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Pös O, Styk J, Buglyó G, Zeman M, Lukyova L, Bernatova K, Hrckova Turnova E, Rendek T, Csók Á, Repiska V, Nagy B, Szemes T. Cross-Kingdom Interaction of miRNAs and Gut Microbiota with Non-Invasive Diagnostic and Therapeutic Implications in Colorectal Cancer. Int J Mol Sci 2023; 24:10520. [PMID: 37445698 DOI: 10.3390/ijms241310520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Colorectal cancer (CRC) has one of the highest incidences among all types of malignant diseases, affecting millions of people worldwide. It shows slow progression, making it preventable. However, this is not the case due to shortcomings in its diagnostic and management procedure and a lack of effective non-invasive biomarkers for screening. Here, we discuss CRC-associated microRNAs (miRNAs) and gut microbial species with potential as CRC diagnostic and therapy biomarkers. We provide rich evidence of cross-kingdom miRNA-mediated interactions between the host and gut microbiome. miRNAs have emerged with the ability to shape the composition and dynamics of gut microbiota. Intestinal microbes can uptake miRNAs, which in turn influence microbial growth and provide the ability to regulate the abundance of various microbial species. In the context of CRC, targeting miRNAs could aid in manipulating the balance of the microbiota. Our findings suggest the need for correlation analysis between the composition of the gut microbiome and the miRNA expression profile.
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Affiliation(s)
- Ondrej Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Jakub Styk
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Michal Zeman
- Comenius University Science Park, 841 04 Bratislava, Slovakia
| | - Lydia Lukyova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 05 Bratislava, Slovakia
| | - Kamila Bernatova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 05 Bratislava, Slovakia
| | - Evelina Hrckova Turnova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Slovgen Ltd., 841 04 Bratislava, Slovakia
| | - Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Ádám Csók
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
- Medirex Group Academy, n.p.o., 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 05 Bratislava, Slovakia
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Yoshikawa Y, Fukunaga M, Takahashi J, Shimizu D, Masuda T, Mizushima T, Yamada K, Mori M, Eguchi H, Doki Y, Ochiya T, Mimori K. Identification of the Minimum Combination of Serum microRNAs to Predict the Recurrence of Colorectal Cancer Cases. Ann Surg Oncol 2023; 30:233-243. [PMID: 36175711 PMCID: PMC9726799 DOI: 10.1245/s10434-022-12355-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/08/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Serum microRNAs (miRNAs) have been recognized as potential stable biomarkers for various types of cancer. Considering the clinical applications, there are certain critical requirements, such as minimizing the number of miRNAs, reproducibility in a longitudinal clinical course, and superiority to conventional tumor markers, such as carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9. This study aimed to identify serum miRNAs that indicate the recurrence of colorectal cancer (CRC), surpassing inter-tumor heterogeneity. METHODS We conducted an analysis of 434 serum samples from 91 patients with CRC and 71 healthy subjects. miRNAs were obtained from Toray Co., Ltd, and miRNA profiles were analyzed using a three-step approach. miRNAs that were highly expressed in patients with CRC than in the healthy controls in the screening phase, and those that were highly expressed in the preoperative samples than in the 1-month postoperative samples in the discovery phase, were extracted. In the validation phase, the extracted miRNAs were evaluated in 323 perioperative samples, in chronological order. RESULTS A total of 12 miRNAs (miR-25-3p, miR-451a, miR-1246, miR-1268b, miR-2392, miR-4480, miR-4648, miR-4732-5p, miR-4736, miR-6131, miR-6776-5p, and miR-6851-5p) were significantly concordant with the clinical findings of tumor recurrence, however their ability to function as biomarkers was comparable with CEA. In contrast, the combination of miR-1246, miR-1268b, and miR-4648 demonstrated a higher area under the curve (AUC) than CEA. These three miRNAs were upregulated in primary CRC tissues. CONCLUSION We identified ideal combinatorial miRNAs to predict CRC recurrence.
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Affiliation(s)
- Yukihiro Yoshikawa
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita Japan ,Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka Japan
| | | | - Junichi Takahashi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita Japan
| | - Dai Shimizu
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka Japan
| | - Kazutaka Yamada
- Coloproctology Center Takano Hospital, Kumamoto, Kumamoto Japan
| | - Masaki Mori
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita Japan
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Zhong M, Chen K, Sun W, Li X, Huang S, Meng Q, Sun B, Huang X, Wang X, Ma X, Ma P. PCDetection: PolyA-CRISPR/Cas12a-based miRNA detection without PAM restriction. Biosens Bioelectron 2022; 214:114497. [DOI: 10.1016/j.bios.2022.114497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022]
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4
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Zygulska AL, Pierzchalski P. Novel Diagnostic Biomarkers in Colorectal Cancer. Int J Mol Sci 2022; 23:852. [PMID: 35055034 DOI: 10.3390/ijms23020852] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/27/2021] [Accepted: 01/03/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is still a leading cause of cancer death worldwide. Less than half of cases are diagnosed when the cancer is locally advanced. CRC is a heterogenous disease associated with a number of genetic or somatic mutations. Diagnostic markers are used for risk stratification and early detection, which might prolong overall survival. Nowadays, the widespread use of semi-invasive endoscopic methods and feacal blood tests characterised by suboptimal accuracy of diagnostic results has led to the detection of cases at later stages. New molecular noninvasive tests based on the detection of CRC alterations seem to be more sensitive and specific then the current methods. Therefore, research aiming at identifying molecular markers, such as DNA, RNA and proteins, would improve survival rates and contribute to the development of personalized medicine. The identification of “ideal” diagnostic biomarkers, having high sensitivity and specificity, being safe, cheap and easy to measure, remains a challenge. The purpose of this review is to discuss recent advances in novel diagnostic biomarkers for tumor tissue, blood and stool samples in CRC patients.
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Kozakiewicz CP, Fraik AK, Patton AH, Ruiz-Aravena M, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Margres MJ, Jones ME, Storfer A. Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection. BMC Genomics 2021; 22:698. [PMID: 34579650 DOI: 10.1186/s12864-021-07994-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/08/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Transmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basis of phenotypic variation. In oncology, transcriptomics studies, which characterize the expression of thousands of genes, have identified processes leading to heterogeneity in cancer phenotypes and individual prognoses. More generally, transcriptomics studies of infectious diseases characterize interactions between host, pathogen, and environment to better predict population-level outcomes. Tasmanian devils have been impacted dramatically by a transmissible cancer (devil facial tumor disease; DFTD) that has led to widespread population declines. Despite initial predictions of extinction, populations have persisted at low levels, due in part to heterogeneity in host responses, particularly between sexes. However, the processes underlying this variation remain unknown. RESULTS We sequenced transcriptomes from healthy and DFTD-infected devils, as well as DFTD tumors, to characterize host responses to DFTD infection, identify differing host-tumor molecular interactions between sexes, and investigate the extent to which tumor gene expression varies among host populations. We found minimal variation in gene expression of devil lip tissues, either with respect to DFTD infection status or sex. However, 4088 genes were differentially expressed in tumors among our sampling localities. Pathways that were up- or downregulated in DFTD tumors relative to normal tissues exhibited the same patterns of expression with greater intensity in tumors from localities that experienced DFTD for longer. No mRNA sequence variants were associated with expression variation. CONCLUSIONS Expression variation among localities may reflect morphological differences in tumors that alter ratios of normal-to-tumor cells within biopsies. Phenotypic variation in tumors may arise from environmental variation or differences in host immune response that were undetectable in lip biopsies, potentially reflecting variation in host-tumor coevolutionary relationships among sites that differ in the time since DFTD arrival.
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Siskova A, Cervena K, Kral J, Hucl T, Vodicka P, Vymetalkova V. Colorectal Adenomas-Genetics and Searching for New Molecular Screening Biomarkers. Int J Mol Sci 2020; 21:ijms21093260. [PMID: 32380676 PMCID: PMC7247353 DOI: 10.3390/ijms21093260] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a malignant disease with an incidence of over 1.8 million new cases per year worldwide. CRC outcome is closely related to the respective stage of CRC and is more favorable at less advanced stages. Detection of early colorectal adenomas is the key to survival. In spite of implemented screening programs showing efficiency in the detection of early precancerous lesions and CRC in asymptomatic patients, a significant number of patients are still diagnosed in advanced stages. Research on CRC accomplished during the last decade has improved our understanding of the etiology and development of colorectal adenomas and revealed weaknesses in the general approach to their detection and elimination. Recent studies seek to find a reliable non-invasive biomarker detectable even in the blood. New candidate biomarkers could be selected on the basis of so-called liquid biopsy, such as long non-coding RNA, microRNA, circulating cell-free DNA, circulating tumor cells, and inflammatory factors released from the adenoma into circulation. In this work, we focused on both genetic and epigenetic changes associated with the development of colorectal adenomas into colorectal carcinoma and we also discuss new possible biomarkers that are detectable even in adenomas prior to cancer development.
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Affiliation(s)
- Anna Siskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
- Correspondence: (A.S.); (P.V.); Tel.: +420-241062251 (A.S.); +420-241062694 (P.V.)
| | - Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
| | - Jan Kral
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute for Clinical and Experimental Medicine, Videnska 1958/9, 14021 Prague, Czech Republic;
| | - Tomas Hucl
- Institute for Clinical and Experimental Medicine, Videnska 1958/9, 14021 Prague, Czech Republic;
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic
- Correspondence: (A.S.); (P.V.); Tel.: +420-241062251 (A.S.); +420-241062694 (P.V.)
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic
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Stevens JR, Herrick JS, Wolff RK, Slattery ML. Power in pairs: assessing the statistical value of paired samples in tests for differential expression. BMC Genomics 2018; 19:953. [PMID: 30572829 PMCID: PMC6302489 DOI: 10.1186/s12864-018-5236-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022] Open
Abstract
Background When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain proportion of subjects to have paired samples. We consider the effect of this paired samples proportion on the statistical power of the study, using characteristics of both count (RNA-Seq) and continuous (microarray) expression data from a colorectal cancer study. Results We demonstrate that a higher proportion of subjects with paired samples yields higher statistical power, for various total numbers of samples, and for various strengths of subject-level confounding factors. In the design scenarios considered, the statistical power in a fully-paired design is substantially (and in many cases several times) greater than in an unpaired design. Conclusions For the many biological systems and research questions where paired samples are feasible and relevant, substantial statistical power gains can be achieved at the study design stage when genomics researchers plan on using paired samples from the largest possible proportion of subjects. Any cost savings in a study design with unpaired samples are likely accompanied by underpowered and possibly biased results. Electronic supplementary material The online version of this article (10.1186/s12864-018-5236-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, UT, USA.
| | - Jennifer S Herrick
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Roger K Wolff
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Martha L Slattery
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
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8
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Roberts BS, Hardigan AA, Moore DE, Ramaker RC, Jones AL, Fitz-Gerald MB, Cooper GM, Wilcox CM, Kimberly RP, Myers RM. Discovery and Validation of Circulating Biomarkers of Colorectal Adenoma by High-Depth Small RNA Sequencing. Clin Cancer Res 2018; 24:2092-2099. [PMID: 29490987 PMCID: PMC5932113 DOI: 10.1158/1078-0432.ccr-17-1960] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 01/02/2018] [Accepted: 02/21/2018] [Indexed: 12/18/2022]
Abstract
Purpose: Colorectal cancer is the third most common cancer worldwide, causing approximately 700,000 deaths each year. The majority of colorectal cancers begin as adenomas. Definitive screening for colorectal adenomas is currently accomplished through colonoscopy but, owing largely to costs and invasiveness, is typically limited to patient groups at higher risk by virtue of age or family history. We sought to determine if blood-based small RNA markers could detect colorectal adenoma.Experimental Design: We applied high-depth small RNA sequencing to plasma from a large (n = 189) cohort of patients, balanced for age, sex, and ancestry. Our analytical methodology allowed for the detection of both microRNAs and other small RNA species. We replicated sequencing results by qPCR on plasma samples from an independent cohort (n = 140).Results: We found several small RNA species with significant associations to colorectal adenoma, including both microRNAs and non-microRNA small RNAs. These associations were robust to correction for patient covariates, including age. Among the adenoma-associated small RNAs, two, a miR-335-5p isoform and an un-annotated small RNA, were validated by qPCR in an independent cohort. A classifier trained on measures of these two RNAs in the discovery cohort yields an AUC of 0.755 (0.775 with age) for adenoma detection in the independent cohort. This classifier accurately detects adenomas in patients under 50 and is robust to sex or ancestry.Conclusions: Circulating small RNAs (including but not limited to miRNAs) discovered by sequencing and validated by qPCR identify patients with colorectal adenomas effectively. Clin Cancer Res; 24(9); 2092-9. ©2018 AACR.
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Affiliation(s)
- Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Dianna E Moore
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Meredith B Fitz-Gerald
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - C Mel Wilcox
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Robert P Kimberly
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.
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Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression predominantly by inhibiting transcription and/or promoting degradation of target mRNAs also in addition to being involved in non-canonical mechanisms regulating transcription, translation and cell signaling processes. Extracellular secretory miRNAs, either in complex with specific proteins or encapsulated in microvesicles called exosomes, are transported between cells as means of intercellular communication. Secretory miRNAs in circulation remain functional after delivery to recipient cells, regulating target genes and their corresponding signaling pathways. Cancer cell secreted miRNA-mediated intercellular communication affects physiological processes associated with the disease, such as, angiogenesis, metabolic reprogramming, immune modulation, metastasis, and chemo-resistance. Given the stability of miRNAs in body fluids and their well-documented roles in deregulating cancer-relevant genetic pathways, there is considerable interest in developing secretory miRNAs as liquid biopsy biomarkers for detection, diagnosis and prognostication of cancer. In this review, we discuss salient features of miRNA biogenesis, secretion and function in cancer as well as the current state of secretory miRNA isolation and profiling methods. Furthermore, we discuss the challenges and opportunities of secretory miRNA biomarker assay development, which need to be addressed for clinical applications.
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Affiliation(s)
- Kazuharu Kai
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Rachel L Dittmar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States; Program in Human and Molecular Genetics, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, United States
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States; Program in Human and Molecular Genetics, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, United States.
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Jung HJ, Lee KP, Milholland B, Shin YJ, Kang JS, Kwon KS, Suh Y. Comprehensive miRNA Profiling of Skeletal Muscle and Serum in Induced and Normal Mouse Muscle Atrophy During Aging. J Gerontol A Biol Sci Med Sci 2017; 72:1483-1491. [PMID: 28329037 DOI: 10.1093/gerona/glx025] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/01/2017] [Indexed: 01/29/2023] Open
Abstract
Age-associated loss of muscle mass and function is a major cause of morbidity and mortality in the elderly adults. Muscular atrophy can also be induced by disuse associated with long-term bed rest or disease. Although miRNAs regulate muscle growth, regeneration, and aging, their potential role in acute muscle atrophy is poorly understood. Furthermore, alterations in circulating miRNA levels have been shown to occur during aging but their potential as noninvasive biomarkers for muscle atrophy remains largely unexplored. Here, we report comprehensive miRNA expression profiles by miRNA-seq analysis in tibialis anterior muscle and serum of a disuse-induced atrophy mouse model, mimicking the acute atrophy following long-term bed rest, as compared to those of young and old mice. Comparative analysis and validation studies have revealed that miR-455-3p was significantly decreased in muscle of both induced-atrophy model and old mice, whereas miR-434-3p was decreased in both serum and muscle of old mice, as compared to young mice. Furthermore, upregulation of miR-455-3p in fully differentiated C2C12 myoblasts induced a hypertrophic phenotype. These results suggest that deregulation of miR-455-3p may play a functional role in muscle atrophy and miR-434-3p could be a candidate serum biomarker of muscle aging.
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Affiliation(s)
- Hwa Jin Jung
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Kwang-Pyo Lee
- Aging Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon.,Department of Biomolecular Science
| | - Brandon Milholland
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Yeo Jin Shin
- Aging Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon
| | - Jae Sook Kang
- Aging Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon
| | - Ki-Sun Kwon
- Aging Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon
| | - Yousin Suh
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
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11
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Moody L, He H, Pan YX, Chen H. Methods and novel technology for microRNA quantification in colorectal cancer screening. Clin Epigenetics 2017; 9:119. [PMID: 29090038 PMCID: PMC5655825 DOI: 10.1186/s13148-017-0420-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/17/2017] [Indexed: 02/08/2023] Open
Abstract
The screening and diagnosis of colorectal cancer (CRC) currently relies heavily on invasive endoscopic techniques as well as imaging and antigen detection tools. More accessible and reliable biomarkers are necessary for early detection in order to expedite treatment and improve patient outcomes. Recent studies have indicated that levels of specific microRNA (miRNA) are altered in CRC; however, measuring miRNA in biological samples has proven difficult, given the complicated and lengthy PCR-based procedures used by most laboratories. In this manuscript, we examine the potential of miRNA as CRC biomarkers, summarize the methods that have commonly been employed to quantify miRNA, and focus on novel strategies that can improve or replace existing technology for feasible implementation in a clinical setting. These include isothermal amplification techniques that can potentially eliminate the need for specialized thermocycling equipment. Additionally, we propose the use of near-infrared (NIR) probes which can minimize autofluorescence and photobleaching and streamline quantification without tedious sample processing. We suggest that novel miRNA quantification tools will be necessary to encourage new discoveries and facilitate their translation to clinical practice.
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Affiliation(s)
- Laura Moody
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 472 Bevier Hall, MC-182, 905 South Goodwin Avenue, Urbana, IL 61801 USA
| | - Hongshan He
- Department of Chemistry, Eastern Illinois University, Charleston, IL 62910 USA
| | - Yuan-Xiang Pan
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 472 Bevier Hall, MC-182, 905 South Goodwin Avenue, Urbana, IL 61801 USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 472 Bevier Hall, MC-182, 905 South Goodwin Avenue, Urbana, IL 61801 USA.,Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Hong Chen
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 472 Bevier Hall, MC-182, 905 South Goodwin Avenue, Urbana, IL 61801 USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 472 Bevier Hall, MC-182, 905 South Goodwin Avenue, Urbana, IL 61801 USA
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12
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Carter JV, Galbraith NJ, Yang D, Burton JF, Walker SP, Galandiuk S. Blood-based microRNAs as biomarkers for the diagnosis of colorectal cancer: a systematic review and meta-analysis. Br J Cancer. 2017;116:762-774. [PMID: 28152545 PMCID: PMC5355921 DOI: 10.1038/bjc.2017.12] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/19/2016] [Accepted: 01/05/2017] [Indexed: 12/13/2022] Open
Abstract
Background: Colorectal cancer (CRC) is common and associated with significant mortality. Current screening methods for CRC lack patient compliance. microRNAs (miRNAs), identified in body fluids, are negative regulators of gene expression and are dysregulated in many cancers, including CRC. This paper summarises studies identifying blood-based miRNAs dysregulated in CRC compared with healthy controls in an attempt to evaluate their use as a screening tool for the diagnosis of CRC. Methods: A search of electronic databases (PubMed and EMBASE) and grey literature was performed between January 2002 and April 2016. Studies reporting plasma or serum miRNAs in the diagnosis of CRC compared with healthy controls were selected. Patient demographics, type of patient sample (serum or plasma), method of miRNA detection, type of normalisation, and the number of significantly dysregulated miRNAs identified were recorded. Statistical evaluation of dysregulated miRNAs using sensitivity, specificity, and area under the curve (AUC) was performed. Results: Thirty-four studies investigating plasma or serum miRNAs in the diagnosis of CRC were included. A total of 31 miRNAs were found to be either upregulated (n=17) or downregulated (n=14) in CRC cases as compared with controls. Fourteen studies identified panels of ⩾2 dysregulated miRNAs. The highest AUC, 0.943, was identified using a panel of 4 miRNAs with 83.3% sensitivity and 93.1% specificity. Meta-analysis of studies identifying a single dysregulated miRNA in CRC cases compared with controls was performed. Overall sensitivity and specificity of 28 individual miRNAs in the diagnosis of CRC were 76% (95% CI 72%–80%) and 76% (95% CI 72%–80%), respectively, indicating good discriminative ability of miRNAs as biomarkers for CRC. These data did not change with sensitivity analyses. Conclusions: Blood-based miRNAs distinguish patients with CRC from healthy controls with high sensitivity and specificity comparable to other common and invasive currently used screening methods for CRC. In future, miRNAs may be used as a relatively non-invasive blood-based marker for detection of CRC.
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Binderup HG, Houlind K, Madsen JS, Brasen CL. Pre-storage centrifugation conditions have significant impact on measured microRNA levels in biobanked EDTA plasma samples. Biochem Biophys Rep 2016; 7:195-200. [PMID: 28955906 PMCID: PMC5613297 DOI: 10.1016/j.bbrep.2016.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/27/2016] [Accepted: 06/06/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In the past few years, an increasing number of studies have reported the potential use of microRNAs (miRNA) as circulating biomarkers for diagnosis or prognosis of a wide variety of diseases. There is, however, a lack of reproducibility between studies. Due to the high miRNA content in platelets this may partly be explained by residual platelets in the plasma samples used. When collecting fresh plasma samples, it is possible to produce cell-free/platelet-poor plasma by centrifugation. In this study, we systematically investigated whether biobanked EDTA plasma samples could be processed to be suitable for miRNA analysis. MATERIALS AND METHODS Blood samples were collected from ten healthy volunteers and centrifuged to produce platelet-poor-plasma (PPP) and standard biobank plasma. After one week at -80 °C the biobanked EDTA plasma was re-centrifuged by different steps to remove residual platelets. Using RT-qPCR the levels of 14 miRNAs in the different plasma preparations were compared to that of PPP. RESULTS We were able to remove residual platelets from biobanked EDTA plasma by re-centrifugation of the thawed samples. Nevertheless, for most of the investigated miRNAs, the miRNA level was significantly higher in the re-centrifuged biobanked plasma compared to PPP, even when the platelet count was reduced to 0-1×109/L. CONCLUSION We found, that pre-storage centrifugation conditions have a significant impact on the measured EDTA plasma level of miRNAs known to be present in platelets. Even for the miRNAs found to be less effected, we showed that a 1.5-3 fold change in plasma levels may possible be caused by or easily overseen due to sample preparation and/or storage.
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Affiliation(s)
- Helle Glud Binderup
- Department of Clinical Immunology and Biochemistry, Lillebaelt Hospital, Kolding, Denmark
| | - Kim Houlind
- Department of Vascular Surgery, Lillebaelt Hospital, Kolding, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Denmark
| | - Jonna Skov Madsen
- Department of Clinical Immunology and Biochemistry, Lillebaelt Hospital, Kolding, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Denmark
| | - Claus Lohman Brasen
- Department of Clinical Immunology and Biochemistry, Lillebaelt Hospital, Kolding, Denmark
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14
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Ostenfeld MS, Jensen SG, Jeppesen DK, Christensen LL, Thorsen SB, Stenvang J, Hvam ML, Thomsen A, Mouritzen P, Rasmussen MH, Nielsen HJ, Ørntoft TF, Andersen CL. miRNA profiling of circulating EpCAM(+) extracellular vesicles: promising biomarkers of colorectal cancer. J Extracell Vesicles 2016; 5:31488. [PMID: 27576678 PMCID: PMC5005366 DOI: 10.3402/jev.v5.31488] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/14/2016] [Accepted: 07/14/2016] [Indexed: 01/06/2023] Open
Abstract
Cancer cells secrete small membranous extracellular vesicles (EVs) into their microenvironment and circulation. These contain biomolecules, including proteins and microRNAs (miRNAs). Both circulating EVs and miRNAs have received much attention as biomarker candidates for non-invasive diagnostics. Here we describe a sensitive analytical method for isolation and subsequent miRNA profiling of epithelial-derived EVs from blood samples of patients with colorectal cancer (CRC). The epithelial-derived EVs were isolated by immunoaffinity-capture using the epithelial cell adhesion molecule (EpCAM) as marker. This approach mitigates some of the specificity issues observed in earlier studies of circulating miRNAs, in particular the negative influence of miRNAs released by erythrocytes, platelets and non-epithelial cells. By applying this method to 2 small-scale patient cohorts, we showed that blood plasma isolated from CRC patients prior to surgery contained elevated levels of 13 EpCAM+-EV miRNAs compared with healthy individuals. Upon surgical tumour removal, the plasma levels of 8 of these were reduced (miR-16-5p, miR-23a-3p, miR-23b-3p, miR-27a-3p, miR-27b-3p, miR-30b-5p, miR-30c-5p and miR-222-3p). These findings indicate that the miRNAs are of tumour origin and may have potential as non-invasive biomarkers for detection of CRC. This work describes a non-invasive blood-based method for sensitive detection of cancer with potential for clinical use in relation to diagnosis and screening. We used the method to study CRC; however, it is not restricted to this disease. It may in principle be used to study any cancer that release epithelial-derived EVs into circulation.
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Affiliation(s)
| | - Steffen Grann Jensen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Stine Buch Thorsen
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Stenvang
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael Lykke Hvam
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | | | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology 360, Hvidovre Hospital, Hvidovre, Denmark
| | - Torben Falck Ørntoft
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
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15
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Abstract
MicroRNAs (miRNAs) are a class of endogenous, evolutionarily conserved small non-coding RNAs, which play a vital role in tumour formation, development, metastasis and recurrence by inducing DNA methylation, changing tumor microenvironment and regulating signal pathways such as Wnt/β-catenin, phosphoinositide3-kinase (PI3K), K-RAS, epithelial mesenchymal transitions (EMT) and so on. Recent studies have found that the expression of many miRNAs is dyregulated in colorectal cancer, and they participate in and control the formation and development of colorectal cancer. Thus, understanding the roles and mechanisms of action of miRNAs in colorectal cancer can provide a new avenue for its early diagnosis, clinical staging, treatment and prognosis evaluation.
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16
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Vychytilova-Faltejskova P, Radova L, Sachlova M, Kosarova Z, Slaba K, Fabian P, Grolich T, Prochazka V, Kala Z, Svoboda M, Kiss I, Vyzula R, Slaby O. Serum-based microRNA signatures in early diagnosis and prognosis prediction of colon cancer. Carcinogenesis 2016; 37:941-950. [PMID: 27485599 DOI: 10.1093/carcin/bgw078] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/28/2016] [Indexed: 12/14/2022] Open
Abstract
Early detection of colorectal cancer is the main prerequisite for successful treatment and reduction of mortality. Circulating microRNAs were previously identified as promising diagnostic, prognostic and predictive biomarkers. The purpose of this study was to identify serum microRNAs enabling early diagnosis and prognosis prediction of colon cancer. In total, serum samples from 427 colon cancer patients and 276 healthy donors were included in three-phase biomarker study. Large-scale microRNA expression profiling was performed using Illumina small RNA sequencing. Diagnostic and prognostic potential of identified microRNAs was validated on independent training and validation sets of samples using RT-qPCR. Fifty-four microRNAs were found to be significantly deregulated in serum of colon cancer patients compared to healthy donors (P < 0.01). A diagnostic four-microRNA signature consisting of miR-23a-3p, miR-27a-3p, miR-142-5p and miR-376c-3p was established (AUC = 0.917), distinguishing colon cancer patients from healthy donors with sensitivity of 89% and specificity of 81% (AUC = 0.922). This panel of microRNAs exhibited high diagnostic performance also when analyzed separately in colon cancer patients in early stages of the disease (T1-4N0M0; AUC = 0.877). Further, a prognostic panel based on the expression of miR-23a-3p and miR-376c-3p independent of TNM stage was established (HR 2.30; 95% CI 1.44-3.66; P < 0.0004). In summary, highly sensitive signatures of circulating microRNAs enabling non-invasive early detection and prognosis prediction of colon cancer were identified.
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Affiliation(s)
- Petra Vychytilova-Faltejskova
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk Memorial Cancer Institute, Masaryk University, Zluty kopec 7, 656 53 Brno, Czech Republic and
| | - Lenka Radova
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Milana Sachlova
- Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk Memorial Cancer Institute, Masaryk University, Zluty kopec 7, 656 53 Brno, Czech Republic and
| | - Zdenka Kosarova
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Katerina Slaba
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Fabian
- Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk Memorial Cancer Institute, Masaryk University, Zluty kopec 7, 656 53 Brno, Czech Republic and
| | - Tomas Grolich
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Department of Surgery, Institutions Shared with the Faculty Hospital Brno, Faculty of Medicine, Masaryk University, Jihlavska 340/20, 625 00 Brno, Czech Republic
| | - Vladimir Prochazka
- Department of Surgery, Institutions Shared with the Faculty Hospital Brno, Faculty of Medicine, Masaryk University, Jihlavska 340/20, 625 00 Brno, Czech Republic
| | - Zdenek Kala
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Department of Surgery, Institutions Shared with the Faculty Hospital Brno, Faculty of Medicine, Masaryk University, Jihlavska 340/20, 625 00 Brno, Czech Republic
| | - Marek Svoboda
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk Memorial Cancer Institute, Masaryk University, Zluty kopec 7, 656 53 Brno, Czech Republic and
| | - Igor Kiss
- Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk Memorial Cancer Institute, Masaryk University, Zluty kopec 7, 656 53 Brno, Czech Republic and
| | - Rostislav Vyzula
- Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk Memorial Cancer Institute, Masaryk University, Zluty kopec 7, 656 53 Brno, Czech Republic and
| | - Ondrej Slaby
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk Memorial Cancer Institute, Masaryk University, Zluty kopec 7, 656 53 Brno, Czech Republic and
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Izzotti A, Carozzo S, Pulliero A, Zhabayeva D, Ravetti JL, Bersimbaev R. Extracellular MicroRNA in liquid biopsy: applicability in cancer diagnosis and prevention. Am J Cancer Res 2016; 6:1461-1493. [PMID: 27508091 PMCID: PMC4969398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 06/06/2023] Open
Abstract
One of the goals of contemporary cancer research is the development of new markers that facilitate earlier and non-invasive diagnosis. MicroRNAs are non-coding RNA molecules that regulate gene expression; studies have shown that their expression levels are altered in cancer. Recently, extra-cellular microRNAs have been detected in biological fluids and studied as possible cancer markers that can be detected by noninvasive procedures. In this review, we analyze the current understanding of extracellular miRNAs based on clinical studies to establish their possible use for the prevention of the most common tumors. Despite discrepancies among different studies of the same cancers, panels of specific extracellular microRNAs are emerging as a new tool for the secondary (selection of high-risk individuals to undergo screening) and tertiary (relapse) prevention of cancer.
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Affiliation(s)
- Alberto Izzotti
- Department of Health Sciences, University of GenoaItaly
- IRCCS AOU San Martino ISTGenoa Italy
| | | | | | - Dinara Zhabayeva
- Department of General Biology and Genomics, Inst. of Cell Biology and Biotechnology, L.N. Gumyliov Eurasian National UniversityAstana, Kazakhstan
| | | | - Rakhmet Bersimbaev
- Department of General Biology and Genomics, Inst. of Cell Biology and Biotechnology, L.N. Gumyliov Eurasian National UniversityAstana, Kazakhstan
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18
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Affiliation(s)
- Rajagopal N Aravalli
- Department of Radiology, University of Minnesota Medical School, Minneapolis, Minn.
| | - Clifford J Steer
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minn; Department of Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, Minn.
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