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Cui L, Zheng J, Lin Y, Lin P, Lu Y, Zheng Y, Guo B, Zhao X. Decoding the ribosome's hidden language: rRNA modifications as key players in cancer dynamics and targeted therapies. Clin Transl Med 2024; 14:e1705. [PMID: 38797935 PMCID: PMC11128715 DOI: 10.1002/ctm2.1705] [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: 01/22/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Ribosomal RNA (rRNA) modifications, essential components of ribosome structure and function, significantly impact cellular proteomics and cancer biology. These chemical modifications transcend structural roles, critically shaping ribosome functionality and influencing cellular protein profiles. In this review, the mechanisms by which rRNA modifications regulate both rRNA functions and broader cellular physiological processes are critically discussed. Importantly, by altering the translational output, rRNA modifications can shift the cellular equilibrium towards oncogenesis, thus playing a key role in cancer development and progression. Moreover, a special focus is placed on the functions of mitochondrial rRNA modifications and their aberrant expression in cancer, an area with profound implications yet largely uncharted. Dysregulation in these modifications can lead to metabolic dysfunction and apoptosis resistance, hallmark traits of cancer cells. Furthermore, the current challenges and future perspectives in targeting rRNA modifications are highlighted as a therapeutic approach for cancer treatment. In conclusion, rRNA modifications represent a frontier in cancer research, offering novel insights and therapeutic possibilities. Understanding and harnessing these modifications can pave the way for breakthroughs in cancer treatment, potentially transforming the approach to combating this complex disease.
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Affiliation(s)
- Li Cui
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
- Division of Oral Biology and Medicine, School of DentistryUniversity of
California, Los AngelesLos AngelesUSA
| | - Jiarong Zheng
- Department of Dentistry, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Yunfan Lin
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Pei Lin
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Ye Lu
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Yucheng Zheng
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Bing Guo
- Department of Dentistry, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Xinyuan Zhao
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
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2
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Chen JL, Leeder WM, Morais P, Adachi H, Yu YT. Pseudouridylation-mediated gene expression modulation. Biochem J 2024; 481:1-16. [PMID: 38174858 DOI: 10.1042/bcj20230096] [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: 10/14/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
RNA-guided pseudouridylation, a widespread post-transcriptional RNA modification, has recently gained recognition for its role in cellular processes such as pre-mRNA splicing and the modulation of premature termination codon (PTC) readthrough. This review provides insights into its mechanisms, functions, and potential therapeutic applications. It examines the mechanisms governing RNA-guided pseudouridylation, emphasizing the roles of guide RNAs and pseudouridine synthases in catalyzing uridine-to-pseudouridine conversion. A key focus is the impact of RNA-guided pseudouridylation of U2 small nuclear RNA on pre-mRNA splicing, encompassing its influence on branch site recognition and spliceosome assembly. Additionally, the review discusses the emerging role of RNA-guided pseudouridylation in regulating PTC readthrough, impacting translation termination and genetic disorders. Finally, it explores the therapeutic potential of pseudouridine modifications, offering insights into potential treatments for genetic diseases and cancer and the development of mRNA vaccine.
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Affiliation(s)
- Jonathan L Chen
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, U.S.A
| | | | | | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, U.S.A
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, U.S.A
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3
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Tan Y, Wang Z, Wang Y, Tian X, Huang Y, Wu G, Lu J. Multi-omics analysis reveals PUS1 triggered malignancy and correlated with immune infiltrates in NSCLC. Aging (Albany NY) 2023; 15:12136-12154. [PMID: 37925171 PMCID: PMC10683629 DOI: 10.18632/aging.205169] [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: 06/19/2023] [Accepted: 09/26/2023] [Indexed: 11/06/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the main pathological type of lung cancer. In this study, multi-omics analysis revealed a significant increase of pseudouridine synthase 1 (PUS1) in NSCLC and the high expression of PUS1 was associated with shorter OS (Overall Survival), PFS (Progression Free Survival), and PPS (Post Progression Survival) of NSCLC patients. Clinical subgroup analysis showed that PUS1 may be involved in the occurrence and development of NSCLC. Besides, TIMER, ESTIMATE, and IPS analysis suggested that PUS1 expression was associated with immune cell infiltration, and the expression of PUS1 was significantly negatively correlated with DC cell infiltration. GESA analysis also indicated PUS1 may involve in DNA_REPAIR, E2F_TARGETS, MYC_TARGETS_V2, G2M_CHECKPOINT and MYC_TARGETS_V1 pathways and triggered NSCLC malignancy through MCM5 or XPO1. Furthermore, PUS1 may be a potential target for NSCLC therapy.
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Affiliation(s)
- Yonghuang Tan
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zhaotong Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, and Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yingzhao Wang
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiaolu Tian
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, and Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yunru Huang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, and Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Guoyong Wu
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jianjun Lu
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
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4
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Grieco JP, Compton SLE, Davis GN, Guinan J, Schmelz EM. Genetic and Functional Modifications Associated with Ovarian Cancer Cell Aggregation and Limited Culture Conditions. Int J Mol Sci 2023; 24:14867. [PMID: 37834315 PMCID: PMC10573375 DOI: 10.3390/ijms241914867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The aggregation of cancer cells provides a survival signal for disseminating cancer cells; however, the underlying molecular mechanisms have yet to be elucidated. Using qPCR gene arrays, this study investigated the changes in cancer-specific genes as well as genes regulating mitochondrial quality control, metabolism, and oxidative stress in response to aggregation and hypoxia in our progressive ovarian cancer models representing slow- and fast-developing ovarian cancer. Aggregation increased the expression of anti-apoptotic, stemness, epithelial-mesenchymal transition (EMT), angiogenic, mitophagic, and reactive oxygen species (ROS) scavenging genes and functions, and decreased proliferation, apoptosis, metabolism, and mitochondrial content genes and functions. The incorporation of stromal vascular cells (SVF) from obese mice into the spheroids increased DNA repair and telomere regulatory genes that may represent a link between obesity and ovarian cancer risk. While glucose had no effect, glutamine was essential for aggregation and supported proliferation of the spheroid. In contrast, low glucose and hypoxic culture conditions delayed adhesion and outgrowth capacity of the spheroids independent of their phenotype, decreased mitochondrial mass and polarity, and induced a shift of mitochondrial dynamics towards mitophagy. However, these conditions did not reduce the appearance of polarized mitochondria at adhesion sites, suggesting that adhesion signals that either reversed mitochondrial fragmentation or induced mitobiogenesis can override the impact of low glucose and oxygen levels. Thus, the plasticity of the spheroids' phenotype supports viability during dissemination, allows for the adaptation to changing conditions such as oxygen and nutrient availability. This may be critical for the development of an aggressive cancer phenotype and, therefore, could represent druggable targets for clinical interventions.
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Affiliation(s)
- Joseph P. Grieco
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061, USA;
| | - Stephanie L. E. Compton
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.E.C.); (G.D.N.)
| | - Grace N. Davis
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.E.C.); (G.D.N.)
| | - Jack Guinan
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.E.C.); (G.D.N.)
| | - Eva M. Schmelz
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.E.C.); (G.D.N.)
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5
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Yu P, Qu N, Zhu R, Hu J, Han P, Wu J, Tan L, Gan H, He C, Fang C, Lei Y, Li J, He C, Lan F, Shi X, Wei W, Wang Y, Ji Q, Yu FX, Wang YL. TERT accelerates BRAF mutant-induced thyroid cancer dedifferentiation and progression by regulating ribosome biogenesis. SCIENCE ADVANCES 2023; 9:eadg7125. [PMID: 37647391 PMCID: PMC10468137 DOI: 10.1126/sciadv.adg7125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023]
Abstract
TERT reactivation occurs frequently in human malignancies, especially advanced cancers. However, in vivo functions of TERT reactivation in cancer progression and the underlying mechanism are not fully understood. In this study, we expressed TERT and/or active BRAF (BRAF V600E) specifically in mouse thyroid epithelium. While BRAF V600E alone induced papillary thyroid cancer (PTC), coexpression of BRAF V600E and TERT resulted in poorly differentiated thyroid carcinoma (PDTC). Spatial transcriptome analysis revealed that tumors from mice coexpressing BRAF V600E and TERT were highly heterogeneous, and cell dedifferentiation was positively correlated with ribosomal biogenesis. Mechanistically, TERT boosted ribosomal RNA (rRNA) expression and protein synthesis by interacting with multiple proteins involved in ribosomal biogenesis. Furthermore, we found that CX-5461, an rRNA transcription inhibitor, effectively blocked proliferation and induced redifferentiation of thyroid cancer. Thus, TERT promotes thyroid cancer progression by inducing cancer cell dedifferentiation, and ribosome inhibition represents a potential strategy to treat TERT-reactivated cancers.
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Affiliation(s)
- Pengcheng Yu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning Qu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rui Zhu
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaqian Hu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peizhen Han
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiahao Wu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Licheng Tan
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hualei Gan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Cong He
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chuantao Fang
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yubin Lei
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Li
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenxi He
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Lan
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Shi
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenjun Wei
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fa-Xing Yu
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Long Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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6
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Tang Q, Li L, Wang Y, Wu P, Hou X, Ouyang J, Fan C, Li Z, Wang F, Guo C, Zhou M, Liao Q, Wang H, Xiang B, Jiang W, Li G, Zeng Z, Xiong W. RNA modifications in cancer. Br J Cancer 2023; 129:204-221. [PMID: 37095185 PMCID: PMC10338518 DOI: 10.1038/s41416-023-02275-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
Currently, more than 170 modifications have been identified on RNA. Among these RNA modifications, various methylations account for two-thirds of total cases and exist on almost all RNAs. Roles of RNA modifications in cancer are garnering increasing interest. The research on m6A RNA methylation in cancer is in full swing at present. However, there are still many other popular RNA modifications involved in the regulation of gene expression post-transcriptionally besides m6A RNA methylation. In this review, we focus on several important RNA modifications including m1A, m5C, m7G, 2'-O-Me, Ψ and A-to-I editing in cancer, which will provide a new perspective on tumourigenesis by peeking into the complex regulatory network of epigenetic RNA modifications, transcript processing, and protein translation.
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Affiliation(s)
- Qiling Tang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Lvyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Pan Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Xiangchan Hou
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Jiawei Ouyang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Chunmei Fan
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Zheng Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Hui Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Weihong Jiang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China.
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Yuan H, Qin X, Yang Q, Liu L, Fang Z, Fan Y, Xu D. Dyskerin and telomerase RNA component are sex-differentially associated with outcomes and Sunitinib response in patients with clear cell renal cell carcinoma. Biol Sex Differ 2023; 14:46. [PMID: 37434223 DOI: 10.1186/s13293-023-00526-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/16/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) displays sex-biased incidence, outcomes, molecular alterations and treatment efficacy; however, clinical managements are largely identical in male and female patients. Moreover, many biomarkers have been identified as predictors for ccRCC outcomes and response to therapeutic drugs, such as multitargeted tyrosine-kinase receptor (TKR) inhibitors, but little is known about their sex-specificity. Dyskerin (DKC1), encoded by the DKC1 gene within Xq28, is a telomerase co-factor stabilizing telomerase RNA component (TERC) and overexpressed in various cancers. Here, we determined whether DKC1 and/or TERC affect ccRCC sex-differentially. METHODS DKC1 and TERC expression in primary ccRCC tumors was assessed using RNA sequencing and qPCR. DKC1 association with molecular alterations and overall or progression-free survival (OS or PFS) was analyzed in the TCGA cohort of ccRCC. The IMmotion 151 and 150 ccRCC cohorts were analyzed to evaluate impacts of DKC1 and TERC on Sunitinib response and PFS. RESULTS DKC1 and TERC expression was significantly upregulated in ccRCC tumors. High DKC1 expression predicts shorter PFS independently in female but not male patients. Tumors in the female DKC1-high group exhibited more frequent alterations in PIK3CA, MYC and TP53 genes. Analyses of the IMmotion 151 ccRCC cohort treated with the TKR inhibitor Sunitinib showed that female patients in the DKC1-high group was significantly associated with lower response rates (P = 0.021) accompanied by markedly shortened PFS (6.1 vs 14.2 months, P = 0.004). DKC1 and TERC expression correlated positively with each other, and higher TERC expression predicted poor Sunitinib response (P = 0.031) and shorter PFS (P = 0.004), too. However, DKC1 rather than TERC acted as an independent predictor (P < 0.001, HR = 2.0, 95% CI 1.480-2.704). In male patients, DKC1 expression was associated with neither Sunitinib response (P = 0.131) nor PFS (P = 0.184), while higher TERC levels did not predict response rates. Similar results were obtained from the analysis of the Sunitinib-treated IMmotion 150 ccRCC patients. CONCLUSIONS DKC1 serves as an independent female-specific predictor for survival and Sunitinib efficacy in ccRCC, which contribute to better understanding of the sex-biased ccRCC pathogenesis and improve personalized interventions of ccRCC.
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Affiliation(s)
- Huiyang Yuan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Xin Qin
- Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Qingya Yang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Li Liu
- School of Nursing, Beijing University of Chinese Medicine, Beijing, 100191, China
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, China.
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, China.
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institute and Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.
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8
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Barozzi C, Zacchini F, Corradini AG, Morara M, Serra M, De Sanctis V, Bertorelli R, Dassi E, Montanaro L. Alterations of ribosomal RNA pseudouridylation in human breast cancer. NAR Cancer 2023; 5:zcad026. [PMID: 37260601 PMCID: PMC10227372 DOI: 10.1093/narcan/zcad026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023] Open
Abstract
RNA modifications are key regulatory factors for several biological and pathological processes. They are abundantly represented on ribosomal RNA (rRNA), where they contribute to regulate ribosomal function in mRNA translation. Altered RNA modification pathways have been linked to tumorigenesis as well as to other human diseases. In this study we quantitatively evaluated the site-specific pseudouridylation pattern in rRNA in breast cancer samples exploiting the RBS-Seq technique involving RNA bisulfite treatment coupled with a new NGS approach. We found a wide variability among patients at different sites. The most dysregulated positions in tumors turned out to be hypermodified with respect to a reference RNA. As for 2'O-methylation level of rRNA modification, we detected variable and stable pseudouridine sites, with the most stable sites being the most evolutionary conserved. We also observed that pseudouridylation levels at specific sites are related to some clinical and bio-pathological tumor features and they are able to distinguish different patient clusters. This study is the first example of the contribution that newly available high-throughput approaches for site specific pseudouridine detection can provide to the understanding of the intrinsic ribosomal changes occurring in human tumors.
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Affiliation(s)
- Chiara Barozzi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Federico Zacchini
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Angelo Gianluca Corradini
- Unit of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Monica Morara
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Margherita Serra
- Unit of Breast Surgery, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Veronica De Sanctis
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Roberto Bertorelli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Lorenzo Montanaro
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
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9
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Kim T. Nucleic Acids in Cancer Diagnosis and Therapy. Cancers (Basel) 2023; 15:cancers15071938. [PMID: 37046599 PMCID: PMC10093127 DOI: 10.3390/cancers15071938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
Nucleic acids include two main classes: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) [...].
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Affiliation(s)
- Taewan Kim
- Department of Anatomy, Histology and Developmental Biology, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518055, China
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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10
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Zacchini F, Venturi G, De Sanctis V, Bertorelli R, Ceccarelli C, Santini D, Taffurelli M, Penzo M, Treré D, Inga A, Dassi E, Montanaro L. Human dyskerin binds to cytoplasmic H/ACA-box-containing transcripts affecting nuclear hormone receptor dependence. Genome Biol 2022; 23:177. [PMID: 35996163 PMCID: PMC9394076 DOI: 10.1186/s13059-022-02746-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 08/11/2022] [Indexed: 12/05/2022] Open
Abstract
Background Dyskerin is a nuclear protein involved in H/ACA box snoRNA-guided uridine modification of RNA. In humans, its defective function is associated with cancer development and induces specific post-transcriptional alterations of gene expression. In this study, we seek to unbiasedly identify mRNAs regulated by dyskerin in human breast cancer-derived cells. Results We find that dyskerin depletion affects the expression and the association with polysomes of selected mRNA isoforms characterized by the retention of H/ACA box snoRNA-containing introns. These snoRNA retaining transcripts (snoRTs) are bound by dyskerin in the cytoplasm in the form of shorter 3′ snoRT fragments. We then characterize the whole cytoplasmic dyskerin RNA interactome and find both H/ACA box snoRTs and protein-coding transcripts which may be targeted by the snoRTs’ guide properties. Since a fraction of these protein-coding transcripts is involved in the nuclear hormone receptor binding, we test to see if this specific activity is affected by dyskerin. Obtained results indicate that dyskerin dysregulation may alter the dependence on nuclear hormone receptor ligands in breast cancer cells. These results are paralleled by consistent observations on the outcome of primary breast cancer patients stratified according to their tumor hormonal status. Accordingly, experiments in nude mice show that the reduction of dyskerin levels in estrogen-dependent cells favors xenograft development in the absence of estrogen supplementation. Conclusions Our work suggests a cytoplasmic function for dyskerin which could affect mRNA post-transcriptional networks relevant for nuclear hormone receptor functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02746-3.
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Affiliation(s)
- Federico Zacchini
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Centro di Ricerca Biomedica Applicata - CRBA, Università̀ di Bologna, Policlinico di Sant'Orsola, I-40138, Bologna, Italy
| | - Giulia Venturi
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Centro di Ricerca Biomedica Applicata - CRBA, Università̀ di Bologna, Policlinico di Sant'Orsola, I-40138, Bologna, Italy
| | - Veronica De Sanctis
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Roberto Bertorelli
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Claudio Ceccarelli
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Unità Operativa di Anatomia e Istologia Patologica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy
| | - Donatella Santini
- Unità Operativa di Anatomia e Istologia Patologica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy
| | - Mario Taffurelli
- Unità Operativa di Chirurgia Senologica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy.,Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy
| | - Marianna Penzo
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Centro di Ricerca Biomedica Applicata - CRBA, Università̀ di Bologna, Policlinico di Sant'Orsola, I-40138, Bologna, Italy
| | - Davide Treré
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy
| | - Alberto Inga
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Erik Dassi
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Lorenzo Montanaro
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy. .,Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy.
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11
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Liu Y, Zhu T, Jiang Y, Bu J, Zhu X, Gu X. The Key Role of RNA Modification in Breast Cancer. Front Cell Dev Biol 2022; 10:885133. [PMID: 35721510 PMCID: PMC9198488 DOI: 10.3389/fcell.2022.885133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/25/2022] [Indexed: 12/09/2022] Open
Abstract
The modulation of the function and expression of epigenetic regulators of RNA modification has gradually become the hotspot of cancer research. Studies have shown that alteration of epigenetic modifications can promote the development and metastasis of breast cancer. This review highlights the progress in characterization of the link between RNA modification and the prognosis, carcinogenesis and treatment of breast cancer, which may provide a new theoretical basis for development of effective strategies for monitoring of breast cancer based on epigenetics.
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12
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Barozzi C, Zacchini F, Asghar S, Montanaro L. Ribosomal RNA Pseudouridylation: Will Newly Available Methods Finally Define the Contribution of This Modification to Human Ribosome Plasticity? Front Genet 2022; 13:920987. [PMID: 35719370 PMCID: PMC9198423 DOI: 10.3389/fgene.2022.920987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
In human rRNA, at least 104 specific uridine residues are modified to pseudouridine. Many of these pseudouridylation sites are located within functionally important ribosomal domains and can influence ribosomal functional features. Until recently, available methods failed to reliably quantify the level of modification at each specific rRNA site. Therefore, information obtained so far only partially explained the degree of regulation of pseudouridylation in different physiological and pathological conditions. In this focused review, we provide a summary of the methods that are now available for the study of rRNA pseudouridylation, discussing the perspectives that newly developed approaches are offering.
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Affiliation(s)
- Chiara Barozzi
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
| | - Federico Zacchini
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
| | - Sidra Asghar
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
| | - Lorenzo Montanaro
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- *Correspondence: Lorenzo Montanaro,
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13
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Wu F, Zhang L, Wu P, Wu Y, Zhang T, Zhang D, Tian J. The Potential Role of Small Nucleolar RNAs in Cancers – An Evidence Map. Int J Gen Med 2022; 15:3851-3864. [PMID: 35431571 PMCID: PMC9005336 DOI: 10.2147/ijgm.s352333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/29/2022] [Indexed: 12/11/2022] Open
Abstract
Purpose Cancer seriously endangers human health in every country of the world. New evidence shows that small nucleolar RNAs play important roles in tumorigenesis. Herein, we created this evidence map to systematically assess the impact of dysregulated snoRNAs on cancers. Methods We searched four databases to February 2022 using the keywords, “carcinoma”, “neoplasms”, “tumor”, “cancer”, “snoRNA”, and “small nucleolar rna”. The research data were independently screened by two reviewers. Bubble plot, mind map, heatmap were used to depict the relationship between snoRNAs and cancers. Results In total, 102 studies met the inclusion criteria and were analyzed in this evidence map. In this study, we found that dysregulated snoRNAs were statistically associated with the clinicopathological characteristics of cancer patients, and affected tumor cell phenotypes. Abnormally expressed snoRNAs were associated with poor survival in cancer patients. Current research confirmed that snoRNAs have good diagnostic efficiency for cancers. snoRNAs could modulate biological processes and signaling pathways of different cancer cells by altering rRNA, regulating mRNA, and recruiting protein factors. Conclusion Taken all together, ectopic snoRNAs may serve as new biomarkers for clinical assessment, diagnostic, prognostic prediction of cancer patients, and provide a potential therapeutic strategy for cancer treatment. This article provided a visual analysis of existing evidence on snoRNAs and cancers, which can offer useful information for different researchers interested in snoRNAs.
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Affiliation(s)
- Fanqi Wu
- Department of Respiratory, Lanzhou University Second Hospital, Lanzhou, Gansu Province, People’s Republic of China
| | - Longguo Zhang
- The Second Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, People’s Republic of China
| | - Pingfan Wu
- Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People’s Liberation Army, Lanzhou, Gansu Province, People’s Republic of China
| | - Yi Wu
- The Second Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, People’s Republic of China
| | - Tao Zhang
- Department of Endocrinology and Metabolism, Lanzhou University Second Hospital, Lanzhou, Gansu Province, People’s Republic of China
| | - Dekui Zhang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, Gansu Province, People’s Republic of China
- Correspondence: Dekui Zhang; Jinhui Tian, Tel +86 139 1978 8616; +86 136 1934 2312, Email ;
| | - Jinhui Tian
- Evidence-Based Medicine Center, Lanzhou University, Lanzhou, Gansu Province, People’s Republic of China
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14
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Cava C, Armaos A, Lang B, Tartaglia GG, Castiglioni I. Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes. Sci Rep 2022; 12:693. [PMID: 35027621 PMCID: PMC8758778 DOI: 10.1038/s41598-021-04664-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is a heterogeneous disease classified into four main subtypes with different clinical outcomes, such as patient survival, prognosis, and relapse. Current genetic tests for the differential diagnosis of BC subtypes showed a poor reproducibility. Therefore, an early and correct diagnosis of molecular subtypes is one of the challenges in the clinic. In the present study, we identified differentially expressed genes, long non-coding RNAs and RNA binding proteins for each BC subtype from a public dataset applying bioinformatics algorithms. In addition, we investigated their interactions and we proposed interacting biomarkers as potential signature specific for each BC subtype. We found a network of only 2 RBPs (RBM20 and PCDH20) and 2 genes (HOXB3 and RASSF7) for luminal A, a network of 21 RBPs and 53 genes for luminal B, a HER2-specific network of 14 RBPs and 30 genes, and a network of 54 RBPs and 302 genes for basal BC. We validated the signature considering their expression levels on an independent dataset evaluating their ability to classify the different molecular subtypes with a machine learning approach. Overall, we achieved good performances of classification with an accuracy >0.80. In addition, we found some interesting novel prognostic biomarkers such as RASSF7 for luminal A, DCTPP1 for luminal B, DHRS11, KLC3, NAGS, and TMEM98 for HER2, and ABHD14A and ADSSL1 for basal. The findings could provide preliminary evidence to identify putative new prognostic biomarkers and therapeutic targets for individual breast cancer subtypes.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, 20090, Segrate-Milan, Milan, Italy.
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, C/ Dr. Aiguader 88, 08003, Barcelona, Spain.,RNA System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano Di Tecnologia (IIT), Via Morego 30, 16163, Genoa, Italy
| | - Benjamin Lang
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, C/ Dr. Aiguader 88, 08003, Barcelona, Spain.,Department of Structural Biology and Center for Data Driven Discovery (C3D), St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Gian G Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, C/ Dr. Aiguader 88, 08003, Barcelona, Spain.,RNA System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano Di Tecnologia (IIT), Via Morego 30, 16163, Genoa, Italy.,Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Isabella Castiglioni
- Department of Physics "Giuseppe Occhialini", University of Milan-Bicocca Piazza dell'Ateneo Nuovo, 1 - 20126, Milan, Italy
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15
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The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells. Cancers (Basel) 2021; 13:cancers13246261. [PMID: 34944881 PMCID: PMC8699117 DOI: 10.3390/cancers13246261] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
Background: The transcriptional activity of estrogen receptor α (ERα) in breast cancer (BC) is extensively characterized. Our group has previously shown that ERα controls the expression of a number of genes in its unliganded form (apoERα), among which a large group of RNA-binding proteins (RBPs) encode genes, suggesting its role in the control of co- and post-transcriptional events. Methods: apoERα-mediated RNA processing events were characterized by the analysis of transcript usage and alternative splicing changes in an RNA-sequencing dataset from MCF-7 cells after siRNA-induced ERα downregulation. Results: ApoERα depletion induced an expression change of 681 RBPs, including 84 splicing factors involved in translation, ribonucleoprotein complex assembly, and 3′end processing. ApoERα depletion results in 758 isoform switching events with effects on 3′end length and the splicing of alternative cassette exons. The functional enrichment of these events shows that post-transcriptional regulation is part of the mechanisms by which apoERα controls epithelial-to-mesenchymal transition and BC cell proliferation. In primary BCs, the inclusion levels of the experimentally identified alternatively spliced exons are associated with overall and disease-free survival. Conclusion: Our data supports the role of apoERα in maintaining the luminal phenotype of BC cells by extensively regulating gene expression at the alternative splicing level.
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16
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Garus A, Autexier C. Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance. RNA (NEW YORK, N.Y.) 2021; 27:1441-1458. [PMID: 34556550 PMCID: PMC8594475 DOI: 10.1261/rna.078953.121] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Dyskerin and its homologs are ancient and conserved enzymes that catalyze the most common post-transcriptional modification found in cells, pseudouridylation. The resulting pseudouridines provide stability to RNA molecules and regulate ribosome biogenesis and splicing events. Dyskerin does not act independently-it is the core component of a protein heterotetramer, which associates with RNAs that contain the H/ACA motif. The variety of H/ACA RNAs that guide the function of this ribonucleoprotein (RNP) complex highlights the diversity of cellular processes in which dyskerin participates. When associated with small nucleolar (sno) RNAs, it regulates ribosomal (r) RNAs and ribosome biogenesis. By interacting with small Cajal body (sca) RNAs, it targets small nuclear (sn) RNAs to regulate pre-mRNA splicing. As a component of the telomerase holoenzyme, dyskerin binds to the telomerase RNA to modulate telomere maintenance. In a disease context, dyskerin malfunction can result in multiple detrimental phenotypes. Mutations in DKC1, the gene that encodes dyskerin, cause the premature aging syndrome X-linked dyskeratosis congenita (X-DC), a still incurable disorder that typically leads to bone marrow failure. In this review, we present the classical and most recent findings on this essential protein, discussing the evolutionary, structural, and functional aspects of dyskerin and the H/ACA RNP. The latest research underscores the role that dyskerin plays in the regulation of gene expression, translation efficiency, and telomere maintenance, along with the impacts that defective dyskerin has on aging, cell proliferation, haematopoietic potential, and cancer.
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Affiliation(s)
- Alexandre Garus
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
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17
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Kumari K, Groza P, Aguilo F. Regulatory roles of RNA modifications in breast cancer. NAR Cancer 2021; 3:zcab036. [PMID: 34541538 PMCID: PMC8445368 DOI: 10.1093/narcan/zcab036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Collectively referred to as the epitranscriptome, RNA modifications play important roles in gene expression control regulating relevant cellular processes. In the last few decades, growing numbers of RNA modifications have been identified not only in abundant ribosomal (rRNA) and transfer RNA (tRNA) but also in messenger RNA (mRNA). In addition, many writers, erasers and readers that dynamically regulate the chemical marks have also been characterized. Correct deposition of RNA modifications is prerequisite for cellular homeostasis, and its alteration results in aberrant transcriptional programs that dictate human disease, including breast cancer, the most frequent female malignancy, and the leading cause of cancer-related death in women. In this review, we emphasize the major RNA modifications that are present in tRNA, rRNA and mRNA. We have categorized breast cancer-associated chemical marks and summarize their contribution to breast tumorigenesis. In addition, we describe less abundant tRNA modifications with related pathways implicated in breast cancer. Finally, we discuss current limitations and perspectives on epitranscriptomics for use in therapeutic strategies against breast and other cancers.
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Affiliation(s)
- Kanchan Kumari
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Paula Groza
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
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