1
|
Silonov SA, Mokin YI, Nedelyaev EM, Smirnov EY, Kuznetsova IM, Turoverov KK, Uversky VN, Fonin AV. On the Prevalence and Roles of Proteins Undergoing Liquid-Liquid Phase Separation in the Biogenesis of PML-Bodies. Biomolecules 2023; 13:1805. [PMID: 38136675 PMCID: PMC10741438 DOI: 10.3390/biom13121805] [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: 11/14/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The formation and function of membrane-less organelles (MLOs) is one of the main driving forces in the molecular life of the cell. These processes are based on the separation of biopolymers into phases regulated by multiple specific and nonspecific inter- and intramolecular interactions. Among the realm of MLOs, a special place is taken by the promyelocytic leukemia nuclear bodies (PML-NBs or PML bodies), which are the intranuclear compartments involved in the regulation of cellular metabolism, transcription, the maintenance of genome stability, responses to viral infection, apoptosis, and tumor suppression. According to the accepted models, specific interactions, such as SUMO/SIM, the formation of disulfide bonds, etc., play a decisive role in the biogenesis of PML bodies. In this work, a number of bioinformatics approaches were used to study proteins found in the proteome of PML bodies for their tendency for spontaneous liquid-liquid phase separation (LLPS), which is usually caused by weak nonspecific interactions. A total of 205 proteins found in PML bodies have been identified. It has been suggested that UBC9, P53, HIPK2, and SUMO1 can be considered as the scaffold proteins of PML bodies. It was shown that more than half of the proteins in the analyzed proteome are capable of spontaneous LLPS, with 85% of the analyzed proteins being intrinsically disordered proteins (IDPs) and the remaining 15% being proteins with intrinsically disordered protein regions (IDPRs). About 44% of all proteins analyzed in this study contain SUMO binding sites and can potentially be SUMOylated. These data suggest that weak nonspecific interactions play a significantly larger role in the formation and biogenesis of PML bodies than previously expected.
Collapse
Affiliation(s)
- Sergey A. Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Yakov I. Mokin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Eugene M. Nedelyaev
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Eugene Y. Smirnov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Alexander V. Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (S.A.S.); (Y.I.M.); (E.M.N.); (E.Y.S.); (I.M.K.); (K.K.T.)
| |
Collapse
|
2
|
Tang B, Dou S. Knockdown of PAF1 reduces cervical cancer cell proliferation, migration and invasion via retarding FLOT2-mediated MEK/ERK1/2 pathway. Cell Adh Migr 2023; 17:1-10. [PMID: 37754347 PMCID: PMC10538450 DOI: 10.1080/19336918.2023.2260641] [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: 08/23/2022] [Accepted: 05/22/2023] [Indexed: 09/28/2023] Open
Abstract
Cervical cancer (CC) is a very usual reproductive malignant tumor in women. RNA polymerase II-associated factor 1 (PAF1) and flotillin-2 (FLOT2) both have been discovered to key participators in cancers' progression. However, the effects of PAF1/FLOT2 axis on CC development have not been probed. In this study, PAF1 and FLOT2 exhibited higher expression, and silencing of PAF1 down-regulated FLOT2 expression in CC. In addition, the regulatory effects of PAF1 suppression on CC progression were reversed after FLOT2 overexpression. Next, inhibition of PAF1 slowed the tumor growth in vivo through modulating FLOT2. Besides, down-regulation of PAF1 reduced FLOT2 expression to retard the MEK/ERK1/2 pathway. In conclusion, knockdown of PAF1 suppressed CC progression via retarding FLOT2-mediated MEK/ERK1/2 pathway. Our findings illustrated that the PAF1/FLOT2 axis may be useful bio-targets for CC treatment.
Collapse
Affiliation(s)
- Bin Tang
- Department of Gynecology, The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Shulan Dou
- Department of Gynecology, The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| |
Collapse
|
3
|
Wu YJ, Huang ST, Chang YH, Lin SY, Lin WL, Chen YJ, Chien ST. SUMO-Activating Enzyme Subunit 1 Is Associated with Poor Prognosis, Tumor Progression, and Radio-Resistance in Colorectal Cancer. Curr Issues Mol Biol 2023; 45:8013-8026. [PMID: 37886949 PMCID: PMC10605852 DOI: 10.3390/cimb45100506] [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: 08/02/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
Concurrent chemoradiotherapy is an effective treatment option for patients with low-grade colorectal cancer (CRC) in the local disease stage. At present, the principle of the Taiwan Medical Center is to treat CRC patients with combination radiotherapy and chemotherapy (high-dose 5-FU) for a period of about five weeks prior to surgery. Radical resection of the tumor is performed at least six to eight weeks after concurrent chemoradiotherapy (CCRT). However, this approach fails to produce the desired therapeutic effect in approximately 20% to 30% of patients, and such patients are unnecessarily exposed to the risks of radiation and drug toxicity posed by this therapy. Therefore, it is crucial to explore new biomarkers to predict the prognosis of CRC. SUMO-activating enzyme subunit 1 (SAE1) plays an important role in SUMOylation, a post-translational modification involved in cellular functions, such as cell proliferation, cell cycle, and apoptosis. In our study, to explore the clinical-pathological role of SAE1 protein in CRC, we evaluated the clinical data and paraffin sections from CRC patients. The expression of SAE1 was evaluated using immunohistochemical analysis, and clinical parameters were analyzed using chi-square and Kaplan-Meier survival tests. The results of in vitro proliferation and radiosensitive assays were compared between control groups and SAE1 siRNA groups. Western blotting was also used to detect the expressions of the SAE1, PARP, cyclin D1, p-NF-κB, and NF-κB proteins. Flow cytometry and colony formation assays were used to detect the effect of SAE-1 on radiosensitivity. In vivo, we detected the growth curve in a mouse xenograft model. The results showed that SAE-1 was revealed to be an independent prognostic biomarker of CRC. SAE1 knockdown inhibited CRC proliferation in vitro and in vivo, and led to the cleavage of PARP, downregulation of cyclin D1 protein expression, and downregulation of p-NF-κB/NF-κB. Additionally, SAE1 knockdown promoted radiosensitivity in CRC cells. Therefore, it was inferred that SAE1 may be used as a potential therapeutic target in CRC treatment.
Collapse
Affiliation(s)
- Yueh-Jung Wu
- Division of Colorectal Surgery, Kaohsiung Armed Forces General Hospital, Kaohsiung 802, Taiwan
| | - Siang-Ting Huang
- Cancer Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 802, Taiwan
| | - Ya-Hui Chang
- Cancer Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 802, Taiwan
| | - Shih-Yi Lin
- Department of Pathology, Kaohsiung Armed Forces General Hospital, Kaohsiung 802, Taiwan
| | - Weng-Ling Lin
- Department of Pathology, Kaohsiung Armed Forces General Hospital, Kaohsiung 802, Taiwan
| | - Ying-Jung Chen
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shang-Tao Chien
- Department of Pathology, Kaohsiung Armed Forces General Hospital, Kaohsiung 802, Taiwan
- Department of Nursing, Fooyin University, Kaohsiung 831, Taiwan
| |
Collapse
|
4
|
Rauth S, Ganguly K, Atri P, Parte S, Nimmakayala RK, Varadharaj V, Nallasamy P, Vengoji R, Ogunleye AO, Lakshmanan I, Chirravuri R, Bessho M, Cox JL, Foster JM, Talmon GA, Bessho T, Ganti AK, Batra SK, Ponnusamy MP. Elevated PAF1-RAD52 axis confers chemoresistance to human cancers. Cell Rep 2023; 42:112043. [PMID: 36709426 PMCID: PMC10374878 DOI: 10.1016/j.celrep.2023.112043] [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: 05/27/2022] [Revised: 11/11/2022] [Accepted: 01/13/2023] [Indexed: 01/30/2023] Open
Abstract
Cisplatin- and gemcitabine-based chemotherapeutics represent a mainstay of cancer therapy for most solid tumors; however, resistance limits their curative potential. Here, we identify RNA polymerase II-associated factor 1 (PAF1) as a common driver of cisplatin and gemcitabine resistance in human cancers (ovarian, lung, and pancreas). Mechanistically, cisplatin- and gemcitabine-resistant cells show enhanced DNA repair, which is inhibited by PAF1 silencing. We demonstrate an increased interaction of PAF1 with RAD52 in resistant cells. Targeting the PAF1 and RAD52 axis combined with cisplatin or gemcitabine strongly diminishes the survival potential of resistant cells. Overall, this study shows clinical evidence that the expression of PAF1 contributes to chemotherapy resistance and worse clinical outcome for lethal cancers.
Collapse
Affiliation(s)
- Sanchita Rauth
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Koelina Ganguly
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Pranita Atri
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Seema Parte
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Rama Krishna Nimmakayala
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Venkatesh Varadharaj
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Palanisamy Nallasamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Raghupathy Vengoji
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Ayoola O Ogunleye
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Ramakanth Chirravuri
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Mika Bessho
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Jesse L Cox
- Department of Pathology and Microbiology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Jason M Foster
- Department of Surgery, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Geoffrey A Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Tadayoshi Bessho
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Apar Kishor Ganti
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA; Division of Oncology-Hematology, Department of Internal Medicine, VA Nebraska Western Iowa Health Care System, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA.
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA.
| |
Collapse
|
5
|
Wen D, Hu M, Guo W, Wu J, Wu Y. Multi-SUMOylation of NAC1 is essential for the growth of prostate cancer cells. Biochem Biophys Res Commun 2023; 641:148-154. [PMID: 36527749 DOI: 10.1016/j.bbrc.2022.12.015] [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: 11/13/2022] [Revised: 11/21/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Nucleus accumbens-associated 1 (NAC1) is a member of pox virus and zinc finger/bric-a-brac tramtrack broad complex (BTB/POZ) gene family. Overexpression of NAC1 is implicated in cancer development, recurrence and chemotherapy resistance. In our previous study, we found NAC1 was a potential small ubiquitin-like modifier (SUMO) substrate in prostate cancer cells. However, there was still lack of evidences to further support and validate the result. In this work, we found that NAC1 is a multi-SUMO-sites acceptor. The SUMO acceptor lysines were K167, K318, K368, K483 and K498. SUMOylation didn't alter the localization of NAC1, but facilitated the formation of NAC1 nuclear bodies. Compared with NAC1 wild type (NAC1 WT), the SUMO-sites mutant of NAC1 (NAC1 SM) suppressed cell proliferation and tumor growth in cellular and animal levels. This work uncovered the function of SUMOylation of NAC1 in prostate cancer cells.
Collapse
Affiliation(s)
- Donghua Wen
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China.
| | - Min Hu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Wenzheng Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Jingjing Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Yingli Wu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital / Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Chinese Academy of Medical Sciences Research Unit 2019RU043, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China.
| |
Collapse
|
6
|
Cao Y, Huang C, Zhao X, Yu J. Regulation of SUMOylation on RNA metabolism in cancers. Front Mol Biosci 2023; 10:1137215. [PMID: 36911524 PMCID: PMC9998694 DOI: 10.3389/fmolb.2023.1137215] [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: 01/04/2023] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Post-translational modifications of proteins play very important roles in regulating RNA metabolism and affect many biological pathways. Here we mainly summarize the crucial functions of small ubiquitin-like modifier (SUMO) modification in RNA metabolism including transcription, splicing, tailing, stability and modification, as well as its impact on the biogenesis and function of microRNA (miRNA) in particular. This review also highlights the current knowledge about SUMOylation regulation in RNA metabolism involved in many cellular processes such as cell proliferation and apoptosis, which is closely related to tumorigenesis and cancer progression.
Collapse
Affiliation(s)
- Yingting Cao
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Caihu Huang
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
7
|
Alamilla-Presuel JC, Burgos-Molina AM, González-Vidal A, Sendra-Portero F, Ruiz-Gómez MJ. Factors and molecular mechanisms of radiation resistance in cancer cells. Int J Radiat Biol 2022; 98:1301-1315. [PMID: 35225732 DOI: 10.1080/09553002.2022.2047825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE The aim of this work is to review the published studies on radiation resistance mechanisms and molecular markers involved in different tumors. The revision has been focused in the last 5 years (2016-2021). CONCLUSIONS Radioresistance is a cause of concern as it causes failure of radiation therapy and subsequent tumor relapse. Combination chemotherapy and radiation therapy are clinically successful in treating many types of tumors. Despite continued improvements in cancer treatment, locoregional recurrence or metastatic spread continues to occur in a high proportion of patients after being treated with radiation therapy or combination treatments. There is strong evidence that cancer stem cells contribute to radiation resistance, contributing to treatment failure. The mechanisms of radiation resistance in different tumors are not fully understood. A better understanding of cancer stem cells and the associated signaling pathways that regulate radiation resistance will open up new strategies for treating cancer by radiation therapy. Radiation can damage malignant cells mainly by the induction of DNA double strand breaks. However, in some tumors appear resistant cells that repopulate the tumor following therapy leading over time to the failure of the treatment. Native mechanisms and induced pathways, are the cause of radiation resistance. It has been described that numerous molecular markers acting through numerous mechanisms of action involved in radiation resistance, such as apoptosis resistance, alterations of cell growth, proliferation and DNA repair, hypoxia, increase in invasiveness and migration capacity, cell cycle alterations and expression of heat shock proteins, among others. Therefore, resistance to radiation is a multifactorial phenomenon that, in different cell types, it occurs through different regulatory mechanisms in which different molecules intervene. Resistance can be acquired by altering different regulatory pathways in different tumors. The knowledge of radiation resistance markers could help in the classification and treatment of patients with more aggressive tumors.
Collapse
Affiliation(s)
- Juan C Alamilla-Presuel
- Departamento de Radiología y Medicina Física, Facultad de Medicina, Universidad de Málaga, Málaga, España
| | - Antonio M Burgos-Molina
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, España
| | - Alejandro González-Vidal
- Departamento de Radiología y Medicina Física, Facultad de Medicina, Universidad de Málaga, Málaga, España
| | - Francisco Sendra-Portero
- Departamento de Radiología y Medicina Física, Facultad de Medicina, Universidad de Málaga, Málaga, España
| | - Miguel J Ruiz-Gómez
- Departamento de Radiología y Medicina Física, Facultad de Medicina, Universidad de Málaga, Málaga, España
| |
Collapse
|