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Janssen FW, Lak NSM, Janda CY, Kester LA, Meister MT, Merks JHM, van den Heuvel-Eibrink MM, van Noesel MM, Zsiros J, Tytgat GAM, Looijenga LHJ. A comprehensive overview of liquid biopsy applications in pediatric solid tumors. NPJ Precis Oncol 2024; 8:172. [PMID: 39097671 PMCID: PMC11297996 DOI: 10.1038/s41698-024-00657-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/15/2024] [Indexed: 08/05/2024] Open
Abstract
Liquid biopsies are emerging as an alternative source for pediatric cancer biomarkers with potential applications during all stages of patient care, from diagnosis to long-term follow-up. While developments within this field are reported, these mainly focus on dedicated items such as a specific liquid biopsy matrix, analyte, and/or single tumor type. To the best of our knowledge, a comprehensive overview is lacking. Here, we review the current state of liquid biopsy research for the most common non-central nervous system pediatric solid tumors. These include neuroblastoma, renal tumors, germ cell tumors, osteosarcoma, Ewing sarcoma, rhabdomyosarcoma and other soft tissue sarcomas, and liver tumors. Within this selection, we discuss the most important or recent studies involving liquid biopsy-based biomarkers, anticipated clinical applications, and the current challenges for success. Furthermore, we provide an overview of liquid biopsy-based biomarker publication output for each tumor type based on a comprehensive literature search between 1989 and 2023. Per study identified, we list the relevant liquid biopsy-based biomarkers, matrices (e.g., peripheral blood, bone marrow, or cerebrospinal fluid), analytes (e.g., circulating cell-free and tumor DNA, microRNAs, and circulating tumor cells), methods (e.g., digital droplet PCR and next-generation sequencing), the involved pediatric patient cohort, and proposed applications. As such, we identified 344 unique publications. Taken together, while the liquid biopsy field in pediatric oncology is still behind adult oncology, potentially relevant publications have increased over the last decade. Importantly, steps towards clinical implementation are rapidly gaining ground, notably through validation of liquid biopsy-based biomarkers in pediatric clinical trials.
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Affiliation(s)
| | | | | | | | - Michael T Meister
- Princess Máxima Center, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Johannes H M Merks
- Princess Máxima Center, Utrecht, the Netherlands
- Division of Imaging and Oncology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Marry M van den Heuvel-Eibrink
- Princess Máxima Center, Utrecht, the Netherlands
- Wilhelmina Children's Hospital-Division of CHILDHEALTH, University Medical Center Utrech, University of Utrecht, Utrecht, the Netherlands
| | - Max M van Noesel
- Princess Máxima Center, Utrecht, the Netherlands
- Division of Imaging and Oncology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | | | - Godelieve A M Tytgat
- Princess Máxima Center, Utrecht, the Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Leendert H J Looijenga
- Princess Máxima Center, Utrecht, the Netherlands.
- Department of Pathology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands.
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2
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Cheng S, Zhou Z, Liu J, Li J, Wang Y, Xiao J, Luo Y. Landscape analysis of alternative splicing in kidney renal clear cell carcinoma and their clinical significance. Aging (Albany NY) 2024; 16:10016-10032. [PMID: 38862257 PMCID: PMC11210227 DOI: 10.18632/aging.205915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/25/2024] [Indexed: 06/13/2024]
Abstract
A growing number of studies reveal that alternative splicing (AS) is associated with tumorigenesis, progression, and metastasis. Systematic analysis of alternative splicing signatures in renal cancer is lacking. In our study, we investigated the AS landscape of kidney renal clear cell carcinoma (KIRC) and identified AS predictive model to improve the prognostic prediction of KIRC. We obtained clinical data and gene expression profiles of KIRC patients from the TCGA database to evaluate AS events. The calculation results for seven types of AS events indicated that 46276 AS events from 10577 genes were identified. Next, we applied Cox regression analysis to identify 5864 prognostic-associated AS events. We used the Metascape database to verify the potential pathways of prognostic-associated AS. Moreover, we constructed KIRC prediction systems with prognostic-associated AS events by the LASSO Cox regression model. AUCs demonstrated that these prediction systems had excellent prognostic accuracy simultaneously. We identified 34 prognostic associated splicing factors (SFs) and constructed homologous regulatory networks. Furthermore, in vitro experiments were performed to validate the favorable effect of SFs FMR1 in KIRC. In conclusion, we overviewed AS events in KIRC and identified AS-based prognostic models to assist the survival prediction of KIRC patients. Our study may provide a novel predictive signature to improve the prognostic prediction of KIRC, which might facilitate KIRC patient counseling and individualized management.
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Affiliation(s)
- Songtao Cheng
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zili Zhou
- Department of Gastrointestinal Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiannan Liu
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jun Li
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Wang
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiantao Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongwen Luo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
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3
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Li J, Fang J, Jiang X, Zhang Y, Vidal-Puig A, Zhang CY. RNAkines are secreted messengers shaping health and disease. Trends Endocrinol Metab 2024; 35:201-218. [PMID: 38160178 DOI: 10.1016/j.tem.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Extracellular noncoding RNAs (ncRNAs) have crucial roles in intercellular communications. The process of ncRNA secretion is highly regulated, with specific ncRNA profiles produced under different physiological and pathological circumstances. These ncRNAs are transported primarily via extracellular vesicles (EVs) from their origin cells to target cells, utilising both endocrine and paracrine pathways. The intercellular impacts of extracellular ncRNAs are essential for maintaining homeostasis and the pathogenesis of various diseases. Given the unique aspects of extracellular ncRNAs, here we propose the term 'RNAkine' to describe these recently identified secreted factors. We explore their roles as intercellular modulators, particularly in their ability to regulate metabolism and influence tumorigenesis, highlighting their definition and importance as a distinct class of secreted factors.
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Affiliation(s)
- Jing Li
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China.
| | - Jingwen Fang
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China
| | - Xiaohong Jiang
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China
| | - Yujing Zhang
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China
| | - Antonio Vidal-Puig
- Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, UK; Cambridge University Nanjing Centre of Technology and Innovation, Nanjing, China.
| | - Chen-Yu Zhang
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China; Research Unit of Extracellular RNA, Chinese Academy of Medical Sciences, Nanjing, Jiangsu 210023, PR China; Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100144, PR China.
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4
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Tomiyama E, Fujita K, Hashimoto M, Uemura H, Nonomura N. Urinary markers for bladder cancer diagnosis: A review of current status and future challenges. Int J Urol 2024; 31:208-219. [PMID: 37968825 DOI: 10.1111/iju.15338] [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: 09/10/2023] [Accepted: 10/26/2023] [Indexed: 11/17/2023]
Abstract
Bladder cancer is a common urological cancer with a high recurrence rate that requires long-term follow-up, and early detection positively affects prognosis. To date, the initial diagnosis and follow-up for bladder cancer rely on cystoscopy, which is an invasive and expensive procedure. Therefore, urinary markers for the detection of bladder cancer have attracted research attention for decades to reduce unnecessary cystoscopies. Urine, which is in continuous contact with bladder cancer, is considered a suitable fluid for providing tumor information. Urinary cytology is the only widely used urinary marker in clinical practice; however, it has poor sensitivity for low-grade tumors; indicating the need for novel urinary markers. Considerable research has been conducted on this topic over the years, resulting in a complex landscape with a wide range of urinary markers, including protein-, exfoliated cell-, RNA-, DNA-, and extracellular vesicle-based markers. Although some of these markers have been approved by the U.S. Food and Drug Administration and are commercially available, their use in clinical practice is limited. To facilitate clinical application, potential urinary markers must withstand prospective clinical trials and be easy for patients and clinicians to understand and utilize in a clinical context. This review provides a comprehensive overview of currently available and recently reported promising urinary markers for bladder cancer. Additionally, the challenges and the prospects of these urinary markers for clinical implementation in bladder cancer treatment were discussed.
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Affiliation(s)
- Eisuke Tomiyama
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazutoshi Fujita
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Urology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Mamoru Hashimoto
- Department of Urology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Hirotsugu Uemura
- Department of Urology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
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5
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Zieren RC, Zondervan PJ, Pienta KJ, Bex A, de Reijke TM, Bins AD. Diagnostic liquid biopsy biomarkers in renal cell cancer. Nat Rev Urol 2024; 21:133-157. [PMID: 37758847 DOI: 10.1038/s41585-023-00818-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
The clinical presentation of renal cell cancer (RCC) is shifting towards incidental and early detection, creating new challenges in RCC diagnosis. Overtreatment might be reduced with the development of new diagnostic biomarkers to distinguish benign from malignant small renal masses (SRMs). Differently from tissue biopsies, liquid biopsies are obtained from a patient's blood or urine and, therefore, are minimally invasive and suitable for longitudinal monitoring. The most promising types of liquid biopsy biomarkers for RCC diagnosis are circulating tumour cells, extracellular vesicles (EVs) and cell-free DNA. Circulating tumour cell assays have the highest specificity, with low processing time and costs. However, the biological characteristics and low sensitivity limit the use of these markers in SRM diagnostics. Cell-free DNA might complement the diagnosis of high-volume RCC, but the potential for clinical application in SRMs is limited. EVs have the highest biological abundance and the highest sensitivity in identifying low-volume disease; moreover, the molecular characteristics of these markers make EVs suitable for multiple analytical applications. Thus, currently, EV assays have the greatest potential for diagnostic application in RCC (including identification of SRMs). All these liquid biomarkers have potential in clinical practice, pending validation studies. Biomarker implementation will be needed to also improve characterization of RCC subtypes. Last, diagnostic biomarkers might be extended to prognostic or predictive applications.
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Affiliation(s)
- Richard C Zieren
- Department of Urology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - Patricia J Zondervan
- Department of Urology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Kenneth J Pienta
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Axel Bex
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London, United Kingdom
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
- The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Theo M de Reijke
- Department of Urology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Adriaan D Bins
- Department of Medical Oncology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
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6
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Postel MD, Darabi S, Howe JR, Liang WS, Craig DW, Demeure MJ. Multiomic sequencing of paired primary and metastatic small bowel carcinoids. F1000Res 2023; 12:417. [PMID: 37954063 PMCID: PMC10632590 DOI: 10.12688/f1000research.130251.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 11/14/2023] Open
Abstract
Background: Small bowel carcinoids are insidious tumors that are often metastatic when diagnosed. Limited mutation landscape studies of carcinoids indicate that these tumors have a relatively low mutational burden. The development of targeted therapies will depend upon the identification of mutations that drive the pathogenesis and metastasis of carcinoid tumors. Methods: Whole exome and RNA sequencing of 5 matched sets of normal tissue, primary small intestine carcinoid tumors, and liver metastases were investigated. Germline and somatic variants included: single nucleotide variants (SNVs), insertions/deletions (indels), structural variants, and copy number alterations (CNAs). The functional impact of mutations was predicted using Ensembl Variant Effect Predictor. Results: Large-scale CNAs were observed including the loss of chromosome 18 in all 5 metastases and 3/5 primary tumors. Certain somatic SNVs were metastasis-specific; including mutations in ATRX, CDKN1B, MXRA5 (leading to the activation of a cryptic splice site and loss of mRNA), SMARCA2, and the loss of UBE4B. Additional mutations in ATRX, and splice site loss of PYGL, leading to intron retention observed in primary and metastatic tumors. Conclusions: We observed novel mutations in primary/metastatic carcinoid tumor pairs, and some have been observed in other types of neuroendocrine tumors. We confirmed a previously observed loss of chromosome 18 and CDKN1B. Transcriptome sequencing added relevant information that would not have been appreciated with DNA sequencing alone. The detection of several splicing mutations on the DNA level and their consequences at the RNA level suggests that RNA splicing aberrations may be an important mechanism underlying carcinoid tumors.
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Affiliation(s)
- Mackenzie D. Postel
- Institute of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Sourat Darabi
- Precision Medicine, Hoag Family Cancer Institute, Newport Beach, CA, 92663, USA
| | - James R. Howe
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | - David W. Craig
- Institute of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michael J. Demeure
- Precision Medicine, Hoag Family Cancer Institute, Newport Beach, CA, 92663, USA
- Translational Genomics Research Institute, Phoenix, AZ, USA
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7
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Wu S, Li R, Jiang Y, Yu J, Zheng J, Li Z, Li M, Xin K, Wang Y, Xu Z, Li S, Chen X. Liquid biopsy in urothelial carcinoma: Detection techniques and clinical applications. Biomed Pharmacother 2023; 165:115027. [PMID: 37354812 DOI: 10.1016/j.biopha.2023.115027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023] Open
Abstract
The types of urothelial carcinoma (UC) include urothelial bladder cancer and upper tract urothelial carcinoma. Current diagnostic techniques cannot meet the needs of patients. Liquid biopsy is an accurate method of determining the molecular profile of UC and is a cutting-edge and popular technique that is expected to complement existing detection techniques and benefit patients with UC. Circulating tumor cells, cell-free DNA, cell-free RNA, extracellular vesicles, proteins, and metabolites can be found in the blood, urine, or other bodily fluids and are examined during liquid biopsies. This article focuses on the components of liquid biopsies and their clinical applications in UC. Liquid biopsies have tremendous potential in multiple aspects of precision oncology, from early diagnosis and treatment monitoring to predicting prognoses. They may therefore play an important role in the management of UC and precision medicine.
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Affiliation(s)
- Siyu Wu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Rong Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Yuanhong Jiang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jiazheng Yu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Mingyang Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Kerong Xin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Yang Wang
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
| | - Zhenqun Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Shijie Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
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8
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Kałafut J, Czerwonka A, Czapla K, Przybyszewska-Podstawka A, Hermanowicz JM, Rivero-Müller A, Borkiewicz L. Regulation of Notch1 Signalling by Long Non-Coding RNAs in Cancers and Other Health Disorders. Int J Mol Sci 2023; 24:12579. [PMID: 37628760 PMCID: PMC10454443 DOI: 10.3390/ijms241612579] [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: 07/12/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Notch1 signalling plays a multifaceted role in tissue development and homeostasis. Currently, due to the pivotal role of Notch1 signalling, the relationship between NOTCH1 expression and the development of health disorders is being intensively studied. Nevertheless, Notch1 signalling is not only controlled at the transcriptional level but also by a variety of post-translational events. First is the ligand-dependent mechanical activation of NOTCH receptors and then the intracellular crosstalk with other signalling molecules-among those are long non-coding RNAs (lncRNAs). In this review, we provide a detailed overview of the specific role of lncRNAs in the modulation of Notch1 signalling, from expression to activity, and their connection with the development of health disorders, especially cancers.
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Affiliation(s)
- Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Arkadiusz Czerwonka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Karolina Czapla
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Alicja Przybyszewska-Podstawka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Justyna Magdalena Hermanowicz
- Department of Pharmacodynamics, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland;
- Department of Clinical Pharmacy, Medical University of Bialystok, Waszyngtona 15, 15-274 Bialystok, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
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9
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Mao Y, Zhang M, Wang L, Lu Y, Hu X, Chen Z. Role of microRNA carried by small extracellular vesicles in urological tumors. Front Cell Dev Biol 2023; 11:1192937. [PMID: 37333986 PMCID: PMC10272383 DOI: 10.3389/fcell.2023.1192937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Small extracellular vesicles (sEVs) are minute vesicles secreted by various cells that are capable of transporting cargo, including microRNAs, between donor and recipient cells. MicroRNAs (miRNAs), small non-coding RNAs approximately 22 nucleotides in length, have been implicated in a wide array of biological processes, including those involved in tumorigenesis. Emerging evidence highlights the pivotal role of miRNAs encapsulated in sEVs in both the diagnosis and treatment of urological tumors, with potential implications in epithelial-mesenchymal transition, proliferation, metastasis, angiogenesis, tumor microenvironment and drug resistance. This review provides a brief overview of the biogenesis and functional mechanisms of sEVs and miRNAs, followed by a summarization of recent empirical findings on miRNAs encapsulated in sEVs from three archetypal urologic malignancies: prostate cancer, clear cell renal cell carcinoma, and bladder cancer. We conclude by underscoring the potential of sEV-enclosed miRNAs as both biomarkers and therapeutic targets, with a particular focus on their detection and analysis in biological fluids such as urine, plasma, and serum.
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Affiliation(s)
- Yiping Mao
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Mengting Zhang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Lanfeng Wang
- Department of Nephrology, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yukang Lu
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xinyi Hu
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Zhiping Chen
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
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10
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Tong Y, Guan B, Sun Z, Dong X, Chen Y, Li Y, Jiang Y, Li J. Ratiometric fluorescent detection of exosomal piRNA-823 based on Au NCs/UiO-66-NH 2 and target-triggered rolling circle amplification. Talanta 2023; 257:124307. [PMID: 36764170 DOI: 10.1016/j.talanta.2023.124307] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
piR-823 is a newly discovered colorectal cancer marker with high diagnostic efficacy. However, the current quantification methods have complicated operations and high cost, which restrict its clinical application. Herein, a metal-organic framework (MOF) with a UiO-66 prototype structure which supports gold nanoclusters (Au NCs), Au NCs/UiO-66-NH2, were prepared as a model nanobiosensing platform for ratiometric detection of exosomal piR-823. The rolling circle amplification process provides high sensitivity and the ratiometric detection process ensures good accuracy of the sensor. Such biosensor showed a wide linear range of 0.04-4 pM, and a low detection limit of 10.2 fM towards piR-823. In addition, piR-823 can be used as an effective supplement to carcinoembryonic antigen (CEA) in clinical diagnosis of colorectal cancer. This study not only provides a potentially valuable ratio fluorescence platform involving enzyme catalytic reaction, but also offers a design blueprint for further expansion of nanotechnology in the diverse biological analysis.
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Affiliation(s)
- Yao Tong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Bingxin Guan
- Department of Pathology, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Zhiwei Sun
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Xiangjun Dong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yuqing Chen
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yanru Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yanyan Jiang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China.
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China.
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11
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The diagnostic role and mechanistic functions of exosomal lncRNAs in prostate cancer. Clin Transl Oncol 2023; 25:592-600. [PMID: 36266385 DOI: 10.1007/s12094-022-02982-w] [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: 07/31/2022] [Accepted: 10/10/2022] [Indexed: 10/24/2022]
Abstract
Exosomes are small membrane-enclosed vesicles that are released by most living cells and harbor a diverse array of proteins, nucleic acids, and lipid cargos. These exosomes offer valuable biomarkers that may offer insights regarding as a range of physiological and pathological processes, including immune responses, cancer development, pregnancy, and diseases of the central nervous system. With the development of high-throughput technologies, the vital functions of long non-coding RNAs (lncRNAs) have been gradually entered people's vision and become new research hotspots. Nowadays, lncRNAs can play important roles in cancer progression by combining with miRNAs, activating molecular targets and other ways, and are also related to the diagnosis, treatment and prognosis for cancer, such as prostate cancer. Current review focused on the summary of diagnostic roles and mechanistic functions about exosomal lncRNAs in prostate cancer.
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Postel MD, Culver JO, Ricker C, Craig DW. Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum. Hum Mutat 2022; 43:1590-1608. [PMID: 35510381 PMCID: PMC9560997 DOI: 10.1002/humu.24394] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
While whole-genome and exome sequencing have transformed our collective understanding of genetics' role in disease pathogenesis, there are certain conditions and populations for whom DNA-level data fails to identify the underlying genetic etiology. Specifically, patients of non-White race and non-European ancestry are disproportionately affected by "variants of unknown/uncertain significance" (VUS), limiting the scope of precision medicine for minority patients and perpetuating health disparities. VUS often include deep intronic and splicing variants which are difficult to interpret from DNA data alone. RNA analysis can illuminate the consequences of VUS, thereby allowing for their reclassification as pathogenic versus benign. Here we review the critical role transcriptome analysis plays in clarifying VUS in both neoplastic and non-neoplastic diseases.
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Affiliation(s)
- Mackenzie D. Postel
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Julie O. Culver
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Charité Ricker
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - David W. Craig
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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13
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Diagnostic Strategies for Urologic Cancer Using Expression Analysis of Various Oncogenic Surveillance Molecules—From Non-Coding Small RNAs to Cancer-Specific Proteins. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12157390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Urinary-tract-related tumors are prone to simultaneous or heterogeneous multiple tumor development within the primary organ. Urologic tumors have a very high risk of recurrence in the long and short term. This may be related to the disruption of homeostasis on the genetic level, such as the induction of genetic mutations due to exposure to various carcinogenic factors and the disruption of cancer suppressor gene functions. It is essential to detect the cancer progression signals caused by genetic abnormalities and find treatment therapies. In this review, we discuss the usefulness of tumor-expressing clinical biomarkers for predicting cancer progression. Furthermore, we discuss various factors associated with disturbed intracellular signals and those targeted by microRNAs, which are representative of non-coding small RNAs.
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Liquid Biopsy as a Source of Nucleic Acid Biomarkers in the Diagnosis and Management of Lynch Syndrome. Int J Mol Sci 2022; 23:ijms23084284. [PMID: 35457101 PMCID: PMC9029375 DOI: 10.3390/ijms23084284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Lynch syndrome (LS) is an autosomal dominant inherited cancer predisposition disorder, which may manifest as colorectal cancer (CRC), endometrial cancer (EC) or other malignancies of the gastrointestinal and genitourinary tract as well as the skin and brain. Its genetic cause is a defect in one of the four key DNA mismatch repair (MMR) loci. Testing of patients at risk is currently based on the absence of MMR protein staining and detection of mutations in cancer tissue and the germline, microsatellite instability (MSI) and the hypermethylated state of the MLH1 promoter. If LS is shown to have caused CRC, lifetime follow-up with regular screening (most importantly, colonoscopy) is required. In recent years, DNA and RNA markers extracted from liquid biopsies have found some use in the clinical diagnosis of LS. They have the potential to greatly enhance the efficiency of the follow-up process by making it minimally invasive, reproducible, and time effective. Here, we review markers reported in the literature and their current clinical applications, and we comment on possible future directions.
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15
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Junker K. [Liquid biopsy to indvidualise therapy in advanced bladder cancer]. Aktuelle Urol 2022; 53:180-187. [PMID: 34875700 DOI: 10.1055/a-1646-9568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Biomarker development is focussing more and more on the analysis of body fluids ("liquid biopsy") due to its advantages compared to tissue analysis. In addition to proteins and lipoproteins, circulating tumour cells (CTCs), extracellular vesicles (EVs) and cell-free nucleic acids (DNA, RNA) can be investigated from body fluids. Treatment of muscle-invasive balder cancer (MIBC) is still challenging. Therefore, new biomarkers are warranted to estimate the metastatic risk, to detect metastatic spread at an early time point and to select the most effective systemic therapy in a given patient. This review gives an overview of liquid biopsy from blood in patients with advanced MIBC and considers CTCs, EVs as well as circulating DNA (ctDNA) and non-coding RNA (ncRNA) and their role for prognostic evaluation and selecting treatment.
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Affiliation(s)
- Kerstin Junker
- Dept of Urology and Pediatric Urology, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany
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16
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Sun CY, Chen GD, He BC, Fu WE, Lee CH, Leu YW, Hsiao SH. Dysregulated HIC1 and RassF1A expression in vitro alters the cell cytoskeleton and exosomal Piwi-interacting RNA. Biochem Biophys Res Commun 2022; 594:109-116. [DOI: 10.1016/j.bbrc.2022.01.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/09/2022] [Accepted: 01/17/2022] [Indexed: 11/02/2022]
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17
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Riffo-Campos AL, Perez-Hernandez J, Ortega A, Martinez-Arroyo O, Flores-Chova A, Redon J, Cortes R. Exosomal and Plasma Non-Coding RNA Signature Associated with Urinary Albumin Excretion in Hypertension. Int J Mol Sci 2022; 23:ijms23020823. [PMID: 35055008 PMCID: PMC8775608 DOI: 10.3390/ijms23020823] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/03/2022] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNA (ncRNA), released into circulation or packaged into exosomes, plays important roles in many biological processes in the kidney. The purpose of the present study is to identify a common ncRNA signature associated with early renal damage and its related molecular pathways. Three individual libraries (plasma and urinary exosomes, and total plasma) were prepared from each hypertensive patient (with or without albuminuria) for ncRNA sequencing analysis. Next, an RNA-based transcriptional regulatory network was constructed. The three RNA biotypes with the greatest number of differentially expressed transcripts were long-ncRNA (lncRNA), microRNA (miRNA) and piwi-interacting RNA (piRNAs). We identified a common 24 ncRNA molecular signature related to hypertension-associated urinary albumin excretion, of which lncRNAs were the most representative. In addition, the transcriptional regulatory network showed five lncRNAs (LINC02614, BAALC-AS1, FAM230B, LOC100505824 and LINC01484) and the miR-301a-3p to play a significant role in network organization and targeting critical pathways regulating filtration barrier integrity and tubule reabsorption. Our study found an ncRNA profile associated with albuminuria, independent of biofluid origin (urine or plasma, circulating or in exosomes) that identifies a handful of potential targets, which may be utilized to study mechanisms of albuminuria and cardiovascular damage.
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Affiliation(s)
- Angela L. Riffo-Campos
- Millennium Nucleus on Sociomedicine (SocioMed) and Vicerrectoría Académica, Universidad de La Frontera, Temuco 4780000, Chile;
- Department of Computer Science, ETSE, University of Valencia, 46010 Valencia, Spain
| | - Javier Perez-Hernandez
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
- Departament of Nutrition and Health, Valencian International University (VIU), 46010 Valencia, Spain
- T-Cell Tolerance, Biomarkers and Therapies in Type 1 Diabetes Team, Institut Cochin, CNRS, INSERM, Université de Paris, 75014 Paris, France
| | - Ana Ortega
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Olga Martinez-Arroyo
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Ana Flores-Chova
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Josep Redon
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
- Internal Medicine Unit, Hospital Clinico Universitario, 46010 Valencia, Spain
- CIBER of Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, Minister of Health, 28029 Madrid, Spain
| | - Raquel Cortes
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
- Correspondence: ; Tel.: +34-961973517
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Small Noncoding RNAs in Reproduction and Infertility. Biomedicines 2021; 9:biomedicines9121884. [PMID: 34944700 PMCID: PMC8698561 DOI: 10.3390/biomedicines9121884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/20/2022] Open
Abstract
Infertility has been reported as one of the most common reproductive impairments, affecting nearly one in six couples worldwide. A large proportion of infertility cases are diagnosed as idiopathic, signifying a deficit in information surrounding the pathology of infertility and necessity of medical intervention such as assisted reproductive therapy. Small noncoding RNAs (sncRNAs) are well-established regulators of mammalian reproduction. Advanced technologies have revealed the dynamic expression and diverse functions of sncRNAs during mammalian germ cell development. Mounting evidence indicates sncRNAs in sperm, especially microRNAs (miRNAs) and transfer RNA (tRNA)-derived small RNAs (tsRNAs), are sensitive to environmental changes and mediate the inheritance of paternally acquired metabolic and mental traits. Here, we review the critical roles of sncRNAs in mammalian germ cell development. Furthermore, we highlight the functions of sperm-borne sncRNAs in epigenetic inheritance. We also discuss evidence supporting sncRNAs as promising biomarkers for fertility and embryo quality in addition to the present limitations of using sncRNAs for infertility diagnosis and treatment.
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Linxweiler J, Kolbinger A, Himbert D, Zeuschner P, Saar M, Stöckle M, Junker K. Organ-Specific Uptake of Extracellular Vesicles Secreted by Urological Cancer Cells. Cancers (Basel) 2021; 13:cancers13194937. [PMID: 34638418 PMCID: PMC8508228 DOI: 10.3390/cancers13194937] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/25/2021] [Accepted: 09/26/2021] [Indexed: 01/06/2023] Open
Abstract
Simple Summary Extracellular vesicles (EVs) play an important role in the communication of cancer cells with their local microenvironment and distant organ systems, in order to promote a supportive tumor microenvironment, as well as to prepare premetastatic niches. In this study, we aimed to analyze if the EVs secreted by urological cancer cells are taken up by specific organ systems, depending on their origin. After the intravenous injection of fluorescence-labeled EVs from benign and malignant prostate, kidney, and bladder cells in immunodeficient mice, their organs were harvested and analyzed for the presence of fluorescent EVs. We could show that (i) EVs are taken up not entirely organ-specifically but in different amounts, depending on their origin; (ii) EVs from malignant cells are taken up more efficiently than EVs from benign cells; and (iii) EVs are taken up very fast. These observations hint to an organotropism in EV uptake, which needs to be further investigated. Abstract Extracellular vesicles (EVs) secreted by cancer cells have been shown to take a pivotal part in the process of local and systemic tumor progression by promoting the formation of a supportive local tumor microenvironment and preparing premetastatic niches in distant organ systems. In this study, we analyzed the organ-specific uptake of EVs secreted by urological cancer cells using an innovative in-vivo approach. EVs from benign and malignant prostate, kidney, and bladder cells were isolated using ultracentrifugation, fluorescence-labeled and injected intravenously in immunodeficient mice. After 12 or 24 h, the animals were sacrificed, their organs were harvested and analyzed for the presence of EVs by high-resolution fluorescence microscopy. Across all entities, EVs were taken up fast (12 h > 24 h), and EVs from malignant cells were taken up more efficiently than EVs from benign cells. Though not entirely organ-specific, EVs were incorporated in different amounts, depending on the entity (prostate: lung > liver > brain; kidney: brain > lung > liver; bladder: lung > liver > brain). EV uptake in other organs than lung, liver, brain, and spleen was not observed. Our results suggest a role of EVs in the formation of premetastatic niches and an organotropism in EV uptake, which have to be examined in more detail in further studies.
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Gareev I, Gileva Y, Dzidzaria A, Beylerli O, Pavlov V, Agaverdiev M, Mazorov B, Biganyakov I, Vardikyan A, Jin M, Ahmad A. Long non-coding RNAs in oncourology. Noncoding RNA Res 2021; 6:139-145. [PMID: 34504983 PMCID: PMC8405895 DOI: 10.1016/j.ncrna.2021.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023] Open
Abstract
For several decades, research in tumor biology has focused on the involvement of genes encoding a protein. Only recently has it been discovered that a whole class of molecules called non-coding RNAs (ncRNAs) play a key regulatory role in health and disease. Long noncoding RNAs (lncRNAs) are a group of noncoding RNAs longer than 200 nucleotides. It has been found that lncRNAs play a fundamental role in the biology of many types of tumors, including tumors of the genitourinary system. As a result, hundreds of clinical trials dedicated to oncourology have begun, using lncRNA as new biomarkers or treatments. Identifying new specific biomarkers, in the form of lncRNAs, will increase the ability to differentiate the tumor and other processes, determine the localization and extent of the tumor, and the ability to predict the course of the disease, and plan treatment. Therapy of tumors, especially malignant ones, is also a difficult task. When surgery and chemotherapy fail, radiation therapy becomes the treatment choice. Therefore, the possibility that lncRNAs could represent innovative therapeutic agents or targets is an exciting idea. However, the possibility of their use in modern clinical practice is limited, and this is associated with several problems at the pre-, analytical and post-analytical stages. Another problem in the study of lncRNAs is the large number and variety of their functions in tumors. Therefore, solving technological problems in lncRNAs study in oncourology may open up new possibilities for lncRNAs use in modern clinical practice.
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Affiliation(s)
- Ilgiz Gareev
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Yulia Gileva
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Aleksandr Dzidzaria
- Urology Department, Russian Scientific Center of Radiology of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Ozal Beylerli
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Valentin Pavlov
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Murad Agaverdiev
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Bakhodur Mazorov
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Ilfat Biganyakov
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Andranik Vardikyan
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Mei Jin
- The First Affiliated Hospital of Harbin Medical University, 23 Youzheng St, Harbin, 150001, Heilongjiang Province, China
| | - Aamir Ahmad
- Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
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21
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Krappinger JC, Bonstingl L, Pansy K, Sallinger K, Wreglesworth NI, Grinninger L, Deutsch A, El-Heliebi A, Kroneis T, Mcfarlane RJ, Sensen CW, Feichtinger J. Non-coding Natural Antisense Transcripts: Analysis and Application. J Biotechnol 2021; 340:75-101. [PMID: 34371054 DOI: 10.1016/j.jbiotec.2021.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Non-coding natural antisense transcripts (ncNATs) are regulatory RNA sequences that are transcribed in the opposite direction to protein-coding or non-coding transcripts. These transcripts are implicated in a broad variety of biological and pathological processes, including tumorigenesis and oncogenic progression. With this complex field still in its infancy, annotations, expression profiling and functional characterisations of ncNATs are far less comprehensive than those for protein-coding genes, pointing out substantial gaps in the analysis and characterisation of these regulatory transcripts. In this review, we discuss ncNATs from an analysis perspective, in particular regarding the use of high-throughput sequencing strategies, such as RNA-sequencing, and summarize the unique challenges of investigating the antisense transcriptome. Finally, we elaborate on their potential as biomarkers and future targets for treatment, focusing on cancer.
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Affiliation(s)
- Julian C Krappinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Lilli Bonstingl
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Katrin Pansy
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Katja Sallinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Nick I Wreglesworth
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Lukas Grinninger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Austrian Biotech University of Applied Sciences, Konrad Lorenz-Straße 10, 3430 Tulln an der Donau, Austria
| | - Alexander Deutsch
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Thomas Kroneis
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Ramsay J Mcfarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Christoph W Sensen
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria; Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; HCEMM Kft., Római blvd. 21, 6723 Szeged, Hungary
| | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
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22
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Gualerzi A, Picciolini S, Carlomagno C, Rodà F, Bedoni M. Biophotonics for diagnostic detection of extracellular vesicles. Adv Drug Deliv Rev 2021; 174:229-249. [PMID: 33887403 DOI: 10.1016/j.addr.2021.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/26/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023]
Abstract
Extracellular Vesicles (EVs) are versatile carriers for biomarkers involved in the pathogenesis of multiple human disorders. Despite the increasing scientific and commercial interest in EV application in diagnostics, traditional biomolecular techniques usually require consistent sample amount, rely on operator-dependent and time- consuming procedures and cannot cope with the nano-size range of EVs, limiting both sensitivity and reproducibility of results. The application of biophotonics, i.e. light-based methods, for the diagnostic detection of EVs has brought to the development of innovative platforms with excellent sensitivity. In this review, we propose an overview of the most promising and emerging technologies used in the field of EV-related biomarker discovery. When tested on clinical samples, the reported biophotonic approaches in most cases have managed to discriminate between nanovesicles and contaminants, achieved much higher resolution compared to traditional procedures, and reached moderate to excellent diagnostic accuracy, thus demonstrating great potentialities for their clinical translation.
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23
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Urine as a Source of Liquid Biopsy for Cancer. Cancers (Basel) 2021; 13:cancers13112652. [PMID: 34071230 PMCID: PMC8199052 DOI: 10.3390/cancers13112652] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Tissue biopsy is essential for diagnosis and characterization of a tumor. Recently circulating tumor cells and other tumor-derived nucleic acid can be detected from blood, which is called liquid biopsy. Now this concept has been expanded to many other body fluids including urine. Urine is the least invasive method to obtain a liquid biopsy and can be done anywhere, which allows longitudinal repeated sampling. Here, we review the latest update on urine liquid biopsy in urological and non-urological cancers. Abstract Tissue biopsy is the gold standard for diagnosis and morphological and immunohistochemical analyses to characterize cancer. However, tissue biopsy usually requires an invasive procedure, and it can be challenging depending on the condition of the patient and the location of the tumor. Even liquid biopsy analysis of body fluids such as blood, saliva, gastric juice, sweat, tears and cerebrospinal fluid may require invasive procedures to obtain samples. Liquid biopsy can be applied to circulating tumor cells (CTCs) or nucleic acids (NAs) in blood. Recently, urine has gained popularity due to its less invasive sampling, ability to easily repeat samples, and ability to follow tumor evolution in real-time, making it a powerful tool for diagnosis and treatment monitoring in cancer patients. With the development and advancements in extraction methods of urinary substances, urinary NAs have been found to be closely related to carcinogenesis, metastasis, and therapeutic response, not only in urological cancers but also in non-urological cancers. This review mainly highlights the components of urine liquid biopsy and their utility and limitations in oncology, especially in non-urological cancers.
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Thrombospondin-2 and LDH Are Putative Predictive Biomarkers for Treatment with Everolimus in Second-Line Metastatic Clear Cell Renal Cell Carcinoma (MARC-2 Study). Cancers (Basel) 2021; 13:cancers13112594. [PMID: 34070677 PMCID: PMC8199288 DOI: 10.3390/cancers13112594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023] Open
Abstract
Simple Summary Treatment of metastatic renal cell carcinoma (mRCC) remains a challenge due to the lack of biomarkers indicating the optimal drug for each patient. This study analyzed blood samples of patients with predominant clear cell mRCC who were treated with the mTOR inhibitor everolimus after failure of one prior tumor therapy. In an exploratory approach, predictive blood biomarkers were searched. We found lower levels of the protein thrombospondin-2 (TSP-2) at the start of the therapy and higher lactate dehydrogenase (LDH) levels in serum two weeks after therapy initiation to be associated with therapy response. Of note, these blood biomarkers had a higher predictive value than baseline patient parameters or risk classifications. Polymorphisms in the mTOR gene appeared to be associated with therapy response, but were not significant. To conclude, it seems feasible to identify patients showing longtime responses to everolimus and possible to increase tumor therapy response rates based on biomarkers for individual therapy selection. Abstract There is an unmet need for predictive biomarkers in metastatic renal cell carcinoma (mRCC) therapy. The phase IV MARC-2 trial searched for predictive blood biomarkers in patients with predominant clear cell mRCC who benefit from second-line treatment with everolimus. In an exploratory approach, potential biomarkers were assessed employing proteomics, ELISA, and polymorphism analyses. Lower levels of angiogenesis-related protein thrombospondin-2 (TSP-2) at baseline (≤665 parts per billion, ppb) identified therapy responders with longer median progression-free survival (PFS; ≤665 ppb at baseline: 6.9 months vs. 1.8, p = 0.005). Responders had higher lactate dehydrogenase (LDH) levels in serum two weeks after therapy initiation (>27.14 nmol/L), associated with a longer median PFS (3.8 months vs. 2.2, p = 0.013) and improved overall survival (OS; 31.0 months vs. 14.0 months, p < 0.001). Baseline TSP-2 levels had a stronger relation to PFS (HR 0.36, p = 0.008) than baseline patient parameters, including IMDC score. Increased serum LDH levels two weeks after therapy initiation were the best predictor for OS (HR 0.21, p < 0.001). mTOR polymorphisms appeared to be associated with therapy response but were not significant. Hence, we identified TSP-2 and LDH as promising predictive biomarkers for therapy response on everolimus after failure of one VEGF-targeted therapy in patients with clear cell mRCC.
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Qiu Y, Li P, Zhang Z, Wu M. Insights Into Exosomal Non-Coding RNAs Sorting Mechanism and Clinical Application. Front Oncol 2021; 11:664904. [PMID: 33987099 PMCID: PMC8111219 DOI: 10.3389/fonc.2021.664904] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Exosomes are natural nanoscale bilayer phospholipid vesicles that can be secreted by almost all types of cells and are detected in almost all types of body fluids. Exosomes are effective mediators of cell–cell signaling communication because of their ability to carry and transfer a variety of bioactive molecules, including non-coding RNAs. Non-coding RNAs have also been found to exert strong effects on a variety of biological processes, including tumorigenesis. Many researchers have established that exosomes encapsulate bioactive non-coding RNAs that alter the biological phenotype of specific target cells in an autocrine or a paracrine manner. However, the mechanism by which the producer cells package non-coding RNAs into exosomes is not well understood. This review focuses on the current research on exosomal non-coding RNAs, including the biogenesis of exosomes, the possible mechanism of sorting non-coding RNAs, their biological functions, and their potential for clinical application in the future.
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Affiliation(s)
- Yi Qiu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Peiyao Li
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, China National Health Commission Key Laboratory of Carcinogenesis, Xiangya Hospital, Central South University, Changsha, China
| | - Zuping Zhang
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Minghua Wu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
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26
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Yang Z, Li Q, Zheng X, Xie L. Long Noncoding RNA Small Nucleolar Host Gene: A Potential Therapeutic Target in Urological Cancers. Front Oncol 2021; 11:638721. [PMID: 33968736 PMCID: PMC8100577 DOI: 10.3389/fonc.2021.638721] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
The incidence of urological cancer has been gradually increasing in the last few decades. However, current diagnostic tools and treatment strategies continue to have limitations. Substantial evidence shows that long noncoding RNAs (lncRNAs) play essential roles in carcinogenesis and the progression, treatment response and prognosis of multiple human cancers, including urological cancers, gastrointestinal tumours, reproductive cancers and respiratory neoplasms. LncRNA small nucleolar RNA host genes (SNHGs), a subgroup of lncRNAs, have been found to be dysregulated in tumour cell biology. In this review, we summarize the impacts of lncRNA SNHGs in urological malignancies and the underlying mechanisms.
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Affiliation(s)
- Zitong Yang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qinchen Li
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangyi Zheng
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liping Xie
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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27
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Vergori L, Martinez MC, Bigot P. Circulating large extracellular vesicles carrying CA9 in the diagnosis and prognosis of clear-cell renal cell carcinoma. Clin Transl Med 2021; 11:e358. [PMID: 33783991 PMCID: PMC8002908 DOI: 10.1002/ctm2.358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 11/10/2022] Open
Affiliation(s)
- Luisa Vergori
- INSERM U1063 SOPAM, University of Angers, Angers, France
| | | | - Pierre Bigot
- Department of Urology, Angers University Hospital, Angers, France
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Da M, Jiang H, Xie Y, Jin W, Han S. The Biological Roles of Exosomal Long Non-Coding RNAs in Cancers. Onco Targets Ther 2021; 14:271-287. [PMID: 33488093 PMCID: PMC7814250 DOI: 10.2147/ott.s281175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
Although it has many treatment strategies, cancer is still one of the most common causes of morbidity and mortality in the world. Exosomes are small extracellular vesicles (EVs) that can be secreted by almost all cells. Exosomes can encapsulate various types of molecules, including lipids, proteins, DNA, messenger RNAs, and non-coding RNAs [microRNAs (miRNAs) and long non-coding RNAs (lncRNAs)]. Exosome release is a way of communication between cells. They act as powerful signaling molecules between cancer cells and the surrounding cells that make up the cancer microenvironment. lncRNAs are a class of non-coding P, with a length of more than 200 bp, which are differentially expressed in many cancers. lncRNAs have been widely regarded as a new medium for cancer behavior. The presence of lncRNAs in circulation can be acellular or encapsulated in exosomal bodies released by cancer cells. Exosomal lncRNAs are functional and can transmit different phenotypic patterns to neighboring cells. Here, we reviewed the molecular mechanism of exosomal lncRNAs in regulating cancer progression, angiogenesis, and chemotherapy resistance, as well as the prospective applications of exosomal lncRNAs in cancer diagnosis, treatment and prognosis. These findings potentially promote the current understanding of exosomal lncRNAs and provide a new research direction for exosomal lncRNAs in cancer prevention, diagnosis, and treatment.
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Affiliation(s)
- Miao Da
- Department of Nursing, Huzhou Third Municipal Hospital, Huzhou, Zhejiang, People's Republic of China
| | - Hao Jiang
- Department of Nursing, Huzhou Third Municipal Hospital, Huzhou, Zhejiang, People's Republic of China
| | - Yangyang Xie
- Key Laboratory of Diagnosis and Treatment of Digestive System Cancers of Zhejiang Province, Ningbo 315000, Zhejiang, People's Republic of China
| | - Weili Jin
- Department of Gastroenterology, Nanxun District People's Hospital, Huzhou, Zhejiang 313009, People's Republic of China
| | - Shuwen Han
- Department of Oncology, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, Huzhou, Zhejiang, People's Republic of China
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29
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Han L, Yao Z, Xie L, Li D, Wang C, Yang Y, Yang J, Huang Z, Li K, Zhang Y, Ye L, Tan Z, Liu Y, Chen Q, Wang T, Yang Z. Transcriptome Sequencing reveals the expressed profiles of mRNA and ncRNAs and regulate network via ceRNA mediated molecular mechanism of lung adenocarcinoma bone metastasis in Xuanwei. Transl Cancer Res 2021; 10:73-87. [PMID: 35116241 PMCID: PMC8799022 DOI: 10.21037/tcr-20-2376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/20/2020] [Indexed: 12/25/2022]
Abstract
Background The most ordinary subtype of lung cancer is lung adenocarcinoma (LuAC), which is characterized by strong metastatic ability. And LuAC rates in Xuanwei leads to the poor prognosis and high death rate. In this study, we systematically explored the molecular mechanism of LuAC bone metastasis in Xuanwei by transcriptome sequencing. Methods RNA Sequencing was conducted to explore the noncoding RNAs (ncRNAs) expression profiles in primary LuAC and LuAC bone metastasis. We identified differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), lncRNAs (DElncRNAs) and circRNAs (DEcircRNAs). Bioinformatics analyses the possible relationships and functions of the LuAC bone metastasis-related competing endogenous RNA (ceRNA). And qRT-PCR was performed to evaluate the expression of these differently expressed genes in serum. Results A total of 2,141 DEmRNAs, 43 DEmiRNAs, 136 DElncRNAs and 706 DEcircRNAs were identified in the Xuanwei patients with primary LuAC vs. LuAC bone metastasis, respectively. The circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA networks of LuAC in Xuanwei with bone metastasis were built, and the gene expression mechanisms regulated by ncRNAs were unveiled via the ceRNA regulatory networks. We observe that lncRNA (ADAMTS9-AS2, TEX41, DLEU2, LINC00152)-miR-223-3p-SCARB1 and hsa_circ_0000053-miR-196a-5p/miR-196b-5p-HOXA5 ceRNA networks might play an important role in bone metastasis of Xuanwei LuAC. Conclusions We comprehensively identified ceRNA regulatory networks of LuAC in Xuanwei with bone metastasis as well as revealed the contribution of different ncRNAs expression profiles. Our data demonstrate the association between mRNAs and ncRNAs in the metastasis mechanism of LuAC in Xuanwei with bone metastasis.
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Affiliation(s)
- Lei Han
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Zhihong Yao
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Lin Xie
- Department of Medical Oncology, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Dongqi Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Cao Wang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Yihao Yang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Jifei Yang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Zeyong Huang
- Medical School, Kunming University of Science and Technology, Kunming, China
| | - Kecheng Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Ya Zhang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Lijuan Ye
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Zunxian Tan
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Yan Liu
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Qiuyun Chen
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Tiying Wang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
| | - Zuozhang Yang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, China
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Himbert D, Zeuschner P, Ayoubian H, Heinzelmann J, Stöckle M, Junker K. Characterization of CD147, CA9, and CD70 as Tumor-Specific Markers on Extracellular Vesicles in Clear Cell Renal Cell Carcinoma. Diagnostics (Basel) 2020; 10:diagnostics10121034. [PMID: 33276608 PMCID: PMC7761541 DOI: 10.3390/diagnostics10121034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/29/2020] [Indexed: 01/04/2023] Open
Abstract
Extracellular vesicles (EVs) are secreted by healthy and tumor cells and are involved in cell–cell communication. Tumor-released EVs could represent a new class of biomarkers from liquid biopsies. The aim of this study was to identify tumor-specific EV markers in clear cell renal carcinoma (ccRCC) using cell lines and patient-derived tissue samples. EVs from ccRCC cell lines (786-O, RCC53, Caki1, and Caki2) and patient tissues were isolated via ultracentrifugation. EVs were characterized using transmission electron microscopy, nanoparticle tracking analysis, and Western blotting using exosome and putative tumor markers (epithelial cell adhesion molecule (EpCAM), carbonic anhydrase 9 (CA9), CD70, CD147). The tumor markers were verified using immunohistochemistry. CA9 was expressed in Caki2 cells and EVs, and CD147 was found in the cells and EVs of all tested ccRCC cell lines. In tumor tissues, we found an increased expression of CA9, CD70, and CD147 were increased in cell lysates and EV fractions compared to normal tissues. In contrast, EpCAM was heterogeneously expressed in tumor samples and positive in normal tissue. To conclude, we developed an effective technique to isolate EVs directly from human tissue samples with high purity and high concentration. In contrast to EpCAM, CA9, CD70, and CD147 could represent promising markers to identify tumor-specific EVs in ccRCC.
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Affiliation(s)
- Dirk Himbert
- Department of Urology and Pediatric Urology, Saarland University, 66421 Homburg/Saar, Germany; (D.H.); (P.Z.); (H.A.); (J.H.); (M.S.)
| | - Philip Zeuschner
- Department of Urology and Pediatric Urology, Saarland University, 66421 Homburg/Saar, Germany; (D.H.); (P.Z.); (H.A.); (J.H.); (M.S.)
| | - Hiresh Ayoubian
- Department of Urology and Pediatric Urology, Saarland University, 66421 Homburg/Saar, Germany; (D.H.); (P.Z.); (H.A.); (J.H.); (M.S.)
| | - Joana Heinzelmann
- Department of Urology and Pediatric Urology, Saarland University, 66421 Homburg/Saar, Germany; (D.H.); (P.Z.); (H.A.); (J.H.); (M.S.)
- Department of Ophthalmology, University Hospital Halle (Saale), Martin-Luther-University Halle-Wittenberg, 06108 Halle/Saale, Germany
| | - Michael Stöckle
- Department of Urology and Pediatric Urology, Saarland University, 66421 Homburg/Saar, Germany; (D.H.); (P.Z.); (H.A.); (J.H.); (M.S.)
| | - Kerstin Junker
- Department of Urology and Pediatric Urology, Saarland University, 66421 Homburg/Saar, Germany; (D.H.); (P.Z.); (H.A.); (J.H.); (M.S.)
- Correspondence:
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Sabo AA, Birolo G, Naccarati A, Dragomir MP, Aneli S, Allione A, Oderda M, Allasia M, Gontero P, Sacerdote C, Vineis P, Matullo G, Pardini B. Small Non-Coding RNA Profiling in Plasma Extracellular Vesicles of Bladder Cancer Patients by Next-Generation Sequencing: Expression Levels of miR-126-3p and piR-5936 Increase with Higher Histologic Grades. Cancers (Basel) 2020; 12:cancers12061507. [PMID: 32527011 PMCID: PMC7352804 DOI: 10.3390/cancers12061507] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is the tenth most frequent cancer worldwide. Due to the need for recurrent cystoscopies and the lack of non-invasive biomarkers, BC is associated with a high management burden. In this respect, small non-coding RNAs (sncRNAs) have been investigated in urine as possible biomarkers for BC, but in plasma their potential has not yet been defined. The expression levels of sncRNAs contained in plasma extracellular vesicles (EVs) from 47 men with BC and 46 healthy controls were assessed by next-generation sequencing. The sncRNA profiles were compared with urinary profiles from the same subjects. miR-4508 resulted downregulated in plasma EVs of muscle-invasive BC patients, compared to controls (adj-p = 0.04). In World Health Organization (WHO) grade 3 (G3) BC, miR-126-3p was upregulated both in plasma EVs and urine, when compared to controls (for both, adj-p < 0.05). Interestingly, two sncRNAs were associated with the risk class: miR-4508 with a downward trend going from controls to high risk BC, and piR-hsa-5936 with an upward trend (adj-p = 0.04 and adj-p = 0.05, respectively). Additionally, BC cases with low expression of miR-185-5p and miR-106a-5p or high expression of miR-10b-5p showed shorter survival (adj-p = 0.0013, adj-p = 0.039 and adj-p = 0.047, respectively). SncRNAs from plasma EVs could be diagnostic biomarkers for BC, especially in advanced grade.
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Affiliation(s)
- Alexandru A. Sabo
- Klinikum Stuttgart, Olgahospital, Zentrum für Kinder, Jugend und Frauenmedizin, Pediatrics 2 (General and Special Pediatrics), 70174 Stuttgart, Germany;
- Department of Pediatrics, Marie Curie Emergency Clinical Hospital for Children, 041434 Bucharest, Romania
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (G.B.); (S.A.); (A.A.); (G.M.)
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM) 10060 Candiolo, Italy; (A.N.); (P.V.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Mihnea P. Dragomir
- Department of Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, 022328 Bucharest, Romania;
| | - Serena Aneli
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (G.B.); (S.A.); (A.A.); (G.M.)
| | - Alessandra Allione
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (G.B.); (S.A.); (A.A.); (G.M.)
| | - Marco Oderda
- Department of Surgical Sciences, University of Turin and Città della Salute e della Scienza, 10126 Turin, Italy; (M.O.); (M.A.); (P.G.)
| | - Marco Allasia
- Department of Surgical Sciences, University of Turin and Città della Salute e della Scienza, 10126 Turin, Italy; (M.O.); (M.A.); (P.G.)
| | - Paolo Gontero
- Department of Surgical Sciences, University of Turin and Città della Salute e della Scienza, 10126 Turin, Italy; (M.O.); (M.A.); (P.G.)
| | | | - Paolo Vineis
- Italian Institute for Genomic Medicine (IIGM) 10060 Candiolo, Italy; (A.N.); (P.V.)
- MRC-HPA Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (G.B.); (S.A.); (A.A.); (G.M.)
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM) 10060 Candiolo, Italy; (A.N.); (P.V.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
- Correspondence:
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Metzenmacher M, Váraljai R, Hegedüs B, Cima I, Forster J, Schramm A, Scheffler B, Horn PA, Klein CA, Szarvas T, Reis H, Bielefeld N, Roesch A, Aigner C, Kunzmann V, Wiesweg M, Siveke JT, Schuler M, Lueong SS. Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer. Cancers (Basel) 2020; 12:cancers12020353. [PMID: 32033141 PMCID: PMC7073169 DOI: 10.3390/cancers12020353] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Early detection of cancer holds high promise for reducing cancer-related mortality. Detection of circulating tumor-specific nucleic acids holds promise, but sensitivity and specificity issues remain with current technology. We studied cell-free RNA (cfRNA) in patients with non-small cell lung cancer (NSCLC; n = 56 stage IV, n = 39 stages I-III), pancreatic cancer (PDAC, n = 20 stage III), malignant melanoma (MM, n = 12 stage III-IV), urothelial bladder cancer (UBC, n = 22 stage II and IV), and 65 healthy controls by means of next generation sequencing (NGS) and real-time droplet digital PCR (RT-ddPCR). We identified 192 overlapping upregulated transcripts in NSCLC and PDAC by NGS, more than 90% of which were noncoding. Previously reported transcripts (e.g., HOTAIRM1) were identified. Plasma cfRNA transcript levels of POU6F2-AS2 discriminated NSCLC from healthy donors (AUC = 0.82 and 0.76 for stages IV and I-III, respectively) and significantly associated (p = 0.017) with the established tumor marker Cyfra 21-1. cfRNA yield and POU6F2-AS transcript abundance discriminated PDAC patients from healthy donors (AUC = 1.0). POU6F2-AS2 transcript was significantly higher in MM (p = 0.044). In summary, our findings support further validation of cfRNA detection by RT-ddPCR as a biomarker for early detection of solid cancers.
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Affiliation(s)
- Martin Metzenmacher
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany; (M.M.); (M.W.); (M.S.)
- Division of Thoracic Oncology, University Medicine Essen-Ruhrlandklinik, University Duisburg-Essen, Tüschener Weg 40, 45239 Essen, Germany
| | - Renáta Váraljai
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany; (R.V.); (A.R.)
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany; (I.C.); (J.F.); (B.S.); (N.B.); (J.T.S.)
| | - Balazs Hegedüs
- Department of Thoracic Surgery, Ruhrlandklinik, University Duisburg-Essen, D-45239 Essen, Germany; (B.H.); (C.A.)
| | - Igor Cima
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany; (I.C.); (J.F.); (B.S.); (N.B.); (J.T.S.)
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45122 Essen, Germany
| | - Jan Forster
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany; (I.C.); (J.F.); (B.S.); (N.B.); (J.T.S.)
- Chair for Genome Informatics, Department of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany
| | - Alexander Schramm
- Laboratory for Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany;
| | - Björn Scheffler
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany; (I.C.); (J.F.); (B.S.); (N.B.); (J.T.S.)
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, 45122 Essen, Germany
| | - Peter A. Horn
- Institute for Transfusion Medicine, University Hospital Essen, 45122 Essen, Germany;
| | - Christoph A. Klein
- Experimental Medicine and Therapy Research, University of Regensburg, 93053 Regensburg, Germany;
- Fraunhofer-Institute for Toxicology and Experimental Medicine, Division of Personalized Tumour Therapy, 93053 Regensburg, Germany
| | - Tibor Szarvas
- Department of Urology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45122 Essen, Germany;
- Department of Urology, Semmelweis University, H-1085 Budapest, Hungary
| | - Hennig Reis
- Institute of Pathology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany;
| | - Nicola Bielefeld
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany; (I.C.); (J.F.); (B.S.); (N.B.); (J.T.S.)
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, 45122 Essen, Germany
| | - Alexander Roesch
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany; (R.V.); (A.R.)
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany; (I.C.); (J.F.); (B.S.); (N.B.); (J.T.S.)
| | - Clemens Aigner
- Department of Thoracic Surgery, Ruhrlandklinik, University Duisburg-Essen, D-45239 Essen, Germany; (B.H.); (C.A.)
| | - Volker Kunzmann
- Department of Internal Medicine II, University Hospital Würzburg, 97080 Würzburg, Germany;
| | - Marcel Wiesweg
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany; (M.M.); (M.W.); (M.S.)
- Division of Thoracic Oncology, University Medicine Essen-Ruhrlandklinik, University Duisburg-Essen, Tüschener Weg 40, 45239 Essen, Germany
| | - Jens T. Siveke
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany; (I.C.); (J.F.); (B.S.); (N.B.); (J.T.S.)
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, 45122 Essen, Germany
| | - Martin Schuler
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany; (M.M.); (M.W.); (M.S.)
- Division of Thoracic Oncology, University Medicine Essen-Ruhrlandklinik, University Duisburg-Essen, Tüschener Weg 40, 45239 Essen, Germany
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany; (I.C.); (J.F.); (B.S.); (N.B.); (J.T.S.)
| | - Smiths S. Lueong
- German Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany; (I.C.); (J.F.); (B.S.); (N.B.); (J.T.S.)
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, 45122 Essen, Germany
- Correspondence: ; Tel.: +49-(201)-723-3139
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Abstract
Extracellular vesicles (EVs) have an essential functional role in local tumour progression, metastatic spread and the emergence of drug resistance in bladder, kidney and prostate cancer. Thus, EVs could be diagnostic, prognostic and predictive biomarkers for these malignancies. Virtually all biomolecules (including DNA, mRNA, microRNA, long non-coding RNA, proteins and lipids) packaged into EVs have been tested as biomarkers in blood and urine samples. The results are very heterogeneous, but promising biomarker candidates have been identified. Differing methods of EV isolation, characterization and analysis of their content have been used owing to a lack of international consensus; hence, comparing study results is challenging. Furthermore, validation of potential biomarkers in independent cohorts or prospective trials has rarely been performed. Future efforts to establish EV-derived biomarkers need to adequately address these points. In addition, emerging technologies such as mass spectroscopy and chip-based approaches can identify surface markers specific for cancer-associated EVs and will enable specific separation from blood and urine EVs, which probably will improve their performance as biomarkers. Moreover, EVs could be harnessed as therapeutic drug delivery vehicles for precise and effective anticancer therapy.
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