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Jin X, Fu C, Qi J, Chen C. Revolutionary multi-omics analysis revealing prognostic signature of thyroid cancer and subsequent in vitro validation of SNAI1 in mediating thyroid cancer progression through EMT. Clin Exp Med 2024; 24:127. [PMID: 38869635 DOI: 10.1007/s10238-024-01387-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
Thyroid carcinoma (TC), the most commonly diagnosed malignancy of the endocrine system, has witnessed a significant rise in incidence over the past few decades. The integration of scRNA-seq with other sequencing approaches offers researchers a distinct perspective to explore mechanisms underlying TC progression. Therefore, it is crucial to develop a prognostic model for TC patients by utilizing a multi-omics approach. We acquired and processed transcriptomic data from the TCGA-THCA dataset, including mRNA expression profiles, lncRNA expression profiles, miRNA expression profiles, methylation chip data, gene mutation data, and clinical data. We constructed a tumor-related risk model using machine learning methods and developed a consensus machine learning-driven signature (CMLS) for accurate and stable prediction of TC patient outcomes. 2 strains of undifferentiated TC cell lines and 1 strain of PTC cell line were utilized for in vitro validation. mRNA, protein levels of hub genes, epithelial-mesenchymal transition (EMT)-associated phenotypes were detected by a series of in vitro experiments. We identified 3 molecular subtypes of TC based on integrated multi-omics clustering algorithms, which were associated with overall survival and displayed distinct molecular features. We developed a CMLS based on 28 hub genes to predict patient outcomes, and demonstrated that CMLS outperformed other prognostic models. TC patients of relatively lower CMLS score had significantly higher levels of T cells, B cells, and macrophages, indicating an immune-activated state. Fibroblasts were predominantly enriched in the high CMLS group, along with markers associated with immune suppression and evasion. We identified several drugs that could be suitable for patients with high CMLS, including Staurosporine_1034, Rapamycin_1084, gemcitabine, and topotecan. SNAI1 was elevated in both undifferentiated TC cell lines, comparing to PTC cells. Knockdown of SNAI1 reduced the cell proliferation and EMT phenotypes of undifferentiated TC cells. Our findings highlight the importance of multi-omics analysis in understanding the molecular subtypes and immune characteristics of TC, and provide a novel prognostic model and potential therapeutic targets for this disease. Moreover, we identified SNAI1 in mediating TC progression through EMT in vitro.
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Affiliation(s)
- Xin Jin
- Department of Breast Surgery, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, 311899, Zhejiang, China
| | - Chunlan Fu
- Department of Hematology, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, 311899, Zhejiang, China
| | - Jiahui Qi
- Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chuanzhi Chen
- Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
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Zeng X, Su H, Liu Z, Wang Y, Lu Z, Cheng S. Integrative analysis of the bladder cancer from a cell cycle NCAM1 perspective at both single cell and bulk resolution. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38581187 DOI: 10.1002/tox.24260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/06/2024] [Accepted: 03/23/2024] [Indexed: 04/08/2024]
Abstract
INTRODUCTION Bladder cancer (BLCA) is a prevalent and deadly form of urinary cancer, and there is a need for effective therapies, particularly for muscle-invasive bladder cancer (MIBC). Cell cycle inhibitors show promise in restoring control of the cell cycle in BLCA cells, but their clinical prognosis evaluation is limited. METHODS Transcriptome and scRNA-seq data were collected from the Cancer Genome Atlas Program (TCGA)-BLCA and GSE190888 cohort, respectively. R software and the Seurat package were used for data analysis, including cell quality control, dimensionality reduction, and identification of differentially expressed genes. Genes related to the cell cycle were obtained from the genecards website, and a protein-protein interaction network analysis was performed using cytoscape software. Functional enrichment analysis, immune infiltration analysis, drug sensitivity analysis, and molecular docking were conducted using various tools and packages. BLCA cell lines were cultured and transfected for in vitro experimental assays, including RT-qPCR analysis, and CCK-8 cell viability assays. RESULTS We identified 32 genes as independent risk or protective factors for BLCA prediction. Functional enrichment analysis revealed their involvement in cell cycle regulation, apoptosis, and various signaling pathways. Using these genes, we developed a nomogram for predicting BLCA survival, which displayed high prognosis stratification efficacy in BLCA patients. Four cell cycle associated key genes identified, including NCAM1, HBB, CKD6, and CTLA4. We also identified the main cell types in BLCA patients and investigated the functional differences between epithelial cells based on their expression levels of key genes. Furthermore, we observed a high positive correlative relationship between the infiltration of cancer-associated fibroblasts and the risk score value. Finally, we conducted in vitro experiments to demonstrate the suppressive role of NCAM1 in BLCA cell proliferation. CONCLUSION These findings suggest that cell cycle associated genes could serve as potential biomarkers for predicting BLCA prognosis and may represent therapeutic targets for the development of more effective therapies. Hopefully, these findings provide valuable insights into the molecular mechanisms and potential therapeutic targets in BLCA from the perspective of cell cycle. Moreover, NCAM1 was a novel cell proliferation suppressor in the BLCA carcinogenesis.
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Affiliation(s)
- Xiangju Zeng
- Department of Outpatient, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hao Su
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ziqi Liu
- Department of Acupuncture and Moxibustion, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Yinhuai Wang
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhijie Lu
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shunhua Cheng
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Teisseire M, Giuliano S, Pagès G. Combination of Anti-Angiogenics and Immunotherapies in Renal Cell Carcinoma Show Their Limits: Targeting Fibrosis to Break through the Glass Ceiling? Biomedicines 2024; 12:385. [PMID: 38397987 PMCID: PMC10886484 DOI: 10.3390/biomedicines12020385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
This review explores treating metastatic clear cell renal cell carcinoma (ccRCC) through current therapeutic modalities-anti-angiogenic therapies and immunotherapies. While these approaches represent the forefront, their limitations and variable patient responses highlight the need to comprehend underlying resistance mechanisms. We specifically investigate the role of fibrosis, prevalent in chronic kidney disease, influencing tumour growth and treatment resistance. Our focus extends to unravelling the intricate interplay between fibrosis, immunotherapy resistance, and the tumour microenvironment for effective therapy development. The analysis centres on connective tissue growth factor (CTGF), revealing its multifaceted role in ccRCC-promoting fibrosis, angiogenesis, and cancer progression. We discuss the potential of targeting CTGF to address the problem of fibrosis in ccRCC. Emphasising the crucial relationship between fibrosis and the immune system in ccRCC, we propose that targeting CTGF holds promise for overcoming obstacles to cancer treatment. However, we recognise that an in-depth understanding of the mechanisms and potential limitations is imperative and, therefore, advocate for further research. This is an essential prerequisite for the successful integration of CTGF-targeted therapies into the clinical landscape.
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Affiliation(s)
| | - Sandy Giuliano
- University Cote d’Azur (UCA), Institute for Research on Cancer and Aging of Nice, CNRS UMR 7284; INSERM U1081, Centre Antoine Lacassagne, 06189 Nice, France;
| | - Gilles Pagès
- University Cote d’Azur (UCA), Institute for Research on Cancer and Aging of Nice, CNRS UMR 7284; INSERM U1081, Centre Antoine Lacassagne, 06189 Nice, France;
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Franco-Valls H, Tusquets-Uxó E, Sala L, Val M, Peña R, Iaconcig A, Villarino Á, Jiménez-Arriola M, Massó P, Trincado JL, Eyras E, Muro AF, Otero J, García de Herreros A, Baulida J. Formation of an invasion-permissive matrix requires TGFβ/SNAIL1-regulated alternative splicing of fibronectin. Breast Cancer Res 2023; 25:143. [PMID: 37964360 PMCID: PMC10647173 DOI: 10.1186/s13058-023-01736-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: 11/08/2022] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND As in most solid cancers, the emergence of cells with oncogenic mutations in the mammary epithelium alters the tissue homeostasis. Some soluble factors, such as TGFβ, potently modify the behavior of healthy stromal cells. A subpopulation of cancer-associated fibroblasts expressing a TGFβ target, the SNAIL1 transcription factor, display myofibroblastic abilities that rearrange the stromal architecture. Breast tumors with the presence of SNAIL1 in the stromal compartment, and with aligned extracellular fiber, are associated with poor survival prognoses. METHODS We used deep RNA sequencing and biochemical techniques to study alternative splicing and human tumor databases to test for associations (correlation t-test) between SNAIL1 and fibronectin isoforms. Three-dimensional extracellular matrices generated from fibroblasts were used to study the mechanical properties and actions of the extracellular matrices on tumor cell and fibroblast behaviors. A metastatic mouse model of breast cancer was used to test the action of fibronectin isoforms on lung metastasis. RESULTS In silico studies showed that SNAIL1 correlates with the expression of the extra domain A (EDA)-containing (EDA+) fibronectin in advanced human breast cancer and other types of epithelial cancers. In TGFβ-activated fibroblasts, alternative splicing of fibronectin as well as of 500 other genes was modified by eliminating SNAIL1. Biochemical analyses demonstrated that SNAIL1 favors the inclusion of the EDA exon by modulating the activity of the SRSF1 splicing factor. Similar to Snai1 knockout fibroblasts, EDA- fibronectin fibroblasts produce an extracellular matrix that does not sustain TGFβ-induced fiber organization, rigidity, fibroblast activation, or tumor cell invasion. The presence of EDA+ fibronectin changes the action of metalloproteinases on fibronectin fibers. Critically, in an mouse orthotopic breast cancer model, the absence of the fibronectin EDA domain completely prevents lung metastasis. CONCLUSIONS Our results support the requirement of EDA+ fibronectin in the generation of a metastasis permissive stromal architecture in breast cancers and its molecular control by SNAIL1. From a pharmacological point of view, specifically blocking EDA+ fibronectin deposition could be included in studies to reduce the formation of a pro-metastatic environment.
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Affiliation(s)
- Héctor Franco-Valls
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Elsa Tusquets-Uxó
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Dr. Aiguader, 88, 08003, Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona, Spain
| | - Laura Sala
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Dr. Aiguader, 88, 08003, Barcelona, Spain
- National Institutes of Health: Intramural Research Program, Bethesda, MD, USA
| | - Maria Val
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Dr. Aiguader, 88, 08003, Barcelona, Spain
- Vall Hebron Institute of Research, Barcelona, Spain
| | - Raúl Peña
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Alessandra Iaconcig
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Álvaro Villarino
- Unitat Biofísica i Bioenginyeria, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Respiratorias, Madrid, Spain
| | - Martín Jiménez-Arriola
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Pere Massó
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Juan L Trincado
- Research Program of Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Eduardo Eyras
- Research Program of Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Andrés F Muro
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Jorge Otero
- Unitat Biofísica i Bioenginyeria, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Respiratorias, Madrid, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Dr. Aiguader, 88, 08003, Barcelona, Spain
- Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Josep Baulida
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Dr. Aiguader, 88, 08003, Barcelona, Spain.
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Abramicheva PA, Semenovich DS, Zorova LD, Pevzner IB, Sokolov IA, Popkov VA, Kazakov EP, Zorov DB, Plotnikov EY. Decreased renal expression of PAQR5 is associated with the absence of a nephroprotective effect of progesterone in a rat UUO model. Sci Rep 2023; 13:12871. [PMID: 37553369 PMCID: PMC10409855 DOI: 10.1038/s41598-023-39848-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
Fibrosis is a severe complication of chronic kidney disease (CKD). Progesterone, like other sex hormones, plays an important role in renal physiology, but its role in CKD is poorly understood. We investigated progesterone effect on renal fibrosis progression in the rat model of unilateral ureteral obstruction (UUO). Female rats were exposed to UUO, ovariectomy and progesterone administration after UUO with ovariectomy. Expression of key fibrosis markers, proinflammatory cytokines, levels of membrane-bound (PAQR5) and nuclear (PGR) progesterone receptors, and matrix metalloproteinase (MMP) activity were analyzed in the obstructed and intact rat kidney. In all groups exposed to UUO, decreased PAQR5 expression was observed in the obstructed kidney while in the contralateral kidney, it remained unaffected. We found increased mRNA levels for profibrotic COL1A1, FN1, MMP2, TIMP1, TIMP2, proinflammatory IL1α, IL1β, and IL18, as well as elevated α-SMA and MMP9 proteins, collagen deposition, and MMP2 activity in all UUO kidneys. Progesterone had slight or no effect on the change in these markers. Thus, we demonstrate for the first time diminished sensitivity of the kidney to progesterone associated with renal fibrosis due to a severe decrease in PAQR5 expression that was accompanied by the lack of nephroprotection in a rat UUO model.
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Affiliation(s)
- P A Abramicheva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234.
| | - D S Semenovich
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - L D Zorova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia, 117997
| | - I B Pevzner
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia, 117997
| | - I A Sokolov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
- Mendeleev University of Chemical Technology of Russia, Moscow, Russia, 125047
| | - V A Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia, 117997
- MSU Institute for Artificial Intelligence, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - E P Kazakov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - D B Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia, 117997
| | - E Y Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234.
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, Russia, 117997.
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Perryman L, Gray SG. Fibrosis in Mesothelioma: Potential Role of Lysyl Oxidases. Cancers (Basel) 2022; 14:cancers14040981. [PMID: 35205728 PMCID: PMC8870010 DOI: 10.3390/cancers14040981] [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: 01/18/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
Immunotherapies (such as checkpoint inhibitors) and standard chemotherapies (such as cisplatin) have limitations in the successful treatment of malignant pleural mesothelioma (MPM). Fibrosis is the accumulation of collagen in the extracellular matrix (ECM) of tissues, making them denser than that of healthy tissues and thereby affecting drug delivery and immune cell infiltration. Moreover, fibrosis severely affects the patient's breathing and quality of life. The production of collagen and its assembly is highly regulated by various enzymes such as lysyl oxidases. Many solid tumors aberrantly express the family of lysyl oxidases (LOX/LOXL). This review examines how LOX/LOXLs were found to be dysregulated in noncancerous and cancerous settings, discusses their roles in solid tumor fibrosis and pathogenesis and explores the role of fibrosis in the development and poor clinical outcomes of patients with MPM. We examine the current preclinical status of drugs targeting LOX/LOXLs and how the incorporation of such drugs may have therapeutic benefits in the treatment and management of patients with MPM.
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Affiliation(s)
- Lara Perryman
- Drug Discovery Department, Pharmaxis Ltd., Sydney, NSW 2086, Australia;
| | - Steven G. Gray
- Thoracic Oncology, Labmed Directorate, St James’s Hospital, D08 RX0X Dublin, Ireland
- Correspondence:
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Kidney Cancer and Chronic Kidney Disease: Too Close for Comfort. Biomedicines 2021; 9:biomedicines9121761. [PMID: 34944574 PMCID: PMC8699019 DOI: 10.3390/biomedicines9121761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 12/11/2022] Open
Abstract
Kidney cancer and chronic kidney disease are two renal pathologies with very different clinical management strategies and therapeutical options. Nonetheless, the cellular and molecular mechanisms underlying both conditions are closely related. Renal physiology is adapted to operate with a limited oxygen supply, making the kidney remarkably equipped to respond to hypoxia. This tightly regulated response mechanism is at the heart of kidney cancer, leading to the onset of malignant cellular phenotypes. Although elusive, the role of hypoxia in chronic kidney diseases is emerging as related to fibrosis, a pivotal factor in decaying renal function. The present review offers a perspective on the common biological traits shared between kidney cancer and chronic kidney disease and the available and prospective therapies for both conditions.
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