1
|
Zhang H, Zhu H, Peng H, Sheng Y. Function of serine/arginine-rich splicing factors in hematopoiesis and hematopoietic malignancies. Cancer Cell Int 2024; 24:257. [PMID: 39034387 PMCID: PMC11265194 DOI: 10.1186/s12935-024-03438-7] [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: 08/27/2023] [Accepted: 07/08/2024] [Indexed: 07/23/2024] Open
Abstract
The serine/arginine-rich splicing factors (SRSFs) play an important role in regulating the alternative splicing of precursor RNA (pre-RNA). During this procedure, introns are removed from the pre-RNA, while the exons are accurately joined together to produce mature mRNA. In addition, SRSFs also involved in DNA replication and transcription, mRNA stability and nuclear export, and protein translation. It is reported that SRSFs participate in hematopoiesis, development, and other important biological process. They are also associated with the development of several diseases, particularly cancers. While the basic physiological functions and the important roles of SRSFs in solid cancer have been extensively reviewed, a comprehensive summary of their significant functions in normal hematopoiesis and hematopoietic malignancies is currently absent. Hence, this review presents a summary of their roles in normal hematopoiesis and hematopoietic malignancies.
Collapse
Affiliation(s)
- Huifang Zhang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, P. R. China.
- Hunan Engineering Research Center of Targeted therapy for Hematopoietic Malignancies, Changsha, 410011, Hunan, P. R. China.
| | - Hongkai Zhu
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, P. R. China
- Hunan Engineering Research Center of Targeted therapy for Hematopoietic Malignancies, Changsha, 410011, Hunan, P. R. China
| | - Hongling Peng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, P. R. China.
- Hunan Engineering Research Center of Targeted therapy for Hematopoietic Malignancies, Changsha, 410011, Hunan, P. R. China.
| | - Yue Sheng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, P. R. China.
- Hunan Engineering Research Center of Targeted therapy for Hematopoietic Malignancies, Changsha, 410011, Hunan, P. R. China.
| |
Collapse
|
2
|
Wu Q, Gu Z, Shang B, Wan D, Zhang Q, Zhang X, Xie P, Cheng S, Zhang W, Zhang K. Circulating tumor cell clustering modulates RNA splicing and polyadenylation to facilitate metastasis. Cancer Lett 2024; 588:216757. [PMID: 38417668 DOI: 10.1016/j.canlet.2024.216757] [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: 10/11/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Circulating tumor cell (CTC) clusters exhibit significantly higher metastatic potential compared to single CTCs. However, the underlying mechanism behind this phenomenon remains unclear, and the role of posttranscriptional RNA regulation in CTC clusters has not been explored. Here, we conducted a comparative analysis of alternative splicing (AS) and alternative polyadenylation (APA) profiles between single CTCs and CTC clusters. We identified 994 and 836 AS events in single CTCs and CTC clusters, respectively, with ∼20% of AS events showing differential regulation between the two cell types. A key event in this differential splicing was observed in SRSF6, which disrupted AS profiles and contributed to the increased malignancy of CTC clusters. Regarding APA, we found a global lengthening of 3' UTRs in CTC clusters compared to single CTCs. This alteration was primarily governed by 14 core APA factors, particularly PPP1CA. The modified APA profiles facilitated the cell cycle progression of CTC clusters and indicated their reduced susceptibility to oxidative stress. Further investigation revealed that the proportion of H2AFY mRNA with long 3' UTR instead of short 3' UTR was higher in CTC clusters than single CTCs. The AU-rich elements (AREs) within the long 3' UTR of H2AFY mRNA enhance mRNA stability and translation activity, resulting in promoting cell proliferation and invasion, which potentially facilitate the establishment and rapid formation of metastatic tumors mediated by CTC clusters. These findings provide new insights into the mechanisms driving CTC cluster metastasis.
Collapse
Affiliation(s)
- Quanyou Wu
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China; State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhaoru Gu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Bingqing Shang
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Duo Wan
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qi Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaoli Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peipei Xie
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Wen Zhang
- Department of Immunology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| |
Collapse
|
3
|
Li D, Yu W, Lai M. Towards understandings of serine/arginine-rich splicing factors. Acta Pharm Sin B 2023; 13:3181-3207. [PMID: 37655328 PMCID: PMC10465970 DOI: 10.1016/j.apsb.2023.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/13/2023] [Accepted: 05/06/2023] [Indexed: 09/02/2023] Open
Abstract
Serine/arginine-rich splicing factors (SRSFs) refer to twelve RNA-binding proteins which regulate splice site recognition and spliceosome assembly during precursor messenger RNA splicing. SRSFs also participate in other RNA metabolic events, such as transcription, translation and nonsense-mediated decay, during their shuttling between nucleus and cytoplasm, making them indispensable for genome diversity and cellular activity. Of note, aberrant SRSF expression and/or mutations elicit fallacies in gene splicing, leading to the generation of pathogenic gene and protein isoforms, which highlights the therapeutic potential of targeting SRSF to treat diseases. In this review, we updated current understanding of SRSF structures and functions in RNA metabolism. Next, we analyzed SRSF-induced aberrant gene expression and their pathogenic outcomes in cancers and non-tumor diseases. The development of some well-characterized SRSF inhibitors was discussed in detail. We hope this review will contribute to future studies of SRSF functions and drug development targeting SRSFs.
Collapse
Affiliation(s)
- Dianyang Li
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Maode Lai
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Science (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| |
Collapse
|
4
|
A critical update on the strategies towards small molecule inhibitors targeting Serine/arginine-rich (SR) proteins and Serine/arginine-rich proteins related kinases in alternative splicing. Bioorg Med Chem 2022; 70:116921. [PMID: 35863237 DOI: 10.1016/j.bmc.2022.116921] [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: 04/21/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
>90% of genes in the human body undergo alternative splicing (AS) after transcription, which enriches protein species and regulates protein levels. However, there is growing evidence that various genetic isoforms resulting from dysregulated alternative splicing are prevalent in various types of cancers. Dysregulated alternative splicing leads to cancer generation and maintenance of cancer properties such as proliferation differentiation, apoptosis inhibition, invasion metastasis, and angiogenesis. Serine/arginine-rich proteins and SR protein-associated kinases mediate splice site recognition and splice complex assembly during variable splicing. Based on the impact of dysregulated alternative splicing on disease onset and progression, the search for small molecule inhibitors targeting alternative splicing is imminent. In this review, we discuss the structure and specific biological functions of SR proteins and describe the regulation of SR protein function by SR protein related kinases meticulously, which are closely related to the occurrence and development of various types of cancers. On this basis, we summarize the reported small molecule inhibitors targeting SR proteins and SR protein related kinases from the perspective of medicinal chemistry. We mainly categorize small molecule inhibitors from four aspects, including targeting SR proteins, targeting Serine/arginine-rich protein-specific kinases (SRPKs), targeting Cdc2-like kinases (CLKs) and targeting dual-specificity tyrosine-regulated kinases (DYRKs), in terms of structure, inhibition target, specific mechanism of action, biological activity, and applicable diseases. With this review, we are expected to provide a timely summary of recent advances in alternative splicing regulated by kinases and a preliminary introduction to relevant small molecule inhibitors.
Collapse
|
5
|
SRSF6 Regulates the Alternative Splicing of the Apoptotic Fas Gene by Targeting a Novel RNA Sequence. Cancers (Basel) 2022; 14:cancers14081990. [PMID: 35454897 PMCID: PMC9025165 DOI: 10.3390/cancers14081990] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Alternative splicing (AS) produces multiple mRNA isoforms from a gene to make a large number of proteins. Fas (Apo-1/CD95) pre-mRNA, a member of TNF receptor family that mediates apoptosis, can generate pro-apoptotic and anti-apoptotic proteins through AS. Here, we identified SRSF6 as an essential regulator protein in Fas AS. We further located a new functional target sequence of SRSF6 in Fas splicing. In addition, our large-scale RNA-seq analysis using GTEX and TCGA indicated that while SRSF6 expression was correlated with Fas expression in normal tissues, the correlation was disrupted in tumors. Our results suggest a novel regulatory mechanisms of Fas AS. Abstract Alternative splicing (AS) is a procedure during gene expression that allows the production of multiple mRNAs from a single gene, leading to a larger number of proteins with various functions. The alternative splicing (AS) of Fas (Apo-1/CD95) pre-mRNA can generate membrane-bound or soluble isoforms with pro-apoptotic and anti-apoptotic functions. SRSF6, a member of the Serine/Arginine-rich protein family, plays essential roles in both constitutive and alternative splicing. Here, we identified SRSF6 as an important regulatory protein in Fas AS. The cassette exon inclusion of Fas was decreased by SRSF6-targeting shRNA treatment, but increased by SRSF6 overexpression. The deletion and substitution mutagenesis of the Fas minigene demonstrated that the UGCCAA sequence in the cassette exon of the Fas gene causes the functional disruption of SRSF6, indicating that these sequences are essential for SRSF6 function in Fas splicing. In addition, biotin-labeled RNA-pulldown and immunoblotting analysis showed that SRSF6 interacted with these RNA sequences. Mutagenesis in the splice-site strength alteration demonstrated that the 5′ splice-site, but not the 3′ splice-site, was required for the SRSF6 regulation of Fas pre-mRNA. In addition, a large-scale RNA-seq analysis using GTEX and TCGA indicated that while SRSF6 expression was correlated with Fas expression in normal tissues, the correlation was disrupted in tumors. Furthermore, high SRSF6 expression was linked to the high expression of pro-apoptotic and immune activation genes. Therefore, we identified a novel RNA target with 5′ splice-site dependence of SRSF6 in Fas pre-mRNA splicing, and a correlation between SRSF6 and Fas expression.
Collapse
|
6
|
She W, Shao J, Jia R. Targeting Splicing Factor SRSF6 for Cancer Therapy. Front Cell Dev Biol 2021; 9:780023. [PMID: 34917618 PMCID: PMC8669609 DOI: 10.3389/fcell.2021.780023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/12/2021] [Indexed: 01/19/2023] Open
Abstract
Aberrant alternative splicing of pre-mRNA is an emerging cancer hallmark. Many cancer-associated genes undergo alternative splicing to produce multiple isoforms with diverse or even antagonistic functions. Oncogenic isoforms are often up-regulated, whereas tumor suppressive isoforms are down-regulated during tumorigenesis. Serine/arginine-rich splicing factor 6 (SRSF6) is an important splicing factor that regulates the alternative splicing of hundreds of target genes, including many cancer-associated genes. The potential roles of SRSF6 in cancers have attracted increasing attentions in the past decade. Accumulated pieces of evidence have shown that SRSF6 is a potential oncogenic gene that promotes oncogenic splicing when overexpressed. Targeting SRSF6 may suppress tumorigenesis. In this review, we describe the gene, mRNA, and protein structure of SRSF6; summarize the current understanding of the expression, functions, and regulatory mechanisms of SRSF6 during tumorigenesis; and discuss the potential application of targeting SRSF6 in cancer treatment.
Collapse
Affiliation(s)
- Wenting She
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Jun Shao
- Department of Breast Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology and Hubei Provincial Clinical Research Center for Breast Cancer, Wuhan, China
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| |
Collapse
|
7
|
Chiu TJ, Chen YJ, Lan J, Chen YY, Chen YC, Lin HW, Tsai HT, Lin YS, Hsiao CC, Chen CH. Downregulation of Notch3 links TIMP3 inhibition to suppress aggressive phenotypes of pancreatic ductal adenocarcinoma. Am J Cancer Res 2021; 11:5609-5624. [PMID: 34873483 PMCID: PMC8640811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), one of the most deadly digestive cancers, has a poor 5-year survival rate and is resistant to chemotherapeutic agents, such as gemcitabine. Notch3 plays an important role in cancer progression, and its expression facilitates chemoresistance in cancers. This study examined the clinical significance of Notch3 and explored the mechanisms through which it may affect disease progression in PDAC. We found Notch3 to be upregulated in PDAC patients in whom it correlated with lymph node stage and poor survival. In vitro and in vivo, functional assays indicated that silencing Notch3 could suppress the growth, migration, invasion of PDAC cells and sensitize PDAC cells to gemcitabine. QPCR array, which was performed to elucidate the Notch3-regulated pathway, revealed that inhibition of Notch3 decreased the transcription and secretion of TIMP3 in PDAC cells. Overexpression of TIMP3 reversed the impaired growth, migration, invasion, and chemosensitivity induced by Notch3 silencing. We also found a positive correlation between Notch3 mRNA expression and TIMP3 expression in patients with PDAC. We concluded that blocking Notch3/TIMP3 pathway could considered a potentially new therapeutic strategy for treating PDAC.
Collapse
Affiliation(s)
- Tai-Jan Chiu
- Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung 83301, Taiwan
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial HospitalKaohsiung 83301, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung UniversityTaoyuan 33302, Taiwan
| | - Yi-Ju Chen
- Department of Anatomic Pathology, E-Da Hospital, I-Shou UniversityKaohsiung 84001, Taiwan
| | - Jui Lan
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of MedicineKaohsiung 83301, Taiwan
| | - Yen-Yang Chen
- Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung 83301, Taiwan
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial HospitalKaohsiung 83301, Taiwan
| | - Yueh-Chiu Chen
- Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung 83301, Taiwan
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial HospitalKaohsiung 83301, Taiwan
| | - Hsiao-Wu Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung 83301, Taiwan
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial HospitalKaohsiung 83301, Taiwan
| | - Hsin-Ting Tsai
- Institute of Medicine, Chung Shan Medical UniversityTaichung 40201, Taiwan
| | - Yu-Sheng Lin
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Chang-Chun Hsiao
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung UniversityTaoyuan 33302, Taiwan
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung 83301, Taiwan
| | - Chang-Han Chen
- Institute of Medicine, Chung Shan Medical UniversityTaichung 40201, Taiwan
- Department of Medical Research, Chung Shan Medical University HospitalTaichung 40201, Taiwan
| |
Collapse
|
8
|
Zhang X, Wang Z, Xu Q, Chen Y, Liu W, Zhong T, Li H, Quan C, Zhang L, Cui CP. Splicing factor Srsf5 deletion disrupts alternative splicing and causes noncompaction of ventricular myocardium. iScience 2021; 24:103097. [PMID: 34622152 PMCID: PMC8482499 DOI: 10.1016/j.isci.2021.103097] [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: 04/09/2021] [Revised: 07/17/2021] [Accepted: 09/06/2021] [Indexed: 11/21/2022] Open
Abstract
The serine/arginine-rich (SR) family of splicing factors plays important roles in mRNA splicing activation, repression, export, stabilization, and translation. SR-splicing factor 5 (SRSF5) is a glucose-inducible protein that promotes tumor cell growth. However, the functional role of SRSF5 in tissue development and disease remains unknown. Here, Srsf5 knockout (Srsf5−/−) mice were generated using CRISPR-Cas9. Mutant mice were perinatally lethal and exhibited cardiac dysfunction with noncompaction of the ventricular myocardium. The left ventricular internal diameter and volume were increased in Srsf5−/− mice during systole. Null mice had abnormal electrocardiogram patterns, indicative of a light atrioventricular block. Mechanistically, Srsf5 promoted the alternative splicing of Myom1 (myomesin-1), a protein that crosslinks myosin filaments to the sarcomeric M-line. The switch between embryonic and adult isoforms of Myom1 could not be completed in Srsf5-deficient heart. These findings indicate that Srsf5-regulated alternative splicing plays a critical role during heart development. Systemic loss of Srsf5 causes perinatal lethality in mice Srsf5 deficiency leads to cardiac dysfunction Alternative splicing of Myom1 in the heart around birth is regulated by Srsf5
Collapse
Affiliation(s)
- Xiaoli Zhang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun, Jilin 130021, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Ze Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Qing Xu
- Core Facilities Centre, Capital Medical University, Beijing 100069, China
| | - Yuhan Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Wen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Tong Zhong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Hongchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Chengshi Quan
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun, Jilin 130021, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Chun-Ping Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| |
Collapse
|
9
|
Tan J, Tao K, Zheng X, Liu D, Ma D, Gao Q. Expression of PAWR predicts prognosis of ovarian cancer. Cancer Cell Int 2020; 20:598. [PMID: 33317551 PMCID: PMC7737345 DOI: 10.1186/s12935-020-01704-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
Background Ovarian cancer greatly threatens the general health of women worldwide. Implementation of predictive prognostic biomarkers aids in ovarian cancer management. Methods Using online databases, the general expression profile, target-disease associations, and interaction network of PAWR were explored. To identify the role of PAWR in ovarian cancer, gene correlation analysis, survival analysis, and combined analysis of drug responsiveness and PAWR expression were performed. The predictive prognostic value of PAWR was further validated in clinical samples. Results PAWR was widely expressed in normal and cancer tissues, with decreased expression in ovarian cancer tissues compared with normal tissues. PAWR was associated with various cancers including ovarian cancer. PAWR formed a regulatory network with a group of proteins and correlated with several genes, which were both implicated in ovarian cancer and drug responsiveness. High PAWR expression denoted better survival in ovarian cancer patients (OS: HR = 0.84, P = 0.0077; PFS, HR = 0.86, P = 0.049). Expression of PAWR could predict platinum responsiveness in ovarian cancer and there was a positive correlation between PAWR gene effect and paclitaxel sensitivity. In 12 paired clinical samples, the cancerous tissues exhibited significantly lower PAWR expression than matched normal fallopian tubes. The predictive prognostic value of PAWR was maintained in a cohort of 50 ovarian cancer patients. Conclusions High PAWR expression indicated better survival and higher drug responsiveness in ovarian cancer patients. PAWR could be exploited as a predictive prognostic biomarker in ovarian cancer.
Collapse
Affiliation(s)
- Jiahong Tan
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, People's Republic of China.,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Kangjia Tao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, People's Republic of China.,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Xu Zheng
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, People's Republic of China.,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Dan Liu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, People's Republic of China.,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Ding Ma
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, People's Republic of China.,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Qinglei Gao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, People's Republic of China. .,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
| |
Collapse
|
10
|
Du JX, Zhu GQ, Cai JL, Wang B, Luo YH, Chen C, Cai CZ, Zhang SJ, Zhou J, Fan J, Zhu W, Dai Z. Splicing factors: Insights into their regulatory network in alternative splicing in cancer. Cancer Lett 2020; 501:83-104. [PMID: 33309781 DOI: 10.1016/j.canlet.2020.11.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022]
Abstract
More than 95% of all human genes are alternatively spliced after transcription, which enriches the diversity of proteins and regulates transcript and/or protein levels. The splicing isoforms produced from the same gene can manifest distinctly, even exerting opposite effects. Mounting evidence indicates that the alternative splicing (AS) mechanism is ubiquitous in various cancers and drives the generation and maintenance of various hallmarks of cancer, such as enhanced proliferation, inhibited apoptosis, invasion and metastasis, and angiogenesis. Splicing factors (SFs) play pivotal roles in the recognition of splice sites and the assembly of spliceosomes during AS. In this review, we mainly discuss the similarities and differences of SF domains, the details of SF function in AS, the effect of SF-driven pathological AS on different hallmarks of cancer, and the main drivers of SF expression level and subcellular localization. In addition, we briefly introduce the application prospects of targeted therapeutic strategies, including small-molecule inhibitors, siRNAs and splice-switching oligonucleotides (SSOs), from three perspectives (drivers, SFs and pathological AS). Finally, we share our insights into the potential direction of research on SF-centric AS-related regulatory networks.
Collapse
Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
| |
Collapse
|
11
|
Johnson GS, Rajendran P, Dashwood RH. CCAR1 and CCAR2 as gene chameleons with antagonistic duality: Preclinical, human translational, and mechanistic basis. Cancer Sci 2020; 111:3416-3425. [PMID: 33403784 PMCID: PMC7540973 DOI: 10.1111/cas.14579] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/04/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022] Open
Abstract
Cell Cycle and Apoptosis Regulator 1 (CCAR1) and Cell Cycle and Apoptosis Regulator 2 (CCAR2) have emerged as key players in physiology and pathophysiology, with critical roles in the DNA damage response, nuclear receptor function, and Wnt signaling, among other activities. Contradictory reports exist on the functional duality of CCAR1 and CCAR2 as either tumor promoters or suppressors, suggesting that CCAR1 and CCAR2 have the hallmarks of gene chameleons. We review herein the mechanistic, preclinical, and human translational findings for CCAR1 and CCAR2, based on available RNA and protein expression data from human studies, The Cancer Genome Atlas (TCGA) data mining, gene knockout mouse models, and cell-based assays. Multiple factors contribute to the divergent activities of CCAR1 and CCAR2, including tissue type, mutation/genetic background, protein-protein interactions, dynamic regulation via posttranslational modifications, and alternative RNA splicing. An array of protein partners interact with CCAR1 and CCAR2 in the context of tumor promotion and suppression, including β-catenin, androgen receptor, p21Cip1/Waf1, tumor protein p53 (p53), sirtuin 1, and histone deacetylase 3. Genetic changes frequently found in cancer, such as TP53 mutation, also serve as critical determinants of survival outcomes in cancer patients. This review seeks to provide the impetus for further investigation into CCAR1 and CCAR2 as potential master regulators of metabolism, aging, and cancer.
Collapse
Affiliation(s)
- Gavin S. Johnson
- Center for Epigenetics & Disease PreventionTexas A&M Health Science CenterHoustonTXUSA
| | - Praveen Rajendran
- Center for Epigenetics & Disease PreventionTexas A&M Health Science CenterHoustonTXUSA
| | - Roderick H. Dashwood
- Center for Epigenetics & Disease PreventionTexas A&M Health Science CenterHoustonTXUSA
- Department of Translational Medical Sciences, Texas A&M College of MedicineTexas A&M UniversityHouston CampusTXUSA
- Department of Clinical Cancer PreventionThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| |
Collapse
|
12
|
Santos RVC, de Sena WLB, Dos Santos FA, da Silva Filho AF, da Rocha Pitta MG, da Rocha Pitta MG, de Melo Rego MB, Pereira MC. Potential Therapeutic Agents Against Par-4 Target for Cancer Treatment: Where Are We Going? Curr Drug Targets 2020; 20:635-654. [PMID: 30474528 DOI: 10.2174/1389450120666181126122440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/15/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
Abstract
One of the greatest challenges of cancer therapeutics nowadays is to find selective targets successfully. Prostate apoptosis response-4 (Par-4) is a selective tumor suppressor protein with an interesting therapeutic potential due to its specificity on inducing apoptosis in cancer cells. Par-4 activity and levels can be downregulated in several tumors and cancer cell types, indicating poor prognosis and treatment resistance. Efforts to increase Par-4 expression levels have been studied, including its use as a therapeutic protein by transfection with adenoviral vectors or plasmids. However, gene therapy is very complex and still presents many hurdles to be overcome. We decided to review molecules and drugs with the capacity to upregulate Par-4 and, thereby, be an alternative to reach this druggable target. In addition, Par-4 localization and function are reviewed in some cancers, clarifying how it can be used as a therapeutic target.
Collapse
Affiliation(s)
- Renata Virgínia Cavalcanti Santos
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE, Brazil
| | - Wanessa Layssa Batista de Sena
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE, Brazil
| | - Flaviana Alves Dos Santos
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE, Brazil
| | - Antônio Felix da Silva Filho
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE, Brazil
| | | | - Maira Galdino da Rocha Pitta
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE, Brazil
| | - Moacyr Barreto de Melo Rego
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE, Brazil
| | - Michelly Cristiny Pereira
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE, Brazil
| |
Collapse
|
13
|
Wang L, Zhao H, Li J, Xu Y, Lan Y, Yin W, Liu X, Yu L, Lin S, Du MY, Li X, Xiao Y, Zhang Y. Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines. Oncogene 2019; 39:677-689. [PMID: 31537905 PMCID: PMC6962092 DOI: 10.1038/s41388-019-1005-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/30/2019] [Accepted: 08/15/2019] [Indexed: 12/15/2022]
Abstract
Epigenetic modifications play critical roles in modulating gene expression, yet their roles in regulatory networks in human cell lines remain poorly characterized. We integrated multiomics data to construct directed regulatory networks with nodes and edges labeled with chromatin states in human cell lines. We observed extensive association of diverse chromatin states and network motifs. The gene expression analysis showed that diverse chromatin states of coherent type-1 feedforward loop (C1-FFL) and incoherent type-1 feedforward loops (I1-FFL) contributed to the dynamic expression patterns of targets. Notably, diverse chromatin state compositions could help C1- or I1-FFL to control a large number of distinct biological functions in human cell lines, such as four different types of chromatin state compositions cooperating with K562-associated C1-FFLs controlling “regulation of cytokinesis,” “G1/S transition of mitotic cell cycle,” “DNA recombination,” and “telomere maintenance,” respectively. Remarkably, we identified six chromatin state-marked C1-FFL instances (HCFC1-NFYA-ABL1, THAP1-USF1-BRCA2, ZNF263-USF1-UBA52, MYC-ATF1-UBA52, ELK1-EGR1-CCT4, and YY1-EGR1-INO80C) could act as prognostic biomarkers of acute myelogenous leukemia though influencing cancer-related biological functions, such as cell proliferation, telomere maintenance, and DNA recombination. Our results will provide novel insight for better understanding of chromatin state-mediated gene regulation and facilitate the identification of novel diagnostic and therapeutic biomarkers of human cancers.
Collapse
Affiliation(s)
- Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China
| | - Jing Li
- Department of Ultrasonic medicine, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, 150040, Harbin, China
| | - Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China
| | - Wenkang Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China
| | - Xiaoqin Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China
| | - Lei Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China
| | - Shihua Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China
| | - Michael Yifei Du
- Weston High School of Massachusetts, 444 Wellesley street, Weston, MA, 02493, USA
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China.
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 150081, Harbin, China.
| |
Collapse
|
14
|
Post-transcriptional regulatory patterns revealed by protein-RNA interactions. Sci Rep 2019; 9:4302. [PMID: 30867517 PMCID: PMC6416249 DOI: 10.1038/s41598-019-40939-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/26/2019] [Indexed: 02/07/2023] Open
Abstract
The coordination of the synthesis of functionally-related proteins can be achieved at the post-transcriptional level by the action of common regulatory molecules, such as RNA–binding proteins (RBPs). Despite advances in the genome-wide identification of RBPs and their binding transcripts, the protein–RNA interaction space is still largely unexplored, thus hindering a broader understanding of the extent of the post-transcriptional regulation of related coding RNAs. Here, we propose a computational approach that combines protein–mRNA interaction networks and statistical analyses to provide an inferred regulatory landscape for more than 800 human RBPs and identify the cellular processes that can be regulated at the post-transcriptional level. We show that 10% of the tested sets of functionally-related mRNAs can be post-transcriptionally regulated. Moreover, we propose a classification of (i) the RBPs and (ii) the functionally-related mRNAs, based on their distinct behaviors in the functional landscape, hinting towards mechanistic regulatory hypotheses. In addition, we demonstrate the usefulness of the inferred functional landscape to investigate the cellular role of both well-characterized and novel RBPs in the context of human diseases.
Collapse
|
15
|
Aburjania Z, Jang S, Whitt J, Jaskula-Stzul R, Chen H, Rose JB. The Role of Notch3 in Cancer. Oncologist 2018; 23:900-911. [PMID: 29622701 PMCID: PMC6156186 DOI: 10.1634/theoncologist.2017-0677] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/19/2018] [Indexed: 12/15/2022] Open
Abstract
The Notch family is a highly conserved gene group that regulates cell-cell interaction, embryogenesis, and tissue commitment. This review article focuses on the third Notch family subtype, Notch3. Regulation via Notch3 signaling was first implicated in vasculogenesis. However, more recent findings suggest that Notch3 signaling may play an important role in oncogenesis, tumor maintenance, and resistance to chemotherapy. Its role is mainly oncogenic, although in some cancers it appears to be tumor suppressive. Despite the wealth of published literature, it remains relatively underexplored and requires further research to shed more light on its role in cancer development, determine its tissue-specific function, and elaborate novel treatment strategies. Herein we summarize the role of Notch3 in cancer, possible mechanisms of its action, and current cancer treatment strategies targeting Notch3 signaling. IMPLICATIONS FOR PRACTICE The Notch family is a highly conserved gene group that regulates cell-cell interaction, embryogenesis, and tissue commitment. This review summarizes the existing data on the third subtype of the Notch family, Notch3. The role of Notch3 in different types of cancers is discussed, as well as implications of its modification and new strategies to affect Notch3 signaling activity.
Collapse
Affiliation(s)
- Zviadi Aburjania
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Samuel Jang
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jason Whitt
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Renata Jaskula-Stzul
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Herbert Chen
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - J Bart Rose
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| |
Collapse
|
16
|
Chen Y, Huang Q, Liu W, Zhu Q, Cui CP, Xu L, Guo X, Wang P, Liu J, Dong G, Wei W, Liu CH, Feng Z, He F, Zhang L. Mutually exclusive acetylation and ubiquitylation of the splicing factor SRSF5 control tumor growth. Nat Commun 2018; 9:2464. [PMID: 29942010 PMCID: PMC6018636 DOI: 10.1038/s41467-018-04815-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/18/2018] [Indexed: 12/30/2022] Open
Abstract
Most tumor cells take up more glucose than normal cells. Splicing dysregulation is one of the molecular hallmarks of cancer. However, the role of splicing factor in glucose metabolism and tumor development remains poorly defined. Here, we show that upon glucose intake, the splicing factor SRSF5 is specifically induced through Tip60-mediated acetylation on K125, which antagonizes Smurf1-mediated ubiquitylation. SRSF5 promotes the alternative splicing of CCAR1 to produce CCAR1S proteins, which promote tumor growth by enhancing glucose consumption and acetyl-CoA production. Conversely, upon glucose starvation, SRSF5 is deacetylated by HDAC1, and ubiquitylated by Smurf1 on the same lysine, resulting in proteasomal degradation of SRSF5. The CCAR1L proteins accumulate to promote apoptosis. Importantly, SRSF5 is hyperacetylated and upregulated in human lung cancers, which correlates with increased CCAR1S expression and tumor progression. Thus, SRSF5 responds to high glucose to promote cancer development, and SRSF5-CCAR1 axis may be valuable targets for cancer therapeutics.
Collapse
Affiliation(s)
- Yuhan Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China.,Affiliated BaYi Children's Hospital, PLA Army General Hospital, National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China
| | - Qingyang Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Wen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qiong Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Chun-Ping Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liang Xu
- Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China.,Department of Biochemistry and Molecular Biology, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xing Guo
- Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China.,Department of Neurobiology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Ping Wang
- Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200072, China
| | - Jingwen Liu
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing, 100853, China
| | - Guanglong Dong
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing, 100853, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhichun Feng
- Affiliated BaYi Children's Hospital, PLA Army General Hospital, National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China. .,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China. .,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China. .,School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China.
| |
Collapse
|
17
|
Bellavia D, Checquolo S, Palermo R, Screpanti I. The Notch3 Receptor and Its Intracellular Signaling-Dependent Oncogenic Mechanisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1066:205-222. [PMID: 30030828 DOI: 10.1007/978-3-319-89512-3_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
During evolution, gene duplication of the Notch receptor suggests a progressive functional diversification. The Notch3 receptor displays a number of structural differences with respect to Notch1 and Notch2, most of which have been reported in the transmembrane and in the intracellular regions, mainly localized in the negative regulatory region (NRR) and trans-activation domain (TAD). Targeted deletion of Notch3 does not result in embryonic lethality, which is in line with its highly restricted tissue expression pattern. Importantly, deregulated Notch3 expression and/or activation, often results in disrupted cell differentiation and/or pathological development, most notably in oncogenesis in different cell contexts. Mechanistically this is due to Notch3-related genetic alterations or epigenetic or posttranslational control mechanisms. In this chapter we discuss the possible relationships between the structural differences and the pathological role of Notch3 in the control of mouse and human cancers. In future, targeting the unique features of Notch3-oncogenic mechanisms could be exploited to develop anticancer therapeutics.
Collapse
Affiliation(s)
- Diana Bellavia
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Saula Checquolo
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Rocco Palermo
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Isabella Screpanti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
| |
Collapse
|
18
|
Shelke GV, Jagtap JC, Kim DK, Shah RD, Das G, Shivayogi M, Pujari R, Shastry P. TNF-α and IFN-γ Together Up-Regulates Par-4 Expression and Induce Apoptosis in Human Neuroblastomas. Biomedicines 2017; 6:biomedicines6010004. [PMID: 29278364 PMCID: PMC5874661 DOI: 10.3390/biomedicines6010004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 01/18/2023] Open
Abstract
The objective of this study was to examine the combined effect of Interferon-gamma (IFN-γ) and Tumor Necrosis factor-alpha (TNF-α) on cytotoxicity and expression of prostate apoptosis response-4 (Par-4) and Par-4 interacting proteins B-cell lymphoma (Bcl-2), nuclear factor kappa-light-chain-enhancer of activated B cells/p65 subunit (NF-κB/p65), Ak mouse strain thymoma (Akt) in human neuroblastoma (NB) cells. Materials and methods included human neuroblastoma cell lines-SK-N-MC, SK-N-SH, and SH-SY5Y, which were treated with IFN-γ and TNF-α individually, or in combination, and were assessed for viability by tetrazolium (MTT) assay. Apoptosis was monitored by hypodiploid population (by flow cytometry), DNA fragmentation, Poly (ADP-ribose) polymerase (PARP) cleavage, and caspase-8 activity. Transcript level of Par-4 was measured by RT-PCR. Protein levels of Par-4 and suppressor of cytokine signaling 3 (SOCS-3) were assessed by immunoblotting. Cellular localization of Par-4 and p65 was examined by immunofluorescence. Unbiased transcript analysis for IFN-γ, TNF-α, and Par-4 were analyzed from three independent clinical datasets from neuroblastoma patients. In terms of results, SK-N-MC cells treated with a combination of, but not individually with, IFN-γ and TNF-α induced apoptosis characterized by hypodiploidy, DNA fragmentation, PARP cleavage, and increased caspase-8 activity. Apoptosis was associated with up-regulation of Par-4 mRNA and protein expression. Immunofluorescence studies revealed that Par-4 was localized exclusively in cytoplasm in SK-N-MC cells cultured for 24 h. but showed nuclear localization at 48 h. Treatment with IFN-γ and TNF-α together enhanced the intensity of nuclear Par-4. In gene expression, data from human neuroblastoma patients, levels of IFN-γ, and TNF-α have strong synergy with Par-4 expression and provide good survival advantage. The findings also demonstrated that apoptosis was associated with reduced level of pro-survival proteins–Bcl-2 and Akt and NF-κB/p65. Furthermore, the apoptotic effect induced by IFN-γ-induced Signal Transducer and Activator of Transcription-1(STAT-1), and could be due to down-regulation of suppressor of cytokine signaling-3 (SOCS3). The study concludes that a combinatorial approach using IFN-γ and TNF-α can be explored to maximize the effect in chemotherapy in neuroblastoma, and implies a role for Par-4 in the process.
Collapse
Affiliation(s)
- Ganesh V Shelke
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
- Current address: Krefting Research Centre, University of Gothenburg, Box-424, SE-405 30 Gothenburg, Sweden.
| | - Jayashree C Jagtap
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India.
| | - Dae-Kyum Kim
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada.
| | - Reecha D Shah
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India.
| | - Gowry Das
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India.
| | | | - Radha Pujari
- Rasayani Biologics Pvt Ltd, 48/7, Mhalunge-Nande Road, Mhalunge, Pune 411045, India.
| | - Padma Shastry
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India.
| |
Collapse
|
19
|
Choudhury M, Ramsey SA. Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation. GENE REGULATION AND SYSTEMS BIOLOGY 2016; 10:105-110. [PMID: 28008225 PMCID: PMC5156548 DOI: 10.4137/grsb.s40768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/03/2016] [Accepted: 11/06/2016] [Indexed: 01/22/2023]
Abstract
We describe a novel computational approach to identify transcription factors (TFs) that are candidate regulators in a human cell type of interest. Our approach involves integrating cell type-specific expression quantitative trait locus (eQTL) data and TF data from chromatin immunoprecipitation-to-tag-sequencing (ChIP-seq) experiments in cell lines. To test the method, we used eQTL data from human monocytes in order to screen for TFs. Using a list of known monocyte-regulating TFs, we tested the hypothesis that the binding sites of cell type-specific TF regulators would be concentrated in the vicinity of monocyte eQTLs. For each of 397 ChIP-seq data sets, we obtained an enrichment ratio for the number of ChIP-seq peaks that are located within monocyte eQTLs. We ranked ChIP-seq data sets according to their statistical significances for eQTL overlap, and from this ranking, we observed that monocyte-regulating TFs are more highly ranked than would be expected by chance. We identified 27 TFs that had significant monocyte enrichment scores and mapped them into a protein interaction network. Our analysis uncovered two novel candidate monocyte-regulating TFs, BCLAF1 and SIN3A. Our approach is an efficient method to identify candidate TFs that can be used for any cell/tissue type for which eQTL data are available.
Collapse
Affiliation(s)
- Mudra Choudhury
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | - Stephen A Ramsey
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| |
Collapse
|
20
|
Shifman AR, Johnson RM, Wilhelm BT. Cascade: an RNA-seq visualization tool for cancer genomics. BMC Genomics 2016; 17:75. [PMID: 26810393 PMCID: PMC4727405 DOI: 10.1186/s12864-016-2389-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/11/2016] [Indexed: 12/20/2022] Open
Abstract
Background Cancer genomics projects are producing ever-increasing amounts of rich and diverse data from patient samples. The ability to easily visualize this data in an integrated an intuitive way is currently limited by the current software available. As a result, users typically must use several different tools to view the different data types for their cohort, making it difficult to have a simple unified view of their data. Results Here we present Cascade, a novel web based tool for the intuitive 3D visualization of RNA-seq data from cancer genomics experiments. The Cascade viewer allows multiple data types (e.g. mutation, gene expression, alternative splicing frequency) to be simultaneously displayed, allowing a simplified view of the data in a way that is tuneable based on user specified parameters. The main webpage of Cascade provides a primary view of user data which is overlaid onto known biological pathways that are either predefined or added by users. A space-saving menu for data selection and parameter adjustment allows users to access an underlying MySQL database and customize the features presented in the main view. Conclusions There is currently a pressing need for new software tools to allow researchers to easily explore large cancer genomics datasets and generate hypotheses. Cascade represents a simple yet intuitive interface for data visualization that is both scalable and customizable. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2389-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Aaron R Shifman
- Laboratory for high throughput genomics, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.
| | - Radia M Johnson
- Laboratory for high throughput genomics, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.
| | - Brian T Wilhelm
- Laboratory for high throughput genomics, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.
| |
Collapse
|
21
|
CARP-1/CCAR1: a biphasic regulator of cancer cell growth and apoptosis. Oncotarget 2016; 6:6499-510. [PMID: 25894788 PMCID: PMC4466629 DOI: 10.18632/oncotarget.3376] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/12/2015] [Indexed: 12/03/2022] Open
Abstract
Targeted cancer therapy using small molecule inhibitors (SMIs) has been useful in targeting the tumor cells while sparing the normal cells. Despite clinical success of many targeted therapies, their off-target effects and development of resistance are emerging as significant and challenging problems. Thus, there is an urgent need to identify targets to devise new means to treat cancers and their drug-resistant phenotypes. CARP-1/CCAR1 (Cell division cycle and apoptosis regulator 1), a peri-nuclear phospho-protein, plays a dynamic role in regulating cell growth and apoptosis by serving as a co-activator of steroid/thyroid nuclear receptors, β-catenin, Anaphase Promoting Complex/Cyclosome (APC/C) E3 ligase, and tumor suppressor p53. CARP-1/CCAR1 also regulates chemotherapy-dependent apoptosis. CARP-1/CCAR1 functional mimetics (CFMs) are a novel SMIs of CARP-1/CCAR1 interaction with APC/C. CFMs promote apoptosis in a manner independent of p53. CFMs are potent inhibitors of a variety of cancer cells including the drug (Adriamycin or Tamoxifen)-resistant breast cancer cells but not the immortalized breast epithelial cells, while a nano-lipid formulation of the lead compound CFM-4 improves its bioavailability and efficacy in vivo when administered orally. This review focuses on the background and pleiotropic roles of CARP-1/CCAR1 as well as its apoptosis signaling mechanisms in response to chemotherapy in cancer cells.
Collapse
|
22
|
Polgárová K, Vášková M, Froňková E, Slámová L, Kalina T, Mejstříková E, Dobiášová A, Fišer K, Hrušák O. Quantitative expression of regulatory and differentiation-related genes in the key steps of human hematopoiesis: The LeukoStage Database. Differentiation 2015; 91:19-28. [PMID: 26674556 DOI: 10.1016/j.diff.2015.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 10/23/2015] [Accepted: 11/13/2015] [Indexed: 11/28/2022]
Abstract
Differentiation during hematopoiesis leads to the generation of many cell types with specific functions. At various stages of maturation, the cells may change pathologically, leading to diseases including acute leukemias (ALs). Expression levels of regulatory molecules (such as the IKZF, GATA, HOX, FOX, NOTCH and CEBP families, as well as SPI-1/PU1 and PAX5) and lineage-specific molecules (including CD2, CD14, CD79A, and BLNK) may be compared between pathological and physiological cells. Although the key steps of differentiation are known, the available databases focus mainly on fully differentiated cells as a reference. Precursor cells may be a more appropriate reference point for diseases that evolve at immature stages. Therefore, we developed a quantitative real-time polymerase chain reaction (qPCR) array to investigate 90 genes that are characteristic of the lymphoid or myeloid lineages and/or are thought to be involved in their regulation. Using this array, sorted cells of granulocytic, monocytic, T and B lineages were analyzed. For each of these lineages, 3-5 differentiation stages were selected (17 stages total), and cells were sorted from 3 different donors per stage. The qPCR results were compared to similarly processed AL cells of lymphoblastic (n=18) or myeloid (n=6) origins and biphenotypic AL cells of B cell origin with myeloid involvement (n=5). Molecules characteristic of each lineage were found. In addition, cells of a newly discovered switching lymphoblastic AL (swALL) were sorted at various phases during the supposed transdifferentiation from an immature B cell to a monocytic phenotype. As demonstrated previously, gene expression changed along with the immunophenotype. The qPCR data are publicly available in the LeukoStage Database in which gene expression in malignant and non-malignant cells of different lineages can be explored graphically and differentially expressed genes can be identified. In addition, the LeukoStage Database can aid the functional analyses of next-generation sequencing data.
Collapse
Affiliation(s)
- K Polgárová
- CLIP - Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic
| | - M Vášková
- CLIP - Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic
| | - E Froňková
- CLIP - Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic
| | - L Slámová
- CLIP - Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic; University Hospital Motol, Czech Republic
| | - T Kalina
- CLIP - Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic; University Hospital Motol, Czech Republic
| | - E Mejstříková
- CLIP - Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic; University Hospital Motol, Czech Republic
| | - A Dobiášová
- CLIP - Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic
| | - K Fišer
- CLIP - Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic
| | - O Hrušák
- CLIP - Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic; University Hospital Motol, Czech Republic.
| |
Collapse
|
23
|
Niu YN, Liu QQ, Zhang SP, Yuan N, Cao Y, Cai JY, Lin WW, Xu F, Wang ZJ, Chen B, Wang JR. Alternative messenger RNA splicing of autophagic gene Beclin 1 in human B-cell acute lymphoblastic leukemia cells. Asian Pac J Cancer Prev 2014; 15:2153-8. [PMID: 24716949 DOI: 10.7314/apjcp.2014.15.5.2153] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Beclin 1 is a key factor for initiation and regulation of autophagy, which is a cellular catabolic process involved in tumorigenesis. To investigate the role of alternative splicing of Beclin1 in the regulation of autophagy in leukemia cells, Beclin1 mRNA from 6 different types of cell lines and peripheral blood mononuclear cells from 2 healthy volunteers was reversely transcribed, subcloned, and screened for alternative splicing. New transcript variants were analyzed by DNA sequencing. A transcript variant of Beclin 1 gene carrying a deletion of exon 11, which encoded a C-terminal truncation of Beclin 1 isoform, was found. The alternative isoform was assessed by bioinformatics, immunoblotting and subcellular localization. The results showed that this variable transcript is generated by alternative 3' splicing, and its translational product displayed a reduced activity in induction of autophagy by starvation, indicating that the spliced isoform might function as a dominant negative modulator of autophagy. Our findings suggest that the alternative splicing of Beclin 1 might play important roles in leukemogenesis regulated by autophagy.
Collapse
Affiliation(s)
- Yu-Na Niu
- Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, School of Medicine, Soochow University, Suzhou, China E-mail : ,
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
The tumor suppressor prostate apoptosis response-4 (Par-4) is regulated by mutant IDH1 and kills glioma stem cells. Acta Neuropathol 2014; 128:723-32. [PMID: 25135281 DOI: 10.1007/s00401-014-1334-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 08/09/2014] [Accepted: 08/09/2014] [Indexed: 10/24/2022]
Abstract
Prostate apoptosis response-4 (Par-4) is an endogenous tumor suppressor that selectively induces apoptosis in a variety of cancers. Although it has been the subject of intensive research in other cancers, less is known about its significance in gliomas, including whether it is regulated by key driver mutations, has therapeutic potential against glioma stem cells (GSCs), and/or is a prognostic marker. We found that patient-derived gliomas with mutant isocitrate dehydrogenase 1 have markedly lower Par-4 expression (P < 0.0001), which was validated by The Cancer Genome Atlas dataset (P = 2.0 E-13). The metabolic product of mutant IDH1, D-2-hydroxyglutarate (2-HG), can suppress Par-4 transcription in vitro via inhibition of promoter activity as well as enhanced mRNA degradation, but interestingly not by direct DNA promoter hypermethylation. The Selective for Apoptosis induction in Cancer cells (SAC) domain within Par-4 is highly active against glioma cells, including orthotopic xenografts of patient-derived primary GSCs (P < 0.0001). Among high-grade gliomas that are IDH1 wild type, those that express more Par-4 have significantly longer median survival (18.4 vs. 8.0 months, P = 0.002), a finding confirmed in two external GBM cohorts. Together, these data suggest that Par-4 is a significant component of the mutant IDH1 phenotype, that the activity of 2-HG is complex and can extend beyond direct DNA hypermethylation, and that Par-4 is a promising therapeutic strategy against GSCs. Furthermore, not every effect of mutant IDH1 necessarily contributes to the overall favorable prognosis seen in such tumors; inhibition of Par-4 may be one such effect.
Collapse
|
25
|
Ortiz-Virumbrales M, Ruiz M, Hone E, Dolios G, Wang R, Morant A, Kottwitz J, Ozelius LJ, Gandy S, Ehrlich ME. Dystonia type 6 gene product Thap1: identification of a 50 kDa DNA-binding species in neuronal nuclear fractions. Acta Neuropathol Commun 2014; 2:139. [PMID: 25231164 PMCID: PMC4177242 DOI: 10.1186/s40478-014-0139-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 09/05/2014] [Indexed: 01/04/2023] Open
Abstract
Mutations in THAP1 result in dystonia type 6, with partial penetrance and variable phenotype. The goal of this study was to examine the nature and expression pattern of the protein product(s) of the Thap1 transcription factor (DYT6 gene) in mouse neurons, and to study the regional and developmental distribution, and subcellular localization of Thap1 protein. The goal was accomplished via overexpression and knock-down of Thap1 in the HEK293T cell line and in mouse striatal primary cultures and western blotting of embryonic Thap1-null tissue. The endogenous and transduced Thap1 isoforms were characterized using three different commercially available anti-Thap1 antibodies and validated by immunoprecipitation and DNA oligonucleotide affinity chromatography. We identified multiple, novel Thap1 species of apparent Mr 32 kDa, 47 kDa, and 50–52 kDa in vitro and in vivo, and verified the previously identified species at 29–30 kDa in neurons. The Thap1 species at the 50 kDa size range was exclusively detected in murine brain and testes and were located in the nuclear compartment. Thus, in addition to the predicted 25 kDa apparent Mr, we identified Thap1 species with greater apparent Mr that we speculate may be a result of posttranslational modifications. The neural localization of the 50 kDa species and its nuclear compartmentalization suggests that these may be key Thap1 species controlling neuronal gene transcription. Dysfunction of the neuronal 50 kDa species may therefore be implicated in the pathogenesis of DYT6.
Collapse
|
26
|
Mondal BC, Shim J, Evans CJ, Banerjee U. Pvr expression regulators in equilibrium signal control and maintenance of Drosophila blood progenitors. eLife 2014; 3:e03626. [PMID: 25201876 PMCID: PMC4185420 DOI: 10.7554/elife.03626] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/05/2014] [Indexed: 12/18/2022] Open
Abstract
Blood progenitors within the lymph gland, a larval organ that supports hematopoiesis in Drosophila melanogaster, are maintained by integrating signals emanating from niche-like cells and those from differentiating blood cells. We term the signal from differentiating cells the 'equilibrium signal' in order to distinguish it from the 'niche signal'. Earlier we showed that equilibrium signaling utilizes Pvr (the Drosophila PDGF/VEGF receptor), STAT92E, and adenosine deaminase-related growth factor A (ADGF-A) (Mondal et al., 2011). Little is known about how this signal initiates during hematopoietic development. To identify new genes involved in lymph gland blood progenitor maintenance, particularly those involved in equilibrium signaling, we performed a genetic screen that identified bip1 (bric à brac interacting protein 1) and Nucleoporin 98 (Nup98) as additional regulators of the equilibrium signal. We show that the products of these genes along with the Bip1-interacting protein RpS8 (Ribosomal protein S8) are required for the proper expression of Pvr.
Collapse
Affiliation(s)
- Bama Charan Mondal
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Jiwon Shim
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Department of Life Science, Hanyang University, Seoul, Republic of Korea
| | - Cory J Evans
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Utpal Banerjee
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, United States
| |
Collapse
|
27
|
Howard JM, Sanford JR. The RNAissance family: SR proteins as multifaceted regulators of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:93-110. [PMID: 25155147 DOI: 10.1002/wrna.1260] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 07/14/2014] [Indexed: 12/29/2022]
Abstract
Serine and arginine-rich (SR) proteins play multiple roles in the eukaryotic gene expression pathway. Initially described as constitutive and alternative splicing factors, now it is clear that SR proteins are key determinants of exon identity and function as molecular adaptors, linking the pre-messenger RNA (pre-mRNA) to the splicing machinery. In addition, now SR proteins are implicated in many aspects of mRNA and noncoding RNA (ncRNA) processing well beyond splicing. These unexpected roles, including RNA transcription, export, translation, and decay, may prove to be the rule rather than the exception. To simply define, this family of RNA-binding proteins as splicing factors belies the broader roles of SR proteins in post-transcriptional gene expression.
Collapse
Affiliation(s)
- Jonathan M Howard
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | | |
Collapse
|