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Mares-Quiñones MD, Galán-Vásquez E, Pérez-Rueda E, Pérez-Ishiwara DG, Medel-Flores MO, Gómez-García MDC. Identification of modules and key genes associated with breast cancer subtypes through network analysis. Sci Rep 2024; 14:12350. [PMID: 38811600 PMCID: PMC11137066 DOI: 10.1038/s41598-024-61908-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Breast cancer is the most common malignancy in women around the world. Intratumor and intertumoral heterogeneity persist in mammary tumors. Therefore, the identification of biomarkers is essential for the treatment of this malignancy. This study analyzed 28,143 genes expressed in 49 breast cancer cell lines using a Weighted Gene Co-expression Network Analysis to determine specific target proteins for Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes. Sixty-five modules were identified, of which five were characterized as having a high correlation with breast cancer subtypes. Genes overexpressed in the tumor were found to participate in the following mechanisms: regulation of the apoptotic process, transcriptional regulation, angiogenesis, signaling, and cellular survival. In particular, we identified the following genes, considered as hubs: IFIT3, an inhibitor of viral and cellular processes; ETS1, a transcription factor involved in cell death and tumorigenesis; ENSG00000259723 lncRNA, expressed in cancers; AL033519.3, a hypothetical gene; and TMEM86A, important for regulating keratinocyte membrane properties, considered as a key in Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes, respectively. The modules and genes identified in this work can be used to identify possible biomarkers or therapeutic targets in different breast cancer subtypes.
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Affiliation(s)
- María Daniela Mares-Quiñones
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Mexico
| | - D Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Del Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico.
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Hogh-Binder SA, Klein D, Wolfsperger F, Huber SM, Hennenlotter J, Stenzl A, Rudner J. Protein Levels of Anti-Apoptotic Mcl-1 and the Deubiquitinase USP9x Are Cooperatively Upregulated during Prostate Cancer Progression and Limit Response of Prostate Cancer Cells to Radiotherapy. Cancers (Basel) 2023; 15:cancers15092496. [PMID: 37173959 PMCID: PMC10177233 DOI: 10.3390/cancers15092496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Radiotherapy constitutes an important therapeutic option for prostate cancer. However, prostate cancer cells often acquire resistance during cancer progression, limiting the cytotoxic effects of radiotherapy. Among factors regulating sensitivity to radiotherapy are members of the Bcl-2 protein family, known to regulate apoptosis at the mitochondrial level. Here, we analyzed the role of anti-apoptotic Mcl-1 and USP9x, a deubiquitinase stabilizing Mcl-1 protein levels, in prostate cancer progression and response to radiotherapy. METHODS Changes in Mcl-1 and USP9x levels during prostate cancer progression were determined by immunohistochemistry. Neutralization of Mcl-1 and USP9x was achieved by siRNA-mediated knockdown. We analyzed Mcl-1 stability after translational inhibition by cycloheximide. Cell death was determined by flow cytometry using an exclusion assay of mitochondrial membrane potential-sensitive dye. Changes in the clonogenic potential were examined by colony formation assay. RESULTS Protein levels of Mcl-1 and USP9x increased during prostate cancer progression, and high protein levels correlated with advanced prostate cancer stages. The stability of Mcl-1 reflected Mcl-1 protein levels in LNCaP and PC3 prostate cancer cells. Moreover, radiotherapy itself affected Mcl-1 protein turnover in prostate cancer cells. Particularly in LNCaP cells, the knockdown of USP9x expression reduced Mcl-1 protein levels and increased sensitivity to radiotherapy. CONCLUSION Posttranslational regulation of protein stability was often responsible for high protein levels of Mcl-1. Moreover, we demonstrated that deubiquitinase USP9x as a factor regulating Mcl-1 levels in prostate cancer cells, thus limiting cytotoxic response to radiotherapy.
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Affiliation(s)
- Sophia A Hogh-Binder
- Department of Radiation Oncology, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
| | - Diana Klein
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Virchowstr. 173, 45147 Essen, Germany
| | - Frederik Wolfsperger
- Department of Radiation Oncology, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
| | - Stephan M Huber
- Department of Radiation Oncology, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
| | - Justine Rudner
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Virchowstr. 173, 45147 Essen, Germany
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Radmanić L, Korać P, Gorenec L, Šimičić P, Bodulić K, Vince A, Lepej SŽ. Distinct Expression Patterns of Genes Coding for Biological Response Modifiers Involved in Inflammatory Responses and Development of Fibrosis in Chronic Hepatitis C: Upregulation of SMAD-6 and MMP-8 and Downregulation of CAV-1, CTGF, CEBPB, PLG, TIMP-3, MMP-1, ITGA-1, ITGA-2 and LOX. Medicina (B Aires) 2022; 58:medicina58121734. [PMID: 36556936 PMCID: PMC9785468 DOI: 10.3390/medicina58121734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Background and Objectives: The aim of this study was to analyze the expression of genes on transcriptomic levels involved in inflammatory immune responses and the development of fibrosis in patients with chronic hepatitis C. Materials and Methods: Expression patterns of 84 selected genes were analyzed with real-time quantitative RT PCR arrays in the peripheral blood of treatment-naive patients with chronic hepatitis C and healthy controls. The panel included pro- and anti-fibrotic genes, genes coding for extracellular matrix (EMC) structural constituents and remodeling enzymes, cell adhesion molecules, inflammatory cytokines, chemokines and growth factors, signal transduction members of the transforming growth factor- beta (TGF-ß) superfamily, transcription factors, and genes involved in epithelial to mesenchymal transition. Results: The expression of SMAD-6 coding for a signal transduction TGF-beta superfamily member as well as MMP-8 coding for an ECM protein were significantly increased in CHC patients compared with controls. Conclusions: Chronic hepatitis C was also characterized by a significant downregulation of a set of genes including CAV-1, CTGF, TIMP-3, MMP-1, ITGA-1, LOX, ITGA-2, PLG and CEBPB encoding various biological response modifiers and transcription factors. Our results suggest that chronic hepatitis C is associated with distinct patterns of gene expression modulation in pathways associated with the regulation of immune responses and development of fibrosis.
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Affiliation(s)
- Leona Radmanić
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases, “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
| | - Petra Korać
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia
| | - Lana Gorenec
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases, “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
| | - Petra Šimičić
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases, “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
| | - Kristian Bodulić
- Research Department, University Hospital for Infectious Diseases, “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
| | - Adriana Vince
- Department of Viral Hepatitis, University Hospital for Infectious Diseases, “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, HR-10000 Zagreb, Croatia
| | - Snježana Židovec Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases, “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-2826-625
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Tan X, Liu Z, Wang Y, Wu Z, Zou Y, Luo S, Tang Y, Chen D, Yuan G, Yao K. miR-138-5p-mediated HOXD11 promotes cell invasion and metastasis by activating the FN1/MMP2/MMP9 pathway and predicts poor prognosis in penile squamous cell carcinoma. Cell Death Dis 2022; 13:816. [PMID: 36151071 PMCID: PMC9508180 DOI: 10.1038/s41419-022-05261-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 01/23/2023]
Abstract
The presence and extent of regional lymph node and distant metastasis are the most fatal prognostic factors in penile squamous cell carcinoma (PSCC). However, the available biomarkers and detailed mechanisms underlying the metastasis of PSCC remain elusive. Here, we explored the expression landscape of HOX genes in twelve paired PSCC tissues, including primary tumors, metastatic lymph nodes and corresponding normal tissues, and highlighted that HOXD11 was indispensable in the progression of PSCC. HOXD11 was upregulated in PSCC cell lines and tumors, especially in metastatic lymph nodes. High HOXD11 expression was associated with aggressive features, such as advanced pN stages, extranodal extension, pelvic lymph node and distant metastasis, and predicted poor survival. Furthermore, tumorigenesis assays demonstrated that knockdown of HOXD11 not only inhibited the capability of cell proliferation, invasion and tumor growth but also reduced the burden of metastatic lymph nodes. Further mechanistic studies indicated that miR-138-5p was a tumor suppressor in PSCC by inhibiting the translation of HOXD11 post-transcriptionally through binding to the 3' untranslated region. Furthermore, HOXD11 activated the transcription of FN1 to decompose the extracellular matrix and to promote epithelial mesenchymal transition-like phenotype metastasis via FN1/MMP2/MMP9 pathways. Our study revealed that HOXD11 is a promising prognostic biomarker and predicts advanced disease with poor outcomes, which could serve as a potential therapeutic target for PSCC.
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Affiliation(s)
- Xingliang Tan
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Zhenhua Liu
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yanjun Wang
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Zhiming Wu
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yuantao Zou
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Sihao Luo
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yi Tang
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Dong Chen
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Gangjun Yuan
- grid.190737.b0000 0001 0154 0904Department of Urology Oncological Surgery, Chongqing University Cancer Hospital, Chongqing, China ,grid.190737.b0000 0001 0154 0904Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Kai Yao
- grid.488530.20000 0004 1803 6191Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in Southern China, Guangzhou, China ,grid.488530.20000 0004 1803 6191Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
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Clinical and Novel Biomarkers in Penile Carcinoma: A Prospective Review. J Pers Med 2022; 12:jpm12091364. [PMID: 36143149 PMCID: PMC9502223 DOI: 10.3390/jpm12091364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Penile carcinoma is a rare urological neoplasia in men compared to other more common tumors, such as prostate, kidney, or bladder tumors. However, this neoplasm continues to affect a large number of patients worldwide, with developing countries presenting the highest incidence and mortality rates. Important risk factors such as the human papilloma virus, a factor affecting a large number of patients, have been described; however, few studies have evaluated screening programs in populations at risk for this disease, which severely affects the quality of life of older men. The management of these patients is usually complex, requiring surgical interventions that are not without risk and that have a great impact on the functionality of the male reproductive system. In addition, in cases of disseminated disease or with significant locoregional involvement, patients are evaluated by multidisciplinary oncological committees that can adjust the application of aggressive neoadjuvant or adjuvant chemotherapy on numerous occasions without clear improvement in survival. Chemotherapy regimens are usually aggressive, and unlike in other urological neoplasms, few advances have been made in the use of immunotherapy in these patients. The study of serological and histological biomarkers may help to better understand the underlying pathophysiology of these tumors and select patients who have a higher risk of metastatic progression. Similarly, the analysis of molecular markers will improve the availability of targeted therapies for the management of patients with disseminated disease that would benefit prognosis. Therefore, the purpose of this article is to summarize the main advances that have occurred in the development of serological and histological markers and their therapeutic implications in patients diagnosed with penile carcinoma, explaining the limitations that have been observed and analyzing future perspectives in the management of this disease.
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Li K, Le X, Wang J, Fan C, Sun J. Tumor Location May Independently Predict Survival in Patients With M0 Squamous Cell Carcinoma of the Penis. Front Oncol 2022; 12:927088. [PMID: 35865480 PMCID: PMC9294313 DOI: 10.3389/fonc.2022.927088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundTo determine the association between tumor location and both clinicopathological characteristics and the survival of patients with M0 squamous cell carcinoma of the penis (SCCP).MethodsData of 455 patients diagnosed with M0 SCCP between 1975 and 2018 were collected from the Surveillance, Epidemiology, and End Results (SEER) database of the United States National Cancer Institute. The effects of tumor location on overall survival (OS) and penile carcinoma-specific survival (PCSS) were analyzed using the Kaplan–Meier method. The Cox proportional hazards regression model was used to determine the impact of tumor location on PCSS.ResultsSCCP was more likely to occur in the prepuce or glans (90%). Although no significant difference was observed between the OS of patients with M0 SCCP in the prepuce or glans and those with M0 SCCP in the body of the penis (p = 0.307), the former had better PCSS (p = 0.024). Moreover, M0 SCCP in the prepuce or glans was also significantly associated with better PCSS in patients with advanced age (age ≥ 60 years, p = 0.011), other ethnicities (p = 0.003), T2–T4 stage (p = 0.036), larger tumors (≥3 cm, p = 0.001), no regional lymph nodes removed (p = 0.044), and radical surgery (p = 0.027). Multivariate analysis confirmed that tumor location is an independent prognostic factor for patients with M0 SCCP [hazard ratio (HR) 1.881, p = 0.026].ConclusionsTumor location is an independent prognostic factor for patients with M0 SCCP, and tumors in the prepuce or glans portend better PCSS.
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Affiliation(s)
| | | | | | - Caibin Fan
- *Correspondence: Caibin Fan, ; Jian Sun,
| | - Jian Sun
- *Correspondence: Caibin Fan, ; Jian Sun,
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Abstract
ABSTRACT Genitourinary (GU) cancers have greatly benefited from immunotherapy treatments, such as immune checkpoint inhibitors. However, the durable clinical response rate for these agents remains relatively low, calling for more innovative immunotherapy approaches. Adoptive cell therapy has shown a significant advancement in the treatment of cancer in recent years and represents a great potential for the treatment of GU cancers. This review summarizes the current advancements in cellular therapy strategies for the treatment of renal cell carcinoma, bladder cancer, and prostate and penile cancers. Further, current and past clinical trials of adoptive cell therapy in GU tumors are reviewed. Finally, a perspective on the future of cell therapy in GU tumors is discussed.
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