programs within gbmMINER significantly augments risk stratification, identifying patients who are super-responders to standard of care and those that would benefit from 2 nd line treatments. In addition to providing mechanistic hypotheses regarding disease prognosis, the activity of programs containing targets of 2 nd line treatments accurately predicted efficacy of 28 drugs in killing glioma stem-like cells from 43 patients. Our findings demonstrate that interpatient heterogeneity manifests from differential activities of transcriptional programs, providing actionable strategies for mechanistically characterizing GBM from a systems perspective and developing better prognostic and predictive biomarkers for personalized medicine.
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Xu B, Sun H, Liu S, Liao L, Song X, Wu Y, Hou Y, Jin W. IFI35 limits antitumor immunity in triple-negative breast cancer via CCL2 secretion. Oncogene 2024; 43:693-702. [PMID: 38216673 PMCID: PMC10907302 DOI: 10.1038/s41388-023-02934-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: 08/06/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 01/14/2024]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with poor prognosis due to the lack of therapeutic targets. Although immunotherapy brings survival benefits to patients diagnosed with TNBC, it remains limited and treatment resistance is widespread. Here we demonstrate that IFI35 is highly expressed in tumor tissues and can be induced by Interferon-γ in a time-dependent and concentration-dependent manner in breast cancer cells. In xenograft models, we reveal that IFI35 dramatically increases myeloid-derived suppressor cells infiltration in tumors, along with depletion and anergy of CD8+T cells. IFI35 ablation leads to prolonged survival of the mice. Mechanistically, RNA-sequencing reveals that IFI35 promotes CCL2 secretion, resulting in the remodeling of TNBC immune microenvironment. Ablation of IFI35 promotes the infiltration of effector CD8+T cells, and thereby sensitizes TNBC to anti-PD-1 immunotherapy. Our data suggest that IFI35 limits antitumor immunity and may be expected to become a new immunotherapy target in TNBC.
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Affiliation(s)
- Baojin Xu
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Breast Surgery, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, 110042, China
| | - Hefen Sun
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Simeng Liu
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Li Liao
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiaoqing Song
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yi Wu
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yifeng Hou
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wei Jin
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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5
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Aracena KA, Lin YL, Luo K, Pacis A, Gona S, Mu Z, Yotova V, Sindeaux R, Pramatarova A, Simon MM, Chen X, Groza C, Lougheed D, Gregoire R, Brownlee D, Boye C, Pique-Regi R, Li Y, He X, Bujold D, Pastinen T, Bourque G, Barreiro LB. Epigenetic variation impacts individual differences in the transcriptional response to influenza infection. Nat Genet 2024; 56:408-419. [PMID: 38424460 DOI: 10.1038/s41588-024-01668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
Humans display remarkable interindividual variation in their immune response to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we performed in-depth genetic, epigenetic and transcriptional profiling on primary macrophages derived from individuals of European and African ancestry before and after infection with influenza A virus. We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to influenza A virus across individuals. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation, with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape can be genetically controlled, even more than gene expression. Lastly, among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, while the remaining genetic variants impact epigenetic marks, stressing the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.
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Affiliation(s)
| | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Alain Pacis
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Saideep Gona
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zepeng Mu
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Vania Yotova
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Renata Sindeaux
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | | | | | - Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
| | - David Lougheed
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Romain Gregoire
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - David Brownlee
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Yang Li
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - David Bujold
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- McGill Genome Centre, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Genomic Medicine Center, Children's Mercy, Kansas City, MO, USA
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada.
- McGill Genome Centre, Montreal, Quebec, Canada.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
| | - Luis B Barreiro
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
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6
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Chai B, Li Y, Guo Y, Zhang Z, Jia K, Chai X, Suo Y. ETV7 promotes colorectal cancer progression through upregulation of IFIT3. Funct Integr Genomics 2024; 24:8. [PMID: 38200280 PMCID: PMC10781848 DOI: 10.1007/s10142-023-01282-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: 10/22/2023] [Revised: 12/04/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024]
Abstract
Members of the E26 transformation-specific (ETS) variant transcription factor family act as either tumor suppressors or oncogenic factors in numerous types of cancer. ETS variant transcription factor 7 (ETV7) participates in the development of malignant tumors, whereas its involvement in colorectal cancer (CRC) is less clear. In this study, The Cancer Genome Atlas (TCGA) and immunochemistry staining were applied to check the clinical relevance of ETV7 and interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) in CRC patients. Overexpression and knockdown of ETV7 and IFIT3 were conducted by transfecting the cells with pCDNA3.1 plasmids and siRNAs, respectively. Western blotting was used to detect the protein expression of ETV7 in CRC cells. Cell Counting Kit-8, cell colony formation, and Transwell assays, as well as flow cytometry, were used to evaluate the proliferation, migration, cell cycle, and apoptosis of CRC cells. Furthermore, western blotting, RT-qPCR, and luciferase assay were used to explore the regulation of ETV7 on IFIT3. Rescue assay was used to investigate the significance of ETV7/IFIT3 axis on CRC progression. We found that ETV7 was upregulated in CRC tissues and cells. Overexpression of ETV7 stimulated the proliferation, migration, and cell cycle amplification, and reduced the apoptosis of CRC cells. Downregulation of ETV7 exerted the opposite effect on CRC cell progression. Moreover, we demonstrated that ETV7 stimulated the transcription activity, the mRNA and protein expression of IFIT3 in CRC cells. There was a positive correlation between ETV7 and IFIT3 in CRC patients. IFIT3 knockdown reversed the promotive effect exerted by overexpression of ETV7 on the amplification and migration of CRC cells. By contrast, overexpression of IFIT3 blocked the inhibitory effect of ETV7-targeting siRNA. In summary, ETV7 induces progression of CRC by activating the transcriptional expression of IFIT3. The EVT7/IFIT3 axis may be a novel target for CRC therapy.
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Affiliation(s)
- Bao Chai
- Department of Gastroenterology, Shanxi Academy of Medical Science, Shanxi Bethune Hospital, Taiyuan, China
| | - Yanjun Li
- Department of Surgery, Shanxi Academy of Medical Science, Shanxi Bethune Hospital, Taiyuan, China
| | - Yarong Guo
- Department of Oncology, The First Affiliated Hospital of Shanxi Medical University, 85 South Jiefang Road, TaiyuanTaiyuan, 030001, Shanxi Province, China.
| | - Zhuowei Zhang
- Medical Imaging Department, Shanxi Medical University, Taiyuan, China
| | - Kai Jia
- Department of Surgery, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, China
| | - Xinhao Chai
- Department of Oncology, The First Affiliated Hospital of Shanxi Medical University, 85 South Jiefang Road, TaiyuanTaiyuan, 030001, Shanxi Province, China
| | - Yuhong Suo
- Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, Taiyuan, China
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7
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Peta KT, Durandt C, van Heerden MB, Joubert AM, Pepper MS, Ambele MA. Effect of 2-methoxyestradiol treatment on early- and late-stage breast cancer progression in a mouse model. Cell Biochem Funct 2023; 41:898-911. [PMID: 37649158 PMCID: PMC10947225 DOI: 10.1002/cbf.3842] [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: 05/11/2023] [Revised: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
The prevalence of breast cancer (BC) continues to increase and is the leading cause of cancer deaths in many countries. Numerous in vitro and in vivo studies have demonstrated that 2-methoxyestradiol (2-ME) has antiproliferative and antiangiogenic effects in BC, thereby inhibiting tumour growth and metastasis. We compared the effect of 2-ME in early- and late-stage BC using a transgenic mouse model-FVB/N-Tg(MMTV-PyVT)-of spontaneously development of aggressive mammary carcinoma with lung metastasis. Mice received 100 mg/kg 2-ME treatment immediately when palpable mammary tumours were identified (early-stage BC; Experimental group 1) and 28 days after palpable mammary tumours were detected (late-stage BC; Experimental group 2). 2-ME was administered via oral gavage three times a week for 28 days after initiation of treatment, whereas control mice received the vehicle containing 10% dimethyl sulfoxide and 90% sunflower oil for the same duration as the treatment group. Mammary tumours were measured weekly over the 28 days and at termination, blood, mammary and lung tissue were collected for analysis. Mice with a tumour volume threshold of 4000 mm3 were killed before the treatment regime was completed. 2-ME treatment of early-stage BC led to lower levels of mammary tumour necrosis, whereas tumour mass and volume were increased. Additionally, necrotic lesions and anti-inflammatory CD163-expressing cells were more frequent in pulmonary metastatic tumours in this group. In contrast, 2-ME treatment of late-stage BC inhibited tumour growth over the 28-day period and resulted in increased CD3+ cell number and tumour necrosis. Furthermore, 2-ME treatment slowed down pulmonary metastasis but did not increase survival of late-stage BC mice. Besides late-stage tumour necrosis, none of the other results were statistically significant. This study demonstrates that 2-ME treatment has an antitumour effect on late-stage BC, however, with no increase in survival rate, whereas the treatment failed to demonstrate any benefit in early-stage BC.
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Affiliation(s)
- Kimberly T. Peta
- Department of Immunology, Institute for Cellular and Molecular Medicine; South African Medical Research Council Extramural Unit for Stem Cell Research and Therapy; Faculty of Health SciencesUniversity of PretoriaArcadiaSouth Africa
| | - Chrisna Durandt
- Department of Immunology, Institute for Cellular and Molecular Medicine; South African Medical Research Council Extramural Unit for Stem Cell Research and Therapy; Faculty of Health SciencesUniversity of PretoriaArcadiaSouth Africa
| | - Marlene B. van Heerden
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Faculty of Health SciencesUniversity of PretoriaPretoriaSouth Africa
| | - Anna M. Joubert
- Department of Physiology, School of Medicine, Faculty of Health SciencesUniversity of PretoriaPretoriaSouth Africa
| | - Michael S. Pepper
- Department of Immunology, Institute for Cellular and Molecular Medicine; South African Medical Research Council Extramural Unit for Stem Cell Research and Therapy; Faculty of Health SciencesUniversity of PretoriaArcadiaSouth Africa
| | - Melvin A. Ambele
- Department of Immunology, Institute for Cellular and Molecular Medicine; South African Medical Research Council Extramural Unit for Stem Cell Research and Therapy; Faculty of Health SciencesUniversity of PretoriaArcadiaSouth Africa
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Faculty of Health SciencesUniversity of PretoriaPretoriaSouth Africa
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8
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Lin F, Ke ZB, Xue YT, Chen JY, Cai H, Lin YZ, Li XD, Wei Y, Xue XY, Xu N. A novel CD8 + T cell-related gene signature for predicting the prognosis and immunotherapy efficacy in bladder cancer. Inflamm Res 2023; 72:1665-1687. [PMID: 37578544 DOI: 10.1007/s00011-023-01772-6] [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: 05/25/2023] [Revised: 05/25/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
OBJECTIVE To identify CD8+ T cell-related molecular clusters and establish a novel gene signature for predicting the prognosis and efficacy of immunotherapy in bladder cancer (BCa). METHODS Transcriptome and clinical data of BCa samples were obtained from the Cancer Genome Atlas (TCGA) and GEO databases. The CD8+ T cell-related genes were screened through the CIBERSORT algorithm and correlation analysis. Consensus clustering analysis was utilized to identified CD8+ T cell-related molecular clusters. A novel CD8+ T cell-related prognostic model was developed using univariate Cox regression analysis and Lasso regression analysis. Internal and external validations were performed and the validity of the model was validated in a real-world cohort. Finally, preliminary experimental verifications were carried out to verify the biological functions of SH2D2A in bladder cancer. RESULTS A total of 52 CD8+ T cell-related prognostic genes were screened and two molecular clusters with notably diverse immune cell infiltration, prognosis and clinical features were developed. Then, a novel CD8+ T cell-related prognostic model was constructed. The patients with high-risk scores exhibited a significantly worse overall survival in training, test, whole TCGA and validating cohort. The AUC was 0.766, 0.725, 0.739 and 0.658 in the four cohorts sequentially. Subgroup analysis suggested that the novel prognostic model has a robust clinical application for selecting high-risk patients. Finally, we confirmed that patients in the low-risk group might benefit more from immunotherapy or chemotherapy, and validated the prognostic model in a real-world immunotherapy cohort. Preliminary experiment showed that SH2D2A was capable of attenuating proliferation, migration and invasion of BCa cells. CONCLUSIONS CD8+ T cell-related molecular clusters were successfully identified. Besides, a novel CD8+ T cell-related prognostic model with an excellent predictive performance in predicting survival rates and immunotherapy efficacy of BCa was developed.
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Affiliation(s)
- Fei Lin
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Zhi-Bin Ke
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yu-Ting Xue
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Jia-Yin Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Hai Cai
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yun-Zhi Lin
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xiao-Dong Li
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yong Wei
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xue-Yi Xue
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
| | - Ning Xu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Urology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
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9
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McCaffrey TA, Toma I, Yang Z, Katz R, Reiner J, Mazhari R, Shah P, Falk Z, Wargowsky R, Goldman J, Jones D, Shtokalo D, Antonets D, Jepson T, Fetisova A, Jaatinen K, Ree N, Ri M. RNAseq profiling of blood from patients with coronary artery disease: Signature of a T cell imbalance. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY PLUS 2023; 4:100033. [PMID: 37303712 PMCID: PMC10256136 DOI: 10.1016/j.jmccpl.2023.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Background Cardiovascular disease had a global prevalence of 523 million cases and 18.6 million deaths in 2019. The current standard for diagnosing coronary artery disease (CAD) is coronary angiography either by invasive catheterization (ICA) or computed tomography (CTA). Prior studies employed single-molecule, amplification-independent RNA sequencing of whole blood to identify an RNA signature in patients with angiographically confirmed CAD. The present studies employed Illumina RNAseq and network co-expression analysis to identify systematic changes underlying CAD. Methods Whole blood RNA was depleted of ribosomal RNA (rRNA) and analyzed by Illumina total RNA sequencing (RNAseq) to identify transcripts associated with CAD in 177 patients presenting for elective invasive coronary catheterization. The resulting transcript counts were compared between groups to identify differentially expressed genes (DEGs) and to identify patterns of changes through whole genome co-expression network analysis (WGCNA). Results The correlation between Illumina amplified RNAseq and the prior SeqLL unamplified RNAseq was quite strong (r = 0.87), but there was only 9 % overlap in the DEGs identified. Consistent with the prior RNAseq, the majority (93 %) of DEGs were down-regulated ~1.7-fold in patients with moderate to severe CAD (>20 % stenosis). DEGs were predominantly related to T cells, consistent with known reductions in Tregs in CAD. Network analysis did not identify pre-existing modules with a strong association with CAD, but patterns of T cell dysregulation were evident. DEGs were enriched for transcripts associated with ciliary and synaptic transcripts, consistent with changes in the immune synapse of developing T cells. Conclusions These studies confirm and extend a novel mRNA signature of a Treg-like defect in CAD. The pattern of changes is consistent with stress-related changes in the maturation of T and Treg cells, possibly due to changes in the immune synapse.
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Affiliation(s)
- Timothy A. McCaffrey
- Department of Medicine, Division of Genomic Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
- The St. Laurent Institute, 317 New Boston Street, Woburn, MA 01801, United States of America
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
- True Bearing Diagnostics, 2450 Virginia Avenue, Washington, DC 20037, United States of America
| | - Ian Toma
- Department of Medicine, Division of Genomic Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
- Department of Clinical Research and Leadership, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
- True Bearing Diagnostics, 2450 Virginia Avenue, Washington, DC 20037, United States of America
| | - Zhaoqing Yang
- Department of Medicine, Division of Genomic Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
| | - Richard Katz
- Department of Medicine, Division of Cardiology, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
| | - Jonathan Reiner
- Department of Medicine, Division of Cardiology, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
| | - Ramesh Mazhari
- Department of Medicine, Division of Cardiology, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
| | - Palak Shah
- INOVA Heart and Vascular Institute, 3300 Gallows Road, Fairfax, VA 22042, United States of America
| | - Zachary Falk
- Department of Medicine, Division of Genomic Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
| | - Richard Wargowsky
- Department of Medicine, Division of Genomic Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
| | - Jennifer Goldman
- Department of Medicine, Division of Genomic Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
| | - Dan Jones
- SeqLL, Inc., 3 Federal Street, Billerica, MA 01821, United States of America
| | - Dmitry Shtokalo
- The St. Laurent Institute, 317 New Boston Street, Woburn, MA 01801, United States of America
- A.P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentyeva Ave, Novosibirsk 630090, Russia
| | - Denis Antonets
- The St. Laurent Institute, 317 New Boston Street, Woburn, MA 01801, United States of America
| | - Tisha Jepson
- Department of Medicine, Division of Genomic Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
- The St. Laurent Institute, 317 New Boston Street, Woburn, MA 01801, United States of America
- True Bearing Diagnostics, 2450 Virginia Avenue, Washington, DC 20037, United States of America
| | - Anastasia Fetisova
- Department of Medicine, Division of Genomic Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
| | - Kevin Jaatinen
- Department of Medicine, Division of Genomic Medicine, The George Washington University, 2300 I Street NW, Washington, DC 20037, United States of America
| | - Natalia Ree
- Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, Kalingrad 236040, Russia
| | - Maxim Ri
- The St. Laurent Institute, 317 New Boston Street, Woburn, MA 01801, United States of America
- A.P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentyeva Ave, Novosibirsk 630090, Russia
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10
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Meškytė EM, Pezzè L, Bartolomei L, Forcato M, Bocci IA, Bertalot G, Barbareschi M, Oliveira-Ferrer L, Bisio A, Bicciato S, Baltriukienė D, Ciribilli Y. ETV7 reduces inflammatory responses in breast cancer cells by repressing the TNFR1/NF-κB axis. Cell Death Dis 2023; 14:263. [PMID: 37041130 PMCID: PMC10089821 DOI: 10.1038/s41419-023-05718-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 04/13/2023]
Abstract
The transcription factor ETV7 is an oncoprotein that is up-regulated in all breast cancer (BC) types. We have recently demonstrated that ETV7 promoted breast cancer progression by increasing cancer cell proliferation and stemness and was also involved in the development of chemo- and radio-resistance. However, the roles of ETV7 in breast cancer inflammation have yet to be studied. Gene ontology analysis previously performed on BC cells stably over-expressing ETV7 demonstrated that ETV7 was involved in the suppression of innate immune and inflammatory responses. To better decipher the involvement of ETV7 in these signaling pathways, in this study, we identified TNFRSF1A, encoding for the main receptor of TNF-α, TNFR1, as one of the genes down-regulated by ETV7. We demonstrated that ETV7 directly binds to the intron I of this gene, and we showed that the ETV7-mediated down-regulation of TNFRSF1A reduced the activation of NF-κB signaling. Furthermore, in this study, we unveiled a potential crosstalk between ETV7 and STAT3, another master regulator of inflammation. While it is known that STAT3 directly up-regulates the expression of TNFRSF1A, here we demonstrated that ETV7 reduces the ability of STAT3 to bind to the TNFRSF1A gene via a competitive mechanism, recruiting repressive chromatin remodelers, which results in the repression of its transcription. The inverse correlation between ETV7 and TNFRSF1A was confirmed also in different cohorts of BC patients. These results suggest that ETV7 can reduce the inflammatory responses in breast cancer through the down-regulation of TNFRSF1A.
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Affiliation(s)
- Erna Marija Meškytė
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Laura Pezzè
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Alia Therapeutics, s.r.l., Trento, Italy
| | - Laura Bartolomei
- Laboratory of Radiobiology, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Irene Adelaide Bocci
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institut für Zellbiologie, Universitätsklinikum Essen, Essen, Germany
| | - Giovanni Bertalot
- Unità Operativa Multizonale di Anatomia Patologica, APSS, Trento, Italy
- Centre for Medical Sciences (CISMed), University of Trento, Trento, Italy
| | - Mattia Barbareschi
- Unità Operativa Multizonale di Anatomia Patologica, APSS, Trento, Italy
- Centre for Medical Sciences (CISMed), University of Trento, Trento, Italy
| | | | - Alessandra Bisio
- Laboratory of Radiobiology, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daiva Baltriukienė
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Yari Ciribilli
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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11
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Wang Y, Huang Z, Sun M, Huang W, Xia L. ETS transcription factors: Multifaceted players from cancer progression to tumor immunity. Biochim Biophys Acta Rev Cancer 2023; 1878:188872. [PMID: 36841365 DOI: 10.1016/j.bbcan.2023.188872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/18/2023] [Accepted: 01/28/2023] [Indexed: 02/26/2023]
Abstract
The E26 transformation specific (ETS) family comprises 28 transcription factors, the majority of which are involved in tumor initiation and development. Serving as a group of functionally heterogeneous gene regulators, ETS factors possess a structurally conserved DNA-binding domain. As one of the most prominent families of transcription factors that control diverse cellular functions, ETS activation is modulated by multiple intracellular signaling pathways and post-translational modifications. Disturbances in ETS activity often lead to abnormal changes in oncogenicity, including cancer cell survival, growth, proliferation, metastasis, genetic instability, cell metabolism, and tumor immunity. This review systematically addresses the basics and advances in studying ETS factors, from their tumor relevance to clinical translational utility, with a particular focus on elucidating the role of ETS family in tumor immunity, aiming to decipher the vital role and clinical potential of regulation of ETS factors in the cancer field.
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Affiliation(s)
- Yufei Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Zhao Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China
| | - Mengyu Sun
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China.
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China.
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12
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Ervin EH, French R, Chang CH, Pauklin S. Inside the stemness engine: Mechanistic links between deregulated transcription factors and stemness in cancer. Semin Cancer Biol 2022; 87:48-83. [PMID: 36347438 DOI: 10.1016/j.semcancer.2022.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/07/2022]
Abstract
Cell identity is largely determined by its transcriptional profile. In tumour, deregulation of transcription factor expression and/or activity enables cancer cell to acquire a stem-like state characterised by capacity to self-renew, differentiate and form tumours in vivo. These stem-like cancer cells are highly metastatic and therapy resistant, thus warranting a more complete understanding of the molecular mechanisms downstream of the transcription factors that mediate the establishment of stemness state. Here, we review recent research findings that provide a mechanistic link between the commonly deregulated transcription factors and stemness in cancer. In particular, we describe the role of master transcription factors (SOX, OCT4, NANOG, KLF, BRACHYURY, SALL, HOX, FOX and RUNX), signalling-regulated transcription factors (SMAD, β-catenin, YAP, TAZ, AP-1, NOTCH, STAT, GLI, ETS and NF-κB) and unclassified transcription factors (c-MYC, HIF, EMT transcription factors and P53) across diverse tumour types, thereby yielding a comprehensive overview identifying shared downstream targets, highlighting unique mechanisms and discussing complexities.
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Affiliation(s)
- Egle-Helene Ervin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Rhiannon French
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Chao-Hui Chang
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
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13
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Lin J, Liu L, Zheng F, Chen S, Yang W, Li J, Mo S, Zeng DY. Exploration the global single-cell ecological landscape of adenomyosis-related cell clusters by single-cell RNA sequencing. Front Genet 2022; 13:1020757. [DOI: 10.3389/fgene.2022.1020757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Adenomyosis (AM) is a common benign uterine disease that threatens the normal life of patients. Cells associated with microenvironmental immune ecology are crucial in AM, although they are not as well understood at the cellular level.Methods: Single-cell sequencing (scRNA-seq) data were used to construct an AM global single-cell map, to further identify relevant cell clusters and infer chromosomal copy number variation (CNV) in AM samples. The biological functions of cell clusters were explored and cellular evolutionary processes were inferred by enrichment analysis and pseudotime analysis. In addition, a gene regulatory network (GRN) analysis was constructed to explore the regulatory role of transcription factors in AM progression.Results: We obtained the expression profiles of 42260 cells and identified 10 cell clusters. By comparing the differences in cell components between AM patients and controls, we found that significant abundance of endometrial cells (EC), epithelial cells (Ep), endothelial cells (En), and smooth muscle cells (SMC) in AM patients. Cell clusters with high CNV levels possessing tumour-like features existed in the ectopic endometrium samples. Moreover, the Ep clusters were significantly involved in leukocyte transendothelial cell migration and apoptosis, suggesting an association with cell apoptosis and migration. En clusters were mainly involved in pathways in cancer and apoptosis, indicating that En has certain malignant features.Conclusion: This study identified cell clusters with immune-related features, investigated the changes in the immune ecology of the microenvironment of these cells during AM, and provided a new strategy for the treatment of AM.
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14
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Restrepo P, Bhalla S, Ghodke-Puranik Y, Aleman A, Leshchenko V, Melnekoff DT, Agte S, Jiang J, Madduri D, Richter J, Richard S, Chari A, Cho HJ, Jagannath S, Walker CJ, Landesman Y, Laganà A, Parekh S. A Three-Gene Signature Predicts Response to Selinexor in Multiple Myeloma. JCO Precis Oncol 2022; 6:e2200147. [PMID: 35704796 PMCID: PMC10530420 DOI: 10.1200/po.22.00147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/21/2022] [Accepted: 05/12/2022] [Indexed: 12/28/2022] Open
Abstract
PURPOSE Selinexor is the first selective inhibitor of nuclear export to be approved for the treatment of relapsed or refractory multiple myeloma (MM). Currently, there are no known genomic biomarkers or assays to help select MM patients at higher likelihood of response to selinexor. Here, we aimed to characterize the transcriptomic correlates of response to selinexor-based therapy. METHODS We performed RNA sequencing on CD138+ cells from the bone marrow of 100 patients with MM who participated in the BOSTON study, followed by differential gene expression and pathway analysis. Using the differentially expressed genes, we used cox proportional hazard models to identify a gene signature predictive of response to selinexor, followed by validation in external cohorts. RESULTS The three-gene signature predicts response to selinexor-based therapy in patients with MM in the BOSTON cohort. Then, we validated this gene signature in 64 patients from the STORM cohort of triple-class refractory MM and additionally in an external cohort of 35 patients treated in a real-world setting outside of clinical trials. We found that the signature tracks with both depth and duration of response, and it also validates in a different tumor type using a cohort of pretreatment tumors from patients with recurrent glioblastoma. Furthermore, the genes involved in the signature, WNT10A, DUSP1, and ETV7, reveal a potential mechanism through upregulated interferon-mediated apoptotic signaling that may prime tumors to respond to selinexor-based therapy. CONCLUSION In this study, we present a present a novel, three-gene expression signature that predicts selinexor response in MM. This signature has important clinical relevance as it could identify patients with cancer who are most likely to benefit from treatment with selinexor-based therapy.
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Affiliation(s)
- Paula Restrepo
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sherry Bhalla
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Adolfo Aleman
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Violetta Leshchenko
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - David T. Melnekoff
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sarita Agte
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Joy Jiang
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Deepu Madduri
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Janssen Pharmaceutical Research and Development, Raritan, NJ
| | - Joshua Richter
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Shambavi Richard
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ajai Chari
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Hearn Jay Cho
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Multiple Myeloma Research Foundation, Norwalk, CT
| | - Sundar Jagannath
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | - Alessandro Laganà
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Samir Parekh
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
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15
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Huang JL, Chen SY, Lin CS. Targeting Cancer Stem Cells through Epigenetic Modulation of Interferon Response. J Pers Med 2022; 12:jpm12040556. [PMID: 35455671 PMCID: PMC9027081 DOI: 10.3390/jpm12040556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/26/2022] [Accepted: 03/30/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer stem cells (CSCs) are a small subset of cancer cells and are thought to play a critical role in the initiation and maintenance of tumor mass. CSCs exhibit similar hallmarks to normal stem cells, such as self-renewal, differentiation, and homeostasis. In addition, CSCs are equipped with several features so as to evade anticancer mechanisms. Therefore, it is hard to eliminate CSCs by conventional anticancer therapeutics that are effective at clearing bulk cancer cells. Interferons are innate cytokines and are the key players in immune surveillance to respond to invaded pathogens. Interferons are also crucial for adaptive immunity for the killing of specific aliens including cancer cells. However, CSCs usually evolve to escape from interferon-mediated immune surveillance and to shape the niche as a “cold” tumor microenvironment (TME). These CSC characteristics are related to their unique epigenetic regulations that are different from those of normal and bulk cancer cells. In this review, we introduce the roles of epigenetic modifiers, focusing on LSD1, BMI1, G9a, and SETDB1, in contributing to CSC characteristics and discussing the interplay between CSCs and interferon response. We also discuss the emerging strategy for eradicating CSCs by targeting these epigenetic modifiers, which can elevate cytosolic nuclei acids, trigger interferon response, and reshape a “hot” TME for improving cancer immunotherapy. The key epigenetic and immune genes involved in this crosstalk can be used as biomarkers for precision oncology.
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Affiliation(s)
- Jau-Ling Huang
- Department of Bioscience Technology, College of Health Science, Chang Jung Christian University, Tainan 711, Taiwan;
| | - Si-Yun Chen
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Chang-Shen Lin
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Correspondence:
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16
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Tadijan A, Precazzini F, Hanžić N, Radić M, Gavioli N, Vlašić I, Ozretić P, Pinto L, Škreblin L, Barban G, Slade N, Ciribilli Y. Altered Expression of Shorter p53 Family Isoforms Can Impact Melanoma Aggressiveness. Cancers (Basel) 2021; 13:cancers13205231. [PMID: 34680379 PMCID: PMC8533715 DOI: 10.3390/cancers13205231] [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: 09/27/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 02/05/2023] Open
Abstract
Cutaneous melanoma is the most aggressive form of skin cancer. Despite the significant advances in the management of melanoma in recent decades, it still represents a challenge for clinicians. The TP53 gene, the guardian of the genome, which is altered in more than 50% of human cancers, is rarely mutated in melanoma. More recently, researchers started to appreciate the importance of shorter p53 isoforms as potential modifiers of the p53-dependent responses. We analyzed the expression of p53 and p73 isoforms both at the RNA and protein level in a panel of melanoma-derived cell lines with different TP53 and BRAF status, in normal conditions or upon treatment with common anti-cancer DNA damaging agents or targeted therapy. Using lentiviral vectors, we also generated stable clones of H1299 p53 null cells over-expressing the less characterized isoforms Δ160p53α, Δ160p53β, and Δ160p53γ. Further, we obtained two melanoma-derived cell lines resistant to BRAF inhibitor vemurafenib. We observed that melanoma cell lines expressed a wide array of p53 and p73 isoforms, with Δ160p53α as the most variable one. We demonstrated for the first time that Δ160p53α, and to a lesser extent Δ160p53β, can be recruited on chromatin, and that Δ160p53γ can localize in perinuclear foci; moreover, all Δ160p53 isoforms can stimulate proliferation and in vitro migration. Lastly, vemurafenib-resistant melanoma cells showed an altered expression of p53 and p73 isoforms, namely an increased expression of potentially pro-oncogenic Δ40p53β and a decrease in tumor-suppressive TAp73β. We therefore propose that p53 family isoforms can play a role in melanoma cells' aggressiveness.
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Affiliation(s)
- Ana Tadijan
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Francesca Precazzini
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
- Laboratory of RNA Biology and Biotechnology, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy
| | - Nikolina Hanžić
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Martina Radić
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Nicolò Gavioli
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
| | - Ignacija Vlašić
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Petar Ozretić
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Lia Pinto
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
| | - Lidija Škreblin
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Giulia Barban
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
| | - Neda Slade
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
- Correspondence: (N.S.); (Y.C.)
| | - Yari Ciribilli
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
- Correspondence: (N.S.); (Y.C.)
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