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Chung J, Xiao S, Gao Y, Soung YH. Recent Technologies towards Diagnostic and Therapeutic Applications of Circulating Nucleic Acids in Colorectal Cancers. Int J Mol Sci 2024; 25:8703. [PMID: 39201393 PMCID: PMC11354501 DOI: 10.3390/ijms25168703] [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: 07/12/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 09/02/2024] Open
Abstract
Liquid biopsy has emerged as a promising noninvasive approach for colorectal cancer (CRC) management. This review focuses on technologies detecting circulating nucleic acids, specifically circulating tumor DNA (ctDNA) and circulating RNA (cfRNA), as CRC biomarkers. Recent advancements in molecular technologies have enabled sensitive and specific detection of tumor-derived genetic material in bodily fluids. These include quantitative real-time PCR, digital PCR, next-generation sequencing (NGS), and emerging nanotechnology-based methods. For ctDNA analysis, techniques such as BEAMing and droplet digital PCR offer high sensitivity in detecting rare mutant alleles, while NGS approaches provide comprehensive genomic profiling. cfRNA detection primarily utilizes qRT-PCR arrays, microarray platforms, and RNA sequencing for profiling circulating microRNAs and discovering novel RNA biomarkers. These technologies show potential in early CRC detection, treatment response monitoring, minimal residual disease assessment, and tumor evolution tracking. However, challenges remain in standardizing procedures, optimizing detection limits, and establishing clinical utility across disease stages. This review summarizes current circulating nucleic acid detection technologies, their CRC applications, and discusses future directions for clinical implementation.
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Affiliation(s)
| | | | | | - Young Hwa Soung
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (J.C.); (S.X.); (Y.G.)
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Molfino A, Beltrà M, Amabile MI, Belli R, Birolo G, Belloni E, De Lucia S, Garcia‐Castillo L, Penna F, Imbimbo G, Nigri G, Pardini B, Costelli P, Muscaritoli M. Small non-coding RNA profiling in patients with gastrointestinal cancer. J Cachexia Sarcopenia Muscle 2023; 14:2692-2702. [PMID: 37743227 PMCID: PMC10751434 DOI: 10.1002/jcsm.13343] [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: 08/05/2022] [Revised: 06/08/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Small non-coding (snc)RNAs, including microRNAs and P-element induced wimpy testis (PIWI)-interacting-RNAs (piRNAs), crucially regulate gene expression in both physiological and pathological conditions. In particular, some muscle-specific microRNAs (myomiRs) have been involved in the pathogenesis of cancer-induced muscle wasting. The aims of the present study were (i) to profile sncRNAs in both skeletal muscle and plasma of gastrointestinal cancer patients and (ii) to investigate the association among differentially expressed sncRNAs and the level of muscularity at body composition analysis. METHODS Surgical patients with gastrointestinal cancer or benign disease were recruited. Blood samples and muscle biopsies (rectus abdominis) were collected during surgery. Low muscularity patients were those at the lowest tertile of skeletal muscle index (SMI; CT-scan), whereas moderate/high muscularity patients were in the middle and highest SMI tertiles. SncRNAs in the muscle were assessed by RNAseq, circulating microRNAs were evaluated by qPCR. RESULTS Cancer patients (n = 25; 13 females, 52%) showed a mean age of 71.6 ± 11.2 years, a median body weight loss of 4.2% and a mean BMI of 27.0 ± 3.2 kg/m2 . Control group (n = 15; 9 females, 60%) showed a mean age 58.1 ± 13.9 years and a mean BMI of 28.0 ± 4.3 kg/m2 . In cancer patients, the median L3-SMI (cm2 /m2 ) was 42.52 (34.42; 49.07). Males showed a median L3-SMI of 46.08 (41.17-51.79) and females a median L3-SMI of 40.77 (33.73-42.87). Moderate-high and low muscularity groups included 17 and 8 patients, respectively. As for circulating microRNAs, miR-21-5p and miR-133a-3p were up-regulated in patients compared with controls, whereas miR-15b-5p resulted down-regulated in the same comparison (about 30% of control values). Sample clustering by muscularity and sex revealed increased miR-133a-3p and miR-206 only in moderate-high muscularity males. SncRNA profiling in the muscle identified 373 microRNAs and 190 piRNAs (72.5% and 18.7% of raw reads, respectively). As for microRNAs, 10 were up-regulated, and 56 were down-regulated in cancer patients versus controls. Among the 24 dysregulated piRNAs, the majority were down-regulated, including the top two most expressed piRNAs in the muscle (piR-12790 and piR-2106). Network analysis on validated mRNA targets of down-regulated microRNAs revealed miR-15b-5p, miR-106a-5p and miR-106b-5p as main interactors of genes related to ubiquitin ligase/transferase activities. CONCLUSIONS These results show dysregulation of both muscle microRNAs and piRNAs in cancer patients compared with controls, the former following a sex-specific pattern. Changes in circulating microRNAs are associated with the degree of muscularity rather than body weight loss.
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Affiliation(s)
- Alessio Molfino
- Department of Translational and Precision MedicineSapienza University of RomeRomeItaly
| | - Marc Beltrà
- Department of Clinical and Biological SciencesUniversity of TorinoTorinoItaly
- Present address:
Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | | | - Roberta Belli
- Department of Translational and Precision MedicineSapienza University of RomeRomeItaly
| | - Giovanni Birolo
- Department of Medical SciencesUniversity of TorinoTorinoItaly
| | - Elena Belloni
- Department of Medical‐Surgical Sciences and Translational MedicineSapienza University of RomeRomeItaly
| | - Serena De Lucia
- Department of Clinical and Biological SciencesUniversity of TorinoTorinoItaly
| | | | - Fabio Penna
- Department of Clinical and Biological SciencesUniversity of TorinoTorinoItaly
| | - Giovanni Imbimbo
- Department of Translational and Precision MedicineSapienza University of RomeRomeItaly
| | - Giuseppe Nigri
- Department of Medical‐Surgical Sciences and Translational MedicineSapienza University of RomeRomeItaly
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM)CandioloItaly
- Candiolo Cancer InstituteFPO‐IRCCSCandioloItaly
| | - Paola Costelli
- Department of Clinical and Biological SciencesUniversity of TorinoTorinoItaly
| | - Maurizio Muscaritoli
- Department of Translational and Precision MedicineSapienza University of RomeRomeItaly
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Fattahi M, Shahrabi S, Saadatpour F, Rezaee D, Beyglu Z, Delavari S, Amrolahi A, Ahmadi S, Bagheri-Mohammadi S, Noori E, Majidpoor J, Nouri S, Aghaei-Zarch SM, Falahi S, Najafi S, Le BN. microRNA-382 as a tumor suppressor? Roles in tumorigenesis and clinical significance. Int J Biol Macromol 2023; 250:125863. [PMID: 37467828 DOI: 10.1016/j.ijbiomac.2023.125863] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/30/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
MicroRNAs (miRNAs) are small single-stranded RNAs belonging to a class of non-coding RNAs with an average length of 18-22 nucleotides. Although not able to encode any protein, miRNAs are vastly studied and found to play role in various human physiologic as well as pathological conditions. A huge number of miRNAs have been identified in human cells whose expression is straightly regulated with crucial biological functions, while this number is constantly increasing. miRNAs are particularly studied in cancers, where they either can act with oncogenic function (oncomiRs) or tumor-suppressors role (referred as tumor-suppressor/oncorepressor miRNAs). miR-382 is a well-studied miRNA, which is revealed to play regulatory roles in physiological processes like osteogenic differentiation, hematopoietic stem cell differentiation and normal hematopoiesis, and liver progenitor cell differentiation. Notably, miR-382 deregulation is reported in pathologic conditions, such as renal fibrosis, muscular dystrophies, Rett syndrome, epidural fibrosis, atrial fibrillation, amelogenesis imperfecta, oxidative stress, human immunodeficiency virus (HIV) replication, and various types of cancers. The majority of oncogenesis studies have claimed miR-382 downregulation in cancers and suppressor impact on malignant phenotype of cancer cells in vitro and in vivo, while a few studies suggest opposite findings. Given the putative role of this miRNA in regulation of oncogenesis, assessment of miR-382 expression is suggested in a several clinical investigations as a prognostic/diagnostic biomarker for cancer patients. In this review, we have an overview to recent studies evaluated the role of miR-382 in oncogenesis as well as its clinical potential.
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Affiliation(s)
- Mehdi Fattahi
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam; School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
| | - Saeid Shahrabi
- Department of Biochemistry and Hematology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Fatemeh Saadatpour
- Pharmaceutical Biotechnology Lab, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Delsuz Rezaee
- School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - Zahra Beyglu
- Department of Genetics, Qom Branch, Islamic Azad University, Qom, Iran
| | - Sana Delavari
- Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Anita Amrolahi
- Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shirin Ahmadi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Bagheri-Mohammadi
- Department of Physiology and Neurophysiology Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Effat Noori
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Shadi Nouri
- Department of Radiology, School of Medicine, Arak University of Medical Sciences, Arak, Iran.
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shahab Falahi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran.
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Binh Nguyen Le
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam; School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
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Duan W, Wang W, He C. A novel potential inflammation-nutrition biomarker for predicting lymph node metastasis in clinically node-negative colon cancer. Front Oncol 2023; 13:995637. [PMID: 37081978 PMCID: PMC10111825 DOI: 10.3389/fonc.2023.995637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 03/20/2023] [Indexed: 04/22/2023] Open
Abstract
Background The purpose of this study is to investigate the predictive significance of (platelet × albumin)/lymphocyte ratio (PALR) for lymph node metastasis (LNM) in patients with clinically node-negative colon cancer (cN0 CC). Methods Data from 800 patients with primary CC who underwent radical surgery between March 2016 and June 2021 were reviewed. The non-linear relationship between PALR and the risk of LNM was explored using a restricted cubic spline (RCS) function while a receiver operating characteristic (ROC) curve was developed to determine the predictive value of PALR. Patients were categorized into high- and low-PALR cohorts according to the optimum cut-off values derived from Youden's index. Univariate and multivariate logistic regression analyses were used to identify the independent indicators of LNM. Sensitivity analysis was performed to repeat the main analyses with the quartile of PALR. Results A total of eligible 269 patients with primary cN0 CC were retrospectively selected. The value of the area under the ROC curve for PALR for predicting LNM was 0.607. RCS visualized the uptrend linear relationship between PALR and the risk of LNM (p-value for non-linearity > 0.05). PALR (odds ratio = 2.118, 95% confidence interval, 1.182-3.786, p = 0.011) was identified as an independent predictor of LNM in patients with cN0 CC. A nomogram incorporating PALR and other independent predictors was constructed with an internally validated concordance index of 0.637. The results of calibration plots and decision curve analysis supported a good performance ability and the sensitivity analysis further confirmed the robustness of our findings. Conclusion PALR has promising clinical applications for predicting LNM in patients with cN0 CC.
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Six Genes Associated with Lymphatic Metastasis in Colon Adenocarcinoma Linked to Prognostic Value and Tumor Immune Cell Infiltration. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4304361. [PMID: 36072412 PMCID: PMC9444393 DOI: 10.1155/2022/4304361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022]
Abstract
Objective. The aim of the study is to explore the relationship between lymphatic metastasis genes, prognosis, and immune cell infiltration in patients with colon cancer. Methods. Based on the Cancer Genome Atlas Program (TCGA) database, differentially expressed genes and prognostic genes related to colon adenocarcinoma (COAD) lymphatic metastasis were screened and intersected. We used lasso and univariate Cox regression analysis to screen core genes and establish a preliminary prediction model. GO and KEGG enrichment analysis was used for lymphatic metastasis-related genes, and single GSEA was used for the final screening results. Finally, we evaluated the relationship between identified genes and immune cell infiltration. Results. A total of 1727 genes were differentially expressed between COAD patients with TNM stages of N0 and N1. After further screening, six core genes (RNU4-2, ZNF556, RNVU1-15, NSA2P6, RN7SL767P, and RN7SL473P) were obtained, and a preliminary prediction model was established, in which ZNF556 was a risk factor, and the rest were protective factors. Single GSEA showed that pathways such as systemic lupus erythematosus might play an important role in the initial lymphatic metastasis of COAD. GO and KEGG enrichment analysis of 1727 genes supported this result. Immune infiltration analysis showed that six genes were significantly correlated with T cell and NK cell families. Conclusion. Six core genes may affect COAD initial lymphatic metastasis through the systemic lupus erythematosus pathway and immune cell infiltration.
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Capriglione F, Verrienti A, Celano M, Maggisano V, Sponziello M, Pecce V, Gagliardi A, Giacomelli L, Aceti V, Durante C, Bulotta S, Russo D. Analysis of serum microRNA in exosomal vehicles of papillary thyroid cancer. Endocrine 2022; 75:185-193. [PMID: 34378123 DOI: 10.1007/s12020-021-02847-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/02/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE In this study, we investigated the profile of microRNAs (miRNAs) contained in exosomes secreted in the serum of patients with papillary thyroid cancer (PTC). METHODS Exosome were isolated by adding ExoQuick Exosome Precipitation Solution. Dynamic light scattering (DLS) and western blotting analysis were used to ensure the quality of exosomes. The expression levels of miRNAs were investigated using custom-designed TaqMan Advanced miRNA Array Cards in the screening cohort and using specific TaqMan Advanced MicroRNA Assays in the validation cohort. RESULTS We identified miR24-3p, miR146a-5p, miR181a-5p and miR382-5p with different expression levels in two different series of 56 and 58 PTC patients as compared with healthy controls. Significant differences in the expression of three PTC exosomal miRNAs, depending on the presence of lymph node metastasis, were detected in only one PTC series. When comparing the expression levels of some PTC-specific exosomal miRNAs with those of the same miRNAs circulating free of any encapsulation, we found a significant correlation for only miR24-3p, suggesting that only select miRNAs are secreted in exosomes. CONCLUSIONS Our findings demonstrate that four miRNAs are differently secreted in the exosomes of PTC patients, whereas no conclusive results were found to characterize PTCs with lymph node metastasis, suggesting caution in the use of circulating exosomal miRNA expression levels as lymph node metastasis biomarkers. Further investigation into the mechanisms governing miRNA secretion in tumor cells are required.
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Affiliation(s)
- Francesca Capriglione
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100, Catanzaro, Italy
| | - Antonella Verrienti
- Department of translational and precision medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Marilena Celano
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100, Catanzaro, Italy
| | - Valentina Maggisano
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100, Catanzaro, Italy
| | - Marialuisa Sponziello
- Department of translational and precision medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Valeria Pecce
- Department of translational and precision medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Agnese Gagliardi
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100, Catanzaro, Italy
| | - Laura Giacomelli
- Department of Surgical Sciences, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Valerio Aceti
- Department of translational and precision medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Cosimo Durante
- Department of translational and precision medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Stefania Bulotta
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100, Catanzaro, Italy
| | - Diego Russo
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100, Catanzaro, Italy.
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Smolarz B, Durczyński A, Romanowicz H, Hogendorf P. The Role of microRNA in Pancreatic Cancer. Biomedicines 2021; 9:biomedicines9101322. [PMID: 34680441 PMCID: PMC8533140 DOI: 10.3390/biomedicines9101322] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small ribonucleic acid molecules that play a key role in regulating gene expression. The increasing number of studies undertaken on the functioning of microRNAs in the tumor formation clearly indicates their important potential in oncological therapy. Pancreatic cancer is one of the deadliest cancers. The expression of miRNAs released into the bloodstream appears to be a good indicator of progression and evaluation of the aggressiveness of pancreatic cancer, as indicated by studies. The work reviewed the latest literature on the importance of miRNAs for pancreatic cancer development.
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Affiliation(s)
- Beata Smolarz
- Laboratory of Cancer Genetics, Department of Pathology, Polish Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland;
- Correspondence: ; Tel.: +48-42-271-1290
| | - Adam Durczyński
- Department of General and Transplant Surgery, N. Barlicki Memorial Clinical Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (A.D.); (P.H.)
| | - Hanna Romanowicz
- Laboratory of Cancer Genetics, Department of Pathology, Polish Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland;
| | - Piotr Hogendorf
- Department of General and Transplant Surgery, N. Barlicki Memorial Clinical Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (A.D.); (P.H.)
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