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Wu XH, Huang XY, You Q, Zhu JM, Qiu QRS, Lin YZ, Xu N, Wei Y, Xue XY, Chen YH, Chen SH, Zheng QS. Liquid-liquid phase separation-related genes associated with prognosis, tumor microenvironment characteristics, and tumor cell features in bladder cancer. Clin Transl Oncol 2024:10.1007/s12094-024-03719-7. [PMID: 39269596 DOI: 10.1007/s12094-024-03719-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024]
Abstract
OBJECTIVE This study aimed to explore the Liquid-liquid phase separation (LLPS)-related genes associated with the prognosis of bladder cancer (BCa) and assess the potential application of LLPS-related prognostic signature for predicting prognosis in BCa patients. METHODS Clinical information and transcriptome data of BCa patients were extracted from the Cancer Genome Atlas-BLCA (TCGA-BLCA) database and the GSE13507 database. Furthermore, 108 BCa patients who received treatment at our institution were subjected to a retrospective analysis. The least absolute shrinkage and selection operator (LASSO) analysis was performed to develop an LLPS-related prognostic signature for BCa. The CCK8, wound healing and Transwell assays were performed. RESULTS Based on 62 differentially expressed LLPS-related genes (DELRGs), three DELRGs were screened by LASSO analysis including kallikrein-related peptidase 5 (KLK5), monoacylglycerol O-acyltransferase 2 (MOGAT2) and S100 calcium-binding protein A7 (S100A7). Based on three DELRGs, a novel LLPS-related prognostic signature was constructed for individualized prognosis assessment. Kaplan-Meier curve analyses showed that LLPS-related prognostic signature was significantly correlated with overall survival (OS) of BCa. ROC analyses demonstrated the LLPS-related prognostic signature performed well in predicting the prognosis of BCa patients in the training group (the area under the curve (AUC) = 0.733), which was externally verified in the validation cohort 1 (AUC = 0.794) and validation cohort 2 (AUC = 0.766). Further experiments demonstrated that inhibiting KLK5 could affect the proliferation, migration, and invasion of BCa cells. CONCLUSIONS In this study, a novel LLPS-related prognostic signature was successfully developed and validated, demonstrating strong performance in predicting the prognosis of BCa patients.
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Affiliation(s)
- Xiao-Hui Wu
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Xu-Yun Huang
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Qi You
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Jun-Ming Zhu
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Qian-Ren-Shun Qiu
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Yun-Zhi Lin
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, 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 Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
- Fujian Key Laboratory of Precision Medicine for Cancer, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Yong Wei
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Xue-Yi Xue
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
- Fujian Key Laboratory of Precision Medicine for Cancer, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Ye-Hui Chen
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China
| | - Shao-Hao Chen
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China.
| | - Qing-Shui Zheng
- Department of Urology, Urology Research Institute, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Fuzhou, 350005, China.
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Chakraborty S, Mishra J, Roy A, Niharika, Manna S, Baral T, Nandi P, Patra S, Patra SK. Liquid-liquid phase separation in subcellular assemblages and signaling pathways: Chromatin modifications induced gene regulation for cellular physiology and functions including carcinogenesis. Biochimie 2024; 223:74-97. [PMID: 38723938 DOI: 10.1016/j.biochi.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024]
Abstract
Liquid-liquid phase separation (LLPS) describes many biochemical processes, including hydrogel formation, in the integrity of macromolecular assemblages and existence of membraneless organelles, including ribosome, nucleolus, nuclear speckles, paraspeckles, promyelocytic leukemia (PML) bodies, Cajal bodies (all exert crucial roles in cellular physiology), and evidence are emerging day by day. Also, phase separation is well documented in generation of plasma membrane subdomains and interplay between membranous and membraneless organelles. Intrinsically disordered regions (IDRs) of biopolymers/proteins are the most critical sticking regions that aggravate the formation of such condensates. Remarkably, phase separated condensates are also involved in epigenetic regulation of gene expression, chromatin remodeling, and heterochromatinization. Epigenetic marks on DNA and histones cooperate with RNA-binding proteins through their IDRs to trigger LLPS for facilitating transcription. How phase separation coalesces mutant oncoproteins, orchestrate tumor suppressor genes expression, and facilitated cancer-associated signaling pathways are unravelling. That autophagosome formation and DYRK3-mediated cancer stem cell modification also depend on phase separation is deciphered in part. In view of this, and to linchpin insight into the subcellular membraneless organelle assembly, gene activation and biological reactions catalyzed by enzymes, and the downstream physiological functions, and how all these events are precisely facilitated by LLPS inducing organelle function, epigenetic modulation of gene expression in this scenario, and how it goes awry in cancer progression are summarized and presented in this article.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Subhajit Patra
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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Peng W, Li Y, Cheng B, Cao M, Liu L, Yang Y, Bai S, Xiong S, Chen W, Zhao Y. Liquid-liquid phase separation-related lncRNA prognostic signature and ZNF32-AS2 as a novel biomarker in hepatocellular carcinoma. Comput Biol Med 2024; 169:107975. [PMID: 38199212 DOI: 10.1016/j.compbiomed.2024.107975] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND Liquid-liquid phase separation (LLPS) enhances oncogenic signaling pathways and advances cancer progression, and has been proposed as a promising cancer biomarker and intervention target. Nevertheless, doubts remain about the prognostic importance of LLPS-related long non-coding RNAs (lncRNAs) in hepatocellular carcinoma (HCC). METHODS An LLPS-related lncRNA prognostic signature was generated by drivers and regulators of LLPS, and was validated in external datasets. The underlying genetic changes and functional enrichment of the signature were assessed. The drug sensitivity and response to immunotherapy were predicted in patients categorized as high-risk and low-risk. Clinical samples, phase separation agonist, and dispersant were used to identify lncRNAs with the most significant expression change. Cancer cells with ZNF32-AS2 expression regulation were subjected to colony formation assay, scratch test assay, migration and invasion assay, sorafenib resistance assay, and xenograft tumor model. RESULTS The signature of LLPS-related hub lncRNAs identified through Weighted Gene Co-Expression Network Analysis showed outstanding performance in training and external validation cohorts consistently, and the molecular characteristics varied between different risk groups. Potential drugs for high-risk individuals were identified, and low-risk individuals demonstrated a more favorable reaction to immunotherapy. ZNF32-AS2 showed the most significant expression change in phase separation agonist and dispersant treatment. ZNF32-AS2 promoted the proliferation, mobility, and sorafenib resistance of liver cancer cells. CONCLUSIONS The LLPS-related lncRNA signature may help assess prognosis and predict treatment efficacy in clinical settings. LLPS-related ZNF32-AS2 promoted the proliferation, mobility, and sorafenib resistance of liver cancer cells, and may be a novel potential biomarker in hepatocellular carcinoma.
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Affiliation(s)
- Wang Peng
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yanling Li
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bin Cheng
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Mengdie Cao
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Luyao Liu
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yilei Yang
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shuya Bai
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Si Xiong
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Chen
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuchong Zhao
- Department of Gastroenterology and Hepatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Li M, Zhang Y, Zhao J, Wang D. The global landscape and research trend of phase separation in cancer: a bibliometric analysis and visualization. Front Oncol 2023; 13:1170157. [PMID: 37333812 PMCID: PMC10272442 DOI: 10.3389/fonc.2023.1170157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
Background Cancer as a deathly disease with high prevalence has impelled researchers to investigate its causative mechanisms in the search for effective therapeutics. Recently, the concept of phase separation has been introduced to biological science and extended to cancer research, which helps reveal various pathogenic processes that have not been identified before. As a process of soluble biomolecules condensed into solid-like and membraneless structures, phase separation is associated with multiple oncogenic processes. However, there are no bibliometric characteristics for these results. To provide future trends and identify new frontiers in this field, a bibliometric analysis was conducted in this study. Methods The Web of Science Core Collection (WoSCC) was used to search for literature on phase separation in cancer from 1/1/2009 to 31/12/2022. After screening the literature, statistical analysis and visualization were carried out by the VOSviewer software (version 1.6.18) and Citespace software (Version 6.1.R6). Results A total of 264 publications, covering 413 organizations and 32 countries, were published in 137 journals, with an increasing trend in publication and citation numbers per year. The USA and China were the two countries with the largest number of publications, and the University of Chinese Academy of Sciences was the most active institution based on the number of articles and cooperations. Molecular Cell was the most frequent publisher with high citations and H-index. The most productive authors were Fox AH, De Oliveira GAP, and Tompa P. Overlay, whilst few authors had a strong collaboration with each other. The combined analysis of concurrent and burst keywords revealed that the future research hotspots of phase separation in cancer were related to tumor microenvironments, immunotherapy, prognosis, p53, and cell death. Conclusion Phase separation-related cancer research remained in the hot streak period and exhibited a promising outlook. Although inter-agency collaboration existed, cooperation among research groups was rare, and no author dominated this field at the current stage. Investigating the interfaced effects between phase separation and tumor microenvironments on carcinoma behaviors, and constructing relevant prognoses and therapeutics such as immune infiltration-based prognosis and immunotherapy might be the next research trend in the study of phase separation and cancer.
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Affiliation(s)
- Mengzhu Li
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Institute of Endocrine and Metabolic Diseases, Jinan, China
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging (Shandong First Medical University), Ministry of Education, Jinan, China
| | - Yizhan Zhang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Institute of Endocrine and Metabolic Diseases, Jinan, China
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging (Shandong First Medical University), Ministry of Education, Jinan, China
| | - Jiajun Zhao
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Institute of Endocrine and Metabolic Diseases, Jinan, China
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging (Shandong First Medical University), Ministry of Education, Jinan, China
| | - Dawei Wang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Institute of Endocrine and Metabolic Diseases, Jinan, China
- Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging (Shandong First Medical University), Ministry of Education, Jinan, China
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Radhakrishnan S, Martin CA, Rammohan A, Vij M, Chandrasekar M, Rela M. Significance of nucleologenesis, ribogenesis, and nucleolar proteome in the pathogenesis and recurrence of hepatocellular carcinoma. Expert Rev Gastroenterol Hepatol 2023; 17:363-378. [PMID: 36919496 DOI: 10.1080/17474124.2023.2191189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION Emerging evidence suggests that enhanced ribosome biogenesis, increased size, and quantitative distribution of nucleoli are associated with dysregulated transcription, which in turn drives a cell into aberrant cellular proliferation and malignancy. Nucleolar alterations have been considered a prognostic histological marker for aggressive tumors. More recently, advancements in the understanding of chromatin network (nucleoplasm viscosity) regulated liquid-liquid phase separation mechanism of nucleolus formation and their multifunctional role shed light on other regulatory processes, apart from ribosomal biogenesis of the nucleolus. AREAS COVERED Using hepatocellular carcinoma as a model to study the role of nucleoli in tumor progression, we review the potential of nucleolus coalescence in the onset and development of tumors through non-ribosomal biogenesis pathways, thereby providing new avenues for early diagnosis and cancer therapy. EXPERT OPINION Molecular-based classifications have failed to identify the nucleolar-based molecular targets that facilitate cell-cycle progression. However, the algorithm-based tumor risk identification with high-resolution medical images suggests prominent nucleoli, karyotheca, and increased nucleus/cytoplasm ratio as largely associated with tumor recurrence. Nonetheless, the role of the non-ribosomal functions of nucleoli in tumorigenesis remains elusive. This clearly indicates the lacunae in the study of the nucleolar proteins pertaining to cancer. [Figure: see text].
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Affiliation(s)
| | | | - Ashwin Rammohan
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mukul Vij
- Department of Pathology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mani Chandrasekar
- Department of Oncology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mohamed Rela
- Cell Laboratory, National Foundation for Liver Research, Chennai, India
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
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Peng Z, Wang J, Guo J, Li X, Wang S, Xie Y, Jiang H, Wang Y, Wang M, Hu M, Li Q, Wang Y, Mi JQ, Liu Z. All-trans retinoic acid improves NSD2-mediated RARα phase separation and efficacy of anti-CD38 CAR T-cell therapy in multiple myeloma. J Immunother Cancer 2023; 11:jitc-2022-006325. [PMID: 36918219 PMCID: PMC10016253 DOI: 10.1136/jitc-2022-006325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Immunotherapies targeting CD38 have demonstrated salient efficacy in relapsed/refractory multiple myeloma (MM). However, loss of CD38 antigen and outgrowth of CD38 negative plasma cells have emerged as a major obstacle in clinics. All-trans retinoic acid (ATRA) has been reported to upregulate CD38 expression, but the mechanism and adaptive genetic background remain unexplored. METHODS The efficacy of ATRA in upregulating CD38 expression in MM cells is evaluated by flow cytometry. The interaction between NSD2 and the RARα is analyzed by immunoprecipitation, and the nuclear condensation of RARα is evaluated under laser confocal microscope. A graft model of MM is established in NOD.Cg-PrkdcscidIl2rgtm1Wjl /SzJ mice, and the tumor burden is assessed by in vivo fluorescence imaging. RESULTS We report that ATRA upregulates MM cells CD38 in a non-linear manner, which is t(4;14) translocation dependent, and t(4;14) translocation-induced NSD2 shows positive correlation with ATRA-induced level of, but not with basal level of CD38 expression. Mechanistically, NSD2 interacts with the ATRA receptor, RARα, and protects it from degradation. Meanwhile, NSD2 enhances the nuclear condensation of RARα and modifies the histone H3 dimethylation at lysine 36 on CD38 promoter. Knockdown of NSD2 attenuates the sensitization of MM against ATRA induced CD38 upregulation. Translationally, ATRA is prone to augment the efficacy of anti-CD38 CAR T cells in NSD2high MM cells in vitro and in vivo. CONCLUSION This study elucidates a mechanism of ATRA in regulating CD38 expression and expands the clinical potential of ATRA in improving immunotherapies against CD38 in patients with MM.Cite Now.
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Affiliation(s)
- Ziyi Peng
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Jingya Wang
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Jing Guo
- Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xin Li
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Sheng Wang
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Ying Xie
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongmei Jiang
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Yixuan Wang
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Mengqi Wang
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Meilin Hu
- School of Stomatology, Tianjin Medical University, Tianjin, China
| | - Qian Li
- Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yafei Wang
- Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jian-Qing Mi
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiqiang Liu
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China .,Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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From the Catastrophic Objective Irreproducibility of Cancer Research and Unavoidable Failures of Molecular Targeted Therapies to the Sparkling Hope of Supramolecular Targeted Strategies. Int J Mol Sci 2023; 24:ijms24032796. [PMID: 36769134 PMCID: PMC9917659 DOI: 10.3390/ijms24032796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The unprecedented non-reproducibility of the results published in the field of cancer research has recently come under the spotlight. In this short review, we try to highlight some general principles in the organization and evolution of cancerous tumors, which objectively lead to their enormous variability and, consequently, the irreproducibility of the results of their investigation. This heterogeneity is also extremely unfavorable for the effective use of molecularly targeted medicine. Against the seemingly comprehensive background of this heterogeneity, we single out two supramolecular characteristics common to all tumors: the clustered nature of tumor interactions with their microenvironment and the formation of biomolecular condensates with tumor-specific distinctive features. We suggest that these features can form the basis of strategies for tumor-specific supramolecular targeted therapies.
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Miné-Hattab J, Liu S, Taddei A. Repair Foci as Liquid Phase Separation: Evidence and Limitations. Genes (Basel) 2022; 13:1846. [PMID: 36292731 PMCID: PMC9602295 DOI: 10.3390/genes13101846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 07/26/2023] Open
Abstract
In response to DNA double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less condensates or "foci". The formation of these foci and their disassembly within the proper time window are essential for genome integrity. However, how these membrane-less sub-compartments are formed, maintained and disassembled remains unclear. Recently, several studies across different model organisms proposed that DNA repair foci form via liquid phase separation. In this review, we discuss the current research investigating the physical nature of repair foci. First, we present the different models of condensates proposed in the literature, highlighting the criteria to differentiate them. Second, we discuss evidence of liquid phase separation at DNA repair sites and the limitations of this model to fully describe structures formed in response to DNA damage. Finally, we discuss the origin and possible function of liquid phase separation for DNA repair processes.
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Affiliation(s)
| | | | - Angela Taddei
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, CEDEX 05, 75248 Paris, France
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Wang J, Meng F, Mao F. Single cell sequencing analysis and transcriptome analysis constructed the liquid-liquid phase separation(LLPS)-related prognostic model for endometrial cancer. Front Oncol 2022; 12:1005472. [PMID: 36185238 PMCID: PMC9515536 DOI: 10.3389/fonc.2022.1005472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background Endometrial cancer is one of the most common gynecological tumors in developed countries. Our understanding of the pathogenesis of endometrial cancer and the changes in the immune microenvironment are still unclear. It is necessary to explore new biomarkers to guide the diagnosis and treatment of endometrial cancer. Methods The GEO database was used to download the endometrial cancer single cell sequencing dataset GSE173682. The UCSC database was used to download transcriptome sequencing data. The validation set was the transcriptome dataset GSE119041, which was retrieved from the GEO database. On the DrLLPS website, liquid-liquid phase separation-related genes can be downloaded. Relevant hub genes were found using weighted co-expression network analysis and dimension reduction clustering analysis. Prognostic models were built using Lasso regression and univariate COX regression. Analyses of immune infiltration were employed to investigate the endometrial cancer immunological microenvironment. The expression of model genes in endometrial cancer was confirmed using a PCR test. Results We created an LLPS-related predictive model for endometrial cancer by extensive study, and it consists of four genes: EIF2S2, SNRPC, PRELID1, and NDUFB9. Patients with endometrial cancer may be classified into high-risk and low-risk groups based on their risk scores, and those in the high-risk group had significantly worse prognoses (P<0.05). Additionally, there were notable variations in the immunological milieu between the groups at high and low risk. EIF2S2, SNRPC, PRELID1, and NDUFB9 were all up-regulated in endometrial cancer tissues, according to PCR results. Conclusions Our study can provide a certain reference for the diagnosis and treatment of endometrial cancer.
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Affiliation(s)
- Jiayang Wang
- Department of Radiotherapy, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
| | - Fei Meng
- Department of Gynaecology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
| | - Fei Mao
- Department of Urology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
- *Correspondence: Fei Mao,
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Sarvari P, Sarvari P, Ramírez-Díaz I, Mahjoubi F, Rubio K. Advances of Epigenetic Biomarkers and Epigenome Editing for Early Diagnosis in Breast Cancer. Int J Mol Sci 2022; 23:ijms23179521. [PMID: 36076918 PMCID: PMC9455804 DOI: 10.3390/ijms23179521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Epigenetic modifications are known to regulate cell phenotype during cancer progression, including breast cancer. Unlike genetic alterations, changes in the epigenome are reversible, thus potentially reversed by epi-drugs. Breast cancer, the most common cause of cancer death worldwide in women, encompasses multiple histopathological and molecular subtypes. Several lines of evidence demonstrated distortion of the epigenetic landscape in breast cancer. Interestingly, mammary cells isolated from breast cancer patients and cultured ex vivo maintained the tumorigenic phenotype and exhibited aberrant epigenetic modifications. Recent studies indicated that the therapeutic efficiency for breast cancer regimens has increased over time, resulting in reduced mortality. Future medical treatment for breast cancer patients, however, will likely depend upon a better understanding of epigenetic modifications. The present review aims to outline different epigenetic mechanisms including DNA methylation, histone modifications, and ncRNAs with their impact on breast cancer, as well as to discuss studies highlighting the central role of epigenetic mechanisms in breast cancer pathogenesis. We propose new research areas that may facilitate locus-specific epigenome editing as breast cancer therapeutics.
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Affiliation(s)
- Pourya Sarvari
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Frouzandeh Mahjoubi
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Correspondence:
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