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Kubota H, Ueno H, Tasaka K, Isobe T, Saida S, Kato I, Umeda K, Hiwatari M, Hasegawa D, Imamura T, Kakiuchi N, Nannya Y, Ogawa S, Hiramatsu H, Takita J. RNA-seq-based miRNA signature as an independent predictor of relapse in pediatric B-cell acute lymphoblastic leukemia. Blood Adv 2024; 8:1258-1271. [PMID: 38127276 PMCID: PMC10918494 DOI: 10.1182/bloodadvances.2023011583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/21/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
ABSTRACT Aberrant micro-RNA (miRNA) expression profiles have been associated with disease progression and clinical outcome in pediatric cancers. However, few studies have analyzed genome-wide dysregulation of miRNAs and messenger RNAs (mRNAs) in pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL). To identify novel prognostic factors, we comprehensively investigated miRNA and mRNA sequencing (miRNA-seq and mRNA-seq) data in pediatric BCP-ALL samples with poor outcome. We analyzed 180 patients, including 43 matched pairs at diagnosis and relapse. Consensus clustering of miRNA expression data revealed a distinct profile characterized by mainly downregulation of miRNAs (referred to as an miR-low cluster [MLC]). The MLC profile was not associated with any known genetic subgroups. Intriguingly, patients classified as MLC had significantly shorter event-free survival (median 21 vs 33 months; log-rank P = 3 ×10-5). Furthermore, this poor prognosis was retained even in hyperdiploid ALL. This poor prognostic MLC profiling was confirmed in the validation cohort. Notably, non-MLC profiling at diagnosis (n = 9 of 23; Fisher exact test, P = .039) often changed into MLC profiling at relapse for the same patient. Integrated analysis of miRNA-seq and mRNA-seq data revealed that the transcriptional profile of MLC was characterized by enrichment of MYC target and oxidative phosphorylation genes, reduced intron retention, and low expression of DICER1. Thus, our miRNA-mRNA integration approach yielded a truly unbiased molecular stratification of pediatric BCP-ALL cases based on a novel prognostic miRNA signature, which may lead to better clinical outcomes.
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Affiliation(s)
- Hirohito Kubota
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroo Ueno
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keiji Tasaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Hematology, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Satoshi Saida
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mitsuteru Hiwatari
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pediatrics, School of Medicine, Teikyo University, Tokyo, Japan
| | - Daiichiro Hasegawa
- Department of Hematology and Oncology, Hyogo Prefectural Kobe Children Hospital, Hyogo, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Hematopoietic Disease Control, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Hidefumi Hiramatsu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Wang S, Sun H, Chen G, Wu C, Sun B, Lin J, Lin D, Zeng D, Lin B, Huang G, Lu X, Lin H, Liang Y. RNA-binding proteins in breast cancer: Biological implications and therapeutic opportunities. Crit Rev Oncol Hematol 2024; 195:104271. [PMID: 38272151 DOI: 10.1016/j.critrevonc.2024.104271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) refer to a class of proteins that participate in alternative splicing, RNA stability, polyadenylation, localization and translation of RNAs, thus regulating gene expression in post-transcriptional manner. Dysregulation of RNA-RBP interaction contributes to various diseases, including cancer. In breast cancer, disorders in RBP expression and function influence the biological characteristics of tumor cells. Targeting RBPs has fostered the development of innovative therapies for breast cancer. However, the RBP-related mechanisms in breast cancer are not completely clear. In this review, we summarize the regulatory mechanisms of RBPs and their signaling crosstalk in breast cancer. Specifically, we emphasize the potential of certain RBPs as prognostic factors due to their effects on proliferation, invasion, apoptosis, and therapy resistance of breast cancer cells. Most importantly, we present a comprehensive overview of the latest RBP-related therapeutic strategies and novel therapeutic targets that have proven to be useful in the treatment of breast cancer.
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Affiliation(s)
- Shimeng Wang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Hexing Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Guanyuan Chen
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Chengyu Wu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Bingmei Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Jiajia Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Danping Lin
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - De Zeng
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - Baohang Lin
- Department of Thyroid, Breast and Vascular Surgery, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Guan Huang
- Department of Pathology, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Xiaofeng Lu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Haoyu Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
| | - Yuanke Liang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
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Skvortsova L, Abdikerim S, Yergali K, Mit N, Perfilyeva A, Omarbayeva N, Zhunussova A, Kachiyeva Z, Sadykova T, Bekmanov B, Kaidarova D, Djansugurova L, Zhunussova G. Association of Genetic Markers with the Risk of Early-Onset Breast Cancer in Kazakh Women. Genes (Basel) 2024; 15:108. [PMID: 38254997 PMCID: PMC10815330 DOI: 10.3390/genes15010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Breast cancer is a global health problem. It is an age-dependent disease, but cases of early-onset breast cancer (eBC) are gradually increasing. There are many unresolved questions regarding eBC risk factors, mechanisms of development and screening. Only 10% of eBC cases are due to mutations in the BRCA1/BRCA2 genes, and 90% have a more complex genetic background. This poses a significant challenge to timely cancer detection in young women and highlights the need for research and awareness. Therefore, identifying genetic risk factors for eBC is essential to solving these problems. This study represents an association analysis of 144 eBC cases and 163 control participants to identify genetic markers associated with eBC risks in Kazakh women. We performed a two-stage approach in association analysis to assess genetic predisposition to eBC. First-stage genome-wide association analysis revealed two risk intronic loci in the CHI3L2 gene (p = 5.2 × 10-6) and MGAT5 gene (p = 8.4 × 10-6). Second-stage exonic polymorphisms haplotype analysis showed significant risks for seven haplotypes (p < 9.4 × 10-4). These results point to the importance of studying medium- and low-penetrant genetic markers in their haplotype combinations for a detailed understanding of the role of detected genetic markers in eBC development and prediction.
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Affiliation(s)
- Liliya Skvortsova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Saltanat Abdikerim
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Kanagat Yergali
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Natalya Mit
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Anastassiya Perfilyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Nazgul Omarbayeva
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Aigul Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Zulfiya Kachiyeva
- Research Institute of Applied and Fundamental Medicine, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan;
| | - Tolkyn Sadykova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Bakhytzhan Bekmanov
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Dilyara Kaidarova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
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