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Strømme O, Heck KA, Brede G, Lindholm HT, Otterlei M, Arum CJ. tRNA-Derived Fragments as Biomarkers in Bladder Cancer. Cancers (Basel) 2024; 16:1588. [PMID: 38672670 PMCID: PMC11049458 DOI: 10.3390/cancers16081588] [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: 03/29/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Bladder cancer (BC) diagnosis is reliant on cystoscopy, an invasive procedure associated with urinary tract infections. This has sparked interest in identifying noninvasive biomarkers in body fluids such as blood and urine. A source of biomarkers in these biofluids are extracellular vesicles (EVs), nanosized vesicles that contain a wide array of molecular cargo, including small noncoding RNA such as transfer RNA-derived fragments (tRF) and microRNA. Here, we performed small-RNA next-generation sequencing from EVs from urine and serum, as well as from serum supernatant. RNA was extracted from 15 non-cancer patients (NCPs) with benign findings in cystoscopy and 41 patients with non-muscle invasive BC. Urine and serum were collected before transurethral resection of bladder tumors (TUR-b) and at routine post-surgery check-ups. We compared levels of tRFs in pre-surgery samples to samples from NCPs and post-surgery check-ups. To further verify our findings, samples from 10 patients with stage T1 disease were resequenced. When comparing tRF expression in urine EVs between T1 stage BC patients and NCPs, 14 differentially expressed tRFs (DEtRFs) were identified. In serum supernatant, six DEtRFs were identified among stage T1 patients when comparing pre-surgery to post-surgery samples and four DEtRFs were found when comparing pre-surgery samples to NCPs. By performing a blast search, we found that sequences of DEtRFs aligned with genomic sequences pertaining to processes relevant to cancer development, such as enhancers, regulatory elements and CpG islands. Our findings display a number of tRFs that may hold potential as biomarkers for the diagnosis and recurrence-free survival of BC.
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Affiliation(s)
- Olaf Strømme
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
| | - Kathleen A. Heck
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
| | - Gaute Brede
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
| | - Håvard T. Lindholm
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
| | - Carl-Jørgen Arum
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
- Department of Urology, St. Olav’s University Hospital, 7030 Trondheim, Norway
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2
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Lee SH, Brianna. Association of microRNA-21 expression with breast cancer subtypes and its potential as an early biomarker. Pathol Res Pract 2024; 254:155073. [PMID: 38218039 DOI: 10.1016/j.prp.2023.155073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/29/2023] [Indexed: 01/15/2024]
Abstract
Breast cancer has become the most diagnosed cancer worldwide in 2020 with high morbidity and mortality rates. The alarming increase in breast cancer incidence has sprung many researchers to focus on developing novel screening tests to identify early breast cancer which will allow clinicians to provide timely and effective treatments. With much evidence supporting the notion that the deregulation of miRNAs (a class of non-coding RNA) greatly contributes to cancer initiation and progression, the promising role of miRNAs as cancer biomarkers is gaining traction in the research world. Among the upregulated miRNAs identified in breast carcinogenesis, miR-21 was shown to be significantly expressed in breast cancer tissues and bodily fluids of breast cancer patients. Therein, this review paper aims to provide an overview of breast cancer, the role and significance of miR-21 in breast cancer pathogenesis, and its potential as a breast cancer biomarker. The paper also discusses the current types of tumor biomarkers and their limitations, the presence of miR-21 in extracellular vesicles and plasma, screening methods available for miRNA detection along with some challenges faced in developing diagnostic miR-21 testing for breast cancer to provide readers with a comprehensive outlook based on using miR-21 in clinical settings.
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Affiliation(s)
- Sau Har Lee
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya 47500, Malaysia; Digital Health and Medical Advancements Impact Lab, Taylor's University, Subang Jaya 47500, Malaysia.
| | - Brianna
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Darul Ehsan, Selangor 47500, Malaysia
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3
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Yang N, Li R, Liu R, Yang S, Zhao Y, Xiong W, Qiu L. The Emerging Function and Promise of tRNA-Derived Small RNAs in Cancer. J Cancer 2024; 15:1642-1656. [PMID: 38370372 PMCID: PMC10869971 DOI: 10.7150/jca.89219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 02/20/2024] Open
Abstract
Fragments derived from tRNA, called tRNA-derived small RNAs (tsRNAs), have attracted widespread attention in the past decade. tsRNAs are widespread in prokaryotic and eukaryotic transcriptome, which contains two main types, tRNA-derived fragments (tRFs) and tRNA-derived stress-inducing RNA (tiRNAs), derived from the precursor tRNAs or mature tRNAs. According to differences in the cleavage position, tRFs can be divided into tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, whereas tiRNAs can be divided into 5'-tiRNA and 3'-tiRNA. Studies have found that tRFs and tiRNAs are abnormally expressed in a variety of human malignant tumors, promote or inhibit the proliferation and apoptosis of cancer cells by regulating the expression of oncogene, and play an important role in the aggressive metastasis and progression of tumors. This article reviews the biological origins of various tsRNAs, introduces their functions and new concepts of related mechanisms, and focuses on the molecular mechanisms of tsRNAs in cancer, including breast cancer, prostate cancer, colorectal cancer, lung cancer, b-cell lymphoma, and chronic lymphoma cell leukemia. Lastly, this article puts forward some unresolved problems and future research prospects.
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Affiliation(s)
- Na Yang
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Ruijun Li
- College of Foreign Languages, Chuxiong Normal University, Chuxiong 675000, China
| | - Ruai Liu
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Shengjie Yang
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Yi Zhao
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Wei Xiong
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Lu Qiu
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
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4
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Gao LJ, Zhu SX, Wei YY, Meng HW, Gu J, Zhang H, Dai LJ. Prognostic, diagnostic and clinicopathological roles of tsRNAs: a meta-analysis in breast cancer. Eur J Med Res 2024; 29:35. [PMID: 38185655 PMCID: PMC10773143 DOI: 10.1186/s40001-023-01617-2] [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: 06/26/2023] [Accepted: 12/24/2023] [Indexed: 01/09/2024] Open
Abstract
Breast cancer (BC) is one of the most common malignancies in women and the leading cause of cancer-related death in women. The newly emerged non-coding RNAs tsRNAs (tRNA-derived small RNAs) play an important role in the occurrence and development of BC. The purpose of this study was to comprehensively evaluate the prognostic, diagnostic and clinicopathological roles of tsRNAs in BC. Through literature screening, a total of 13 BC-related tsRNA studies were included in this meta-analysis, all of which passed quality assessment. Prognostic studies showed upregulated tsRNAs to be associated with poor survival outcomes (HR = 1.64, 95%CI 1.51-1.77) and downregulated tsRNAs to be associated with better outcomes (HR = 0.58, 95%CI 0.50-0.68). Results of diagnostic studies showed a combined sensitivity of 72% (95%CI 68-76%) and combined specificity of 64% (95%CI 61-67%); the AUC was 0.72 (95%CI 0.68-0.75) and the DOR 4.62 (95%CI 3.76-5.68). Finally, correlation analysis of clinicopathological features showed that downregulation of tsRNAs correlated significantly with age, TNM stage and lymphatic metastasis. Sensitivity analysis and publication bias showed no significant difference. In conclusion, BC-associated tsRNAs are closely related to the prognosis and clinicopathological features of patients with this disease and can be used to assist in early diagnosis of BC. Therefore, tsRNAs are potential targets for the diagnosis and treatment of BC.
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Affiliation(s)
- Lu-Jue Gao
- Taicang Hospital of Traditional Chinese Medicine, Suzhou, China
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Si-Xun Zhu
- Jiangyin Traditional Chinese Medicine Hospital, Jiangyin, China
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Ying-Yi Wei
- Taicang Hospital of Traditional Chinese Medicine, Suzhou, China
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Hua-Wei Meng
- Taicang Hospital of Traditional Chinese Medicine, Suzhou, China
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing Gu
- Taicang Hospital of Traditional Chinese Medicine, Suzhou, China
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Hao Zhang
- Taicang Hospital of Traditional Chinese Medicine, Suzhou, China.
- Nanjing University of Chinese Medicine, Nanjing, China.
| | - Li-Juan Dai
- Taicang Hospital of Traditional Chinese Medicine, Suzhou, China.
- Nanjing University of Chinese Medicine, Nanjing, China.
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5
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Yu M, Yi J, Qiu Q, Yao D, Li J, Yang J, Mi C, Zhou L, Lu B, Lu W, Ying K, Chen W, Chen E, Zhang H, Lu Z, Lu Y, Liu P. Pan-cancer tRNA-derived fragment CAT1 coordinates RBPMS to stabilize NOTCH2 mRNA to promote tumorigenesis. Cell Rep 2023; 42:113408. [PMID: 37943661 DOI: 10.1016/j.celrep.2023.113408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/20/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Transfer RNA-derived fragments (tRFs) are a class of small non-coding regulatory RNAs that are involved in the pathophysiology of many diseases. However, the role of tRFs in cancer progression remains largely elusive. Here, we demonstrate that a pan-cancer 3'-tRF, CAT1 (cancer associated tRF 1), is ubiquitously upregulated in tumors and associated with poor prognosis of a variety of cancers, including lung cancer. The upregulated CAT1 in cancer cells binds to RNA-binding protein with multiple splicing (RBPMS) and displaces NOTCH2 association from RBPMS, thereby inhibiting the subsequent CCR4-NOT deadenylation-complex-mediated NOTCH2 mRNA decay. The CAT1-enhanced NOTCH2 expression promotes lung cancer cell proliferation and metastasis in vitro and in vivo. In addition, plasma CAT1 levels are substantially increased in patients with lung cancer compared to non-cancer control subjects. Our findings reveal an intrinsic connection between cancer-specific upregulation of CAT1 and cancer progression, show the regulation of NOTCH signaling in cancer by a 3'-tRF, and highlight its great clinical potential.
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Affiliation(s)
- Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Jiani Yi
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Qiongzi Qiu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Dongxia Yao
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Jia Li
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Juze Yang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Chunyi Mi
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Liyuan Zhou
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Bingjian Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Weiguo Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Kejing Ying
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Wantao Chen
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200011, China
| | - Enguo Chen
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Honghe Zhang
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Zhimin Lu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China.
| | - Yan Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China.
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China; Department of Physiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA.
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6
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Muñoz JP, Pérez-Moreno P, Pérez Y, Calaf GM. The Role of MicroRNAs in Breast Cancer and the Challenges of Their Clinical Application. Diagnostics (Basel) 2023; 13:3072. [PMID: 37835815 PMCID: PMC10572677 DOI: 10.3390/diagnostics13193072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
MicroRNAs (miRNAs) constitute a subclass of non-coding RNAs that exert substantial influence on gene-expression regulation. Their tightly controlled expression plays a pivotal role in various cellular processes, while their dysregulation has been implicated in numerous pathological conditions, including cancer. Among cancers affecting women, breast cancer (BC) is the most prevalent malignant tumor. Extensive investigations have demonstrated distinct expression patterns of miRNAs in normal and malignant breast cells. Consequently, these findings have prompted research efforts towards leveraging miRNAs as diagnostic tools and the development of therapeutic strategies. The aim of this review is to describe the role of miRNAs in BC. We discuss the identification of oncogenic, tumor suppressor and metastatic miRNAs among BC cells, and their impact on tumor progression. We describe the potential of miRNAs as diagnostic and prognostic biomarkers for BC, as well as their role as promising therapeutic targets. Finally, we evaluate the current use of artificial intelligence tools for miRNA analysis and the challenges faced by these new biomedical approaches in its clinical application. The insights presented in this review underscore the promising prospects of utilizing miRNAs as innovative diagnostic, prognostic, and therapeutic tools for the management of BC.
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Affiliation(s)
- Juan P. Muñoz
- Laboratorio de Bioquímica, Departamento de Química, Facultad de Ciencias, Universidad de Tarapacá, Arica 1000007, Chile
| | - Pablo Pérez-Moreno
- Programa de Comunicación Celular en Cáncer, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7780272, Chile
| | - Yasmín Pérez
- Laboratorio de Bioquímica, Departamento de Química, Facultad de Ciencias, Universidad de Tarapacá, Arica 1000007, Chile
| | - Gloria M. Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile
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7
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Zayakin P, Sadovska L, Eglītis K, Romanchikova N, Radoviča-Spalviņa I, Endzeliņš E, Liepniece-Karele I, Eglītis J, Linē A. Extracellular Vesicles-A Source of RNA Biomarkers for the Detection of Breast Cancer in Liquid Biopsies. Cancers (Basel) 2023; 15:4329. [PMID: 37686605 PMCID: PMC10487078 DOI: 10.3390/cancers15174329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Over the past decade, extracellular vesicles (EVs) have emerged as a promising source of cancer-derived RNAs for liquid biopsies. However, blood contains a pool of heterogeneous EVs released by a variety of cell types, making the identification of cancer RNA biomarkers challenging. Here, we performed deep sequencing of plasma EV RNA cargo in 32 patients with locally advanced breast cancer (BC) at diagnosis and 7 days after breast surgery and in 30 cancer-free healthy controls (HCs). To identify BC-derived RNA biomarkers, we searched for RNAs that had higher levels in BC EVs at the time of diagnosis compared with HCs and decreased after surgery. Data analysis showed that the fractions of miRNAs, snRNAs, snoRNAs, and tRFs were increased, but the fraction of lncRNAs was decreased in BC EVs as compared to HCs. BC-derived biomarker candidates were identified across various RNA biotypes. Considered individually, they had very high specificity but moderate sensitivity for the detection of BC, whereas a biomarker model composed of eight RNAs: SNORD3H, SNORD1C, SNORA74D, miR-224-5p, piR-32949, lnc-IFT-122-2, lnc-C9orf50-4, and lnc-FAM122C-3 was able to distinguish BC from HC EVs with an AUC of 0.902 (95% CI = 0.872-0.931, p = 3.4 × 10-9) in leave-one-out cross-validation. Furthermore, a number of RNA biomarkers were correlated with the ER and HER2 expression and additional biomarker models were created to predict hormone receptor and HER2 status. Overall, this study demonstrated that the RNA composition of plasma EVs is altered in BC patients and that they contain cancer-derived RNA biomarkers that can be used for BC detection and monitoring using liquid biopsies.
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Affiliation(s)
- Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | - Lilite Sadovska
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | - Kristaps Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, LV-1038 Riga, Latvia; (K.E.)
| | - Nadezhda Romanchikova
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | | | - Edgars Endzeliņš
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | | | - Jānis Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, LV-1038 Riga, Latvia; (K.E.)
| | - Aija Linē
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
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8
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Murillo Carrasco AG, Otake AH, Macedo-da-Silva J, Feijoli Santiago V, Palmisano G, Andrade LNDS, Chammas R. Deciphering the Functional Status of Breast Cancers through the Analysis of Their Extracellular Vesicles. Int J Mol Sci 2023; 24:13022. [PMID: 37629204 PMCID: PMC10455604 DOI: 10.3390/ijms241613022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/10/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Breast cancer (BC) accounts for the highest incidence of tumor-related mortality among women worldwide, justifying the growing search for molecular tools for the early diagnosis and follow-up of BC patients under treatment. Circulating extracellular vesicles (EVs) are membranous nanocompartments produced by all human cells, including tumor cells. Since minimally invasive methods collect EVs, which represent reservoirs of signals for cell communication, these particles have attracted the interest of many researchers aiming to improve BC screening and treatment. Here, we analyzed the cargoes of BC-derived EVs, both proteins and nucleic acids, which yielded a comprehensive list of potential markers divided into four distinct categories, namely, (i) modulation of aggressiveness and growth; (ii) preparation of the pre-metastatic niche; (iii) epithelial-to-mesenchymal transition; and (iv) drug resistance phenotype, further classified according to their specificity and sensitivity as vesicular BC biomarkers. We discuss the therapeutic potential of and barriers to the clinical implementation of EV-based tests, including the heterogeneity of EVs and the available technologies for analyzing their content, to present a consistent, reproducible, and affordable set of markers for further evaluation.
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Affiliation(s)
- Alexis Germán Murillo Carrasco
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 01246-000, Brazil; (A.G.M.C.); (A.H.O.); (L.N.d.S.A.)
- Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Andreia Hanada Otake
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 01246-000, Brazil; (A.G.M.C.); (A.H.O.); (L.N.d.S.A.)
- Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Janaina Macedo-da-Silva
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil; (J.M.-d.-S.); (V.F.S.); (G.P.)
| | - Veronica Feijoli Santiago
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil; (J.M.-d.-S.); (V.F.S.); (G.P.)
| | - Giuseppe Palmisano
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil; (J.M.-d.-S.); (V.F.S.); (G.P.)
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Luciana Nogueira de Sousa Andrade
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 01246-000, Brazil; (A.G.M.C.); (A.H.O.); (L.N.d.S.A.)
- Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Roger Chammas
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 01246-000, Brazil; (A.G.M.C.); (A.H.O.); (L.N.d.S.A.)
- Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo 01246-000, Brazil
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9
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Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
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10
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Maqueda JJ, Santos M, Ferreira M, Marinho S, Rocha S, Rocha M, Saraiva N, Bonito N, Carvalho J, Oliveira C. NGS Data Repurposing Allows Detection of tRNA Fragments as Gastric Cancer Biomarkers in Patient-Derived Extracellular Vesicles. Int J Mol Sci 2023; 24:ijms24108961. [PMID: 37240307 DOI: 10.3390/ijms24108961] [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: 03/15/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Transfer RNA fragments (tRFs) have gene silencing effects similarly to miRNAs, can be sorted into extracellular vesicles (EVs) and are emerging as potential circulating biomarkers for cancer diagnoses. We aimed at analyzing the expression of tRFs in gastric cancer (GC) and understanding their potential as biomarkers. We explored miRNA datasets from gastric tumors and normal adjacent tissues (NATs) from TCGA repository, as well as proprietary 3D-cultured GC cell lines and corresponding EVs, in order to identify differentially represented tRFs using MINTmap and R/Bioconductor packages. Selected tRFs were validated in patient-derived EVs. We found 613 Differentially Expressed (DE)-tRFs in the TCGA dataset, of which 19 were concomitantly upregulated in TCGA gastric tumors and present in 3D cells and EVs, but barely expressed in NATs. Moreover, 20 tRFs were expressed in 3D cells and EVs and downregulated in TCGA gastric tumors. Of these 39 DE-tRFs, 9 tRFs were also detected in patient-derived EVs. Interestingly, the targets of these 9 tRFs affect neutrophil activation and degranulation, cadherin binding, focal adhesion and the cell-substrate junction, highlighting these pathways as major targets of EV-mediated crosstalk with the tumor microenvironment. Furthermore, as they are present in four distinct GC datasets and can be detected even in low quality patient-derived EV samples, they hold promise as GC biomarkers. By repurposing already available NGS data, we could identify and cross-validate a set of tRFs holding potential as GC diagnosis biomarkers.
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Affiliation(s)
- Joaquín J Maqueda
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Bioinf2Bio LDA, 4200-150 Porto, Portugal
| | - Mafalda Santos
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Marta Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Sérgio Marinho
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Sara Rocha
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Mafalda Rocha
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Nadine Saraiva
- Instituto Português de Oncologia de Coimbra Francisco Gentil, E.P.E. (IPOCFG, E.P.E.), 3000-075 Coimbra, Portugal
| | - Nuno Bonito
- Instituto Português de Oncologia de Coimbra Francisco Gentil, E.P.E. (IPOCFG, E.P.E.), 3000-075 Coimbra, Portugal
| | - Joana Carvalho
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Carla Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Bioinf2Bio LDA, 4200-150 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
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11
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Jiang Y, Liu X, Ye J, Ma Y, Mao J, Feng D, Wang X. Migrasomes, a new mode of intercellular communication. Cell Commun Signal 2023; 21:105. [PMID: 37158915 PMCID: PMC10165304 DOI: 10.1186/s12964-023-01121-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/30/2023] [Indexed: 05/10/2023] Open
Abstract
Migrasomes are newly discovered extracellular vesicles (EVs) that are formed in migrating cells and mediate intercellular communication. However, their size, biological generation, cargo packaging, transport, and effects on recipient cells by migrasomes are different from those of other EVs. In addition to mediating organ morphogenesis during zebrafish gastrulation, discarding damaged mitochondria, and lateral transport of mRNA and proteins, growing evidence has demonstrated that migrasomes mediate a variety of pathological processes. In this review, we summarize the discovery, mechanisms of formation, isolation, identification, and mediation of cellular communication in migrasomes. We discuss migrasome-mediated disease processes, such as osteoclast differentiation, proliferative vitreoretinopathy, tumor cell metastasis by PD-L1 transport, immune cell chemotaxis to the site of infection by chemokines, angiogenesis promotion via angiogenic factors by immune cells, and leukemic cells chemotaxis to the site of mesenchymal stromal cells. Moreover, as new EVs, we propose the potential of migrasomes for disease diagnosis and treatment. Video Abstract.
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Affiliation(s)
- Yuyun Jiang
- Department of Central Laboratory, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Xi Liu
- Department of Central Laboratory, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Jixian Ye
- Department of Central Laboratory, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Yongbin Ma
- Department of Central Laboratory, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
- Department of Central Laboratory, Jintan Hospital, Jiangsu University, 500 Avenue Jintan, Jintan, 213200, People's Republic of China.
| | - Jiahui Mao
- Department of Central Laboratory, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Dingqi Feng
- Department of Central Laboratory, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Xuefeng Wang
- Department of Central Laboratory, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
- Department of Nuclear Medicine and Institute of Digestive Diseases, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
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12
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Fan S, Poetsch A. Proteomic Research of Extracellular Vesicles in Clinical Biofluid. Proteomes 2023; 11:proteomes11020018. [PMID: 37218923 DOI: 10.3390/proteomes11020018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/14/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Extracellular vesicles (EVs), the lipid bilayer membranous structures of particles, are produced and released from almost all cells, including eukaryotes and prokaryotes. The versatility of EVs has been investigated in various pathologies, including development, coagulation, inflammation, immune response modulation, and cell-cell communication. Proteomics technologies have revolutionized EV studies by enabling high-throughput analysis of their biomolecules to deliver comprehensive identification and quantification with rich structural information (PTMs, proteoforms). Extensive research has highlighted variations in EV cargo depending on vesicle size, origin, disease, and other features. This fact has sparked activities to use EVs for diagnosis and treatment to ultimately achieve clinical translation with recent endeavors summarized and critically reviewed in this publication. Notably, successful application and translation require a constant improvement of methods for sample preparation and analysis and their standardization, both of which are areas of active research. This review summarizes the characteristics, isolation, and identification approaches for EVs and the recent advances in EVs for clinical biofluid analysis to gain novel knowledge by employing proteomics. In addition, the current and predicted future challenges and technical barriers are also reviewed and discussed.
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Affiliation(s)
- Shipan Fan
- School of Basic Medical Sciences, Nanchang University, Nanchang 330021, China
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang 330021, China
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13
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Fu M, Gu J, Wang M, Zhang J, Chen Y, Jiang P, Zhu T, Zhang X. Emerging roles of tRNA-derived fragments in cancer. Mol Cancer 2023; 22:30. [PMID: 36782290 PMCID: PMC9926655 DOI: 10.1186/s12943-023-01739-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
tRNA-derived fragments (tRFs) are an emerging category of small non-coding RNAs that are generated from cleavage of mature tRNAs or tRNA precursors. The advance in high-throughput sequencing has contributed to the identification of increasing number of tRFs with critical functions in distinct physiological and pathophysiological processes. tRFs can regulate cell viability, differentiation, and homeostasis through multiple mechanisms and are thus considered as critical regulators of human diseases including cancer. In addition, increasing evidence suggest the extracellular tRFs may be utilized as promising diagnostic and prognostic biomarkers for cancer liquid biopsy. In this review, we focus on the biogenesis, classification and modification of tRFs, and summarize the multifaceted functions of tRFs with an emphasis on the current research status and perspectives of tRFs in cancer.
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Affiliation(s)
- Min Fu
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China ,grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jianmei Gu
- grid.260483.b0000 0000 9530 8833Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, 226361 Jiangsu China
| | - Maoye Wang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jiahui Zhang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Yanke Chen
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Pengcheng Jiang
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China
| | - Taofeng Zhu
- Department of Pulmonary and Critical Care Medicine, Yixing Hospital Affiliated to Jiangsu University, Yixing, 214200, Jiangsu, China.
| | - Xu Zhang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, China. .,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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14
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Addressing the Clinical Feasibility of Adopting Circulating miRNA for Breast Cancer Detection, Monitoring and Management with Artificial Intelligence and Machine Learning Platforms. Int J Mol Sci 2022; 23:ijms232315382. [PMID: 36499713 PMCID: PMC9736108 DOI: 10.3390/ijms232315382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Detecting breast cancer (BC) at the initial stages of progression has always been regarded as a lifesaving intervention. With modern technology, extensive studies have unraveled the complexity of BC, but the current standard practice of early breast cancer screening and clinical management of cancer progression is still heavily dependent on tissue biopsies, which are invasive and limited in capturing definitive cancer signatures for more comprehensive applications to improve outcomes in BC care and treatments. In recent years, reviews and studies have shown that liquid biopsies in the form of blood, containing free circulating and exosomal microRNAs (miRNAs), have become increasingly evident as a potential minimally invasive alternative to tissue biopsy or as a complement to biomarkers in assessing and classifying BC. As such, in this review, the potential of miRNAs as the key BC signatures in liquid biopsy are addressed, including the role of artificial intelligence (AI) and machine learning platforms (ML), in capitalizing on the big data of miRNA for a more comprehensive assessment of the cancer, leading to practical clinical utility in BC management.
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15
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Rhim J, Baek W, Seo Y, Kim JH. From Molecular Mechanisms to Therapeutics: Understanding MicroRNA-21 in Cancer. Cells 2022; 11:cells11182791. [PMID: 36139366 PMCID: PMC9497241 DOI: 10.3390/cells11182791] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that play an important role in regulating gene expression at a posttranscriptional level. As one of the first discovered oncogenic miRNAs, microRNA-21 (miR-21) has been highlighted for its critical role in cancers, such as glioblastoma, pancreatic adenocarcinoma, non-small cell lung cancer, and many others. MiR-21 targets many vital components in a wide range of cancers and acts on various cellular processes ranging from cancer stemness to cell death. Expression of miR-21 is elevated within cancer tissues and circulating miR-21 is readily detectable in biofluids, making it valuable as a cancer biomarker with significant potential for use in diagnosis and prognosis. Advances in RNA-based therapeutics have revealed additional avenues by which miR-21 can be utilized as a promising target in cancer. The purpose of this review is to outline the roles of miR-21 as a key modulator in various cancers and its potential as a therapeutic target.
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Affiliation(s)
- Jiho Rhim
- Cancer Molecular Biology Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Korea
- Department of Cancer Biomedical Science, National Cancer Center, Graduate School of Cancer Science and Policy, Goyang 10408, Korea
| | - Woosun Baek
- Cancer Molecular Biology Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Korea
- Department of Cancer Biomedical Science, National Cancer Center, Graduate School of Cancer Science and Policy, Goyang 10408, Korea
| | - Yoona Seo
- Cancer Molecular Biology Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Korea
- Department of Cancer Biomedical Science, National Cancer Center, Graduate School of Cancer Science and Policy, Goyang 10408, Korea
| | - Jong Heon Kim
- Cancer Molecular Biology Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Korea
- Department of Cancer Biomedical Science, National Cancer Center, Graduate School of Cancer Science and Policy, Goyang 10408, Korea
- Correspondence: ; Tel.: +82-31-920-2204
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16
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Paterson E, Blenkiron C, Danielson K, Henry C. Recommendations for extracellular vesicle miRNA biomarker research in the endometrial cancer context. Transl Oncol 2022; 23:101478. [PMID: 35820359 PMCID: PMC9284453 DOI: 10.1016/j.tranon.2022.101478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/06/2022] [Accepted: 07/03/2022] [Indexed: 11/05/2022] Open
Abstract
Endometrial cancer (EC) is the most common gynaecological malignancy in the developed world, and concerningly incidence is rising, particularly in younger people. Therefore, there is increased interest in novel diagnostic and prognostic biomarkers. Extracellular vesicles (EVs) are membrane-bound particles present in bodily fluids that have the potential to facilitate non-invasive, early diagnosis of EC and could aid with monitoring of recurrence and treatment response. EV cargo provides molecular insight into the tumor, with the lipid bilayer providing stability for RNA species usually prone to degradation. miRNAs have recently become a focus for EV biomarker research due to their ability to regulate cancer related pathways and influence cancer development and progression. This review evaluates the current literature on EV miRNA biomarkers with a focus on EC, and discusses the challenges facing this research. This review finally highlights areas of focus for EV miRNA biomarker research going forward, such as standardization of normalization approaches, sample storage and processing, extensive reporting of methodologies and moving away from single miRNA biomarkers.
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Affiliation(s)
- Emily Paterson
- Department of Obstetrics, Gynaecology and Women's Health, University of Otago, Wellington, New Zealand
| | - Cherie Blenkiron
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Kirsty Danielson
- Department of Surgery and Anaesthesia, University of Otago, Wellington, New Zealand
| | - Claire Henry
- Department of Obstetrics, Gynaecology and Women's Health, University of Otago, Wellington, New Zealand.
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Liu X, Papukashvili D, Wang Z, Liu Y, Chen X, Li J, Li Z, Hu L, Li Z, Rcheulishvili N, Lu X, Ma J. Potential utility of miRNAs for liquid biopsy in breast cancer. Front Oncol 2022; 12:940314. [PMID: 35992785 PMCID: PMC9386533 DOI: 10.3389/fonc.2022.940314] [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: 05/10/2022] [Accepted: 07/04/2022] [Indexed: 12/18/2022] Open
Abstract
Breast cancer (BC) remains the most prevalent malignancy due to its incidence rate, recurrence, and metastasis in women. Conventional strategies of cancer detection– mammography and tissue biopsy lack the capacity to detect the complete cancer genomic landscape. Besides, they often give false- positive or negative results. The presence of this and other disadvantages such as invasiveness, high-cost, and side effects necessitates developing new strategies to overcome the BC burden. Liquid biopsy (LB) has been brought to the fore owing to its early detection, screening, prognosis, simplicity of the technique, and efficient monitoring. Remarkably, microRNAs (miRNAs)– gene expression regulators seem to play a major role as biomarkers detected in the samples of LB. Particularly, miR-21 and miR-155 among other possible candidates seem to serve as favorable biomarkers in the diagnosis and prognosis of BC. Hence, this review will assess the potential utility of miRNAs as biomarkers and will highlight certain promising candidates for the LB approach in the diagnosis and management of BC that may optimize the patient outcome.
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Affiliation(s)
- Xiangrong Liu
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Dimitri Papukashvili
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhixiang Wang
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Yan Liu
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Xiaoxia Chen
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jianrong Li
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Zhiyuan Li
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Linjie Hu
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Zheng Li
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Nino Rcheulishvili
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xiaoqing Lu
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
- *Correspondence: Xiaoqing Lu, ; Jinfeng Ma,
| | - Jinfeng Ma
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
- *Correspondence: Xiaoqing Lu, ; Jinfeng Ma,
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18
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Li Y, Cui S, Xu Z, Zhang Y, Wu T, Zhang J, Chen Y. Exosomal tRF-Leu-AAG-001 derived from mast cell as a potential non-invasive diagnostic biomarker for endometriosis. BMC Womens Health 2022; 22:253. [PMID: 35752827 PMCID: PMC9233364 DOI: 10.1186/s12905-022-01827-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The diagnosis of endometriosis (EMs) is still based on laparoscopic observation. This study tries to verify whether exosomal tRNA-derived fragments (tRFs) in leucorrhea can be used as non-invasive diagnostic markers. METHODS Endometrial tissues and leucorrhea were sampled from women hospitalized in Ningbo University Affiliated Hospital from January 2021 to July 2021 with (n = 26) and without endometriosis (n = 25). Exosomes were isolated from samples by differential centrifugation. The small RNA sequencing was performed to detect the exosomal tRNA halves (tiRNAs)&tRFs. RNA probe and immunofluorescence antibody were used to localize the origin of tRFs. From mast cell lines infected with tRF-Leu-AAG-001 siRNA, we observed the change in vascular capacity and expression of inflammatory factors. The specificity and sensitivity tRF were determined by receiver operating characteristic analyses. RESULTS 63 up-regulated and 45 down-regulated tRFs&tiRNAs were identified in ectopic exosomes. We selected tRF-Leu-AAG-001 as a candidate marker through KEGG pathway enrichment and PCR verification. We found that mast cells highly expressed tRF-Leu-AAG-001 in ectopic foci by immunofluorescence staining. We used siRNA to silenced tRF-Leu-AAG-001 expression in luva, qPCR analysis showed IL-6, IL-10, IL-1β, and TNF-α were significantly decreased. Meanwhile, tRF-Leu-AAG-001 siRNA dramatically reduced the angiogenic ability of luva. Finally, we examined the expression of exosomal tRF-Leu-AAG-001 in the leucorrhea. It was found exosomal tRF-Leu-AAG-001 had high specificity and sensitivity for predicting the occurrence of ectopic disease. CONCLUSIONS Exosomal tRF-Leu-AAG-001 derived from mast cells in ectopic foci might promote inflammation and angiogenesis. Meanwhile, leucorrhea exosomal tRF-Leu-AAG-001 could be a potential diagnostic biomarker for endometriosis.
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Affiliation(s)
- Yingxue Li
- Ningbo Institute of Medical Sciences, Ningbo, China.,Ningbo University, Ningbo, China
| | - Shuling Cui
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Zemin Xu
- Addiction Research of Zhejiang Province, Ningbo Kangning Hospital, School of Medicine, Ningbo University, Ningbo, China
| | | | - Tao Wu
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Jing Zhang
- Ningbo Women&Children's Hospital, Ningbo, China
| | - Yichen Chen
- Ningbo Women&Children's Hospital, Ningbo, China. .,Ningbo Institute of Medical Sciences, Ningbo, China. .,Ningbo University, Ningbo, China.
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Jing W, Wang H, Zhan L, Yan W. Extracellular Vesicles, New Players in Sepsis and Acute Respiratory Distress Syndrome. Front Cell Infect Microbiol 2022; 12:853840. [PMID: 35463634 PMCID: PMC9021632 DOI: 10.3389/fcimb.2022.853840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/14/2022] [Indexed: 11/15/2022] Open
Abstract
Sepsis refers to a complex syndrome associated with physiological, pathological, and biochemical abnormalities resulted from infection. Sepsis is the major cause of acute respiratory distress syndrome (ARDS). Extracellular vesicles (EVs) are serving as new messengers to mediate cell-cell communication in vivo. Non-coding RNAs, proteins and metabolites encapsulated by EVs could result in either pro-inflammatory or anti-inflammatory effects in the recipient cells. Pathogens or host cells derived EVs play an important role in pathogens infection during the occurrence and development of sepsis and ARDS. Additionally, we summarize the potential application for EVs in diagnosis, prevention and treatment for sepsis and ARDS.
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Affiliation(s)
- Wenqiang Jing
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huijuan Wang
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, China
| | - Liying Zhan
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Liying Zhan, ; Wei Yan,
| | - Wei Yan
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- *Correspondence: Liying Zhan, ; Wei Yan,
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Liu DSK, Yang QZC, Asim M, Krell J, Frampton AE. The Clinical Significance of Transfer RNAs Present in Extracellular Vesicles. Int J Mol Sci 2022; 23:ijms23073692. [PMID: 35409051 PMCID: PMC8998272 DOI: 10.3390/ijms23073692] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 12/19/2022] Open
Abstract
Extracellular vesicles (EVs) are important for intercellular signalling in multi-cellular organisms. However, the role of mature transfer RNAs (tRNAs) and tRNA fragments in EVs has yet to be characterised. This systematic review aimed to identify up-to-date literature on tRNAs present within human EVs and explores their potential clinical significance in health and disease. A comprehensive and systematic literature search was performed, and the study was conducted in accordance with PRISMA guidelines. Electronic databases MEDLINE and EMBASE were searched up until 1 January 2022. From 685 papers, 60 studies were identified for analysis. The majority of papers reviewed focussed on the role of EV tRNAs in cancers (31.7%), with numerous other conditions represented. Blood and cell lines were the most common EV sources, representing 85.9% of protocols used. EV isolation methods included most known methods, precipitation being the most common (49.3%). The proportion of EV tRNAs was highly variable, ranging between 0.04% to >95% depending on tissue source. EV tRNAs are present in a multitude of sources and show promise as disease markers in breast cancer, gastrointestinal cancers, and other diseases. EV tRNA research is an emerging field, with increasing numbers of papers highlighting novel methodologies for tRNA and tRNA fragment discovery.
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Affiliation(s)
- Daniel S. K. Liu
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0HS, UK; (D.S.K.L.); (Q.Z.C.Y.); (J.K.)
| | - Qi Zhi Clayton Yang
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0HS, UK; (D.S.K.L.); (Q.Z.C.Y.); (J.K.)
| | - Mohammad Asim
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7WG, UK;
| | - Jonathan Krell
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0HS, UK; (D.S.K.L.); (Q.Z.C.Y.); (J.K.)
| | - Adam E. Frampton
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0HS, UK; (D.S.K.L.); (Q.Z.C.Y.); (J.K.)
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7WG, UK;
- HPB Surgical Unit, Royal Surrey County Hospital NHS Foundation Trust, Guildford, Surrey GU2 7XX, UK
- Correspondence: or
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21
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Weng Q, Wang Y, Xie Y, Yu X, Zhang S, Ge J, Li Z, Ye G, Guo J. Extracellular vesicles-associated tRNA-derived fragments (tRFs): biogenesis, biological functions, and their role as potential biomarkers in human diseases. J Mol Med (Berl) 2022; 100:679-695. [PMID: 35322869 PMCID: PMC9110440 DOI: 10.1007/s00109-022-02189-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 02/10/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023]
Abstract
Traditionally, transfer RNAs (tRNAs) specifically decoded messenger RNA (mRNA) and participated in protein translation. tRNA-derived fragments (tRFs), also known as tRNA-derived small RNAs (tsRNAs), are generated by the specific cleavage of pre- and mature tRNAs and are a class of newly defined functional small non-coding RNAs (sncRNAs). Following the different cleavage positions of precursor or mature tRNA, tRFs are classified into seven types, 5′-tRNA half, 3′-tRNA half, tRF-1, 5′U-tRF, 3′-tRF, 5′-tRF, and i-tRF. It has been demonstrated that tRFs have a diverse range of biological functions in cellular processes, which include inhibiting protein translation, modulating stress response, regulating gene expression, and involvement in cell cycles and epigenetic inheritance. Emerging evidences have indicated that tRFs in extracellular vesicles (EVs) seem to act as regulatory molecules in various cellular processes and play essential roles in cell-to-cell communication. Furthermore, the dysregulation of EV-associated tRFs has been associated with the occurrence and progression of a variety of cancers and they can serve as novel potential biomarkers for cancer diagnosis. In this review, the biogenesis and classification of tRFs are summarized, and the biological functions of EV-associated tRFs and their roles as potential biomarkers in human diseases are discussed.
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Affiliation(s)
- Qiuyan Weng
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Yao Wang
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Yaoyao Xie
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Xiuchong Yu
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Shuangshuang Zhang
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Jiaxin Ge
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Zhe Li
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Guoliang Ye
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China. .,Institute of Digestive Diseases of Ningbo University, Ningbo, 315020, China.
| | - Junming Guo
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China. .,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China. .,Institute of Digestive Diseases of Ningbo University, Ningbo, 315020, China.
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22
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Gao L, Xu L, Wang X. A Systematic Review of tRNA-Derived Small non-Coding RNAs as Diagnostic and Prognostic Markers in Cancer. Technol Cancer Res Treat 2022; 21:15330338211072989. [PMID: 35506562 DOI: 10.1177/15330338211072989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Objectives: tRNA-derived small non-coding RNAs (tsncRNAs) are one of mysterious small non-coding RNAs. Dysregulated tsncRNAs can led to all kinds of cancers. Recently, tsncRNAs were postulated to be potentially useful biomarkers for tumor diagnosis and prognosis. However, there were no systematic reviews of prognostic and diagnostic tsncRNAs in neoplasms. The study aimed to decipher the relationships between tsncRNAs expression, diagnostic and prognostic outcome in tumors. Methods: This study systematically searched Google Scholar, MEDLINE, Scopus, PubMed, Embase, ScienceDirect, Ovid-Medline, Chinese National Knowledge Infrastructure, WanFang and SinoMed databases for relevant articles published before September 21, 2020. Results: The study is registered in PROSPERO (CRD42020213863). Fourteen relevant studies were included in the meta-analysis: 12 on diagnosis and 5 on prognosis. The pooled add ratio, 95% confidence intervals (Cl) and hazard ratios (HR) of the studies were used to investigate the clinical parameters and overall survival (OS) of cancer patients. The area under the curve (AUC), sensitivity, and specificity was 0.79, 72%, and 73% in tumors, respectively. Though abnormally expressed tsncRNAs were associated with poor and unfavorable impacts on the OS time of cancer patients, the oncogenic tsncRNA may be a favorable impact on overall survival (OS: HR = 0.67, 95% Cl: 0.48-0.94, P = 0.02), and tumor-suppressor tsncRNA might have an unfavorable impact on overall survival (OS: HR = 1.41, 95% Cl: 0.84-2.37, P = 0.19). Conclusion: These results strongly suggested that tsncRNAs were potential novel prognostic and diagnostic indicators in tumors.
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Affiliation(s)
| | - Lin Xu
- 71220Jiujiang University, China
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23
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Liu H, Bian QZ, Zhang W, Cui HB. Circulating microRNA-103a-3p could be a diagnostic and prognostic biomarker for breast cancer. Oncol Lett 2021; 23:38. [PMID: 34966454 PMCID: PMC8669650 DOI: 10.3892/ol.2021.13156] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
Breast cancer (BC) is the most frequent cancer for women worldwide. Recently, a spectrum of cell-free circulating microRNAs (miR) has been recognized as promising biomarkers for BC diagnosis and prognosis, among which miR-103a-3p has been reported in several types of human cancer. However, the role of miR-103a-3p in BC remains unknown. A total of 112 patients with BC and 59 healthy controls were recruited into the present study. The expression level of serum miR-103a-3p was evaluated using reverse transcription-quantitative PCR. Receiver operating characteristic curves were utilized to calculate diagnostic accuracy. Survival curves were generated to analyze survival outcomes. It was found that circulating miR-103a-3p level was upregulated in patients with BC compared with that in healthy controls, and its expression was decreased following surgery. In addition, miR-103a-3p expression level was also associated with advanced clinicopathological features, including positive epidermal growth factor receptor 2 status, metastasis and an advanced TNM stage. The circulating serum miR-103a-3p level could be used to discriminate between patients with BC and the healthy controls prior to surgery using an area under curve [(AUC), 0.697; 95% confidence intervals (CI), 0.615-0.778], and distinguish patients with BC and metastasis from those without metastasis (AUC, 0.936; 95% CI, 0.892-0.980). In addition, high expression level of miR-103a-3p was associated with worse survival outcomes in patients with BC. In conclusion, the present study suggests that miR-103a-3p could be a potential non-invasive diagnostic and prognostic biomarker for BC.
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Affiliation(s)
- Hui Liu
- Department of Thyroid and Breast Surgery, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Qing-Zhao Bian
- Department of Thyroid and Breast Surgery, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Wei Zhang
- Department of Thyroid and Breast Surgery, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Hai-Bin Cui
- Department of Thyroid and Breast Surgery, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
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Shi L, Feng L, Tong Y, Jia J, Li T, Wang J, Jiang Z, Yu M, Xia H, Jin Q, Jiang X, Cheng Y, Ju L, Liu J, Zhang Q, Lou J. Genome wide profiling of miRNAs relevant to the DNA damage response induced by hexavalent chromium exposure (DDR-related miRNAs in response to Cr (VI) exposure). ENVIRONMENT INTERNATIONAL 2021; 157:106782. [PMID: 34329887 DOI: 10.1016/j.envint.2021.106782] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
AIM We aimed to explore the expression of miRNAs and their potential roles in the DNA damage response (DDR) induced by Cr (VI) exposure in human B lymphoblast cells (HMy2.CIR cells) and in a population of Cr (VI)-exposed humans. METHODS Differentially expressed miRNAs were found by a combination of miRNA sequencing and RT-qPCR validation in HMy2.CIR cells treated with K2Cr2O7. Differentially expressed miRNAs related to DDR were selected for functional study. The expression levels of differential miRNAs were also investigated in chromate workers. RESULTS A total of 214 differentially expressed miRNAs were identified by sequencing, and the expression of 5 miRNAs among 25 associated with DDR was found to be consistent between sequencing and validation studies.Functional studies showed that miR-148a-3p, miR-21-5p, and miR-424-3p might be related to Cr (VI)-induced cell apoptosis, and miR-221-3p might participate in Cr (VI)-induced DDR. We also found that the expression of miR-21-5p and miR-424-3p was upregulated in chromate workers. CONCLUSIONS Cr (VI) exposure could significantly impact miRNAs expression in vitro and in chromate workers. Functional studies showed that miR-148a-3p, miR-21-5p and miR-221-3p might take a crucial role in the cellular DDR induced by Cr (VI) exposure.
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Affiliation(s)
- Li Shi
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Lingfang Feng
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Yan Tong
- Affiliated Hangzhou First People's Hospital, Zhejiang University, School of Medicine, Hangzhou, Zhejiang, China
| | - Junlin Jia
- Center for Biostatistics, Bioinformatics and Big Data, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tao Li
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Jing Wang
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Zhaoqiang Jiang
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Min Yu
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Hailing Xia
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Qi Jin
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Xiyi Jiang
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Yongran Cheng
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Li Ju
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Jiaqi Liu
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China
| | - Quan Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Jianlin Lou
- School of Public Health (Institute of Occupational Diseases), Hangzhou Medical College (Zhejiang Academy of Medical Sciences), Hangzhou, Zhejiang, China.
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Dynamic Landscape of Extracellular Vesicle-Associated Proteins Is Related to Treatment Response of Patients with Metastatic Breast Cancer. MEMBRANES 2021; 11:membranes11110880. [PMID: 34832109 PMCID: PMC8619728 DOI: 10.3390/membranes11110880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022]
Abstract
Breast cancer is the leading cause of cancer death in women. The majority of these deaths are due to disease metastasis, in which cancer cells disseminate to multiple organs and disrupt vital physiological functions. It is widely accepted that breast cancer cells secrete extracellular vesicles (EVs), which contain dynamic molecular cargo that act as versatile mediators of intercellular communication. Therefore, Evs. secreted by breast cancer cells could be involved in the development of metastatic disease and resistance to treatment. Moreover, changes in EV cargo could reflect the effects of therapy on their parent tumor cells. The aim of this feasibility study was to quantitatively profile the proteomes of Evs. isolated from blood samples taken from treatment sensitive and resistant metastatic breast cancer patients to identify proteins associated with responses. Three serial blood samples were collected from three patients with metastatic breast cancer receiving systemic therapy including a responder, a non-responder, and a mixed-responder. Evs. were isolated from plasma using size exclusion chromatography and their protein cargo was prepared for tandem mass tag (TMT)-labelling and quantitative analyses using two-dimensional high-performance liquid chromatography followed by tandem mass spectrometry. After filtering, we quantitatively identified 286 proteins with high confidence using a q value of 0.05. Of these, 149 were classified as EV associated candidate proteins and 137 as classical, high abundant plasma proteins. After comparing EV protein abundance between the responder and non-responder, we identified 35 proteins with unique de-regulated abundance patterns that was conserved at multiple time points. We propose that this proof-of-concept approach can be used to identify proteins which have potential as predictors of metastatic breast cancer response to treatment.
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Zelli V, Compagnoni C, Capelli R, Corrente A, Cornice J, Vecchiotti D, Di Padova M, Zazzeroni F, Alesse E, Tessitore A. Emerging Role of isomiRs in Cancer: State of the Art and Recent Advances. Genes (Basel) 2021; 12:genes12091447. [PMID: 34573429 PMCID: PMC8469436 DOI: 10.3390/genes12091447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
The advent of Next Generation Sequencing technologies brought with it the discovery of several microRNA (miRNA) variants of heterogeneous lengths and/or sequences. Initially ascribed to sequencing errors/artifacts, these isoforms, named isomiRs, are now considered non-canonical variants that originate from physiological processes affecting the canonical miRNA biogenesis. To date, accurate IsomiRs abundance, biological activity, and functions are not completely understood; however, the study of isomiR biology is an area of great interest due to their high frequency in the human miRNome, their putative functions in cooperating with the canonical miRNAs, and potential for exhibiting novel functional roles. The discovery of isomiRs highlighted the complexity of the small RNA transcriptional landscape in several diseases, including cancer. In this field, the study of isomiRs could provide further insights into the miRNA biology and its implication in oncogenesis, possibly providing putative new cancer diagnostic, prognostic, and predictive biomarkers as well. In this review, a comprehensive overview of the state of research on isomiRs in different cancer types, including the most common tumors such as breast cancer, colorectal cancer, melanoma, and prostate cancer, as well as in the less frequent tumors, as for example brain tumors and hematological malignancies, will be summarized and discussed.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Corrente
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Jessica Cornice
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Davide Vecchiotti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Monica Di Padova
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence: ; Tel.: +39-0862433518; Fax: +39-0862433131
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Li X, Liu X, Zhao D, Cui W, Wu Y, Zhang C, Duan C. tRNA-derived small RNAs: novel regulators of cancer hallmarks and targets of clinical application. Cell Death Discov 2021; 7:249. [PMID: 34537813 PMCID: PMC8449783 DOI: 10.1038/s41420-021-00647-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/19/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
tRNAs are a group of conventional noncoding RNAs (ncRNAs) with critical roles in the biological synthesis of proteins. Recently, tRNA-derived small RNAs (tsRNAs) were found to have important biological functions in the development of human diseases including carcinomas, rather than just being considered pure degradation material. tsRNAs not only are abnormally expressed in the cancer tissues and serum of cancer patients, but also have been suggested to regulate various vital cancer hallmarks. On the other hand, the application of tsRNAs as biomarkers and therapeutic targets is promising. In this review, we focused on the basic characteristics of tsRNAs, and their biological functions known thus far, and explored the regulatory roles of tsRNAs in cancer hallmarks including proliferation, apoptosis, metastasis, tumor microenvironment, drug resistance, cancer stem cell phenotype, and cancer cell metabolism. In addition, we also discussed the research progress on the application of tsRNAs as tumor biomarkers and therapeutic targets.
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Affiliation(s)
- Xizhe Li
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Xianyu Liu
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Deze Zhao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Weifang Cui
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Yingfang Wu
- Centre of Stomatology, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China. .,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China. .,National Clinical Research Center for Geriatric Disorders, Changsha, 410008, Hunan, P. R. China.
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China. .,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China. .,Institute of Medical Sciences, Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P. R. China.
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Koyano K, Bahn JH, Xiao X. Extracellular microRNA 3' end modification across diverse body fluids. Epigenetics 2021; 16:1000-1015. [PMID: 33092484 PMCID: PMC8451466 DOI: 10.1080/15592294.2020.1834922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/03/2020] [Accepted: 08/21/2020] [Indexed: 01/19/2023] Open
Abstract
microRNAs (miRNAs) are small non-coding RNAs that play critical roles in gene regulation. The presence of miRNAs in extracellular biofluids is increasingly recognized. However, most previous characterization of extracellular miRNAs focused on their overall expression levels. Alternative sequence isoforms and modifications of miRNAs were rarely considered in the extracellular space. Here, we developed a highly accurate bioinformatic method, called miNTA, to identify 3' non-templated additions (NTAs) of miRNAs using small RNA-sequencing data. Using miNTA, we conducted an in-depth analysis of miRNA 3' NTA profiles in 1047 extracellular RNA-sequencing data sets of 4 types of biofluids. This analysis identified hundreds of miRNAs with 3' uridylation or adenylation, with the former being more prevalent. Among these miRNAs, up to 53% (22%) had an average 3' uridylation (adenylation) level of at least 10% in a specific biofluid. Strikingly, we found that 3' uridylation levels enabled segregation of different types of biofluids, more effectively than overall miRNA expression levels. This observation suggests that 3' NTA levels possess fluid-specific information relatively robust to batch effects. In addition, we observed that extracellular miRNAs with 3' uridylations are enriched in processes related to angiogenesis, apoptosis, and inflammatory response, and this type of modification may stabilize base-pairing between miRNAs and their target genes. Together, our study provides a comprehensive landscape of miRNA NTAs in human biofluids, which paves way for further biomarker discoveries. The insights generated in our work built a foundation for future functional, mechanistic, and translational discoveries.
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Affiliation(s)
- Kikuye Koyano
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, California, USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, California, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, California, USA
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, California, USA
- Molecular Biology Institute; UCLA, Los Angeles, California, USA
- Institute for Quantitative and Computational Sciences, UCLA, California, CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, California, CA, US
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29
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isomiRs-Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them? Biomolecules 2020; 11:biom11010041. [PMID: 33396892 PMCID: PMC7823672 DOI: 10.3390/biom11010041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/22/2020] [Accepted: 12/26/2020] [Indexed: 02/06/2023] Open
Abstract
Numerous studies on microRNAs (miRNA) in cancer and other diseases have been accompanied by diverse computational approaches and experimental methods to predict and validate miRNA biological and clinical significance as easily accessible disease biomarkers. In recent years, the application of the next-generation deep sequencing for the analysis and discovery of novel RNA biomarkers has clearly shown an expanding repertoire of diverse sequence variants of mature miRNAs, or isomiRs, resulting from alternative post-transcriptional processing events, and affected by (patho)physiological changes, population origin, individual's gender, and age. Here, we provide an in-depth overview of currently available bioinformatics approaches for the detection and visualization of both mature miRNA and cognate isomiR sequences. An attempt has been made to present in a systematic way the advantages and downsides of in silico approaches in terms of their sensitivity and accuracy performance, as well as used methods, workflows, and processing steps, and end output dataset overlapping issues. The focus is given to the challenges and pitfalls of isomiR expression analysis. Specifically, we address the availability of tools enabling research without extensive bioinformatics background to explore this fascinating corner of the small RNAome universe that may facilitate the discovery of new and more reliable disease biomarkers.
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30
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Yu M, Lu B, Zhang J, Ding J, Liu P, Lu Y. tRNA-derived RNA fragments in cancer: current status and future perspectives. J Hematol Oncol 2020; 13:121. [PMID: 32887641 PMCID: PMC7487644 DOI: 10.1186/s13045-020-00955-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/24/2020] [Indexed: 01/02/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have been the focus of many studies over the last few decades, and their fundamental roles in human diseases have been well established. Transfer RNAs (tRNAs) are housekeeping ncRNAs that deliver amino acids to ribosomes during protein biosynthesis. tRNA fragments (tRFs) are a novel class of small ncRNAs produced through enzymatic cleavage of tRNAs and have been shown to play key regulatory roles similar to microRNAs. Development and application of high-throughput sequencing technologies has provided accumulating evidence of dysregulated tRFs in cancer. Aberrant expression of tRFs has been found to participate in cell proliferation, invasive metastasis, and progression in several human malignancies. These newly identified functional tRFs also have great potential as new biomarkers and therapeutic targets for cancer treatment. In this review, we focus on the major biological functions of tRFs including RNA silencing, translation regulation, and epigenetic regulation; summarize recent research on the roles of tRFs in different types of cancer; and discuss the potential of using tRFs as clinical biomarkers for cancer diagnosis and prognosis and as therapeutic targets for cancer treatment.
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Affiliation(s)
- Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Bingjian Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Jisong Zhang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Jinwang Ding
- Department of Head and Neck Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, China
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China.,Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.
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31
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Koi Y, Tsutani Y, Nishiyama Y, Ueda D, Ibuki Y, Sasada S, Akita T, Masumoto N, Kadoya T, Yamamoto Y, Takahashi RU, Tanaka J, Okada M, Tahara H. Predicting the presence of breast cancer using circulating small RNAs, including those in the extracellular vesicles. Cancer Sci 2020; 111:2104-2115. [PMID: 32215990 PMCID: PMC7293081 DOI: 10.1111/cas.14393] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 12/26/2022] Open
Abstract
Emerging evidence indicates that small RNAs, including microRNAs (miRNAs) and their isoforms (isomiRs), and transfer RNA fragments (tRFs), are differently expressed in breast cancer (BC) and can be detected in blood circulation. Circulating small RNAs and small RNAs in extracellular vesicles (EVs) have emerged as ideal markers in small RNA‐based applications for cancer detection. In this study, we first undertook small RNA sequencing to assess the expression of circulating small RNAs in the serum of BC patients and cancer‐free individuals (controls). Expression of 3 small RNAs, namely isomiR of miR‐21‐5p (3′ addition C), miR‐23a‐3p and tRF‐Lys (TTT), was significantly higher in BC samples and was validated by small RNA sequencing in an independent cohort. Our constructed model using 3 small RNAs showed high diagnostic accuracy with an area under the receiver operating characteristic curve of 0.92 and discriminated early‐stage BCs at stage 0 from control. To test the possibility that these small RNAs are released from cancer cells, we next examined EVs from the serum of BC patients and controls. Two of the 3 candidate small RNAs were identified, and shown to be abundant in EVs of BC patients. Interestingly, these 2 small RNAs are also more abundantly detected in culture media of breast cancer cell lines (MCF‐7 and MDA‐MB‐231). The same tendency in selective elevation seen in total serum, serum EV, and EV derived from cell culture media could indicate the efficiency of this model using total serum of patients. These findings indicate that small RNAs serve as significant biomarkers for BC detection.
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Affiliation(s)
- Yumiko Koi
- Surgical Oncology, Division of Radiation Biology and Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yasuhiro Tsutani
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yukie Nishiyama
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Daisuke Ueda
- Surgical Oncology, Division of Radiation Biology and Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yuta Ibuki
- Surgical Oncology, Division of Radiation Biology and Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Shinsuke Sasada
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Tomoyuki Akita
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Norio Masumoto
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takayuki Kadoya
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yuki Yamamoto
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ryou-U Takahashi
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Junko Tanaka
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Collaborative laboratory of Liquid Biopsy, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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