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Lu Q, Wang J, Tao Y, Zhong J, Zhang Z, Feng C, Wang X, Li T, He R, Wang Q, Xie Y. Small Cajal Body-Specific RNA12 Promotes Carcinogenesis through Modulating Extracellular Matrix Signaling in Bladder Cancer. Cancers (Basel) 2024; 16:483. [PMID: 38339238 PMCID: PMC10854576 DOI: 10.3390/cancers16030483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Background: Small Cajal body-specific RNAs (scaRNAs) are a specific subset of small nucleolar RNAs (snoRNAs) that have recently emerged as pivotal contributors in diverse physiological and pathological processes. However, their defined roles in carcinogenesis remain largely elusive. This study aims to explore the potential function and mechanism of SCARNA12 in bladder cancer (BLCA) and to provide a theoretical basis for further investigations into the biological functionalities of scaRNAs. Materials and Methods: TCGA, GEO and GTEx data sets were used to analyze the expression of SCARNA12 and its clinicopathological significance in BLCA. Quantitative real-time PCR (qPCR) and in situ hybridization were applied to validate the expression of SCARNA12 in both BLCA cell lines and tissues. RNA sequencing (RNA-seq) combined with bioinformatics analyses were conducted to reveal the changes in gene expression patterns and functional pathways in BLCA patients with different expressions of SCARNA12 and T24 cell lines upon SCARNA12 knockdown. Single-cell mass cytometry (CyTOF) was then used to evaluate the tumor-related cell cluster affected by SCARNA12. Moreover, SCARNA12 was stably knocked down in T24 and UMUC3 cell lines by lentivirus-mediated CRISPR/Cas9 approach. The biological effects of SCARNA12 on the proliferation, clonogenic, migration, invasion, cell apoptosis, cell cycle, and tumor growth were assessed by in vitro MTT, colony formation, wound healing, transwell, flow cytometry assays, and in vivo nude mice xenograft models, respectively. Finally, a chromatin isolation by RNA purification (ChIRP) experiment was further conducted to delineate the potential mechanisms of SCARNA12 in BLCA. Results: The expression of SCARNA12 was significantly up-regulated in both BLCA tissues and cell lines. RNA-seq data elucidated that SCARAN12 may play a potential role in cell adhesion and extracellular matrix (ECM) related signaling pathways. CyTOF results further showed that an ECM-related cell cluster with vimentin+, CD13+, CD44+, and CD47+ was enriched in BLCA patients with high SCARNA12 expression. Additionally, SCARNA12 knockdown significantly inhibited the proliferation, colony formation, migration, and invasion abilities in T24 and UMUC3 cell lines. SCARNA12 knockdown prompted cell arrest in the G0/G1 and G2/M phase and promoted apoptosis in T24 and UMUC3 cell lines. Furthermore, SCARNA12 knockdown could suppress the in vivo tumor growth in nude mice. A ChIRP experiment further suggested that SCARNA12 may combine transcription factors H2AFZ to modulate the transcription program and then affect BLCA progression. Conclusions: Our study is the first to propose aberrant alteration of SCARNA12 and elucidate its potential oncogenic roles in BLCA via the modulation of ECM signaling. The interaction of SCARNA12 with the transcriptional factor H2AFZ emerges as a key contributor to the carcinogenesis and progression of BLCA. These findings suggest SCARNA12 may serve as a diagnostic biomarker and potential therapeutic target for the treatment of BLCA.
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Affiliation(s)
- Qinchen Lu
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (Q.L.); (J.W.)
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, China
| | - Jiandong Wang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (Q.L.); (J.W.)
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, China
| | - Yuting Tao
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
| | - Jialing Zhong
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;
| | - Chao Feng
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
| | - Xi Wang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
| | - Tianyu Li
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China;
| | - Rongquan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China;
| | - Qiuyan Wang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
| | - Yuanliang Xie
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (Q.L.); (J.W.)
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Gao L, Fan J, He J, Che X, Wang X, Han C. Small Nucleolar RNAs as Diagnostic and Prognostic Biomarkers in Cancer: A Systematic Review and Meta-Analysis. Technol Cancer Res Treat 2024; 23:15330338241245939. [PMID: 38752263 PMCID: PMC11102679 DOI: 10.1177/15330338241245939] [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: 09/16/2023] [Revised: 01/14/2024] [Accepted: 02/12/2024] [Indexed: 05/21/2024] Open
Abstract
OBJECTIVES Small nucleolar RNAs (snoRNAs) form clusters within the genome, representing a mysterious category of small non-coding RNAs. Research has demonstrated that aberrant snoRNAs can contribute to the development of various types of cancers. Recent studies have identified snoRNAs as potentially valuable biomarkers for the diagnosis or/and prognosis of cancers. However, there has been a lack of comprehensive reviews on prognostic and diagnostic snoRNAs across different types of cancers. METHODS We conducted a systematic search of various databases including Google Scholar, Medline, Cochrane, Scopus, PubMed, Embase, ScienceDirect, Ovid-Medline, Chinese National Knowledge Infrastructure, WanFang, and SinoMed with a time frame reception to December 30, 2022. A total of 49 relevant articles were included in our analysis, consisting of 21 articles focusing on diagnostic aspects and 41 articles focusing on prognostic aspects. Pooled odds ratio, 95% confidence intervals (CIs), and hazard ratio (HR) were utilized to evaluate clinical parameters and overall survival (OS), respectively. RESULT The findings indicated that area under the curve, sensitivity, and specificity were 0.85, 75%, and 80% in cancer, respectively. There was a possibility that snoRNAs had a positive impact on the diagnosis (risk ratio, RR = 2.95, 95% CI: 2.75-3.16, P = 0.000) and OS (HR = 1) in cancer. Additionally, abnormally expressed snoRNAs were associated with a positive impact on OS time for chronic lymphocytic leukemia (HR: 0.88, 95%Cl: 0.69-1.11, P < 0.00001), colon adenocarcinoma (HR: 0.97, 95%Cl: 0.91-1.03, P < 0.0001), and ovarian cancer (HR: 0.98, 95%Cl: 0.98-0.99, P < 0.00001). However, dysregulated snoRNAs of colon cancer and colorectal cancer had a negative impact on OS time (HR = 3.01 and 1.01 respectively, P < 0.0001). CONCLUSION The results strongly suggested that snoRNAs could serve as potential novel indicators for prognosis and diagnosis in cancers. This systematic review followed the guidelines of the Transparent Reporting of Systematic Review and Meta-Analyses (PROSPERO register: CRD42020209096).
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Affiliation(s)
- Liyun Gao
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
- Jiangxi Provincial Key Laboratory of Cell Precision Therapy, School of Basic Medical Sciences, Jiujiang University, China
| | - Junfei Fan
- School of Humanities, Shangluo University, Shangluo, China
| | - Jiayin He
- School of Literature and Journalism, South-central Minzu University, Wuhan, China
| | - Xiangxin Che
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Xin Wang
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Chunhua Han
- Internal Medicine, Jiujiang First People's Hospital, Jiujiang, China
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Beňačka R, Szabóová D, Guľašová Z, Hertelyová Z, Radoňak J. Non-Coding RNAs in Human Cancer and Other Diseases: Overview of the Diagnostic Potential. Int J Mol Sci 2023; 24:16213. [PMID: 38003403 PMCID: PMC10671391 DOI: 10.3390/ijms242216213] [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: 09/30/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are abundant single-stranded RNA molecules in human cells, involved in various cellular processes ranging from DNA replication and mRNA translation regulation to genome stability defense. MicroRNAs are multifunctional ncRNA molecules of 18-24 nt in length, involved in gene silencing through base-pair complementary binding to target mRNA transcripts. piwi-interacting RNAs are an animal-specific class of small ncRNAs sized 26-31 nt, responsible for the defense of genome stability via the epigenetic and post-transcriptional silencing of transposable elements. Long non-coding RNAs are ncRNA molecules defined as transcripts of more than 200 nucleotides, their function depending on localization, and varying from the regulation of cell differentiation and development to the regulation of telomere-specific heterochromatin modifications. The current review provides recent data on the several forms of small and long non-coding RNA's potential to act as diagnostic, prognostic or therapeutic target for various human diseases.
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Affiliation(s)
- Roman Beňačka
- Department of Pathophysiology, Medical Faculty, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (R.B.); (D.S.)
| | - Daniela Szabóová
- Department of Pathophysiology, Medical Faculty, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (R.B.); (D.S.)
| | - Zuzana Guľašová
- Center of Clinical and Preclinical Research MEDIPARK, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (Z.G.); (Z.H.)
| | - Zdenka Hertelyová
- Center of Clinical and Preclinical Research MEDIPARK, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (Z.G.); (Z.H.)
| | - Jozef Radoňak
- 1st Department of Surgery, Faculty of Medicine, Louis Pasteur University Hospital (UNLP) and Pavol Jozef Šafarik University, 04011 Košice, Slovakia
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Zhang H, Liu X, Zhang W, Deng J, Lin C, Qi Z, Li Y, Gu Y, Wang Q, Shen L, Wang Z. Oncogene SCARNA12 as a potential diagnostic biomarker for colorectal cancer. MOLECULAR BIOMEDICINE 2023; 4:37. [PMID: 37907779 PMCID: PMC10618143 DOI: 10.1186/s43556-023-00147-x] [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: 07/28/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive system, and represents a severe threat to the life and health of individuals. Increasing evidence supports the role of small nucleolar RNAs (snoRNAs) as critical regulatory gene in cancer development. Small Cajal body-specific RNAs (scaRNAs), a subtype of snoRNAs, are named for their subcellular localization within Cajal bodies. SCARNA12, which located at the intronic region of PHB2 in chromosome 12p13.31 with 270 nucleotides (nt) in length. It has been reported function as a diagnostic marker for cervical cancer. However, its biological functions and molecular mechanisms in CRC have yet to be elucidated. In this study, bioinformatics analysis revealed that SCARNA12 was highly expressed in CRC and positively correlated with poor prognosis in CRC patients. Additionally, SCARNA12 showed upregulated expression in CRC cell lines and clinical CRC tissue samples. Moreover, SCARNA12 overexpression in SW620 cells accelerated cell proliferation, suppressed the apoptosis rate, and enhanced tumorigenesis in vivo. The knockdown of SCARNA12 expression in HCT116 and HT29 cells resulted in contrasting effects. The functioning of SCARNA12 is mechanically independent of its host gene PHB2. Notably, the overexpression of SCARNA12 activated PI3K/AKT pathway in SW620 cells, and the malignancy degree of CRC cells was attenuated after treatment with MK2206 (a specific AKT inhibitor). Our findings demonstrated that SCARNA12 plays an oncogenic role in CRC progression and can be used as a potential diagnostic biomarker for CRC.
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Affiliation(s)
- Hong Zhang
- Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China
| | - Xin Liu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China
| | - Wencheng Zhang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China
| | - Jiarong Deng
- Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China
| | - Chuxian Lin
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China
| | - Zhenhua Qi
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China
| | - Yaqiong Li
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China
| | - Yongqing Gu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China
| | - Qi Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China.
| | - Liping Shen
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China.
| | - Zhidong Wang
- Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100039, China.
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Challakkara MF, Chhabra R. snoRNAs in hematopoiesis and blood malignancies: A comprehensive review. J Cell Physiol 2023; 238:1207-1225. [PMID: 37183323 DOI: 10.1002/jcp.31032] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNA molecules of highly variable size, usually ranging from 60 to 150 nucleotides. They are classified into H/ACA box snoRNAs, C/D box snoRNAs, and scaRNAs. Their functional profile includes biogenesis of ribosomes, processing of rRNAs, 2'-O-methylation and pseudouridylation of RNAs, alternative splicing and processing of mRNAs and the generation of small RNA molecules like miRNA. The snoRNAs have been observed to have an important role in hematopoiesis and malignant hematopoietic conditions including leukemia, lymphoma, and multiple myeloma. Blood malignancies arise in immune system cells or the bone marrow due to chromosome abnormalities. It has been estimated that annually over 1.25 million cases of blood cancer occur worldwide. The snoRNAs often show a differential expression profile in blood malignancies. Recent reports associate the abnormal expression of snoRNAs with the inhibition of apoptosis, uncontrolled cell proliferation, angiogenesis, and metastasis. This implies that targeting snoRNAs could be a potential way to treat hematologic malignancies. In this review, we describe the various functions of snoRNAs, their role in hematopoiesis, and the consequences of their dysregulation in blood malignancies. We also evaluate the potential of the dysregulated snoRNAs as biomarkers and therapeutic targets for blood malignancies.
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Affiliation(s)
- Mohamed Fahad Challakkara
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
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6
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Xiao H, Feng X, Liu M, Gong H, Zhou X. SnoRNA and lncSNHG: Advances of nucleolar small RNA host gene transcripts in anti-tumor immunity. Front Immunol 2023; 14:1143980. [PMID: 37006268 PMCID: PMC10050728 DOI: 10.3389/fimmu.2023.1143980] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
The small nucleolar RNA host genes (SNHGs) are a group of genes that can be transcript into long non-coding RNA SNHG (lncSNHG) and further processed into small nucleolar RNAs (snoRNAs). Although lncSNHGs and snoRNAs are well established to play pivotal roles in tumorigenesis, how lncSNHGs and snoRNAs regulate the immune cell behavior and function to mediate anti-tumor immunity remains further illustrated. Certain immune cell types carry out distinct roles to participate in each step of tumorigenesis. It is particularly important to understand how lncSNHGs and snoRNAs regulate the immune cell function to manipulate anti-tumor immunity. Here, we discuss the expression, mechanism of action, and potential clinical relevance of lncSNHGs and snoRNAs in regulating different types of immune cells that are closely related to anti-tumor immunity. By uncovering the changes and roles of lncSNHGs and snoRNAs in different immune cells, we aim to provide a better understanding of how the transcripts of SNHGs participate in tumorigenesis from an immune perspective.
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Affiliation(s)
- Hao Xiao
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Xin Feng
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Mengjun Liu
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Hanwen Gong
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Xiao Zhou
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- *Correspondence: Xiao Zhou,
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Ghazimoradi MH, Karimpour-Fard N, Babashah S. The Promising Role of Non-Coding RNAs as Biomarkers and Therapeutic Targets for Leukemia. Genes (Basel) 2023; 14:131. [PMID: 36672872 PMCID: PMC9859176 DOI: 10.3390/genes14010131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023] Open
Abstract
Early-stage leukemia identification is crucial for effective disease management and leads to an improvement in the survival of leukemia patients. Approaches based on cutting-edge biomarkers with excellent accuracy in body liquids provide patients with the possibility of early diagnosis with high sensitivity and specificity. Non-coding RNAs have recently received a great deal of interest as possible biomarkers in leukemia due to their participation in crucial oncogenic processes such as proliferation, differentiation, invasion, apoptosis, and their availability in body fluids. Recent studies have revealed a strong correlation between leukemia and the deregulated non-coding RNAs. On this basis, these RNAs are also great therapeutic targets. Based on these advantages, we tried to review the role of non-coding RNAs in leukemia. Here, the significance of several non-coding RNA types in leukemia is highlighted, and their potential roles as diagnostic, prognostic, and therapeutic targets are covered.
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Affiliation(s)
- Mohammad H. Ghazimoradi
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
| | - Naeim Karimpour-Fard
- Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
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Park S, Lee J, Kim J, Kim D, Lee JH, Pack SP, Seo M. Benchmark study for evaluating the quality of reference genomes and gene annotations in 114 species. Front Vet Sci 2023; 10:1128570. [PMID: 36896291 PMCID: PMC9988948 DOI: 10.3389/fvets.2023.1128570] [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: 12/20/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Introduction For reference genomes and gene annotations are key materials that can determine the limits of the molecular biology research of a species; however, systematic research on their quality assessment remains insufficient. Methods We collected reference assemblies, gene annotations, and 3,420 RNA-sequencing (RNA-seq) data from 114 species and selected effective indicators to simultaneously evaluate the reference genome quality of various species, including statistics that can be obtained empirically during the mapping process of short reads. Furthermore, we newly presented and applied transcript diversity and quantification success rates that can relatively evaluate the quality of gene annotations of various species. Finally, we proposed a next-generation sequencing (NGS) applicability index by integrating a total of 10 effective indicators that can evaluate the genome and gene annotation of a specific species. Results and discussion Based on these effective evaluation indicators, we successfully evaluated and demonstrated the relative accessibility of NGS applications in all species, which will directly contribute to determining the technological boundaries in each species. Simultaneously, we expect that it will be a key indicator to examine the direction of future development through relative quality evaluation of genomes and gene annotations in each species, including countless organisms whose genomes and gene annotations will be constructed in the future.
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Affiliation(s)
- Sinwoo Park
- Department of Computer and Information Science, Korea University, Sejong City, Republic of Korea
| | - Jinbaek Lee
- Department of Computer Convergence Software, Korea University, Sejong City, Republic of Korea
| | - Jaeryeong Kim
- Department of Computer and Information Science, Korea University, Sejong City, Republic of Korea
| | - Dohyeon Kim
- Department of Computer and Information Science, Korea University, Sejong City, Republic of Korea
| | - Jin Hyup Lee
- Department of Food and Biotechnology, Korea University, Sejong City, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong City, Republic of Korea
| | - Minseok Seo
- Department of Computer and Information Science, Korea University, Sejong City, Republic of Korea.,Department of Computer Convergence Software, Korea University, Sejong City, Republic of Korea
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Midsize noncoding RNAs in cancers: a new division that clarifies the world of noncoding RNA or an unnecessary chaos? Rep Pract Oncol Radiother 2022; 27:1077-1093. [PMID: 36632289 PMCID: PMC9826665 DOI: 10.5603/rpor.a2022.0123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/18/2022] [Indexed: 12/31/2022] Open
Abstract
Most of the human genome is made out of noncoding RNAs (ncRNAs). These ncRNAs do not code for proteins but carry a vast number of important functions in human cells such as: modification and processing other RNAs (tRNAs, rRNAs, snRNAs, snoRNAs, miRNAs), help in the synthesis of ribosome proteins, initiation of DNA replication, regulation of transcription, processing of pre-messenger mRNA during its maturation and much more. The ncRNAs also have a significant impact on many events that occur during carcinogenesis in cancer cells, such as: regulation of cell survival, cellular signaling, apoptosis, proliferation or even influencing the metastasis process. The ncRNAs may be divided based on their length, into short and long, where 200 nucleotides is the "magic" border. However, a new division was proposed, suggesting the creation of the additional group called midsize noncoding RNAs, with the length ranging from 50-400 nucleotides. This new group may include: transfer RNA (tRNA), small nuclear RNAs (snRNAs) with 7SK and 7SL, small nucleolar RNAs (snoRNAs), small Cajal body-specific RNAs (scaRNAs) and YRNAs. In this review their structure, biogenesis, function and influence on carcinogenesis process will be evaluated. What is more, a question will be answered of whether this new division is a necessity that clears current knowledge or just creates an additional misunderstanding in the ncRNA world?
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Dong J, Wang H, Zhang Z, Yang L, Qian X, Qian W, Han Y, Huang H, Qian P. Small but strong: Pivotal roles and potential applications of snoRNAs in hematopoietic malignancies. Front Oncol 2022; 12:939465. [PMID: 36033520 PMCID: PMC9413531 DOI: 10.3389/fonc.2022.939465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) belong to a family of noncoding RNAs that are 60-300 nucleotides in length, and they are classified into two classes according to their structure and function: C/D box snoRNAs, playing an essential role in 2’-O-methylation modification on ribosomal RNA; H/ACA box snoRNAs, involved in the pseudouridylation of rRNA. SnoRNAs with unclear functions, no predictable targets, and unusual subcellular locations are called orphan snoRNAs. Recent studies have revealed abnormal expression and demonstrated the pivotal roles of snoRNAs and their host genes in various types of hematological malignancies. This review discusses recent discoveries concerning snoRNAs in a variety of hematological malignancies, including multiple myeloma, lymphoma and leukemia, and sheds light on the application of snoRNAs as diagnostic and prognostic markers as well as therapeutic targets of hematological malignancies in the future.
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Affiliation(s)
- Jian Dong
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Hui Wang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Zhaoru Zhang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Lin Yang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Xinyue Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Wenchang Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Yingli Han
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - He Huang
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Pengxu Qian, ; He Huang,
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
- *Correspondence: Pengxu Qian, ; He Huang,
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11
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Small noncoding RNAs play superior roles in maintaining hematopoietic stem cell homeostasis. BLOOD SCIENCE 2022; 4:125-132. [DOI: 10.1097/bs9.0000000000000123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022] Open
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12
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Dysregulation of Small Nucleolar RNAs in B-Cell Malignancies. Biomedicines 2022; 10:biomedicines10061229. [PMID: 35740251 PMCID: PMC9219770 DOI: 10.3390/biomedicines10061229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/17/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) are responsible for post-transcriptional modification of ribosomal RNAs, transfer RNAs and small nuclear RNAs, and thereby have important regulatory functions in mRNA splicing and protein translation. Several studies have shown that snoRNAs are dysregulated in human cancer and may play a role in cancer initiation and progression. In this review, we focus on the role of snoRNAs in normal and malignant B-cell development. SnoRNA activity appears to be essential for normal B-cell differentiation and dysregulated expression of sno-RNAs is determined in B-cell acute lymphoblastic leukemia, chronic lymphocytic leukemia, B-cell non-Hodgkin’s lymphoma, and plasma cell neoplasms. SnoRNA expression is associated with cytogenetic/molecular subgroups and clinical outcome in patients with B-cell malignancies. Translocations involving snoRNAs have been described as well. Here, we discuss the different aspects of snoRNAs in B-cell malignancies and report on their role in oncogenic transformation, which may be useful for the development of novel diagnostic biomarkers or therapeutic targets.
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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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Abstract
Glioma, also known as glioblastoma multiforme (GBM), is the most prevalent and most lethal primary brain tumor in adults. Gliomas are highly invasive tumors with the highest death rate among all primary brain malignancies. Metastasis occurs as the tumor cells spread from the site of origin to another site in the brain. Metastasis is a multifactorial process, which depends on alterations in metabolism, genetic mutations, and the cancer microenvironment. During recent years, the scientific study of non-coding RNAs (ncRNAs) has led to new insight into the molecular mechanisms involved in glioma. Many studies have reported that ncRNAs play major roles in many biological procedures connected with the development and progression of glioma. Long ncRNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) are all types of ncRNAs, which are commonly dysregulated in GBM. Dysregulation of ncRNAs can facilitate the invasion and metastasis of glioma. The present review highlights some ncRNAs that have been associated with metastasis in GBM. miRNAs, circRNAs, and lncRNAs are discussed in detail with respect to their relevant signaling pathways involved in metastasis.
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Rastorgueva E, Liamina D, Panchenko I, Iurova E, Beloborodov E, Pogodina E, Dmitrii S, Slesarev S, Saenko Y. The effect of chromosome abnormalities on expression of SnoRNA in radioresistant and radiosensitive cell lines after irradiation. Cancer Biomark 2022; 34:545-553. [PMID: 35275519 DOI: 10.3233/cbm-210092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In this paper, we have studied the role of chromosomal abnormalities in the expression of small nucleolar RNAs (snoRNAs) of radioresistant (K562) and radiosensitive (HL-60) leukemia cell line. Cells were exposed to an X-ray dose of 4 Gy. SnoRNA expression was investigated using NGS sequencing. The distribution of expressed snoRNAs on chromosomes has been found to be different for two cell lines. The most significant differences in the expression of snoRNAs were found in the K562 cell line based on the analysis of the dynamics of log2fc values. The type of clustering, the number and type of snoRNAs slightly differed in the chromosomes with trisomy and monosomy and had a pronounced difference in pairs with marker chromosomes in both cell lines. In this study, we have demonstrated that chromosomal abnormalities alter the expression of snoRNA after irradiation. Trisomies and monosomies do not have such a noticeable effect on the expression of snoRNAs as the presence of marker chromosomes.
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Affiliation(s)
- Eugenia Rastorgueva
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian.,Department of General and Clinical Pharmacology and Microbiology, Faculty of Medicine, Ulyanovsk State University, Ulyanovsk, Russian
| | - Daria Liamina
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Ivan Panchenko
- Second Surgical Department, Ulyanovsk Oncology Center, Ulyanovsk, Russian
| | - Elena Iurova
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Evgenii Beloborodov
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Evgeniya Pogodina
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Sugak Dmitrii
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Sergei Slesarev
- Department of Biology, Ecology and Natural Resources Management, Faculty of Ecology, Ulyanovsk State University, Ulyanovsk, Russia
| | - Yury Saenko
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
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16
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Zhang S, Ding Y, Sun Z, Ge Y, Li Y, Han X, Xu Q, Zhou L, Chen Y, Xu H, Bai Y, Xu C, Ding H, Yan S, Wang W. Identification of Expression Pattern and Clinical Significance of the Small Cajal Body-specific RNA SCARNA16 in Hepatocellular Carcinoma. J Clin Transl Hepatol 2022; 10:104-111. [PMID: 35233378 PMCID: PMC8845156 DOI: 10.14218/jcth.2021.00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/21/2021] [Accepted: 04/27/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND AND AIMS For high morbidity and mortality, hepatocellular carcinoma (HCC) becomes a major health issue worldwide. Nowadays, numerous non-coding RNAs (ncRNAs) are known to regulate the occurrence and pathogenesis of tumors. Some ncRNAs have also been developed as tumor biomarkers and therapeutic targets. However, the potential function of the small Cajal body-specific RNA (scaRNA) SCARNA16, a newly identified ncRNA, remains to be explored in HCC. METHODS In both HCC cell lines and specimens from 120 enrolled patients, the expression values of SCARNA16 were detected. We divided patients into SCARNA16 high and low expression subgroups, and then analyzed the difference of various clinical characteristics and prognosis data between subgroups. RESULTS Compared to paired controls, SCARNA16 was significantly down-regulated in HCC cell lines and clinical specimens (p<0.01). Besides, HCC patients with lower SCARNA16 expression commonly presented with larger and more tumor lesions, more vessel carcinoma emboli, more capsular invasion and higher TNM stages (p<0.05). Moreover, SCARNA16 expression was negatively correlated with postoperative prognosis of HCC patients in 5-year follow-up, including tumor-free survival (TFS) (median time of low vs. high subgroups: 14 vs. 48 months, p=0.006) and overall survival (OS) (median time of low vs. high subgroups: 39 vs. 52 months, p=0.001). Besides, SCARNA16 acted as an independent prognostic biomarker in TFS (hazard ratio [HR]: 0.578, 95% CI: 0.345-0.969, p=0.038) and OS (HR: 0.366, 95% CI: 0.178-0.752, p=0.006). CONCLUSIONS Low expression patterns of SCARNA16 remarkably associated with severe clinical status and poor survival of patients, suggesting that SCARNA16 possesses potency as a novel biomarker for HCC.
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Affiliation(s)
- Sitong Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Zhongquan Sun
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Yao Ge
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Yanjie Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Xin Han
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Qianhui Xu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Liuzhi Zhou
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Yining Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Hao Xu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Yang Bai
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Chang Xu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Hao Ding
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Sheng Yan
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
- Correspondence to: Weilin Wang, Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88 Jiefang Road, Hangzhou, Zhejiang 310009, China. ORCID: https://orcid.org/0000-0001-9432-2649. Tel: +86-571-8778-3820, Fax: +86-571-8706-8001, E-mail: ; Sheng Yan, Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88 Jiefang Road, Hangzhou, Zhejiang 310009, China. ORCID: https://orcid.org/0000-0002-4153-3546. Tel: +86-571-8723-6688, Fax: +86-571-8723-6765, E-mail:
| | - Weilin Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
- Correspondence to: Weilin Wang, Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88 Jiefang Road, Hangzhou, Zhejiang 310009, China. ORCID: https://orcid.org/0000-0001-9432-2649. Tel: +86-571-8778-3820, Fax: +86-571-8706-8001, E-mail: ; Sheng Yan, Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88 Jiefang Road, Hangzhou, Zhejiang 310009, China. ORCID: https://orcid.org/0000-0002-4153-3546. Tel: +86-571-8723-6688, Fax: +86-571-8723-6765, E-mail:
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Huang R, Liao X, Li Q. Integrative genomic analysis of a novel small nucleolar RNAs prognostic signature in patients with acute myelocytic leukemia. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:2424-2452. [PMID: 35240791 DOI: 10.3934/mbe.2022112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This study mainly used The Cancer Genome Atlas (TCGA) RNA sequencing dataset to screen prognostic snoRNAs of acute myeloid leukemia (AML), and used for the construction of prognostic snoRNAs signature for AML. A total of 130 AML patients with RNA sequencing dataset were used for prognostic snoRNAs screenning. SnoRNAs co-expressed genes and differentially expressed genes (DEGs) were used for functional annotation, as well as gene set enrichment analysis (GSEA). Connectivity Map (CMap) also used for potential targeted drugs screening. Through genome-wide screening, we identified 30 snoRNAs that were significantly associated with the prognosis of AML. Then we used the step function to screen a prognostic signature composed of 14 snoRNAs (SNORD72, SNORD38, U3, SNORA73B, SNORD79, SNORA73, SNORD12B, SNORA74, SNORD116-12, SNORA65, SNORA14, snoU13, SNORA75, SNORA31), which can significantly divide AML patients into high- and low-risk groups. Through GSEA, snoRNAs co-expressed genes and DEGs functional enrichment analysis, we screened a large number of potential functional mechanisms of this prognostic signature in AML, such as phosphatidylinositol 3-kinase-Akt, Wnt, epithelial to mesenchymal transition, T cell receptors, NF-kappa B, mTOR and other classic cancer-related signaling pathways. In the subsequent targeted drug screening using CMap, we also identified six drugs that can be used for AML targeted therapy, they were alimemazine, MG-262, fluoxetine, quipazine, naltrexone and oxybenzone. In conclusion, our current study was constructed an AML prognostic signature based on the 14 prognostic snoRNAs, which may serve as a novel prognostic biomarker for AML.
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Affiliation(s)
- Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Qiaochuan Li
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
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18
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Genetic Profiling in Children With Acute Lymphoblastic Leukemia Referred for Allogeneic Hematopoietic Stem Cell Transplantation. Cancer Control 2022; 29:10732748211064776. [PMID: 35470705 PMCID: PMC9052811 DOI: 10.1177/10732748211064776] [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] [Indexed: 11/23/2022] Open
Abstract
Introduction Hematopoietic stem cell transplantation (HSCT) is the essential and often the
only curative therapeutic option in high risk and relapsed pediatric acute
lymphoblastic leukemia (ALL). Methods The objective of the study was to investigate whole-genome expression in
children with high risk or relapsed ALL referred for HSCT. Gene expression
was assessed in 18 children with ALL referred for HSCT (10 high risk, 8
relapsed; median age of 9.4 years) and in a control group of 38 obese
children (median age of 14.1 years). Whole-genome expression was assessed in
leukocytes using GeneChip® HumanGene 1.0 ST microarray. Results The analysis of genomic profiles revealed a significantly lower expression of
21 genes with a defined function, involved in immunoglobulin production,
lymphocyte function, or regulation of DNA processing in ALL patients
referred for HSCT compared with the control group. Conclusion Genome expression of patients with ALL in remission referred to HSCT revealed
deep immunosuppression of both B-cell and T-cell lineages, which may
increase the probability of donor cell engraftment.
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Barros-Silva D, Klavert J, Jenster G, Jerónimo C, Lafontaine DLJ, Martens-Uzunova ES. The role of OncoSnoRNAs and Ribosomal RNA 2'-O-methylation in Cancer. RNA Biol 2021; 18:61-74. [PMID: 34775914 PMCID: PMC8677010 DOI: 10.1080/15476286.2021.1991167] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ribosomes are essential nanomachines responsible for all protein production in cells. Ribosome biogenesis and function are energy costly processes, they are tightly regulated to match cellular needs. In cancer, major pathways that control ribosome biogenesis and function are often deregulated to ensure cell survival and to accommodate the continuous proliferation of tumour cells. Ribosomal RNAs (rRNAs) are abundantly modified with 2'-O-methylation (Nm, ribomethylation) being one of the most common modifications. In eukaryotic ribosomes, ribomethylation is performed by the methyltransferase Fibrillarin guided by box C/D small nucleolar RNAs (snoRNAs). Accumulating evidences indicate that snoRNA expression and ribosome methylation profiles are altered in cancer. Here we review our current knowledge on differential snoRNA expression and rRNA 2ʹ-O methylation in the context of human malignancies, and discuss the consequences and opportunities for cancer diagnostics, prognostics, and therapeutics.
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Affiliation(s)
- Daniela Barros-Silva
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Jonathan Klavert
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (Icbas-up), Porto, Portugal
| | - Denis L J Lafontaine
- Rna Molecular Biology, Fonds De La Recherche Scientifique (F.r.s./fnrs), Université Libre De Bruxelles (Ulb), BioPark Campus, Gosselies, Belgium
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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Fitz NF, Wang J, Kamboh MI, Koldamova R, Lefterov I. Small nucleolar RNAs in plasma extracellular vesicles and their discriminatory power as diagnostic biomarkers of Alzheimer's disease. Neurobiol Dis 2021; 159:105481. [PMID: 34411703 PMCID: PMC9382696 DOI: 10.1016/j.nbd.2021.105481] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
The clinical diagnosis of Alzheimer's disease, at its early stage, remains a difficult task. Advanced imaging technologies and laboratory assays to detect Aβ peptides Aβ42 and Aβ40, total and phosphorylated tau in CSF provide a set of biomarkers of developing AD brain pathology and facilitate the diagnostic process. The search for biofluid biomarkers, other than in CSF, and the development of biomarker assays have accelerated significantly and now represent the fastest-growing field in AD research. The goal of this study was to determine the differential enrichment of noncoding RNAs (ncRNAs) in plasma-derived extracellular vesicles (EV) of AD patients and Cognitively Normal controls (NC). Using RNA-seq, we profiled four significant classes of ncRNAs: miRNAs, snoRNAs, tRNAs, and piRNAs. We report a significant enrichment of SNORDs - a group of snoRNAs, in AD samples compared to NC. To verify the differential enrichment of two clusters of SNORDs - SNORD115 and SNORD116, localized on human chromosome 15q11-q13, we used plasma samples of an independent group of AD patients and NC. We applied ddPCR technique and identified SNORD115 and SNORD116 with a high discriminatory power to differentiate AD samples from NC. The results of our study present evidence that AD is associated with changes in the enrichment of SNORDs, transcribed from imprinted genomic loci, in plasma EV and provide a rationale to further explore the validity of those SNORDs as plasma biomarkers of AD.
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Affiliation(s)
- Nicholas F Fitz
- Department of Environmental & Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
| | - Jiebiao Wang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
| | - M Ilyas Kamboh
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
| | - Radosveta Koldamova
- Department of Environmental & Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America.
| | - Iliya Lefterov
- Department of Environmental & Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America.
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21
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Calvo Sánchez J, Köhn M. Small but Mighty-The Emerging Role of snoRNAs in Hematological Malignancies. Noncoding RNA 2021; 7:68. [PMID: 34842767 PMCID: PMC8629011 DOI: 10.3390/ncrna7040068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Over recent years, the long known class of small nucleolar RNAs (snoRNAs) have gained interest among the scientific community, especially in the clinical context. The main molecular role of this interesting family of non-coding RNAs is to serve as scaffolding RNAs to mediate site-specific RNA modification of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). With the development of new sequencing techniques and sophisticated analysis pipelines, new members of the snoRNA family were identified and global expression patterns in disease backgrounds could be determined. We will herein shed light on the current research progress in snoRNA biology and their clinical role by influencing disease outcome in hematological diseases. Astonishingly, in recent studies snoRNAs emerged as potent biomarkers in a variety of these clinical setups, which is also highlighted by the frequent deregulation of snoRNA levels in the hema-oncological context. However, research is only starting to reveal how snoRNAs might influence cellular functions and the connected disease hallmarks in hematological malignancies.
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Affiliation(s)
| | - Marcel Köhn
- Junior Research Group ‘RBPs and ncRNAs in Human Diseases’, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Saale, Germany;
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22
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Small nucleolar RNA is potential as a novel player in leukemogenesis and clinical application. BLOOD SCIENCE 2021; 3:122-131. [PMID: 35402848 PMCID: PMC8975097 DOI: 10.1097/bs9.0000000000000091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/21/2021] [Indexed: 12/19/2022] Open
Abstract
Lack of clarity of the mechanisms that underlie leukemogenesis obstructs the diagnosis, prognosis, and treatment of leukemia. Research has found that small nuclear RNA (snoRNA) plays an essential role in leukemia. These small non-coding RNAs are involved in ribosome biogenesis, including the 2′-O-methylation and pseudouridylation of precursor ribosomal RNA (pre-rRNA), and pre-rRNA splicing. Recently, many snoRNAs were found to be orphans that have no predictable RNA modification targets, but these RNAs have always been found to be located in different subcellular organelles, and they play diverse roles. Using high-throughput technology, snoRNA expression profiles have been revealed in leukemia, and some of the deregulated snoRNAs may regulate the cell cycle, differentiation, proliferation, and apoptosis in leukemic cells and confer drug resistance during leukemia treatment. In this review, we discuss the expression profiles and functions of snoRNAs, particularly orphan snoRNAs, in leukemia. It is possible that the dysregulated snoRNAs are promising diagnosis and prognosis markers for leukemia, which may serve as potential therapeutic targets in leukemia treatment.
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23
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Morabito F, Tripepi G, Moia R, Recchia AG, Boggione P, Mauro FR, Bossio S, D'Arrigo G, Martino EA, Vigna E, Storino F, Fronza G, Di Raimondo F, Rossi D, Condoluci A, Colombo M, Fais F, Fabris S, Foa R, Cutrona G, Gentile M, Montserrat E, Gaidano G, Ferrarini M, Neri A. Lymphocyte Doubling Time As A Key Prognostic Factor To Predict Time To First Treatment In Early-Stage Chronic Lymphocytic Leukemia. Front Oncol 2021; 11:684621. [PMID: 34408978 PMCID: PMC8366564 DOI: 10.3389/fonc.2021.684621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/05/2021] [Indexed: 12/23/2022] Open
Abstract
The prognostic role of lymphocyte doubling time (LDT) in chronic lymphocytic leukemia (CLL) was recognized more than three decades ago when the neoplastic clone’s biology was almost unknown. LDT was defined as the time needed for the peripheral blood lymphocyte count to double the of the initial observed value. Herein, the LDT prognostic value for time to first treatment (TTFT) was explored in our prospective O-CLL cohort and validated in in two additional CLL cohorts. Specifically, newly diagnosed Binet stage A CLL patients from 40 Italian Institutions, representative of the whole country, were prospectively enrolled into the O-CLL1-GISL protocol (clinicaltrial.gov identifier: NCT00917540). Two independent cohorts of newly diagnosed CLL patients recruited respectively at the Division of Hematology in Novara, Italy, and at the Hospital Clinic in Barcelona, Spain, were utilized as validation cohorts. In the training cohort, TTFT of patients with LDT >12 months was significantly longer related to those with a shorter LDT. At Cox multivariate regression model, LDT ≤ 12 months maintained a significant independent relationship with shorter TTFT along with IGHV unmutated (IGHVunmut) status, 11q and 17p deletions, elevated β2M, Rai stage I-II, and NOTCH1 mutations. Based on these statistics, two regression models were constructed including the same prognostic factors with or without the LDT. The model with the LTD provided a significantly better data fitting (χ2 = 8.25, P=0.0041). The risk prediction developed including LDT had better prognostic accuracy than those without LDT. Moreover, the Harrell’C index for the scores including LDT were higher than those without LDT, although the accepted 0.70 threshold exceeded in both cases. These findings were also confirmed when the same analysis was carried out according to TTFT’s explained variation. When data were further analyzed based on the combination between LDT and IGHV mutational status in the training and validation cohorts, IGHVunmut and LDT>12months group showed a predominant prognostic role over IGHVmut LTD ≤ 12 months (P=0.006) in the O-CLL validation cohort. However, this predominance was of borden-line significance (P=0.06) in the Barcelona group, while the significant prognostic impact was definitely lost in the Novara group. Overall, in this study, we demonstrated that LDT could be re-utilized together with the more sophisticated prognostic factors to manage the follow-up plans for Binet stage A CLL patients.
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Affiliation(s)
- Fortunato Morabito
- Department of Onco-Hematology Azienda Ospedaliera (AO) Cosenza, Biotechnology Research Unit, Cosenza, Italy.,Department of Hematology and Bone Marrow Transplant Unit, Augusta Victoria Hospital, Jerusalem, Israel
| | - Giovanni Tripepi
- Centro Nazionale Ricerca Istituto di Fisiologia Clinica (CNR-IFC), Research Unit of Reggio Calabria, Reggio Calabria, Italy
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Anna Grazia Recchia
- Department of Onco-Hematology Azienda Ospedaliera (AO) Cosenza, Biotechnology Research Unit, Cosenza, Italy
| | - Paola Boggione
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Francesca Romana Mauro
- Hematology, Department of Translational and Precision Medicine, 'Sapienza' University, Rome, Italy
| | - Sabrina Bossio
- Department of Onco-Hematology Azienda Ospedaliera (AO) Cosenza, Biotechnology Research Unit, Cosenza, Italy
| | - Graziella D'Arrigo
- Centro Nazionale Ricerca Istituto di Fisiologia Clinica (CNR-IFC), Research Unit of Reggio Calabria, Reggio Calabria, Italy
| | | | - Ernesto Vigna
- Department of Onco-Hematology AO Cosenza, Hematology Unit AO of Cosenza, Cosenza, Italy
| | - Francesca Storino
- Department of Onco-Hematology Azienda Ospedaliera (AO) Cosenza, Biotechnology Research Unit, Cosenza, Italy
| | - Gilberto Fronza
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Francesco Di Raimondo
- Division of Hematology, Policlinico, Department of Surgery and Medical Specialties, University of Catania, Catania, Italy
| | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Adalgisa Condoluci
- Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Monica Colombo
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Franco Fais
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Sonia Fabris
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Robin Foa
- Hematology, Department of Translational and Precision Medicine, 'Sapienza' University, Rome, Italy
| | - Giovanna Cutrona
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Massimo Gentile
- Department of Onco-Hematology AO Cosenza, Hematology Unit AO of Cosenza, Cosenza, Italy
| | - Emili Montserrat
- Department of Hematology, Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Manlio Ferrarini
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Antonino Neri
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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Sugai T, Osakabe M, Habano W, Tanaka Y, Eizuka M, Sugimoto R, Yanagawa N, Matsumoto T, Suzuki H. A genome-wide analysis of the molecular alterations occurring in the adenomatous and carcinomatous components of the same tumor based on the adenoma-carcinoma sequence. Pathol Int 2021; 71:582-593. [PMID: 34263942 PMCID: PMC8518074 DOI: 10.1111/pin.13129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/19/2021] [Indexed: 12/24/2022]
Abstract
Identification of molecular alterations occurring in the adenomatous and carcinomatous components within the same tumor would greatly enhance understanding of the neoplastic progression of colorectal cancer. We examined somatic copy number alterations (SCNAs) and mRNA expression at the corresponding loci involved in the adenoma–carcinoma sequence in the isolated adenomatous and cancer glands of the same tumor in 15 cases of microsatellite‐stable “carcinoma in adenoma,” using genome‐wide SNP and global gene expression arrays. Multiple copy‐neutral loss of heterozygosity events were detected at 4q13.2, 15q15.1, and 14q24.3 in the adenomatous component and at 4q13.2, 15q15.1, and 14q24.3 in the carcinomatous component. There were significant differences in the copy number (CN) gain frequencies at 20q11.21–q13.33, 8q13.3, 8p23.1, and 8q21.2–q22.2 between the adenomatous and carcinomatous components. Finally, we found a high frequency of five genotypes involving CN gain with upregulated expression of the corresponding gene (RPS21, MIR3654, RSP20, SNORD54, or ASPH) in the carcinomatous component, whereas none of these genotypes were detected in the adenomatous component. This finding is interesting in that CN gain with upregulated gene expression may enhance gene function and play a crucial role in the progression of an adenoma into a carcinomatous lesion.
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Affiliation(s)
- Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Mitsumasa Osakabe
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Wataru Habano
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Yoshihito Tanaka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Makoto Eizuka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Ryo Sugimoto
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Naoki Yanagawa
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal Medicine, Shiwagun'yahabachou, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, School of Medicine, Sapporo Medical University, Cyuuouku, Sapporo, Japan
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25
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Beneventi G, Munita R, Cao Thi Ngoc P, Madej M, Cieśla M, Muthukumar S, Krogh N, Nielsen H, Swaminathan V, Bellodi C. The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells. NAR Cancer 2021; 3:zcab026. [PMID: 34316713 PMCID: PMC8271217 DOI: 10.1093/narcan/zcab026] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/19/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023] Open
Abstract
Small Cajal body-specific RNAs (scaRNAs) guide post-transcriptional modification of spliceosomal RNA and, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here, we uncover that SCARNA15 directs alternative splicing (AS) and stress adaptation in cancer cells. Specifically, we find that SCARNA15 guides critical pseudouridylation (Ψ) of U2 spliceosomal RNA to fine-tune AS of distinct transcripts enriched for chromatin and transcriptional regulators in malignant cells. This critically impacts the expression and function of the key tumor suppressors ATRX and p53. Significantly, SCARNA15 loss impairs p53-mediated redox homeostasis and hampers cancer cell survival, motility and anchorage-independent growth. In sum, these findings highlight an unanticipated role for SCARNA15 and Ψ in directing cancer-associated splicing programs.
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Affiliation(s)
- Giulia Beneventi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Magdalena Madej
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Maciej Cieśla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Vinay Swaminathan
- Division of Oncology, Department of Clinical Sciences, Lund University, 22184, Lund, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
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26
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Deng T, Gong Y, Liao X, Wang X, Zhou X, Zhu G, Mo L. Integrative Analysis of a Novel Eleven-Small Nucleolar RNA Prognostic Signature in Patients With Lower Grade Glioma. Front Oncol 2021; 11:650828. [PMID: 34164339 PMCID: PMC8215672 DOI: 10.3389/fonc.2021.650828] [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: 01/08/2021] [Accepted: 05/12/2021] [Indexed: 12/13/2022] Open
Abstract
Objective The present study used the RNA sequencing (RNA-seq) dataset to identify prognostic snoRNAs and construct a prognostic signature of The Cancer Genome Atla (TCGA) lower grade glioma (LGG) cohort, and comprehensive analysis of this signature. Methods RNA-seq dataset of 488 patients from TCGA LGG cohort were included in this study. Comprehensive analysis including function enrichment, gene set enrichment analysis (GSEA), immune infiltration, cancer immune microenvironment, and connectivity map (CMap) were used to evaluate the snoRNAs prognostic signature. Results We identified 21 LGG prognostic snoRNAs and constructed a novel eleven-snoRNA prognostic signature for LGG patients. Survival analysis suggests that this signature is an independent prognostic risk factor for LGG, and the prognosis of LGG patients with a high-risk phenotype is poor (adjusted P = 0.003, adjusted hazard ratio = 2.076, 95% confidence interval = 1.290–3.340). GSEA and functional enrichment analysis suggest that this signature may be involved in the following biological processes and signaling pathways: such as cell cycle, Wnt, mitogen-activated protein kinase, janus kinase/signal transducer and activator of tran-ions, T cell receptor, nuclear factor-kappa B signaling pathway. CMap analysis screened out ten targeted therapy drugs for this signature: 15-delta prostaglandin J2, MG-262, vorinostat, 5155877, puromycin, anisomycin, withaferin A, ciclopirox, chloropyrazine and megestrol. We also found that high- and low-risk score phenotypes of LGG patients have significant differences in immune infiltration and cancer immune microenvironment. Conclusions The present study identified a novel eleven-snoRNA prognostic signature of LGG and performed a integrative analysis of its molecular mechanisms and relationship with tumor immunity.
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Affiliation(s)
- Teng Deng
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yizhen Gong
- Evidence-based Medicine Teaching and Research Section, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ligen Mo
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
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27
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Seddon AR, Liau Y, Pace PE, Miller AL, Das AB, Kennedy MA, Hampton MB, Stevens AJ. Genome-wide impact of hydrogen peroxide on maintenance DNA methylation in replicating cells. Epigenetics Chromatin 2021; 14:17. [PMID: 33761969 PMCID: PMC7992848 DOI: 10.1186/s13072-021-00388-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 12/22/2022] Open
Abstract
Background Environmental factors, such as oxidative stress, have the potential to modify the epigenetic landscape of cells. We have previously shown that DNA methyltransferase (DNMT) activity can be inhibited by sublethal doses of hydrogen peroxide (H2O2). However, site-specific changes in DNA methylation and the reversibility of any changes have not been explored. Using bead chip array technology, differential methylation was assessed in Jurkat T-lymphoma cells following exposure to H2O2. Results Sublethal H2O2 exposure was associated with an initial genome-wide decrease in DNA methylation in replicating cells, which was largely corrected 72 h later. However, some alterations were conserved through subsequent cycles of cell division. Significant changes to the variability of DNA methylation were also observed both globally and at the site-specific level. Conclusions This research indicates that increased exposure to H2O2 can result in long-term alterations to DNA methylation patterns, providing a mechanism for environmental factors to have prolonged impact on gene expression. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00388-6.
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Affiliation(s)
- Annika R Seddon
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand.
| | - Yusmiati Liau
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Paul E Pace
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Allison L Miller
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Andrew B Das
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Mark B Hampton
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Aaron J Stevens
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand.
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28
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Rodriguez PD, Paculova H, Kogut S, Heath J, Schjerven H, Frietze S. Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2021; 22:ijms22052683. [PMID: 33799946 PMCID: PMC7961854 DOI: 10.3390/ijms22052683] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.
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Affiliation(s)
- Princess D. Rodriguez
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Sophie Kogut
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Jessica Heath
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Department of Pediatrics, University of Vermont, Burlington, VT 05405, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA;
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Correspondence:
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29
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Transcriptomic Changes in Endothelial Cells Triggered by Na,K-ATPase Inhibition: A Search for Upstream Na +i/K +i Sensitive Genes. Int J Mol Sci 2020; 21:ijms21217992. [PMID: 33121152 PMCID: PMC7662270 DOI: 10.3390/ijms21217992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 12/14/2022] Open
Abstract
Stimulus-dependent elevation of intracellular Ca2+ affects gene expression via well-documented calmodulin-mediated signaling pathways. Recently, we found that the addition of extra- and intracellular Ca2+ chelators increased, rather than decreased, the number of genes expressed, and that this is affected by the elevation of [Na+]i/[K+]i-ratio. This assumes the existence of a novel Na+i/K+i-mediated Ca2+i-independent mechanism of excitation-transcription coupling. To identify upstream Na+i/K+i-sensitive genes, we examined the kinetics of transcriptomic changes in human umbilical vein endothelial cells (HUVEC) subjected to Na,K-ATPase inhibition by ouabain or K+-free medium. According to our data, microRNAs, transcription factors, and proteins involved in immune response and inflammation might be considered as key components of Na+i/K+i-mediated excitation-transcription coupling. Special attention was focused on the FOS gene and the possible mechanism of transcription regulation via G-quadruplexes, non-canonical secondary structures of nucleic acids, whose stability depends on [Na+]i/[K+]i-ratio. Verification of the [Na+]i/[K+]i-sensitive transcription regulation mechanism should be continued in forthcoming studies.
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30
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McCann KL, Kavari SL, Burkholder AB, Phillips BT, Hall TMT. H/ACA snoRNA levels are regulated during stem cell differentiation. Nucleic Acids Res 2020; 48:8686-8703. [PMID: 32710630 DOI: 10.1093/nar/gkaa612] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022] Open
Abstract
H/ACA small nucleolar RNAs (snoRNAs) guide pseudouridylation as part of a small nucleolar ribonucleoprotein complex (snoRNP). Disruption of H/ACA snoRNA levels in stem cells impairs pluripotency, yet it remains unclear how H/ACA snoRNAs contribute to differentiation. To determine if H/ACA snoRNA levels are dynamic during differentiation, we comprehensively profiled H/ACA snoRNA abundance in multiple murine cell types and during differentiation in three cellular models, including mouse embryonic stem cells and mouse myoblasts. We determined that the profiles of H/ACA snoRNA abundance are cell-type specific, and we identified a subset of snoRNAs that are specifically regulated during differentiation. Additionally, we demonstrated that a decrease in Snora27 abundance upon differentiation corresponds to a decrease in pseudouridylation of its target site within the E-site transfer RNA (tRNA) binding region of the 28S ribosomal RNA (rRNA) in the large ribosomal subunit. Together, these data point toward a potential model in which H/ACA snoRNAs are specifically regulated during differentiation to alter pseudouridylation and fine tune ribosome function.
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Affiliation(s)
- Kathleen L McCann
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Sanam L Kavari
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Adam B Burkholder
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Bart T Phillips
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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31
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Epitranscriptomics in Normal and Malignant Hematopoiesis. Int J Mol Sci 2020; 21:ijms21186578. [PMID: 32916783 PMCID: PMC7555315 DOI: 10.3390/ijms21186578] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/05/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Epitranscriptomics analyze the biochemical modifications borne by RNA and their downstream influence. From this point of view, epitranscriptomics represent a new layer for the control of genetic information and can affect a variety of molecular processes including the cell cycle and the differentiation. In physiological conditions, hematopoiesis is a tightly regulated process that produces differentiated blood cells starting from hematopoietic stem cells. Alteration of this process can occur at different levels in the pathway that leads from the genetic information to the phenotypic manifestation producing malignant hematopoiesis. This review focuses on the role of epitranscriptomic events that are known to be implicated in normal and malignant hematopoiesis, opening a new pathophysiological and therapeutic scenario. Moreover, an evolutionary vision of this mechanism will be provided.
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32
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Han C, Sun LY, Wang WT, Sun YM, Chen YQ. Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications. J Mol Cell Biol 2020; 11:886-898. [PMID: 31361891 PMCID: PMC6884712 DOI: 10.1093/jmcb/mjz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 12/25/2022] Open
Abstract
Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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33
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NEAT1 Long Isoform Is Highly Expressed in Chronic Lymphocytic Leukemia Irrespectively of Cytogenetic Groups or Clinical Outcome. Noncoding RNA 2020; 6:ncrna6010011. [PMID: 32182990 PMCID: PMC7151605 DOI: 10.3390/ncrna6010011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/19/2020] [Accepted: 03/08/2020] [Indexed: 12/15/2022] Open
Abstract
The biological role and therapeutic potential of long non-coding RNAs (lncRNAs) in chronic lymphocytic leukemia (CLL) are still open questions. Herein, we investigated the significance of the lncRNA NEAT1 in CLL. We examined NEAT1 expression in 310 newly diagnosed Binet A patients, in normal CD19+ B-cells, and other types of B-cell malignancies. Although global NEAT1 expression level was not statistically different in CLL cells compared to normal B cells, the median ratio of NEAT1_2 long isoform and global NEAT1 expression in CLL samples was significantly higher than in other groups. NEAT1_2 was more expressed in patients carrying mutated IGHV genes. Concerning cytogenetic aberrations, NEAT1_2 expression in CLL with trisomy 12 was lower with respect to patients without alterations. Although global NEAT1 expression appeared not to be associated with clinical outcome, patients with the lowest NEAT1_2 expression displayed the shortest time to first treatment; however, a multivariate regression analysis showed that the NEAT1_2 risk model was not independent from other known prognostic factors, particularly the IGHV mutational status. Overall, our data prompt future studies to investigate whether the increased amount of the long NEAT1_2 isoform detected in CLL cells may have a specific role in the pathology of the disease.
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34
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Huang H, Weng H, Deng X, Chen J. RNA Modifications in Cancer: Functions, Mechanisms, and Therapeutic Implications. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020. [DOI: 10.1146/annurev-cancerbio-030419-033357] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over 170 chemical modifications have been identified in protein-coding and noncoding RNAs and shown to exhibit broad impacts on gene expression. Dysregulation of RNA modifications caused by aberrant expression of or mutations in RNA modifiers aberrantly reprograms the epitranscriptome and skews global gene expression, which in turn leads to tumorigenesis and drug resistance. Here we review current knowledge of the functions and underlying mechanisms of aberrant RNA modifications in human cancers, particularly several common RNA modifications, including N6-methyladenosine (m6A), A-to-I editing, pseudouridine (ψ), 5-methylcytosine (m5C), 5-hydroxymethylcytosine (hm5C), N1-methyladenosine (m1A), and N4-acetylcytidine (ac4C), providing insights into therapeutic implications of targeting RNA modifications and the associated machineries for cancer therapy.
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Affiliation(s)
- Huilin Huang
- Department of Systems Biology and The Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California 91010, USA
| | - Hengyou Weng
- Department of Systems Biology and The Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California 91010, USA
| | - Xiaolan Deng
- Department of Systems Biology and The Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California 91010, USA
| | - Jianjun Chen
- Department of Systems Biology and The Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California 91010, USA
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35
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Kaur G, Ruhela V, Rani L, Gupta A, Sriram K, Gogia A, Sharma A, Kumar L, Gupta R. RNA-Seq profiling of deregulated miRs in CLL and their impact on clinical outcome. Blood Cancer J 2020; 10:6. [PMID: 31932582 PMCID: PMC6957689 DOI: 10.1038/s41408-019-0272-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Abnormal expression patterns of regulatory small non-coding RNA (sncRNA) molecules such as microRNAs (miRs), piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs) play an important role in the development and progression of cancer. Identification of clinically relevant sncRNA signatures could, therefore, be of tremendous translational value. In the present study, genome-wide small RNA sequencing identified a unique pattern of differential regulation of eight miRs in Chronic Lymphocytic Leukemia (CLL). Among these, three were up-regulated (miR-1295a, miR-155, miR-4524a) and five were down-regulated (miR-30a, miR-423, miR-486*, let-7e, and miR-744) in CLL. Altered expression of all these eight differentially expressed miRs (DEMs) was validated by RQ-PCR. Besides, seven novel sequences identified to have elevated expression levels in CLL turned out to be transfer RNA (tRNA)/piRNAs (piRNA-30799, piRNA-36225)/snoRNA (SNORD43) related. Multivariate analysis showed that miR-4524a (HR: 1.916, 95% CI: 1.080–3.4, p value: 0.026) and miR-744 (HR: 0.415, 95% CI: 0.224–0.769, p value: 0.005) were significantly associated with risk and time to first treatment. Further investigations could help establish the scope of integration of these DEM markers into risk stratification designs and prognostication approaches for CLL.
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Affiliation(s)
- Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Ruhela
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-D), Delhi, India
| | - Lata Rani
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Anubha Gupta
- SBILab, Department of Electronics and Communication Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-D), Delhi, India.
| | - Krishnamachari Sriram
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-D), Delhi, India
| | - Ajay Gogia
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Atul Sharma
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Lalit Kumar
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences, New Delhi, India.
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36
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Lv P, Yang S, Liu W, Qin H, Tang X, Wu F, Liu Z, Gao H, Liu X. Circulating plasma lncRNAs as novel markers of EGFR mutation status and monitors of epidermal growth factor receptor-tyrosine kinase inhibitor therapy. Thorac Cancer 2019; 11:29-40. [PMID: 31691525 PMCID: PMC6938758 DOI: 10.1111/1759-7714.13216] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/23/2022] Open
Abstract
Background Epidermal growth factor receptor (EGFR) gene mutations predict tumor response to EGFR tyrosine kinase inhibitors (EGFR‐TKIs) in non‐small cell lung cancer (NSCLC). However, even patients with EGFR‐sensitive mutations in NSCLC have limited efficacy with EGFR‐TKI. Studies have shown that long noncoding RNA (lncRNA) is related to diagnosis and prognosis with NSCLC. This study aimed to explore the correlation between lncRNA in NSCLC patients with EGFR mutation status and EGFR‐TKI efficacy. Methods The amplification‐refractory mutation system method was used to test the EGFR mutation status in tumor tissues and pleural effusions of NSCLC patients. Three EGFR‐mutant patients and three EGFR wild‐type patients were selected. Differential lncRNA was performed on the pleural effusions of the two selected groups of patients using Clariom D Human chip technology. Five lncRNAs significantly associated with EGFR mutation status were screened by FC value and GO analysis, and then evaluated by real‐time quantitative polymerase chain reaction in NSCLC patients' pleural effusions. Three were further analyzed in NSCLC patients' plasma. Results There were 61 significant differences in lncRNA between EGFR mutation‐positive and wild‐type patients. Among them, SCARNA7, MALAT1, NONHSAT017369, NONHSAT051892, and FTH1P2 were significantly associated with EGFR mutation status. SCARNA7, MALAT1, and NONHSAT017369 showed consistent results with plasma in pleural effusions compared to EGFR wild‐type, all upregulated in the EGFR mutation group. Conclusion This study shows that lncRNAs can be used not only as potential biomarkers for predicting the mutation status of EGFR and the efficacy of EGFR‐TKI, but also for monitoring the efficacy of EGFR‐TKI.
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Affiliation(s)
- Panpan Lv
- Academy of Military Medical Science, Beijing, China.,PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Shaoxing Yang
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Wenjing Liu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Haifeng Qin
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Xiuhua Tang
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Fangfang Wu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Zeyuan Liu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Hongjun Gao
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Xiaoqing Liu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
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37
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McMahon M, Contreras A, Holm M, Uechi T, Forester CM, Pang X, Jackson C, Calvert ME, Chen B, Quigley DA, Luk JM, Kelley RK, Gordan JD, Gill RM, Blanchard SC, Ruggero D. A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS. eLife 2019; 8:48847. [PMID: 31478838 PMCID: PMC6776443 DOI: 10.7554/elife.48847] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/02/2019] [Indexed: 12/19/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a diverse group of non-coding RNAs that direct chemical modifications at specific residues on other RNA molecules, primarily on ribosomal RNA (rRNA). SnoRNAs are altered in several cancers; however, their role in cell homeostasis as well as in cellular transformation remains poorly explored. Here, we show that specific subsets of snoRNAs are differentially regulated during the earliest cellular response to oncogenic RASG12V expression. We describe a novel function for one H/ACA snoRNA, SNORA24, which guides two pseudouridine modifications within the small ribosomal subunit, in RAS-induced senescence in vivo. We find that in mouse models, loss of Snora24 cooperates with RASG12V to promote the development of liver cancer that closely resembles human steatohepatitic hepatocellular carcinoma (HCC). From a clinical perspective, we further show that human HCCs with low SNORA24 expression display increased lipid content and are associated with poor patient survival. We next asked whether ribosomes lacking SNORA24-guided pseudouridine modifications on 18S rRNA have alterations in their biophysical properties. Single-molecule Fluorescence Resonance Energy Transfer (FRET) analyses revealed that these ribosomes exhibit perturbations in aminoacyl-transfer RNA (aa-tRNA) selection and altered pre-translocation ribosome complex dynamics. Furthermore, we find that HCC cells lacking SNORA24-guided pseudouridine modifications have increased translational miscoding and stop codon readthrough frequencies. These findings highlight a role for specific snoRNAs in safeguarding against oncogenic insult and demonstrate a functional link between H/ACA snoRNAs regulated by RAS and the biophysical properties of ribosomes in cancer.
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Affiliation(s)
- Mary McMahon
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Adrian Contreras
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Mikael Holm
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
| | - Tamayo Uechi
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Craig M Forester
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States.,Division of Pediatric Allergy, Immunology & Bone Marrow Transplantation, University of California, San Francisco, San Francisco, United States
| | - Xiaming Pang
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Cody Jackson
- Gladstone Histology and Light Microscopy Core, Gladstone Institutes, San Francisco, United States
| | - Meredith E Calvert
- Gladstone Histology and Light Microscopy Core, Gladstone Institutes, San Francisco, United States
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, United States.,Department of Pharmacology and Toxicology, Michigan State University, Grand Rapids, United States
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States
| | - John M Luk
- Arbele Corporation, Seattle, United States
| | - R Kate Kelley
- Helen Diller Family Comprehensive Cancer Center, Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center, Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Ryan M Gill
- Department of Pathology, University of California, San Francisco, San Francisco, United States
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
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38
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Liang J, Wen J, Huang Z, Chen XP, Zhang BX, Chu L. Small Nucleolar RNAs: Insight Into Their Function in Cancer. Front Oncol 2019; 9:587. [PMID: 31338327 PMCID: PMC6629867 DOI: 10.3389/fonc.2019.00587] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/17/2019] [Indexed: 02/04/2023] Open
Abstract
Small nucleolar RNAs (SnoRNAs) are a class of non-coding RNAs divided into two classes: C/D box snoRNAs and H/ACA box snoRNAs. The canonical function of C/D box and H/ACA box snoRNAs are 2'-O-ribose methylation and pseudouridylation of ribosomal RNAs (rRNAs), respectively. Emerging evidence has demonstrated that snoRNAs are involved in various physiological and pathological cellular processes. Mutations and aberrant expression of snoRNAs have been reported in cell transformation, tumorigenesis, and metastasis, indicating that snoRNAs may serve as biomarkers and/or therapeutic targets of cancer. Hence, further study of the functions and underlying mechanism of snoRNAs is valuable. In this review, we summarize the biogenesis and functions of snoRNAs, as well as the association of snoRNAs in different types of cancers and their potential roles in cancer diagnosis and therapy.
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Affiliation(s)
- Junnan Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingyuan Wen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhao Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Ping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bi-Xiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Chu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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39
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Abstract
While only a small part of the human genome encodes for proteins, biological functions for the so-called junk genome are increasingly being recognized through high-throughput technologies and mechanistic experimental studies. Indeed, novel mechanisms of gene regulation are being discovered that require coordinated interaction between DNA, RNA, and proteins. Therefore, interdisciplinary efforts are still needed to decipher these complex transcriptional networks. In this review, we discuss how non-coding RNAs (ncRNAs) are epigenetically regulated in cancer and metastases and consequently how ncRNAs participate in the sculpting of the epigenetic profile of a cancer cell, thus modulating the expression of other RNA molecules. In the latter case, ncRNAs not only affect the DNA methylation status of certain genomic loci but also interact with histone-modifying complexes, changing the structure of the chromatin itself. We present several examples of epigenetic changes causing aberrant expression of ncRNAs in the context of tumor progression. Interestingly, there are also important epigenetic changes and transcriptional regulatory effects derived from their aberrant expression. As ncRNAs can also be used as biomarkers for diagnosis and prognosis or explored as potential targets, we present insights into the use of ncRNAs for targeted cancer therapy.
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40
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Zhu Q, Yang H, Cheng P, Han Q. Bioinformatic analysis of the prognostic value of the lncRNAs encoding snoRNAs in hepatocellular carcinoma. Biofactors 2019; 45:244-252. [PMID: 30537372 DOI: 10.1002/biof.1478] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 12/14/2022]
Abstract
Some lncRNAs can encode small nucleolar RNAs (snoRNAs), called small nucleolar RNA host genes (SNHGs), which exert diverse regulatory effects on cellular processes. In this study, using RNA-seq and survival data in the Cancer Genome Atlas (TCGA)-Liver Hepatocellular Carcinoma (LIHC), we examined the expression profile of some SNHG genes and explored their prognostic value in hepatocellular carcinoma (HCC). Level-3 RNA-sequencing data, the clinicopathological and survival data of patients with primary HCC were downloaded from the UCSC Xena browser (https://xenabrowser.net/), for a secondary analysis. Results showed that SNHG1, GAS5, SNHG3-7 and SNHG10-12 were significantly upregulated in HCC tissues (N = 49) compared with adjacent normal tissues (N = 49). After adjustment for confounding factors, the multivariate analysis confirmed that increased SNHG4 expression was independently associated with shorter OS (HR: 1.319, 95%CI: 1.131-1.537, P < 0.001), while increased GAS5 expression was an independent predictor of shorter RFS (HR: 1.287, 95% CI: 1.027-1.612, P = 0.028). Using the methylation data obtained from the Infinium HumanMethylation450 BeadChip, we found that SNHG4 expression was not likely to be modulated by methylation in HCC. In comparison, the methylation status of 5 CpG sites (cg07177756, cg17025683, cg16290996, cg03044573 and cg06644515) showed a moderately negative correlation (Pearson's r = -0.54, P < 0.001) with GAS5 expression. Based on these findings, we infer that SNHG4 and GAS5 might be valuable prognostic markers in HCC. DNA hypomethylation might play an important role in elevated GAS5 transcription in HCC. © 2018 BioFactors, 45(2):244-252, 2019.
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Affiliation(s)
- Qingyao Zhu
- Department of Oncology Radiotherapy, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hongjie Yang
- Department of Oncology Radiotherapy, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Peng Cheng
- Department of Oncology Radiotherapy, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Qian Han
- Department of Oncology Radiotherapy, Henan Provincial People's Hospital, Zhengzhou, Henan, China
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41
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Rynkeviciene R, Simiene J, Strainiene E, Stankevicius V, Usinskiene J, Miseikyte Kaubriene E, Meskinyte I, Cicenas J, Suziedelis K. Non-Coding RNAs in Glioma. Cancers (Basel) 2018; 11:cancers11010017. [PMID: 30583549 PMCID: PMC6356972 DOI: 10.3390/cancers11010017] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
Glioma is the most aggressive brain tumor of the central nervous system. The ability of glioma cells to migrate, rapidly diffuse and invade normal adjacent tissue, their sustained proliferation, and heterogeneity contribute to an overall survival of approximately 15 months for most patients with high grade glioma. Numerous studies indicate that non-coding RNA species have critical functions across biological processes that regulate glioma initiation and progression. Recently, new data emerged, which shows that the cross-regulation between long non-coding RNAs and small non-coding RNAs contribute to phenotypic diversity of glioblastoma subclasses. In this paper, we review data of long non-coding RNA expression, which was evaluated in human glioma tissue samples during a five-year period. Thus, this review summarizes the following: (I) the role of non-coding RNAs in glioblastoma pathogenesis, (II) the potential application of non-coding RNA species in glioma-grading, (III) crosstalk between lncRNAs and miRNAs (IV) future perspectives of non-coding RNAs as biomarkers for glioma.
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Affiliation(s)
- Ryte Rynkeviciene
- Nacional Cancer Institute, Santariskiu str. 1, LT-08660 Vilnius, Lithuania.
| | - Julija Simiene
- Nacional Cancer Institute, Santariskiu str. 1, LT-08660 Vilnius, Lithuania.
- Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio ave. 7, LT-08412 Vilnius, Lithuania.
| | - Egle Strainiene
- Nacional Cancer Institute, Santariskiu str. 1, LT-08660 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Sauletekio ave. 11, LT-10122 Vilnius, Lithuania.
| | - Vaidotas Stankevicius
- Nacional Cancer Institute, Santariskiu str. 1, LT-08660 Vilnius, Lithuania.
- Institute of Biotechnology, Vilnius University, LT-10257 Vilnius, Lithuania.
| | - Jurgita Usinskiene
- Nacional Cancer Institute, Santariskiu str. 1, LT-08660 Vilnius, Lithuania.
| | - Edita Miseikyte Kaubriene
- Nacional Cancer Institute, Santariskiu str. 1, LT-08660 Vilnius, Lithuania.
- Faculty of Medicine, Vilnius University, M.K. Cˇiurlionio 21, LT-03101 Vilnius, Lithuania.
| | - Ingrida Meskinyte
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.
- MAP Kinase Resource, Bioinformatics, Melchiorstrasse 9, 3027 Bern, Switzerland.
| | - Jonas Cicenas
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.
- MAP Kinase Resource, Bioinformatics, Melchiorstrasse 9, 3027 Bern, Switzerland.
- Energy and Biotechnology Engineering Institute, Aleksandro Stulginskio University, Studentų g. 11, LT-53361 Akademija, Lithuania.
| | - Kestutis Suziedelis
- Nacional Cancer Institute, Santariskiu str. 1, LT-08660 Vilnius, Lithuania.
- Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio ave. 7, LT-08412 Vilnius, Lithuania.
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Guide snoRNAs: Drivers or Passengers in Human Disease? BIOLOGY 2018; 8:biology8010001. [PMID: 30577491 PMCID: PMC6466398 DOI: 10.3390/biology8010001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 01/17/2023]
Abstract
In every domain of life, RNA-protein interactions play a significant role in co- and post-transcriptional modifications and mRNA translation. RNA performs diverse roles inside the cell, and therefore any aberrancy in their function can cause various diseases. During maturation from its primary transcript, RNA undergoes several functionally important post-transcriptional modifications including pseudouridylation and ribose 2′-O-methylation. These modifications play a critical role in the stability of the RNA. In the last few decades, small nucleolar RNAs (snoRNAs) were revealed to be one of the main components to guide these modifications. Due to their active links to the nucleoside modification, deregulation in the snoRNA expressions can cause multiple disorders in humans. Additionally, host genes carrying snoRNA-encoding sequences in their introns also show differential expression in disease. Although few reports support a causal link between snoRNA expression and disease manifestation, this emerging field will have an impact on the way we think about biomarkers or identify novel targets for therapy. This review focuses on the intriguing aspect of snoRNAs that function as a guide in post-transcriptional RNA modification, and regulation of their host genes in human disease.
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43
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Chamorro-Petronacci C, Perez-Sayáns M, Padín-Iruegas ME, Marichalar-Mendia X, Gallas-Torreira M, García García A. Differential expression of snoRNAs in oral squamous cell carcinomas: new potential diagnostic markers. J Enzyme Inhib Med Chem 2018; 33:424-427. [PMID: 29372649 PMCID: PMC6010090 DOI: 10.1080/14756366.2018.1426574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/07/2018] [Accepted: 01/08/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Small nucleolar RNAs (snoRNAs) are small non-coding RNA sequences whose most studied function is ribosome biogenesis. The altered expression of snoRNA is observed in tumoral processes such as breast cancer and multiple myeloma. However, we have not found any references to snoRNAs in oral squamous cell carcinomas (OSCC) in the literature at the time this article was written. MATERIAL AND METHODS We have analyzed snoRNA expression in frozen OSCC tissue samples and have compared them to healthy controls. RNA was extracted from a total of eight OSCC samples and eight control samples, measuring the differential expression of small RNAs with the Affymetrix® miRNA 4.1 Array Plate microarray platform. RESULTS Results were analyzed using the Transcriptome Analysis Console 3.0 (TAC) software. We obtained a total of 16 deregulated snoRNAs of which one was over expressed and 15 were under expressed. SnoRNAs expression was altered in OSCC and could serve as a diagnostic marker.
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Affiliation(s)
- Cintia Chamorro-Petronacci
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Mario Perez-Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Maria Elena Padín-Iruegas
- Anatomy and Human Embryology, Functional Biology and Health Science Department, Vigo University, Vigo, Spain
| | - Xabier Marichalar-Mendia
- Faculty of Medicine and Dentistry, Stomatology Department, Universidad del Pais Vasco/Euskal Herriko Unibertsitatea, Bilbao, Spain
| | - Mercedes Gallas-Torreira
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Abel García García
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
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44
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Kaur S, Abu-Shahba AG, Paananen RO, Hongisto H, Hiidenmaa H, Skottman H, Seppänen-Kaijansinkko R, Mannerström B. Small non-coding RNA landscape of extracellular vesicles from human stem cells. Sci Rep 2018; 8:15503. [PMID: 30341351 PMCID: PMC6195565 DOI: 10.1038/s41598-018-33899-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/08/2018] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are reported to be involved in stem cell maintenance, self-renewal, and differentiation. Due to their bioactive cargoes influencing cell fate and function, interest in EVs in regenerative medicine has rapidly increased. EV-derived small non-coding RNA mimic the functions of the parent stem cells, regulating the maintenance and differentiation of stem cells, controlling the intercellular regulation of gene expression, and eventually affecting the cell fate. In this study, we used RNA sequencing to provide a comprehensive overview of the expression profiles of small non-coding transcripts carried by the EVs derived from human adipose tissue stromal/stem cells (AT-MSCs) and human pluripotent stem cells (hPSCs), both human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSC). Both hPSCs and AT-MSCs were characterized and their EVs were extracted using standard protocols. Small non-coding RNA sequencing from EVs showed that hPSCs and AT-MSCs showed distinct profiles, unique for each stem cell source. Interestingly, in hPSCs, most abundant miRNAs were from specific miRNA families regulating pluripotency, reprogramming and differentiation (miR-17-92, mir-200, miR-302/367, miR-371/373, CM19 microRNA cluster). For the AT-MSCs, the highly expressed miRNAs were found to be regulating osteogenesis (let-7/98, miR-10/100, miR-125, miR-196, miR-199, miR-615-3p, mir-22-3p, mir-24-3p, mir-27a-3p, mir-193b-5p, mir-195-3p). Additionally, abundant small nuclear and nucleolar RNA were detected in hPSCs, whereas Y- and tRNA were found in AT-MSCs. Identification of EV-miRNA and non-coding RNA signatures released by these stem cells will provide clues towards understanding their role in intracellular communication, and well as their roles in maintaining the stem cell niche.
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Affiliation(s)
- Sippy Kaur
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ahmed G Abu-Shahba
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Tanta University, Tanta, Egypt
| | - Riku O Paananen
- Helsinki Eye Lab, Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Heidi Hongisto
- Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere, Finland
| | - Hanna Hiidenmaa
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Heli Skottman
- Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere, Finland
| | - Riitta Seppänen-Kaijansinkko
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Bettina Mannerström
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
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45
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Chuang TD, Xie Y, Yan W, Khorram O. Next-generation sequencing reveals differentially expressed small noncoding RNAs in uterine leiomyoma. Fertil Steril 2018; 109:919-929. [PMID: 29778390 PMCID: PMC6445395 DOI: 10.1016/j.fertnstert.2018.01.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date. DESIGN Laboratory-based investigation. SETTING Academic center. PATIENT(S) Women undergoing hysterectomy for benign indications. INTERVENTION(S) Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). MAIN OUTCOME MEASURE(S) Expression profile of sncRNAs in leiomyoma and matched myometrium. RESULT(S) Screening our previously determined RNA sequencing data with the sncRNA database resulted in identification of 15 small nuclear (sn) RNAs, 284 small nucleolar (sno) RNAs, 98 Piwi-interacting (pi) RNAs, 152 transfer (t) RNAs, and 45 ribosomal (r) RNAs, of which 15 snoRNAs, 24 piRNAs, 7 tRNAs, and 6 rRNAs were differentially expressed at a 1.5-fold change cutoff in leiomyoma compared with myometrium. We selected 5 snoRNAs, 4 piRNAs, 1 tRNA, and 1 rRNA that were differentially expressed and confirmed their expression in paired tissues (n = 20) from both phases of the menstrual cycle with the use of qRT-PCR. The results indicated up-regulation of the snoRNAs (SNORD30, SNORD27, SNORA16A, SNORD46, and SNORD56) and down-regulation of the piRNAs (piR-1311, piR-16677, piR-20365, piR-4153), tRNA (TRG-GCC5-1), and rRNA (RNA5SP202) expression in leiomyoma compared with myometrium (P<.05). The pattern of expression of these sncRNAs was similar to RNA sequencing analysis, with no menstrual cycle-dependent differences detected except for SNORD30. Because Argonaute 2 (AGO2) is required for sncRNA-mediated gene silencing, we determined its expression and found greater abundance in leiomyoma. CONCLUSION(S) Our results provide the first evidence for the differential expression of additional classes of sncRNAs and AGO2 in leiomyoma, implicating their roles as a gene regulatory mechanism.
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Affiliation(s)
- Tsai-Der Chuang
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and LA-Biomed Research Institute, Torrance, California
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Omid Khorram
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and LA-Biomed Research Institute, Torrance, California.
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46
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Vendramini E, Giordan M, Giarin E, Michielotto B, Fazio G, Cazzaniga G, Biondi A, Silvestri D, Valsecchi MG, Muckenthaler MU, Kulozik AE, Gattei V, Izraeli S, Basso G, Te Kronnie G. High expression of miR-125b-2 and SNORD116 noncoding RNA clusters characterize ERG-related B cell precursor acute lymphoblastic leukemia. Oncotarget 2018; 8:42398-42413. [PMID: 28415578 PMCID: PMC5522075 DOI: 10.18632/oncotarget.16392] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/04/2017] [Indexed: 12/19/2022] Open
Abstract
ERG-related leukemia is a B cell precursor acute lymphoblastic leukemia (BCP ALL) subtype characterized by aberrant expression of DUX4 and ERG transcription factors, and highly recurrent ERG intragenic deletions. ERG-related patients have remarkably favorable outcome despite a high incidence of inauspicious IKZF1 aberrations. We describe clinical and genomic features of the ERG-related cases in an unselected cohort of B-other BCP ALL pediatric patients enrolled in the AIEOP ALL 2000 therapeutic protocol. We report a small noncoding RNA signature specific of ERG-related group, with up-regulation of miR-125b-2 cluster on chromosome 21 and several snoRNAs in the Prader-Willi locus at 15q11.2, including the orphan SNORD116 cluster.
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Affiliation(s)
- Elena Vendramini
- Department of Women's and Children's Health, University of Padova, Padova, Italy.,Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Marco Giordan
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Emanuela Giarin
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Barbara Michielotto
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Grazia Fazio
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | - Andrea Biondi
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | - Daniela Silvestri
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | | | - Martina U Muckenthaler
- Department of Pediatric Oncology Hematology, University of Heidelberg, Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology Hematology, University of Heidelberg, Heidelberg, Germany
| | - Valter Gattei
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., Aviano (PN), Italy
| | - Shai Izraeli
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Giuseppe Basso
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Geertruy Te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
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47
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Fernández-Martínez JL, deAndrés-Galiana EJ, Sonis ST. Genomic data integration in chronic lymphocytic leukemia. J Gene Med 2018; 19. [PMID: 27928896 DOI: 10.1002/jgm.2936] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 10/04/2016] [Accepted: 11/26/2016] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND B-cell chronic lymphocytic leukemia (CLL) is a heterogeneous disease and the most common adult leukemia in western countries. IgVH mutational status distinguishes two major types of CLL, each associated with a different prognosis and survival. Sequencing identified NOTCH1 and SF3B1 as the two main recurrent mutations. We described a novel method to clarify how these mutations affect gene expression by finding small-scale signatures that predict the IgVH, NOTCH1 and SF3B1 mutations. We subsequently defined the biological pathways and correlation networks involved in disease development, with the potential goal of identifying new drugable targets. METHODS We modeled a microarray dataset consisting of 48807 probes derived from 163 samples. The use of Fisher's ratio and fold change combined with feature elimination allowed us to identify the minimum number of genes with the highest predictive mutation power and, subsequently, we applied network and pathway analyses of these genes to identify their biological roles. RESULTS The mutational status of the patients was accurately predicted (94-99%) using small-scale gene signatures: 13 genes for IgVH, 60 for NOTCH1 and 22 for SF3B1. LPL plays an important role in the case of the IgVH mutation, whereas MSI2, LTK, TFEC and CNTAP2 are involved in the NOTCH1 mutation, and RPL32 and PLAGL1 are involved in the SF3B1 mutation. Four high discriminatory genes (IGHG1, MYBL1, NRIP1 and RGS1) are common to these three mutations. The IL-4-mediated signaling events pathway appears to be involved as a common mechanism and suggests an important role of the immune response mechanisms and antigen presentation. CONCLUSIONS This retrospective analysis served to provide a deeper understanding of the effects of the different mutations in CLL disease progression, with the expectation that these findings will be clinically applied in the near future to the development of new drugs.
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Affiliation(s)
- Juan Luis Fernández-Martínez
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo, Oviedo, Asturias, Spain
| | - Enrique J deAndrés-Galiana
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo, Oviedo, Asturias, Spain.,Artificial Intelligence Center, University of Oviedo, Oviedo, Asturias, Spain
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48
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Ren C, Liu F, Ouyang Z, An G, Zhao C, Shuai J, Cai S, Bo X, Shu W. Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease. Sci Rep 2017; 7:15518. [PMID: 29138457 PMCID: PMC5686184 DOI: 10.1038/s41598-017-15822-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/03/2017] [Indexed: 12/28/2022] Open
Abstract
Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and underlying mechanisms of eRNAs, it remains an open question whether eRNAs are mere transcriptional noise or relevant biologically functional species. Here, we identified a catalogue of eRNAs in a broad range of human cell/tissue types and extended our understanding of eRNAs by demonstrating their multi-omic signatures. Gene Ontology (GO) analysis revealed that eRNAs play key roles in human cell identity. Furthermore, we detected numerous known and novel functional RNA structures within eRNA regions. To better characterize the cis-regulatory effects of non-coding variation in these structural ncRNAs, we performed a comprehensive analysis of the genetic variants of structural ncRNAs in eRNA regions that are associated with inflammatory autoimmune diseases. Disease-associated variants of the structural ncRNAs were disproportionately enriched in immune-specific cell types. We also identified riboSNitches in lymphoid eRNAs and investigated the potential pathogenic mechanisms by which eRNAs might function in autoimmune diseases. Collectively, our findings offer valuable insights into the function of eRNAs and suggest that eRNAs might be effective diagnostic and therapeutic targets for human diseases.
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Affiliation(s)
- Chao Ren
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Feng Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China.,Department of Information, The 188th Hospital of ChaoZhou, ChaoZhou, China
| | - Zhangyi Ouyang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Gaole An
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Chenghui Zhao
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jun Shuai
- Department of Information, The 188th Hospital of ChaoZhou, ChaoZhou, China
| | - Shuhong Cai
- Department of Information, The 188th Hospital of ChaoZhou, ChaoZhou, China
| | - Xiaochen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Wenjie Shu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China.
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49
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Berardocco M, Radeghieri A, Busatto S, Gallorini M, Raggi C, Gissi C, D'Agnano I, Bergese P, Felsani A, Berardi AC. RNA-seq reveals distinctive RNA profiles of small extracellular vesicles from different human liver cancer cell lines. Oncotarget 2017; 8:82920-82939. [PMID: 29137313 PMCID: PMC5669939 DOI: 10.18632/oncotarget.20503] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/29/2017] [Indexed: 12/20/2022] Open
Abstract
Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome. Here are reported genome wide data of the expression level of coding and non-coding transcripts, microRNAs, isomiRs and snoRNAs providing the first comprehensive overview of the extracellular-vesicle RNA cargo released from LC cell lines. The EV-RNA expression profiles of the four liver cancer cell lines share a similar background, but cell-specific features clearly emerge showing the marked heterogeneity of the EV-cargo among the individual cell lines, evident both for the coding and non-coding RNA species.
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Affiliation(s)
- Martina Berardocco
- U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy
| | - Annalisa Radeghieri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Sara Busatto
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Chiara Raggi
- Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Italy
| | - Clarissa Gissi
- U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy
| | - Igea D'Agnano
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Armando Felsani
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Italy.,Genomnia Srl, Bresso, Italy
| | - Anna C Berardi
- U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy
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50
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Cao T, Rajasingh S, Samanta S, Dawn B, Bittel DC, Rajasingh J. Biology and clinical relevance of noncoding sno/scaRNAs. Trends Cardiovasc Med 2017; 28:81-90. [PMID: 28869095 DOI: 10.1016/j.tcm.2017.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/18/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are a group of noncoding RNAs that perform various biological functions, including biochemical modifications of other RNAs, precursors of miRNA, splicing, and telomerase activity. The small Cajal body-associated RNAs (scaRNAs) are a subset of the snoRNA family and collect in the Cajal body where they perform their canonical function to biochemically modify spliceosomal RNAs prior to maturation. Failure of sno/scaRNAs have been implicated in pathology such as congenital heart anomalies, neuromuscular disorders, and various malignancies. Thus, understanding of sno/scaRNAs demonstrates the clinical value.
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Affiliation(s)
- Thuy Cao
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | - Sheeja Rajasingh
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | - Saheli Samanta
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | - Buddhadeb Dawn
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | | | - Johnson Rajasingh
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS.
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