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Boychev N, Lee S, Yeung V, Ross AE, Kuang L, Chen L, Dana R, Ciolino JB. Contact lenses as novel tear fluid sampling vehicles for total RNA isolation, precipitation, and amplification. Sci Rep 2024; 14:11727. [PMID: 38778161 PMCID: PMC11111455 DOI: 10.1038/s41598-024-62215-8] [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: 03/08/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
The tear fluid is a readily accessible, potential source for biomarkers of disease and could be used to monitor the ocular response to contact lens (CL) wear or ophthalmic pathologies treated by therapeutic CLs. However, the tear fluid remains largely unexplored as a biomarker source for RNA-based molecular analyses. Using a rabbit model, this study sought to determine whether RNA could be collected from commercial CLs and whether the duration of CL wear would impact RNA recovery. The results were referenced to standardized strips of filtered paper (e.g., Shirmer Strips) placed in the inferior fornix. By performing total RNA isolation, precipitation, and amplification with commercial kits and RT-PCR methods, CLs were found to have no significant differences in RNA concentration and purity compared to Schirmer Strips. The study also identified genes that could be used to normalize RNA levels between tear samples. Of the potential control genes or housekeeping genes, GAPDH was the most stable. This study, which to our knowledge has never been done before, provides a methodology for the detection of RNA and gene expression changes from tear fluid that could be used to monitor or study eye diseases.
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Affiliation(s)
- Nikolay Boychev
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, and Harvard Medical School, Boston, USA.
| | - Seokjoo Lee
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, and Harvard Medical School, Boston, USA
| | - Vincent Yeung
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, and Harvard Medical School, Boston, USA
| | - Amy E Ross
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, and Harvard Medical School, Boston, USA
| | - Liangju Kuang
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, and Harvard Medical School, Boston, USA
| | - Lin Chen
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Ophthalmology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Reza Dana
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, and Harvard Medical School, Boston, USA
| | - Joseph B Ciolino
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, and Harvard Medical School, Boston, USA
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2
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Joshi M, Chandel R, Kumar V, Sharma S, Baithalu RK, Singh D, Onteru SK. Detection and quantification of TIMP1 and miR-141 through RT-LAMP and TT-LAMP in serum samples during estrous cycle in buffalo. Reprod Biol 2023; 23:100820. [PMID: 37931338 DOI: 10.1016/j.repbio.2023.100820] [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: 04/12/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023]
Abstract
Estrus identification is a common problem in the reproductive management of farm animals. Hence, several studies have been conducted to explore biomarkers for estrus detection. One of our previous studies identified the abundance of RNA biomarkers such as TIMP1 and miR-141 in buffalo saliva during the estrus stage. However, the level of these RNA biomarkers in buffalo serum during estrous cycle is undetected. Therefore, the present study was designed to quantify TIMP1 and miR-141 in serum during buffalo estrous cycle. Blood samples were collected in different stages of estrous cycle from four healthy cyclic buffaloes. The quantification of TIMP1 and miR-141 was performed with direct serum using RT-LAMP and TT-LAMP technologies, respectively. The LAMP amplification was confirmed by agarose gel electrophoresis and the color change was quantified in comparison to a non-template control using ImageJ software. A decreased abundance of TIMP1 at the diestrus stage and a decreasing trend of miR-141 from proestrus to diestrus stages were observed, which was further reinforced by simulated random populations generated with R programming. Specifically, TIMP1 was found significantly (P < 0.0001) abundant at estrus and metestrus stages as compared to the diestrus stage, whereas miR-141 was significantly (P < 0.001) higher during the proestrus stage as compared to the other stages of estrous cycle. The ROC curve analysis showed miR-141 to be a better biomarker than TIMP1 as it distinguished the proestrus stage from diestrus with a sensitivity and specificity of 83 % and 98 %. This study also marked the first use of TT-LAMP technology for rapid miRNA detection in livestock.
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Affiliation(s)
- Mansi Joshi
- Molecular Endocrinology, Functional Genomics & Systems Biology Laboratory, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Rajeev Chandel
- Molecular Endocrinology, Functional Genomics & Systems Biology Laboratory, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Varun Kumar
- Molecular Endocrinology, Functional Genomics & Systems Biology Laboratory, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Sanjay Sharma
- Molecular Endocrinology, Functional Genomics & Systems Biology Laboratory, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Rubina Kumari Baithalu
- Molecular Endocrinology, Functional Genomics & Systems Biology Laboratory, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India; Department of Animal Reproduction, Gynaecology and Obstetrics, ICAR- National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Dheer Singh
- Molecular Endocrinology, Functional Genomics & Systems Biology Laboratory, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Suneel Kumar Onteru
- Molecular Endocrinology, Functional Genomics & Systems Biology Laboratory, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India.
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3
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Yang IS, Jang I, Yang JO, Choi J, Kim MS, Kim KK, Seung BJ, Cheong JH, Sur JH, Nam H, Lee B, Kim J, Kim S. CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris). BMC Genomics 2023; 24:613. [PMID: 37828501 PMCID: PMC10571338 DOI: 10.1186/s12864-023-09655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete. RESULTS We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns. CONCLUSIONS CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ .
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Affiliation(s)
- In Seok Yang
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Insu Jang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Jin Ok Yang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Jinhyuk Choi
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Min-Seo Kim
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Ka-Kyung Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Byung-Joon Seung
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Korea
| | - Jae-Ho Cheong
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Jung-Hyang Sur
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Korea
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Korea
| | - Byungwook Lee
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea.
| | - Junho Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea.
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4
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Xing S, Zhu Y, You Y, Wang S, Wang H, Ning M, Jin H, Liu Z, Zhang X, Yu C, Lu ZJ. Cell-free RNA for the liquid biopsy of gastrointestinal cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1791. [PMID: 37086051 DOI: 10.1002/wrna.1791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Gastrointestinal (GI) cancer includes many cancer types, such as esophageal, liver, gastric, pancreatic, and colorectal cancer. As the cornerstone of personalized medicine for GI cancer, liquid biopsy based on noninvasive biomarkers provides promising opportunities for early diagnosis and dynamic treatment management. Recently, a growing number of studies have demonstrated the potential of cell-free RNA (cfRNA) as a new type of noninvasive biomarker in body fluids, such as blood, saliva, and urine. Meanwhile, transcriptomes based on high-throughput RNA detection technologies keep discovering new cfRNA biomarkers. In this review, we introduce the origins and applications of cfRNA, describe its detection and qualification methods in liquid biopsy, and summarize a comprehensive list of cfRNA biomarkers in different GI cancer types. Moreover, we also discuss perspective studies of cfRNA to overcome its current limitations in clinical applications. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute for Precision Medicine, Tsinghua University, Beijing, China
| | - Yumin Zhu
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Population Health and Aristogenics, Department of Maternal & Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Yaxian You
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongke Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Meng Ning
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Heyue Jin
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Population Health and Aristogenics, Department of Maternal & Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Zhengxia Liu
- Department of General Surgery, SIR RUN RUN Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Geriatrics, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xinhua Zhang
- Department of Health Care, Jiangsu Women and Children Health Hospital, the First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, Jiangsu, China
| | - Chunzhao Yu
- Department of General Surgery, SIR RUN RUN Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Geriatrics, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute for Precision Medicine, Tsinghua University, Beijing, China
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5
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Mathur Y, Shafie A, Alharbi B, Ashour AA, Al-Soud WA, Alhassan HH, Alharethi SH, Anjum F. Genome-Wide Analysis of Kidney Renal Cell Carcinoma: Exploring Differentially Expressed Genes for Diagnostic and Therapeutic Targets. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:393-401. [PMID: 37624678 DOI: 10.1089/omi.2023.0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Kidney renal cell carcinoma (KIRC) is the most common type of renal cancer. Kidney malignancies have been ranked in the top 10 most frequently occurring cancers. KIRC is a prevalent malignancy with a poor prognosis. The disease has risen for the last 40 years, and robust biomarkers for KIRC are needed for precision/personalized medicine. In this bioinformatics study, we utilized genomic data of KIRC patients from The Cancer Genome Atlas for biomarker discovery. A total of 314 samples were used in this study. We identified many differentially expressed genes (DEGs) categorized as upregulated or downregulated. A protein-protein interaction network for the DEGs was then generated and analyzed using the Search Tool for the Retrieval of Interacting Genes plugin of Cytoscape. A set of 10 hub genes was selected based on the Maximum Clique Centrality score defined by the CytoHubba plugin. The elucidated set of genes, that is, CALCA, CRH, TH, CHAT, SLC18A3, FSHB, MYH6, CAV3, KCNA4, and GBX2, were then categorized as potential candidates to be explored as KIRC biomarkers. The survival analysis plots for each gene suggested that alterations in CHAT, CAV3, CRH, MYH6, SLC18A3, and FSHB resulted in decreased survival of KIRC patients. In all, the results suggest that genomic alterations in selected genes can be explored to inform biomarker discovery and for therapeutic predictions in KIRC.
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Affiliation(s)
- Yash Mathur
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Bandar Alharbi
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Hail, Saudi Arabia
| | - Amal Adnan Ashour
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Science, College of Applied Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Hassan H Alhassan
- Department of Clinical Laboratory Science, College of Applied Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran, Saudi Arabia
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
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6
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Salim R, Husby S, Winther Eskelund C, Scott DW, Holte H, Kolstad A, Räty R, Ek S, Jerkeman M, Geisler C, Sommer Kristensen L, Dahl M, Grønbæk K. Exploring new prognostic biomarkers in Mantle Cell Lymphoma: a comparison of the circSCORE and the MCL35 score. Leuk Lymphoma 2023; 64:1414-1423. [PMID: 37259807 DOI: 10.1080/10428194.2023.2216819] [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: 04/18/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
Mantle cell lymphoma (MCL) is a biologically and clinically heterogeneous disease, emphasizing the need for prognostic biomarkers. In this study we aimed at comparing the prognostic value of two RNA-based risk scores, circSCORE and MCL35, in 149 patients from the MCL2 (ISRCTN87866680) and MCL3 (NCT00514475) patient cohorts. Both risk scores provided significant stratification of high versus low risk for progression free survival (PFS) and overall survival (OS). The circSCORE retained significant prognostic value in adjusted multivariable Cox regressions for PFS, but not for OS. Furthermore, circSCORE added significant prognostic value to MIPI in the pooled cohort (MCL2 and MCL3) for PFS and OS, and for PFS in MCL3 alone, outperforming Ki67 and MCL35. We suggest a new, combined MIPI-circSCORE with improved prognostic value, and with potential for future clinical implementation, if validated in a larger, independent cohort.
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Affiliation(s)
- Ruth Salim
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre, BRIC, University of Copenhagen, Copenhagen, Denmark
| | - Simon Husby
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre, BRIC, University of Copenhagen, Copenhagen, Denmark
| | | | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - Harald Holte
- Department of Oncology, Oslo University Hospital, Norway and KG Jebsen Centre for B-cell malignancies, Oslo, Norway
| | - Arne Kolstad
- Department of Oncology, Division Gjøvik-Lillehammer, Innlandet Hospital Trust, Innlandet, Norway
| | - Riikka Räty
- Department of Hematology, Helsinki University Hospital, Helsinki, Finland
| | - Sara Ek
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Mats Jerkeman
- Department of Oncology, Lund University, Lund, Sweden
| | | | | | - Mette Dahl
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre, BRIC, University of Copenhagen, Copenhagen, Denmark
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre, BRIC, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health science, University of Copenhagen, Copenhagen, Denmark
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7
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Shukla N, Kour B, Sharma D, Vijayvargiya M, Sadasukhi TC, Medicherla KM, Malik B, Bissa B, Vuree S, Lohiya NK, Suravajhala P. Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian Prostate Cancer Cohort. Diseases 2023; 11:diseases11020072. [PMID: 37218885 DOI: 10.3390/diseases11020072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers among men in India. Although studies on PCa have dealt with genetics, genomics, and the environmental influence in the causality of PCa, not many studies employing the Next Generation Sequencing (NGS) approaches of PCa have been carried out. In our previous study, we identified some causal genes and mutations specific to Indian PCa using Whole Exome Sequencing (WES). In the recent past, with the help of different cancer consortiums such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC), along with differentially expressed genes (DEGs), many cancer-associated novel non-coding RNAs have been identified as biomarkers. In this work, we attempt to identify differentially expressed genes (DEGs) including long non-coding RNAs (lncRNAs) associated with signature pathways from an Indian PCa cohort using the RNA-sequencing (RNA-seq) approach. From a cohort of 60, we screened six patients who underwent prostatectomy; we performed whole transcriptome shotgun sequencing (WTSS)/RNA-sequencing to decipher the DEGs. We further normalized the read counts using fragments per kilobase of transcript per million mapped reads (FPKM) and analyzed the DEGs using a cohort of downstream regulatory tools, viz., GeneMANIA, Stringdb, Cytoscape-Cytohubba, and cbioportal, to map the inherent signatures associated with PCa. By comparing the RNA-seq data obtained from the pairs of normal and PCa tissue samples using our benchmarked in-house cuffdiff pipeline, we observed some important genes specific to PCa, such as STEAP2, APP, PMEPA1, PABPC1, NFE2L2, and HN1L, and some other important genes known to be involved in different cancer pathways, such as COL6A1, DOK5, STX6, BCAS1, BACE1, BACE2, LMOD1, SNX9, CTNND1, etc. We also identified a few novel lncRNAs such as LINC01440, SOX2OT, ENSG00000232855, ENSG00000287903, and ENST00000647843.1 that need to be characterized further. In comparison with publicly available datasets, we have identified characteristic DEGs and novel lncRNAs implicated in signature PCa pathways in an Indian PCa cohort which perhaps have not been reported. This has set a precedent for us to validate candidates further experimentally, and we firmly believe this will pave a way toward the discovery of biomarkers and the development of novel therapies.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhumandeep Kour
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144001, India
| | - Devendra Sharma
- Department of Urology, Rukmani Birla Hospital, Jaipur 302018, India
| | - Maneesh Vijayvargiya
- Department of Pathology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - T C Sadasukhi
- Department of Urology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Bioengineering, Birla Institute of Technology, Mesra Jaipur Campus, 27-Malaviya Industrial Area, Jaipur 302017, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhawana Bissa
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Sugunakar Vuree
- Bioclues.org, Hyderabad 500072, India
- MNR Foundation for Research & Innovation, MNR University, Sangareddy 502294, India
| | - Nirmal Kumar Lohiya
- Department of Zoology, Center for Advanced Studies, University of Rajasthan, Jaipur 302004, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
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8
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Arriaga-Canon C, Contreras-Espinosa L, Aguilar-Villanueva S, Bargalló-Rocha E, García-Gordillo JA, Cabrera-Galeana P, Castro-Hernández C, Jiménez-Trejo F, Herrera LA. The Clinical Utility of lncRNAs and Their Application as Molecular Biomarkers in Breast Cancer. Int J Mol Sci 2023; 24:ijms24087426. [PMID: 37108589 PMCID: PMC10138835 DOI: 10.3390/ijms24087426] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Given their tumor-specific and stage-specific gene expression, long non-coding RNAs (lncRNAs) have demonstrated to be potential molecular biomarkers for diagnosis, prognosis, and treatment response. Particularly, the lncRNAs DSCAM-AS1 and GATA3-AS1 serve as examples of this because of their high subtype-specific expression profile in luminal B-like breast cancer. This makes them candidates to use as molecular biomarkers in clinical practice. However, lncRNA studies in breast cancer are limited in sample size and are restricted to the determination of their biological function, which represents an obstacle for its inclusion as molecular biomarkers of clinical utility. Nevertheless, due to their expression specificity among diseases, such as cancer, and their stability in body fluids, lncRNAs are promising molecular biomarkers that could improve the reliability, sensitivity, and specificity of molecular techniques used in clinical diagnosis. The development of lncRNA-based diagnostics and lncRNA-based therapeutics will be useful in routine medical practice to improve patient clinical management and quality of life.
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Affiliation(s)
- Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C.P. 14080, Mexico
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C.P. 14080, Mexico
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Mexico City C.P. 04510, Mexico
| | - Sergio Aguilar-Villanueva
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, Tlalpan, Mexico City C.P. 14080, Mexico
| | - Enrique Bargalló-Rocha
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, Tlalpan, Mexico City C.P. 14080, Mexico
| | - José Antonio García-Gordillo
- Departamento de Oncología Médica de Mama, Instituto Nacional de Cancerología, Tlalpan, Mexico City C.P. 14080, Mexico
| | - Paula Cabrera-Galeana
- Departamento de Oncología Médica de Mama, Instituto Nacional de Cancerología, Tlalpan, Mexico City C.P. 14080, Mexico
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C.P. 14080, Mexico
| | | | - L A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C.P. 14080, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey C.P. 64710, Mexico
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9
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Kumar R, Mondal R, Lahiri T, Pal MK. Application of sequence semantic and integrated cellular geography approach to study alternative biogenesis of exonic circular RNA. BMC Bioinformatics 2023; 24:148. [PMID: 37069509 PMCID: PMC10108499 DOI: 10.1186/s12859-023-05279-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Concurrent existence of lncRNA and circular RNA at both nucleus and cytosol within a cell at different proportions is well reported. Previous studies showed that circular RNAs are synthesized in nucleus followed by transportation across the nuclear membrane and the export is primarily defined by their length. lncRNAs primarily originated through inefficient splicing and seem to use NXF1 for cytoplasm export. However, it is not clear whether circularization of lncRNA happens only in nucleus or it also occurs in cytoplasm. Studies indicate that circular RNAs arise when the splicing apparatus undergoes a phenomenon of back splicing. Minor spliceosome (U12 type) mediated splicing occurs in cytoplasm and is responsible for the splicing of 0.5% of introns of human cells. Therefore, possibility of cRNA biogenesis mediated by minor spliceosome at cytoplasm cannot be ruled out. Secondly, information on genes transcribing both circular and lncRNAs along with total number of RBP binding sites for both of these RNA types is extractable from databases. This study showed how these apparently unconnected pieces of reports could be put together to build a model for exploring biogenesis of circular RNA. RESULTS As a result of this study, a model was built under the premises that, sequences with special semantics were molecular precursors in biogenesis of circular RNA which occurred through catalytic role of some specific RBPs. The model outcome was further strengthened by fulfillment of three logical lemmas which were extracted and assimilated in this work using a novel data analytic approach, Integrated Cellular Geography. Result of the study was found to be in well agreement with proposed model. Furthermore this study also indicated that biogenesis of circular RNA was a post-transcriptional event. CONCLUSIONS Overall, this study provides a novel systems biology based model under the paradigm of Integrated Cellular Geography which can assimilate independently performed experimental results and data published by global researchers on RNA biology to provide important information on biogenesis of circular RNAs considering lncRNAs as precursor molecule. This study also suggests the possible RBP-mediated circularization of RNA in the cytoplasm through back-splicing using minor spliceosome.
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Affiliation(s)
- Rajnish Kumar
- Department of Pathology and Laboratory Medicine, Medical Center, University of Kansas, Kansas City, 66160, USA
| | - Rajkrishna Mondal
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland, 797112, India
| | - Tapobrata Lahiri
- Room No. 4302, Department of Applied Sciences, Computer Centre - II, Indian Institute of Information Technology-Allahabad, Allahabad, 211015, India.
| | - Manoj Kumar Pal
- Faculty of Engineering and Technology, United University Prayagraj, Prayagraj, UP, 211012, India
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10
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Molecular Diagnosis and Cancer Prognosis-A Concise Review. Diagnostics (Basel) 2023; 13:diagnostics13040766. [PMID: 36832253 PMCID: PMC9955694 DOI: 10.3390/diagnostics13040766] [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: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Cancer is a complicated disease. Globally, it is one of the major causes for morbidity and mortality. A critical challenge associated with it is the difficulty to accurately diagnose it at an early stage. The malignancy due to multistage and heterogeneity that result from genetic and epigenetic modifications poses critical challenge to diagnose and monitor the progress at an early stage. Current diagnostic techniques normally suggest invasive biopsy procedure that can cause further infections and bleeding. Therefore, noninvasive diagnostic methods with high accuracy, safety and earliest detection are the needs of the hour. Herein, we provide a detailed review on the advanced methodologies and protocols developed for the detection of cancer biomarkers based on proteins, nucleic acids and extracellular vesicles. Furthermore, existing challenges and the improvements essential for the rapid, sensitive and noninvasive detection have also been discussed.
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11
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Through the Looking Glass: Updated Insights on Ovarian Cancer Diagnostics. Diagnostics (Basel) 2023; 13:diagnostics13040713. [PMID: 36832201 PMCID: PMC9955065 DOI: 10.3390/diagnostics13040713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/30/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is the deadliest gynaecological malignancy and the eighth most prevalent cancer in women, with an abysmal mortality rate of two million worldwide. The existence of multiple overlapping symptoms with other gastrointestinal, genitourinary, and gynaecological maladies often leads to late-stage diagnosis and extensive extra-ovarian metastasis. Due to the absence of any clear early-stage symptoms, current tools only aid in the diagnosis of advanced-stage patients, wherein the 5-year survival plummets further to less than 30%. Therefore, there is a dire need for the identification of novel approaches that not only allow early diagnosis of the disease but also have a greater prognostic value. Toward this, biomarkers provide a gamut of powerful and dynamic tools to allow the identification of a spectrum of different malignancies. Both serum cancer antigen 125 (CA-125) and human epididymis 4 (HE4) are currently being used in clinics not only for EOC but also peritoneal and GI tract cancers. Screening of multiple biomarkers is gradually emerging as a beneficial strategy for early-stage diagnosis, proving instrumental in administration of first-line chemotherapy. These novel biomarkers seem to exhibit an enhanced potential as a diagnostic tool. This review summarizes existing knowledge of the ever-growing field of biomarker identification along with potential future ones, especially for ovarian cancer.
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12
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Altman J, Jones G, Ahmed S, Sharma S, Sharma A. Tear Film MicroRNAs as Potential Biomarkers: A Review. Int J Mol Sci 2023; 24:3694. [PMID: 36835108 PMCID: PMC9962948 DOI: 10.3390/ijms24043694] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
MicroRNAs are non-coding RNAs that serve as regulatory molecules in a variety of pathways such as inflammation, metabolism, homeostasis, cell machinery, and development. With the progression of sequencing methods and modern bioinformatics tools, novel roles of microRNAs in regulatory mechanisms and pathophysiological states continue to expand. Advances in detection methods have further enabled larger adoption of studies utilizing minimal sample volumes, allowing the analysis of microRNAs in low-volume biofluids, such as the aqueous humor and tear fluid. The reported abundance of extracellular microRNAs in these biofluids has prompted studies to explore their biomarker potential. This review compiles the current literature reporting microRNAs in human tear fluid and their association with ocular diseases including dry eye disease, Sjögren's syndrome, keratitis, vernal keratoconjunctivitis, glaucoma, diabetic macular edema, and diabetic retinopathy, as well as non-ocular diseases, including Alzheimer's and breast cancer. We also summarize the known roles of these microRNAs and shed light on the future progression of this field.
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Affiliation(s)
- Jeremy Altman
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Garrett Jones
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Saleh Ahmed
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Shruti Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Ophthalmology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Ophthalmology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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13
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Expression of Epithelial and Mesenchymal Markers in Plasmatic Extracellular Vesicles as a Diagnostic Tool for Neoplastic Processes. Int J Mol Sci 2023; 24:ijms24043578. [PMID: 36834987 PMCID: PMC9964693 DOI: 10.3390/ijms24043578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Tumor-derived extracellular vesicles (TD-EVs) have active roles as cancer hallmark enablers. EVs RNA of epithelial and stromal cells carry information that facilitates the communication processes that contribute to oncological progression, so the objective of this work was to validate by RT-PCR the presence of epithelial (KRT19; CEA) and stromal (COL1A2; COL11A1) markers in RNA of plasmatic EVs in healthy and diverse-malignancy patients for the development of a non-invasive cancer diagnosis system using liquid biopsy. Ten asymptomatic controls and 20 cancer patients were included in the study, and results showed that the isolated plasmatic EVs by scanning transmission electron microscopy (STEM) andBiomedical Research Institute A Coruña nanoparticle tracking analysis (NTA) contained most exosome structures with also a considerable percentage of microvesicles. No differences were found in concentration and size distribution between the two cohorts of patients, but significant gene expression in epithelial and mesenchymal markers between healthy donors and patients with active oncological disease was shown. Results of quantitative RT-PCR are solid and reliable for KRT19, COL1A2, and COL11A1, so the analysis of RNA extracted from TD-EVs could be a correct approach to develop a diagnostic tool in oncological processes.
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14
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Zhao X, Wang Z, Ji X, Bu S, Fang P, Wang Y, Wang M, Yang Y, Zhang W, Leung AY, Shi P. Discrete single-cell microRNA analysis for phenotyping the heterogeneity of acute myeloid leukemia. Biomaterials 2022; 291:121869. [DOI: 10.1016/j.biomaterials.2022.121869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/28/2022]
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15
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Weaver C, Bin Satter K, Richardson KP, Tran LKH, Tran PMH, Purohit S. Diagnostic and Prognostic Biomarkers in Renal Clear Cell Carcinoma. Biomedicines 2022; 10:biomedicines10112953. [PMID: 36428521 PMCID: PMC9687861 DOI: 10.3390/biomedicines10112953] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Renal clear cell carcinoma (ccRCC) comprises over 75% of all renal tumors and arises in the epithelial cells of the proximal convoluted tubule. Molecularly ccRCC is characterized by copy number alterations (CNAs) such as the loss of chromosome 3p and VHL inactivation. Additional driver mutations (SETD2, PBRM1, BAP1, and others) promote genomic instability and tumor cell metastasis through the dysregulation of various metabolic and immune-response pathways. Many researchers identified mutation, gene expression, and proteomic signatures for early diagnosis and prognostics for ccRCC. Despite a tremendous influx of data regarding DNA alterations, gene expression, and protein expression, the incorporation of these analyses for diagnosis and prognosis of RCC into the clinical application has not been implemented yet. In this review, we focused on the molecular changes associated with ccRCC development, along with gene expression and protein signatures, to emphasize the utilization of these molecular profiles in clinical practice. These findings, in the context of machine learning and precision medicine, may help to overcome some of the barriers encountered for implementing molecular profiles of tumors into the diagnosis and treatment of ccRCC.
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Affiliation(s)
- Chaston Weaver
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
| | - Khaled Bin Satter
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
| | - Katherine P. Richardson
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Department of Interdisciplinary Health Science, College of Allied Health Sciences, Augusta University, 1120 15th St., Augusta, GA 30912, USA
| | - Lynn K. H. Tran
- Department of Urology, Baylor College of Medicine, Houston, TX 76798, USA
| | - Paul M. H. Tran
- Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Sharad Purohit
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Department of Interdisciplinary Health Science, College of Allied Health Sciences, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Department of Undergraduate Health Professionals, College of Allied Health Sciences, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Correspondence:
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16
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Wang J, Li J, Chen Y, Liu R, Wu Y, Liu J, Yang X, Wang K, Huang J. Size-Controllable and Self-Assembled DNA Nanosphere for Amplified MicroRNA Imaging through ATP-Fueled Cyclic Dissociation. NANO LETTERS 2022; 22:8216-8223. [PMID: 36194690 DOI: 10.1021/acs.nanolett.2c02934] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Visualizing intracellular microRNA (miRNA) is of great importance for revealing its roles in the development of disease. However, cell membrane barrier, complex intracellular environment and low abundance of target miRNA are three main challenges for efficient imaging of intracellular miRNA. Here, we report a size-controllable and self-assembled DNA nanosphere with ATP-fueled dissociation property for amplified miRNA imaging in live cells and mice. The DNA nanosphere was self-assembled from Y-shaped DNA (Y-DNA) monomers through predesigned base pair hybridization, and the size could be easily controlled by varying the concentration of Y-DNA. Once the nanosphere was internalized into cells, the intracellular specific target miRNA would trigger the cyclic dissociation of the DNA nanosphere driven by ATP, resulting in amplified FRET signal. The programmable DNA nanosphere has been proven to work well for detecting the expression of miRNA in cancer cells and in mice, which demonstrates its fairish cell penetration, stability and sensitivity.
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Affiliation(s)
- Jiaoli Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Juan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Yu Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Ruiting Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Yixuan Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
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17
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Chen Z, Wang WT, Wang W, Huang J, Liao JY, Zeng S, Qian L. Sensitive Imaging of Cellular RNA via Cascaded Proximity-Induced Fluorogenic Reactions. ACS APPLIED MATERIALS & INTERFACES 2022; 14:44054-44064. [PMID: 36153979 DOI: 10.1021/acsami.2c10355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Owing to its important biological functions, RNA has become a promising molecular biomarker of various diseases. With a dynamic change in its expression level and a relatively low amount within the complicated biological matrix, signal amplification detection based on DNA probes has been put forward, which is helpful for early diagnosis and prognostic prediction. However, conventional methods are confined to cell lysates or dead cells and are not only time-consuming in sample preparation but also inaccessible to the spatial-temporal information of target RNAs. To achieve live-cell imaging of specific RNAs, both the detection sensitivity and intracellular delivery issues should be addressed. Herein, a new cascaded fluorogenic system based on the combination of hybridization chain reactions (HCRs) and proximity-induced bioorthogonal chemistry is developed, in which a bioorthogonal reaction pair (a tetrazine-quenched dye and its complementary dienophile) is brought into spatial proximity upon target RNA triggering the HCR to turn on and amplify the fluorescence in one step, sensitively indicating the cellular distribution of RNA with minimal false positive results caused by unspecific degradation. Facilitated by a biodegradable carrier based on black phosphorus with high loading capacity and excellent biocompatibility, the resulting imaging platform allows wash-free tracking of target RNAs inside living cells.
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Affiliation(s)
- Zhiyan Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wen-Tao Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wenchao Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jinsong Huang
- Department of Liver Disease, Hangzhou Xixi Hospital, Hangzhou 310023, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
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18
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The Future of Biomarkers in Veterinary Medicine: Emerging Approaches and Associated Challenges. Animals (Basel) 2022; 12:ani12172194. [PMID: 36077913 PMCID: PMC9454634 DOI: 10.3390/ani12172194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary In this review we seek to outline the role of new technologies in biomarker discovery, particularly within the veterinary field and with an emphasis on ‘omics’, as well as to examine why many biomarkers-despite much excitement-have not yet made it to clinical practice. Further we emphasise the critical need for close collaboration between clinicians, researchers and funding bodies and the need to set clear goals for biomarker requirements and realistic application in the clinical setting, ensuring that biomarker type, method of detection and clinical utility are compatible, and adequate funding, time and sample size are available for all phases of development. Abstract New biomarkers promise to transform veterinary practice through rapid diagnosis of diseases, effective monitoring of animal health and improved welfare and production efficiency. However, the road from biomarker discovery to translation is not always straightforward. This review focuses on molecular biomarkers under development in the veterinary field, introduces the emerging technological approaches transforming this space and the role of ‘omics platforms in novel biomarker discovery. The vast majority of veterinary biomarkers are at preliminary stages of development and not yet ready to be deployed into clinical translation. Hence, we examine the major challenges encountered in the process of biomarker development from discovery, through validation and translation to clinical practice, including the hurdles specific to veterinary practice and to each of the ‘omics platforms–transcriptomics, proteomics, lipidomics and metabolomics. Finally, recommendations are made for the planning and execution of biomarker studies with a view to assisting the success of novel biomarkers in reaching their full potential.
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19
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González-Vasconcellos I, Cobos-Fernández MA, Atkinson MJ, Fernandez-Piqueras J, Santos J. Quantifying telomeric lncRNAs using PNA-labelled RNA-Flow FISH (RNA-Flow). Commun Biol 2022; 5:513. [PMID: 35614335 PMCID: PMC9132901 DOI: 10.1038/s42003-022-03452-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Here we present a method to detect and quantify long non-coding RNAs, in particular those related to telomeres. By coupling the specificity of a peptide nucleic acid (PNA) probe with flow cytometry we have quantified cellular levels of TERRA and TERC lncRNAs in culture cell lines and PBMCs. This easy-to-use method appointed RNA-Flow allows reliable lncRNA quantification with broad applications in basic research and clinical diagnostics. In addition, the staining protocol presented here was proven useful for the detection and quantification of such lncRNAs on unfixed cells using confocal microscopy. Telomeric-associated long non-coding RNAs TERRA and TERC can be quantified in culture cell lines and human PBMCs using peptide nucleic acid probes with flow cytometry (RNA-Flow).
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Affiliation(s)
- Iria González-Vasconcellos
- Genome Dynamics and Function Programme, Genome Decoding Research Unit, Centro de Biología Molecular Severo Ochoa (CBMSO), Madrid, Spain. .,Institute for Molecular Biology-IUBM (Autonomous University of Madrid), Madrid, Spain. .,Biology Department, faculty of science. Autonomous University of Madrid (UAM). Canto Blanco Campus, Madrid, Spain.
| | - María A Cobos-Fernández
- Genome Dynamics and Function Programme, Genome Decoding Research Unit, Centro de Biología Molecular Severo Ochoa (CBMSO), Madrid, Spain.,Institute for Molecular Biology-IUBM (Autonomous University of Madrid), Madrid, Spain.,Biology Department, faculty of science. Autonomous University of Madrid (UAM). Canto Blanco Campus, Madrid, Spain
| | - Michael J Atkinson
- Chair of Radiation Biology, Technical University of Munich, 81675, Munich, Germany
| | - José Fernandez-Piqueras
- Genome Dynamics and Function Programme, Genome Decoding Research Unit, Centro de Biología Molecular Severo Ochoa (CBMSO), Madrid, Spain.,Institute for Molecular Biology-IUBM (Autonomous University of Madrid), Madrid, Spain.,Biology Department, faculty of science. Autonomous University of Madrid (UAM). Canto Blanco Campus, Madrid, Spain.,Institute of Health Research Jiménez Díaz Foundation, Madrid, 28040, Spain
| | - Javier Santos
- Genome Dynamics and Function Programme, Genome Decoding Research Unit, Centro de Biología Molecular Severo Ochoa (CBMSO), Madrid, Spain.,Institute for Molecular Biology-IUBM (Autonomous University of Madrid), Madrid, Spain.,Biology Department, faculty of science. Autonomous University of Madrid (UAM). Canto Blanco Campus, Madrid, Spain.,Institute of Health Research Jiménez Díaz Foundation, Madrid, 28040, Spain
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20
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Ujfaludi Z, Kuthi L, Pankotai-Bodó G, Bankó S, Sükösd F, Pankotai T. Novel Diagnostic Value of Driver Gene Transcription Signatures to Characterise Clear Cell Renal Cell Carcinoma, ccRCC. Pathol Oncol Res 2022; 28:1610345. [PMID: 35586183 PMCID: PMC9108154 DOI: 10.3389/pore.2022.1610345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/12/2022] [Indexed: 11/22/2022]
Abstract
Routine molecular tumour diagnostics are augmented by DNA-based qualitative and quantitative molecular techniques detecting mutations of DNA. However, in the past decade, it has been unravelled that the phenotype of cancer, as it’s an extremely complex disease, cannot be fully described and explained by single or multiple genetic variants affecting only the coding regions of the genes. Moreover, studying the manifestation of these somatic mutations and the altered transcription programming—driven by genomic rearrangements, dysregulation of DNA methylation and epigenetic landscape—standing behind the tumorigenesis and detecting these changes could provide a more detailed characterisation of the tumour phenotype. Consequently, novel comparative cancer diagnostic pipelines, including DNA- and RNA-based approaches, are needed for a global assessment of cancer patients. Here we report, that by monitoring the expression patterns of key tumour driver genes by qPCR, the normal and the tumorous samples can be separated into distinct categories. Furthermore, we also prove that by examining the transcription signatures of frequently affected genes at 3p25, 3p21 and 9p21.3 genomic regions, the ccRCC (clear cell renal cell carcinoma) and non-tumorous kidney tissues can be distinguished based on the mRNA level of the selected genes. Our results open new diagnostics possibilities where the mRNA signatures of tumour drivers can supplement the DNA-based approaches providing a more precise diagnostics opportunity leading to determine more precise therapeutic protocols.
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Affiliation(s)
- Zsuzsanna Ujfaludi
- Albert Szent-Györgyi Clinical Center, Albert Szent-Györgyi Medical School, Institute of Pathology, University of Szeged, Szeged, Hungary
| | - Levente Kuthi
- Albert Szent-Györgyi Clinical Center, Albert Szent-Györgyi Medical School, Institute of Pathology, University of Szeged, Szeged, Hungary
| | - Gabriella Pankotai-Bodó
- Albert Szent-Györgyi Clinical Center, Albert Szent-Györgyi Medical School, Institute of Pathology, University of Szeged, Szeged, Hungary
| | - Sarolta Bankó
- Albert Szent-Györgyi Clinical Center, Albert Szent-Györgyi Medical School, Institute of Pathology, University of Szeged, Szeged, Hungary
| | - Farkas Sükösd
- Albert Szent-Györgyi Clinical Center, Albert Szent-Györgyi Medical School, Institute of Pathology, University of Szeged, Szeged, Hungary
| | - Tibor Pankotai
- Albert Szent-Györgyi Clinical Center, Albert Szent-Györgyi Medical School, Institute of Pathology, University of Szeged, Szeged, Hungary
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21
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RNAscope for VEGF-A Detection in Human Tumor Bioptic Specimens. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2475:143-155. [PMID: 35451755 DOI: 10.1007/978-1-0716-2217-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Different pro-angiogenic factors, such as vascular endothelial growth factor-A (VEGF-A), have been related to microvascular density, clinicopathologic factors, and poor prognosis in many tumors. VEGF-A binds its receptor 2 (VEGFR2) to induce neo-angiogenesis, a constant hallmark of tumor initiation and progression. Based on VEGF-A/VEGFR2 relevance in tumor angiogenesis, several inhibitors were developed. However, the clinical benefits of anti-angiogenic therapies are limited because tumors activate different mechanisms of drug resistance.The need for understanding tumor biology, limitation or failure of anti-angiogenic therapies, and the demand for a personalized therapeutic approach has boosted the search for robust biomarkers for patient stratification as responder or non-responder to anti-VEGF therapies.This chapter presents a detailed protocol to perform chromogenic VEGF-A mRNA detection and quantification in human tumor bioptic specimens using RNAscope technology and RNA-in situ hybridization (ISH) algorithm. RNAscope for VEGF-A detection, even for small amounts, is compatible with precious clinical samples and diagnostic laboratory workflows.
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22
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Li J, Huang J. Fuel‐powered DNA nanomachines for biosensing and cancer therapy. Chempluschem 2022; 87:e202200098. [DOI: 10.1002/cplu.202200098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/12/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jing Li
- Yangzhou University School of Chemistry and Chemical Engineering CHINA
| | - Jin Huang
- Hunan University Chemistry lushan road 410082 Changsha CHINA
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23
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Grätz C, Bui MLU, Thaqi G, Kirchner B, Loewe RP, Pfaffl MW. Obtaining Reliable RT-qPCR Results in Molecular Diagnostics—MIQE Goals and Pitfalls for Transcriptional Biomarker Discovery. Life (Basel) 2022; 12:life12030386. [PMID: 35330136 PMCID: PMC8953338 DOI: 10.3390/life12030386] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
In this review, we discuss the development pipeline for transcriptional biomarkers in molecular diagnostics and stress the importance of a reliable gene transcript quantification strategy. Hence, a further focus is put on the MIQE guidelines and how to adapt them for biomarker discovery, from signature validation up to routine diagnostic applications. First, the advantages and pitfalls of the holistic RNA sequencing for biomarker development will be described to establish a candidate biomarker signature. Sequentially, the RT-qPCR confirmation process will be discussed to validate the discovered biomarker signature. Examples for the successful application of RT-qPCR as a fast and reproducible quantification method in routinemolecular diagnostics are provided. Based on the MIQE guidelines, the importance of “key steps” in RT-qPCR is accurately described, e.g., reverse transcription, proper reference gene selection and, finally, the application of automated RT-qPCR data analysis software. In conclusion, RT-qPCR proves to be a valuable tool in the establishment of a disease-specific transcriptional biomarker signature and will have a great future in molecular diagnostics or personalized medicine.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | - Maria L. U. Bui
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | - Granit Thaqi
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | | | - Michael W. Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- Correspondence: or
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24
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Cannistraci A, Hascoet P, Ali A, Mundra P, Clarke NW, Pavet V, Marais R. MiR-378a inhibits glucose metabolism by suppressing GLUT1 in prostate cancer. Oncogene 2022; 41:1445-1455. [PMID: 35039635 PMCID: PMC8897193 DOI: 10.1038/s41388-022-02178-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/07/2021] [Accepted: 01/05/2022] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is the fifth leading cause of cancer related deaths worldwide, in part due to a lack of molecular stratification tools that can distinguish primary tumours that will remain indolent from those that will metastasise. Amongst potential molecular biomarkers, microRNAs (miRs) have attracted particular interest because of their high stability in body fluids and fixed tissues. These small non-coding RNAs modulate several physiological and pathological processes, including cancer progression. Herein we explore the prognostic potential and the functional role of miRs in localised PCa and their relation to nodal metastasis. We define a 7-miR signature that is associated with poor survival independently of age, Gleason score, pathological T state, N stage and surgical margin status and that is also prognostic for disease-free survival in patients with intermediate-risk localised disease. Within our 7-miR signature, we show that miR-378a-3p (hereafter miR-378a) levels are low in primary tumours compared to benign prostate tissue, and also lower in Gleason score 8-9 compared to Gleason 6-7 PCa. We demonstrate that miR-378a impairs glucose metabolism and reduces proliferation in PCa cells through independent mechanisms, and we identify glucose transporter 1 (GLUT1) messenger RNA as a direct target of miR-378a. We show that GLUT1 inhibition hampers glycolysis, leading to cell death. Our data provides a rational for a new PCa stratification strategy based on miR expression, and it reveals that miR-378a and GLUT1 are potential therapeutic targets in highly aggressive glycolytic PCa.
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Affiliation(s)
- A Cannistraci
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - P Hascoet
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - A Ali
- Genito-Urinary Cancer Research Group and the FASTMAN Prostate Cancer Centre for Excellence, Division of Cancer Sciences, Manchester Cancer Research Centre, The University of Manchester, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - P Mundra
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - N W Clarke
- Genito-Urinary Cancer Research Group and the FASTMAN Prostate Cancer Centre for Excellence, Division of Cancer Sciences, Manchester Cancer Research Centre, The University of Manchester, 555 Wilmslow Road, Manchester, M20 4GJ, UK.,The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - V Pavet
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.
| | - R Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.
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25
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Smith BJ, Silva-Costa LC, Martins-de-Souza D. Human disease biomarker panels through systems biology. Biophys Rev 2021; 13:1179-1190. [PMID: 35059036 PMCID: PMC8724340 DOI: 10.1007/s12551-021-00849-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022] Open
Abstract
As more uses for biomarkers are sought after for an increasing number of disease targets, single-target biomarkers are slowly giving way for biomarker panels. These panels incorporate various sources of biomolecular and clinical data to guarantee a higher robustness and power of separation for a clinical test. Multifactorial diseases such as psychiatric disorders show great potential for clinical use, assisting medical professionals during the analysis of risk and predisposition, disease diagnosis and prognosis, and treatment applicability and efficacy. More specific tests are also being developed to assist in ruling out, distinguishing between, and confirming suspicions of multifactorial diseases, as well as to predict which therapy option may be the best option for a given patient's biochemical profile. As more complex datasets are entering the field, involving multi-omic approaches, systems biology has stepped in to facilitate the discovery and validation steps during biomarker panel generation. Filtering biomolecules and clinical data, pre-validating and cross-validating potential biomarkers, generating final biomarker panels, and testing the robustness and applicability of those panels are all beginning to rely on machine learning and systems biology and research in this area will only benefit from advances in these approaches.
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Affiliation(s)
- Bradley J. Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Licia C. Silva-Costa
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores Em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico E Tecnológico, Sao Paulo, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, Brazil
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26
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Yang Q, Yang F, Dai W, Meng X, Wei W, Cheng Y, Dong J, Lu H, Dong H. DNA Logic Circuits for Multiple Tumor Cells Identification Using Intracellular MicroRNA Molecular Bispecific Recognition. Adv Healthc Mater 2021; 10:e2101130. [PMID: 34486246 DOI: 10.1002/adhm.202101130] [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: 06/10/2021] [Revised: 08/11/2021] [Indexed: 12/19/2022]
Abstract
The aberrant expression level of intracellular microRNAs (miRNAs) holds great promise for differentiating cell types at the molecular level. However, cell subtype discrimination based on a single miRNA molecular level is not sufficient and reliable. Herein, multiple identifiable and reporting modules are integrated into a single DNA circuit for multiple cancer cell subtypes identification based on miRNAs bispecific recognition. The DNA three-dimensional (3D) logic gate nano-hexahedron framework extends three recognition modules and three reporting modules to form three "AND" logic gates. Each Boolean operator "AND" returns an "ON" signal in the presence of bispecific miRNAs, simultaneously enabling three types of cell subtype identification. It not only enables the discrimination of cancer cells A549 and MCF-7 from normal cells NHDF but also successfully distinguishes different types of cancer cells. The bispecific intracellular miRNA controllable DNA circuit, with low signal-to-noise ratio, easily extends to various cell type discrimination by adjusting the miRNA species, provides huge opportunities for accurately differentiating multiple cell types at the molecular level.
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Affiliation(s)
- Qiqi Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Yaru Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Jinhong Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Huiting Lu
- Department of Chemistry School of Chemistry and Bioengineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
- Department of Chemistry School of Chemistry and Bioengineering University of Science and Technology Beijing Beijing 100083 P. R. China
- Marshall Laboratory of Biomedical Engineering School of Biomedical Engineering Health Science Centre Shenzhen University Shenzhen 518071 P. R. China
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27
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Functional and Clinical Significance of Dysregulated microRNAs in Liver Cancer. Cancers (Basel) 2021; 13:cancers13215361. [PMID: 34771525 PMCID: PMC8582514 DOI: 10.3390/cancers13215361] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Liver cancer has a high mortality rate. Here, we retrospectively discuss the current progress and dilemmas in the clinical research and treatment of liver cancer. We primarily focus on microRNAs because of their extremely high value in applications and research. We discuss whether microRNAs can be used for the development of better biomarkers and/or therapeutic drugs, and address the difficulties, requirements for improved diagnostic technologies, and side effects related to microRNA-based drugs. Abstract Liver cancer is the leading cause of cancer-related mortality in the world. This mainly reflects the lack of early diagnosis tools and effective treatment methods. MicroRNAs (miRNAs) are a class of non-transcribed RNAs, some of which play important regulatory roles in liver cancer. Here, we discuss microRNAs with key impacts on liver cancer, such as miR-122, miR-21, miR-214, and miR-199. These microRNAs participate in various physiological regulatory pathways of liver cancer cells, and their modulation can have non-negligible effects in the treatment of liver cancer. We discuss whether these microRNAs can be used for better clinical diagnosis and/or drug development. With the advent of novel technologies, fast, inexpensive, and non-invasive RNA-based biomarker research has become a new mainstream approach. However, the clinical application of microRNA-based markers has been limited by the high sequence similarity among them and the potential for off-target problems. Therefore, researchers particularly value microRNAs that are specific to or have special functions in liver cancer. These include miR-122, which is specifically expressed in the liver, and miR-34, which is necessary for the replication of the hepatitis C virus in liver cancer. Clinical treatment drugs have been developed based on miR-34 and miR-122 (MRX34 and Miravirsen, respectively), but their side effects have not yet been overcome. Future research is needed to address these weaknesses and establish a feasible microRNA-based treatment strategy for liver cancer.
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28
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Shah JA, Khattak S, Rauf MA, Cai Y, Jin J. Potential Biomarkers of miR-371-373 Gene Cluster in Tumorigenesis. Life (Basel) 2021; 11:life11090984. [PMID: 34575133 PMCID: PMC8465240 DOI: 10.3390/life11090984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
microRNAs (miRNAs) are small non-coding RNA transcripts (20–24 nucleotides) that bind to their complementary sequences in the 3′-untranslated regions (3′-UTR) of targeted genes to negatively or positively regulate their expression. miRNAs affect the expression of genes in cells, thereby contributing to several important biological processes, including tumorigenesis. Identifying the miRNA cluster as a human embryonic stem cell (hESC)-specific miRNAs initially led to the identification of miR-371, miR-372, miR-373, and miR-373*, which can ultimately be translated into mature miRNAs. Recent evidence suggests that miR-371–373 genes are abnormally expressed in various cancers and act either as oncogenes or tumor suppressors, indicating they may be suitable as molecular biomarkers for cancer diagnosis and prevention. In this article, we summarize recent studies linking miR-371–373 functions to tumorigenesis and speculate on the potential applications of miR-371–373 as biomarkers for cancer diagnosis and treatment.
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Affiliation(s)
- Junaid Ali Shah
- School of Life Sciences, Jilin University, Changchun 130012, China; (J.A.S.); (Y.C.)
| | - Saadullah Khattak
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China;
| | - Mohd Ahmar Rauf
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; or
| | - Yong Cai
- School of Life Sciences, Jilin University, Changchun 130012, China; (J.A.S.); (Y.C.)
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun 130012, China; (J.A.S.); (Y.C.)
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
- Correspondence:
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29
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Dong C, Rao N, Du W, Gao F, Lv X, Wang G, Zhang J. mRBioM: An Algorithm for the Identification of Potential mRNA Biomarkers From Complete Transcriptomic Profiles of Gastric Adenocarcinoma. Front Genet 2021; 12:679612. [PMID: 34386038 PMCID: PMC8354214 DOI: 10.3389/fgene.2021.679612] [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: 03/12/2021] [Accepted: 05/06/2021] [Indexed: 12/09/2022] Open
Abstract
Purpose In this work, an algorithm named mRBioM was developed for the identification of potential mRNA biomarkers (PmBs) from complete transcriptomic RNA profiles of gastric adenocarcinoma (GA). Methods mRBioM initially extracts differentially expressed (DE) RNAs (mRNAs, miRNAs, and lncRNAs). Next, mRBioM calculates the total information amount of each DE mRNA based on the coexpression network, including three types of RNAs and the protein-protein interaction network encoded by DE mRNAs. Finally, PmBs were identified according to the variation trend of total information amount of all DE mRNAs. Four PmB-based classifiers without learning and with learning were designed to discriminate the sample types to confirm the reliability of PmBs identified by mRBioM. PmB-based survival analysis was performed. Finally, three other cancer datasets were used to confirm the generalization ability of mRBioM. Results mRBioM identified 55 PmBs (41 upregulated and 14 downregulated) related to GA. The list included thirteen PmBs that have been verified as biomarkers or potential therapeutic targets of gastric cancer, and some PmBs were newly identified. Most PmBs were primarily enriched in the pathways closely related to the occurrence and development of gastric cancer. Cancer-related factors without learning achieved sensitivity, specificity, and accuracy of 0.90, 1, and 0.90, respectively, in the classification of the GA and control samples. Average accuracy, sensitivity, and specificity of the three classifiers with machine learning ranged within 0.94–0.98, 0.94–0.97, and 0.97–1, respectively. The prognostic risk score model constructed by 4 PmBs was able to correctly and significantly (∗∗∗p < 0.001) classify 269 GA patients into the high-risk (n = 134) and low-risk (n = 135) groups. GA equivalent classification performance was achieved using the complete transcriptomic RNA profiles of colon adenocarcinoma, lung adenocarcinoma, and hepatocellular carcinoma using PmBs identified by mRBioM. Conclusions GA-related PmBs have high specificity and sensitivity and strong prognostic risk prediction. MRBioM has also good generalization. These PmBs may have good application prospects for early diagnosis of GA and may help to elucidate the mechanism governing the occurrence and development of GA. Additionally, mRBioM is expected to be applied for the identification of other cancer-related biomarkers.
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Affiliation(s)
- Changlong Dong
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Nini Rao
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenju Du
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Fenglin Gao
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoqin Lv
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Guangbin Wang
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Junpeng Zhang
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
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30
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Riquier S, Bessiere C, Guibert B, Bouge AL, Boureux A, Ruffle F, Audoux J, Gilbert N, Xue H, Gautheret D, Commes T. Kmerator Suite: design of specific k-mer signatures and automatic metadata discovery in large RNA-seq datasets. NAR Genom Bioinform 2021; 3:lqab058. [PMID: 34179780 PMCID: PMC8221386 DOI: 10.1093/nargab/lqab058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 05/10/2021] [Accepted: 06/17/2021] [Indexed: 11/12/2022] Open
Abstract
The huge body of publicly available RNA-sequencing (RNA-seq) libraries is a treasure of functional information allowing to quantify the expression of known or novel transcripts in tissues. However, transcript quantification commonly relies on alignment methods requiring a lot of computational resources and processing time, which does not scale easily to large datasets. K-mer decomposition constitutes a new way to process RNA-seq data for the identification of transcriptional signatures, as k-mers can be used to quantify accurately gene expression in a less resource-consuming way. We present the Kmerator Suite, a set of three tools designed to extract specific k-mer signatures, quantify these k-mers into RNA-seq datasets and quickly visualize large dataset characteristics. The core tool, Kmerator, produces specific k-mers for 97% of human genes, enabling the measure of gene expression with high accuracy in simulated datasets. KmerExploR, a direct application of Kmerator, uses a set of predictor gene-specific k-mers to infer metadata including library protocol, sample features or contaminations from RNA-seq datasets. KmerExploR results are visualized through a user-friendly interface. Moreover, we demonstrate that the Kmerator Suite can be used for advanced queries targeting known or new biomarkers such as mutations, gene fusions or long non-coding RNAs for human health applications.
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Affiliation(s)
- Sébastien Riquier
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | - Chloé Bessiere
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | - Benoit Guibert
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | | | - Anthony Boureux
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | - Florence Ruffle
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | | | - Nicolas Gilbert
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
| | - Haoliang Xue
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Thérèse Commes
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, 34295, Montpellier, France
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31
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Yao T, Wang R, Meng Y, Hun X. Photoelectrochemical Sensing of α-Synuclein Based on a AuNPs/Graphdiyne-Modified Electrode Coupled with a Nanoprobe. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26515-26521. [PMID: 34060317 DOI: 10.1021/acsami.1c07617] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We developed a method for photoelectrochemical (PEC) sensing based on a AuNPs/graphdiyne, as a low background signal composite material, modified electrode coupled with a nanoprobe (probe DNA/DA/MBA/WSe2) for sensitive α-synuclein (α-Syn) detection. A tungsten selenide (WSe2) nanoflower was first produced with a one-pot solvothermal method and employed as a signal amplification element and the modified substrate of the nanoprobe. The synergy effect between the WSe2 nanoflower and graphdiyne (GDY) can reduce the photoinduced electron-hole recombination and expedite the spatial charge separation. Due to the synergistic effect of AuNPs/GDY and WSe2, this detection strategy provides a high signal-to-noise ratio and good performance. The signal indicator, dopamine/4-mercaptophenyl boronic acid/WSe2 (DA/MBA/WSe2), was generated with the recognition of boron-diol. In the presence of the α-Syn oligomer, the target triggered cycle I strand displacement amplification and achieved the conversion of the α-Syn oligomer to a massive output of false-target DNA (FT). The output FT was used for the cycle II catalytic hairpin assembly onto the electrode which was modified with AuNPs/GDY and triple-stranded DNA (TsDNA); thereby, plenty of PEC nanoprobes which are composed of probe DNA and the signal indicator are captured, and the photocurrent response is produced correspondingly. This PEC biosensor generated a strong photocurrent with low blank (27.6 nA) and was sensitive to α-Syn oligomer. The limit of detection was 3.3 aM, and the relative standard deviation (RSD) was 3.7% at 100 aM. Moreover, it also has good selectivity, indicating promising potential in clinical diagnostics.
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Affiliation(s)
- Ting Yao
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China
| | - Ruhao Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China
| | - Yuchan Meng
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China
| | - Xu Hun
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China
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32
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Fattahi F, Kiani J, Alemrajabi M, Soroush A, Naseri M, Najafi M, Madjd Z. Overexpression of DDIT4 and TPTEP1 are associated with metastasis and advanced stages in colorectal cancer patients: a study utilizing bioinformatics prediction and experimental validation. Cancer Cell Int 2021; 21:303. [PMID: 34107956 PMCID: PMC8191213 DOI: 10.1186/s12935-021-02002-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Various diagnostic and prognostic tools exist in colorectal cancer (CRC) due to multiple genetic and epigenetic alterations causing the disease. Today, the expression of RNAs is being used as prognostic markers for cancer. METHODS In the current study, various dysregulated RNAs in CRC were identified via bioinformatics prediction. Expression of several of these RNAs were measured by RT-qPCR in 48 tissues from CRC patients as well as in colorectal cancer stem cell-enriched spheroids derived from the HT-29 cell line. The relationships between the expression levels of these RNAs and clinicopathological features were analyzed. RESULTS Our bioinformatics analysis determined 11 key mRNAs, 9 hub miRNAs, and 18 lncRNAs which among them 2 coding RNA genes including DDIT4 and SULF1 as well as 3 non-coding RNA genes including TPTEP1, miR-181d-5p, and miR-148b-3p were selected for the further investigations. Expression of DDIT4, TPTEP1, and miR-181d-5p showed significantly increased levels while SULF1 and miR-148b-3p showed decreased levels in CRC tissues compared to the adjacent normal tissues. Positive relationships between DDIT4, SULF1, and TPTEP1 expression and metastasis and advanced stages of CRC were observed. Additionally, our results showed significant correlations between expression of TPTEP1 with DDIT4 and SULF1. CONCLUSIONS Our findings demonstrated increased expression levels of DDIT4 and TPTEP1 in CRC were associated with more aggressive tumor behavior and more advanced stages of the disease. The positive correlations between TPTEP1 as non-coding RNA and both DDIT4 and SULF1 suggest a regulatory effect of TPTEP1 on these genes.
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Affiliation(s)
- Fahimeh Fattahi
- Oncopathology Research Center, Iran University of Medical Sciences, (IUMS), Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, (IUMS), Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahdi Alemrajabi
- Firoozgar Clinical Research Development Center (FCRDC), Iran University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Soroush
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Naseri
- Oncopathology Research Center, Iran University of Medical Sciences, (IUMS), Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Najafi
- Biochemistry Department, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran.
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences, (IUMS), Tehran, Iran. .,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Raza M, Kumar N, Nair U, Luthra G, Bhattacharyya U, Jayasundar S, Jayasundar R, Sehrawat S. Current updates on precision therapy for breast cancer associated brain metastasis: Emphasis on combination therapy. Mol Cell Biochem 2021; 476:3271-3284. [PMID: 33886058 DOI: 10.1007/s11010-021-04149-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/01/2021] [Indexed: 12/12/2022]
Abstract
Cancer therapies have undergone a tremendous progress over the past decade. Precision medicine provides a more tailored approach, making the combination of existing therapies more precise. Different types of cancers are characterized by unique biomarkers that are targeted using various genomic approaches by clinicians and companies worldwide to achieve efficient treatment with minimal side effects. Precision medicine has two broad approaches namely stratified and personalized medicine. The driver mutations could vary within a subtype while the same driver mutations could be found across different subtypes. Precision medicine has recently gained a lot of importance for breast cancer therapy. Various kinds of mutations like hotspot mutations, gene alterations, gene amplification mutations are targeted to design a more specific therapy. Apart from these known gene mutations there are various unknown mutations. Thus, tumor heterogeneity can pose a challenge to precision medicine. For breast cancer, one of the most successful models developed in case of precision medicine is the anti-HER2 therapies as HER2 was considered to have the worst prognosis being highly malignant. But now due to the advent of HER2 receptor targeted therapies, it has a good prognosis. Moreover, precision medicine helps in identifying if the drug molecules being used for the treatment of one kind of cancer can be beneficial in the treatment of another kind of cancer as well, considering the signaling pathways and machinery is similar in most of the cancers. This reduces the time for new drug development and is economically more feasible. Precision medicine will prove to be very advantageous in case of brain metastasis.
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Affiliation(s)
- Masoom Raza
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Delhi NCR, India
| | - Naveen Kumar
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Delhi NCR, India
| | - Uttara Nair
- Department of Women's and Reproductive Health, Oxford Fertility, Oxford Business Park North, University of Oxford, Oxford, OX4 2HW, UK
| | - Gehna Luthra
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Delhi NCR, India
| | - Ushosi Bhattacharyya
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Delhi NCR, India
| | - Smruthi Jayasundar
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Delhi NCR, India
| | - Rama Jayasundar
- Department of Nuclear Magnetic Resonance & MRI, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Seema Sehrawat
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Delhi NCR, India.
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Alladin-Mustan BS, Liu Y, Li Y, de Almeida DRQ, Yuzik J, Mendes CF, Gibbs JM. Reverse transcription lesion-induced DNA amplification: An instrument-free isothermal method to detect RNA. Anal Chim Acta 2021; 1149:238130. [PMID: 33551053 DOI: 10.1016/j.aca.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 10/22/2022]
Abstract
One challenge in point-of-care (POC) diagnostics is the lack of room-temperature methods for RNA detection based on enzymatic amplification and visualization steps. Here we perform reverse transcription lesion-induced DNA amplification (RT-LIDA), an isothermal amplification method that only requires T4 DNA ligase. RT-LIDA involves the RNA-templated ligation of DNA primers to form complementary DNA (cDNA) followed by toehold-mediated strand displacement of the cDNA and its exponential amplification via our isothermal ligase chain reaction LIDA. Each step is tuned to proceed at 28 °C, which falls within the range of global room temperatures. Using RT-LIDA, we can detect as little as ∼100 amol target RNA and can distinguish RNA target from total cellular RNA. Finally, we demonstrate that the resulting DNA amplicons can be detected colorimetrically, also at room temperature, by rapid, target-triggered disassembly of DNA-modified gold nanoparticles. This integrated amplification/detection platform requires no heating or visualization instrumentation, which is an important step towards realizing instrument-free POC testing.
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Affiliation(s)
| | - Yuning Liu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Yimeng Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Daria R Q de Almeida
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Jesse Yuzik
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Camilla F Mendes
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2.
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Advani D, Sharma S, Kumari S, Ambasta RK, Kumar P. Precision Oncology, Signaling and Anticancer Agents in Cancer Therapeutics. Anticancer Agents Med Chem 2021; 22:433-468. [PMID: 33687887 DOI: 10.2174/1871520621666210308101029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/05/2021] [Accepted: 01/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The global alliance for genomics and healthcare facilities provides innovational solutions to expedite research and clinical practices for complex and incurable health conditions. Precision oncology is an emerging field explicitly tailored to facilitate cancer diagnosis, prevention and treatment based on patients' genetic profile. Advancements in "omics" techniques, next-generation sequencing, artificial intelligence and clinical trial designs provide a platform for assessing the efficacy and safety of combination therapies and diagnostic procedures. METHOD Data were collected from Pubmed and Google scholar using keywords: "Precision medicine", "precision medicine and cancer", "anticancer agents in precision medicine" and reviewed comprehensively. RESULTS Personalized therapeutics including immunotherapy, cancer vaccines, serve as a groundbreaking solution for cancer treatment. Herein, we take a measurable view of precision therapies and novel diagnostic approaches targeting cancer treatment. The contemporary applications of precision medicine have also been described along with various hurdles identified in the successful establishment of precision therapeutics. CONCLUSION This review highlights the key breakthroughs related to immunotherapies, targeted anticancer agents, and target interventions related to cancer signaling mechanisms. The success story of this field in context to drug resistance, safety, patient survival and in improving quality of life is yet to be elucidated. We conclude that, in the near future, the field of individualized treatments may truly revolutionize the nature of cancer patient care.
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Affiliation(s)
- Dia Advani
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Sudhanshu Sharma
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
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Lam CK, Wu JC. Clinical Trial in a Dish: Using Patient-Derived Induced Pluripotent Stem Cells to Identify Risks of Drug-Induced Cardiotoxicity. Arterioscler Thromb Vasc Biol 2021; 41:1019-1031. [PMID: 33472401 PMCID: PMC11006431 DOI: 10.1161/atvbaha.120.314695] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Drug-induced cardiotoxicity is a significant clinical issue, with many drugs in the market being labeled with warnings on cardiovascular adverse effects. Treatments are often prematurely halted when cardiotoxicity is observed, which limits their therapeutic potential. Moreover, cardiotoxicity is a major reason for abandonment during drug development, reducing available treatment options for diseases and creating a significant financial burden and disincentive for drug developers. Thus, it is important to minimize the cardiotoxic effects of medications that are in use or in development. To this end, identifying patients at a higher risk of developing cardiovascular adverse effects for the drug of interest may be an effective strategy. The discovery of human induced pluripotent stem cells has enabled researchers to generate relevant cell types that retain a patient's own genome and examine patient-specific disease mechanisms, paving the way for precision medicine. Combined with the rapid development of pharmacogenomic analysis, the ability of induced pluripotent stem cell-derivatives to recapitulate patient-specific drug responses provides a powerful platform to identify subsets of patients who are particularly vulnerable to drug-induced cardiotoxicity. In this review, we will discuss the current use of patient-specific induced pluripotent stem cells in identifying populations who are at risk to drug-induced cardiotoxicity and their potential applications in future precision medicine practice. Graphic Abstract: A graphic abstract is available for this article.
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Affiliation(s)
- Chi Keung Lam
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
- Department of Biological Sciences, University of Delaware, Newark, DE
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
- Department of Radiology, Stanford University School of Medicine, Stanford, CA
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37
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Lan L, Huang J, Liu M, Yin Y, Wei C, Cai Q, Meng X. Polymerization and isomerization cyclic amplification for nucleic acid detection with attomolar sensitivity. Chem Sci 2021; 12:4509-4518. [PMID: 34163716 PMCID: PMC8179492 DOI: 10.1039/d0sc05457g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/11/2020] [Indexed: 12/25/2022] Open
Abstract
DNA amplification is one of the most valuable tools for the clinical diagnosis of nucleic acid-related diseases, but current techniques for DNA amplification are based on intermolecular polymerization reactions, resulting in the risk of errors in the intermolecular reaction pattern. In this article, we introduce the concept of intramolecular polymerization and isomerization cyclic amplification (PICA), which extends a short DNA strand to a long strand containing periodic repeats of a sequence through cyclic alternating polymerization and isomerization. To the best of our knowledge, this is the first time that a real ssDNA self-extension method without any additional auxiliary oligonucleotides has been reported. By interfacing PICA with external molecular elements, it can be programmed to respond to different targets. Herein, we designed two distinct types of amplified nucleic acid detection platforms that can be implemented with PICA, including cyclic reverse transcription (CRT) and cyclic replication (CR). We experimentally demonstrate the mechanisms of CRT-PICA and CR-PICA using mammalian miRNA and virus DNA. The results showed that this proposed detection platform has excellent sensitivity, selectivity, and reliability. The detection level could reach the aM level, that is, several copies of target molecules can be detected if a small volume is taken into account.
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Affiliation(s)
- Lin Lan
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Jin Huang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Mengtan Liu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Yao Yin
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Can Wei
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Qinyun Cai
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Xiangxian Meng
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
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38
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Supplitt S, Karpinski P, Sasiadek M, Laczmanska I. Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine. Int J Mol Sci 2021; 22:1422. [PMID: 33572595 PMCID: PMC7866970 DOI: 10.3390/ijms22031422] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Over the last decades, transcriptome profiling emerged as one of the most powerful approaches in oncology, providing prognostic and predictive utility for cancer management. The development of novel technologies, such as revolutionary next-generation sequencing, enables the identification of cancer biomarkers, gene signatures, and their aberrant expression affecting oncogenesis, as well as the discovery of molecular targets for anticancer therapies. Transcriptomics contribute to a change in the holistic understanding of cancer, from histopathological and organic to molecular classifications, opening a more personalized perspective for tumor diagnostics and therapy. The further advancement on transcriptome profiling may allow standardization and cost reduction of its analysis, which will be the next step for transcriptomics to become a canon of contemporary cancer medicine.
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Affiliation(s)
- Stanislaw Supplitt
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
| | - Pawel Karpinski
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
- Laboratory of Genomics and Bioinformatics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Maria Sasiadek
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
| | - Izabela Laczmanska
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
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Jeevanandam J, Sabbih G, Tan KX, Danquah MK. Oncological Ligand-Target Binding Systems and Developmental Approaches for Cancer Theranostics. Mol Biotechnol 2021; 63:167-183. [PMID: 33423212 DOI: 10.1007/s12033-020-00296-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Targeted treatment of cancer hinges on the identification of specific intracellular molecular receptors on cancer cells to stimulate apoptosis for eventually inhibiting growth; the development of novel ligands to target biomarkers expressed by the cancer cells; and the creation of novel multifunctional carrier systems for targeted delivery of anticancer drugs to specific malignant sites. There are numerous receptors, antigens, and biomarkers that have been discovered as oncological targets (oncotargets) for cancer diagnosis and treatment applications. Oncotargets are critically important to navigate active anticancer drug ingredients to specific disease sites with no/minimal effect on surrounding normal cells. In silico techniques relating to genomics, proteomics, and bioinformatics have catalyzed the discovery of oncotargets for various cancer types. Effective oncotargeting requires high-affinity probes engineered for specific binding of receptors associated with the malignancy. Computational methods such as structural modeling and molecular dynamic (MD) simulations offer opportunities to structurally design novel ligands and optimize binding affinity for specific oncotargets. This article proposes a streamlined approach for the development of ligand-oncotarget bioaffinity systems via integrated structural modeling and MD simulations, making use of proteomics, genomic, and X-ray crystallographic resources, to support targeted diagnosis and treatment of cancers and tumors.
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Affiliation(s)
- Jaison Jeevanandam
- CQM-Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, 9020-105, Funchal, Portugal
| | - Godfred Sabbih
- Chemical Engineering Department, University of Tennessee, Chattanooga, TN, 37403, USA
| | - Kei X Tan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Michael K Danquah
- Chemical Engineering Department, University of Tennessee, Chattanooga, TN, 37403, USA.
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Dell'Olio F, Su J, Huser T, Sottile V, Cortés-Hernández LE, Alix-Panabières C. Photonic technologies for liquid biopsies: recent advances and open research challenges. LASER & PHOTONICS REVIEWS 2021; 15:2000255. [PMID: 35360260 PMCID: PMC8966629 DOI: 10.1002/lpor.202000255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The recent development of sophisticated techniques capable of detecting extremely low concentrations of circulating tumor biomarkers in accessible body fluids, such as blood or urine, could contribute to a paradigm shift in cancer diagnosis and treatment. By applying such techniques, clinicians can carry out liquid biopsies, providing information on tumor presence, evolution, and response to therapy. The implementation of biosensing platforms for liquid biopsies is particularly complex because this application domain demands high selectivity/specificity and challenging limit-of-detection (LoD) values. The interest in photonics as an enabling technology for liquid biopsies is growing owing to the well-known advantages of photonic biosensors over competing technologies in terms of compactness, immunity to external disturbance, and ultra-high spatial resolution. Some encouraging experimental results in the field of photonic devices and systems for liquid biopsy have already been achieved by using fluorescent labels and label-free techniques and by exploiting super-resolution microscopy, surface plasmon resonance, surface-enhanced Raman scattering, and whispering gallery mode resonators. This paper critically reviews the current state-of-the-art, starting from the requirements imposed by the detection of the most common circulating biomarkers. Open research challenges are considered together with competing technologies, and the most promising paths of improvement are discussed for future applications.
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Affiliation(s)
- Francesco Dell'Olio
- Department of Electrical and Information Engineering, Polytechnic University of Bari, 70125, Italy
| | - Judith Su
- Department of Biomedical Engineering, College of Optical Sciences, and BIO5 Institute, University of Arizona, 85721, USA
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Germany
| | - Virginie Sottile
- Department of Molecular Medicine, University of Pavia, 27100, Italy
| | | | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Center of Montpellier, 34093 CEDEX 5, France
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Zhu Y, Wang S, Xi X, Zhang M, Liu X, Tang W, Cai P, Xing S, Bao P, Jin Y, Zhao W, Chen Y, Zhao H, Jia X, Lu S, Lu Y, Chen L, Yin J, Lu ZJ. Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. Theranostics 2021; 11:181-193. [PMID: 33391469 PMCID: PMC7681086 DOI: 10.7150/thno.48206] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/06/2020] [Indexed: 12/11/2022] Open
Abstract
Rationale: Long extracellular RNAs (exRNAs) in plasma can be profiled by new sequencing technologies, even with low abundance. However, cancer-related exRNAs and their variations remain understudied. Methods: We investigated different variations (i.e. differential expression, alternative splicing, alternative polyadenylation, and differential editing) in diverse long exRNA species (e.g. long noncoding RNAs and circular RNAs) using 79 plasma exosomal RNA-seq (exoRNA-seq) datasets of multiple cancer types. We then integrated 53 exoRNA-seq datasets and 65 self-profiled cell-free RNA-seq (cfRNA-seq) datasets to identify recurrent variations in liver cancer patients. We further combined TCGA tissue RNA-seq datasets and validated biomarker candidates by RT-qPCR in an individual cohort of more than 100 plasma samples. Finally, we used machine learning models to identify a signature of 3 noncoding RNAs for the detection of liver cancer. Results: We found that different types of RNA variations identified from exoRNA-seq data were enriched in pathways related to tumorigenesis and metastasis, immune, and metabolism, suggesting that cancer signals can be detected from long exRNAs. Subsequently, we identified more than 100 recurrent variations in plasma from liver cancer patients by integrating exoRNA-seq and cfRNA-seq datasets. From these datasets, 5 significantly up-regulated long exRNAs were confirmed by TCGA data and validated by RT-qPCR in an independent cohort. When using machine learning models to combine two of these validated circular and structured RNAs (SNORD3B-1, circ-0080695) with a miRNA (miR-122) as a panel to classify liver cancer patients from healthy donors, the average AUROC of the cross-validation was 89.4%. The selected 3-RNA panel successfully detected 79.2% AFP-negative samples and 77.1% early-stage liver cancer samples in the testing and validation sets. Conclusions: Our study revealed that different types of RNA variations related to cancer can be detected in plasma and identified a 3-RNA detection panel for liver cancer, especially for AFP-negative and early-stage patients.
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Affiliation(s)
- Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Provincial Key Laboratory of Population Health and Aristogenics, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaochen Xi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minfeng Zhang
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai 200433, China
| | - Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weina Tang
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Peng Cai
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yunfan Jin
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weihao Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yinghui Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huanan Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaodong Jia
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Shanshan Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Yinying Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Lei Chen
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
- National Center for Liver Cancer, Shanghai 201805, China
| | - Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Hisey CL, Tomek P, Nursalim YNS, Chamley LW, Leung E. Towards establishing extracellular vesicle-associated RNAs as biomarkers for HER2+ breast cancer. F1000Res 2020; 9:1362. [PMID: 33447385 DOI: 10.12688/f1000research.27393.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 01/07/2023] Open
Abstract
Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs BIRC5 (Survivin) and YBX1, as well as long-noncoding RNAs HOTAIR, ZFAS1, and AGAP2-AS1 were detected in BT-474 EVs by quantitative RT-PCR. Bioinformatics meta-analyses showed that BIRC5 and HOTAIR RNAs were substantially upregulated in breast tumours compared to non-tumour breast tissue, warranting further studies to explore their usefulness as biomarkers in patient EV samples. We envision this effective procedure for obtaining large amounts of cancer-specific EVs will accelerate discovery of EV-associated RNA biomarkers for cancers including HER2+ breast cancer.
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Affiliation(s)
- Colin L Hisey
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
- Hub for Extracellular Vesicle Investigations, University of Auckland, Auckland, New Zealand
| | - Petr Tomek
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Yohanes N S Nursalim
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
| | - Lawrence W Chamley
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
- Hub for Extracellular Vesicle Investigations, University of Auckland, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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43
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Hisey CL, Tomek P, Nursalim YNS, Chamley LW, Leung E. Towards establishing extracellular vesicle-associated RNAs as biomarkers for HER2+ breast cancer. F1000Res 2020; 9:1362. [PMID: 33447385 PMCID: PMC7780337 DOI: 10.12688/f1000research.27393.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs
BIRC5 (Survivin) and
YBX1,
as well as long-noncoding RNAs
HOTAIR,
ZFAS1, and
AGAP2-AS1 were detected in BT-474 EVs by quantitative RT-PCR. Bioinformatics meta-analyses showed that
BIRC5 and
HOTAIR RNAs were substantially upregulated in breast tumours compared to non-tumour breast tissue, warranting further studies to explore their usefulness as biomarkers in patient EV samples. We envision this effective procedure for obtaining large amounts of cancer-specific EVs will accelerate discovery of EV-associated RNA biomarkers for cancers including HER2+ breast cancer.
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Affiliation(s)
- Colin L Hisey
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand.,Hub for Extracellular Vesicle Investigations, University of Auckland, Auckland, New Zealand
| | - Petr Tomek
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Yohanes N S Nursalim
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
| | - Lawrence W Chamley
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand.,Hub for Extracellular Vesicle Investigations, University of Auckland, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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You T, Song K, Guo W, Fu Y, Wang K, Zheng H, Yang J, Jin L, Qi L, Guo Z, Zhao W. A Qualitative Transcriptional Signature for Predicting CpG Island Methylator Phenotype Status of the Right-Sided Colon Cancer. Front Genet 2020; 11:971. [PMID: 33193579 PMCID: PMC7658404 DOI: 10.3389/fgene.2020.00971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/31/2020] [Indexed: 12/24/2022] Open
Abstract
A part of colorectal cancer which is characterized by simultaneous numerous hypermethylation CpG islands sites is defined as CpG island methylator phenotype (CIMP) status. Stage II and III CIMP−positive (CIMP+) right-sided colon cancer (RCC) patients have a better prognosis than CIMP−negative (CIMP−) RCC treated with surgery alone. However, there is no gold standard available in defining CIMP status. In this work, we selected the gene pairs whose relative expression orderings (REOs) were associated with the CIMP status, to develop a qualitative transcriptional signature to individually predict CIMP status for stage II and III RCC. Based on the REOs of gene pairs, a signature composed of 19 gene pairs was developed to predict the CIMP status of RCC through a feature selection process. A sample is predicted as CIMP+ when the gene expression orderings of at least 12 gene pairs vote for CIMP+; otherwise the CIMP−. The difference of prognosis between the predicted CIMP+ and CIMP− groups was more significantly different than the original CIMP status groups. There were more differential methylation and expression characteristics between the two predicted groups. The hierarchical clustering analysis showed that the signature could perform better for predicting CIMP status of RCC than current methods. In conclusion, the qualitative transcriptional signature for classifying CIMP status at the individualized level can predict outcome and guide therapy for RCC patients.
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Affiliation(s)
- Tianyi You
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Song
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenbing Guo
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yelin Fu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Wang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hailong Zheng
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Yang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liangliang Jin
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lishuang Qi
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zheng Guo
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory on Hematology, Fujian Medical University, Fuzhou, China
| | - Wenyuan Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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45
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Rashed WM, Kandeil MA, Mahmoud MO, Maher D, Ezzat S, Abdel-Rahman MH. MET canonical transcript expression is a predictive biomarker for chemo-sensitivity to MET-inhibitors in hepatocellular carcinoma cell lines. J Cancer Res Clin Oncol 2020; 147:167-175. [PMID: 32980960 DOI: 10.1007/s00432-020-03395-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022]
Abstract
PURPOSE Long interspersed nuclear element 1 (LINE-1 or L1) is a dominant non-long terminal repeat (non-LTR) retrotransposon in the human genome that has been implicated in the overexpression of MET. Both the canonical MET and L1-MET transcripts are considered to play a role in hepatocellular carcinoma (HCC) development. The aim of this study was to assess the utility of canonical MET, L1-MET, and MET protein expressions as predictive biomarkers for chemo-sensitivity to MET-inhibitors in HCC cell lines in vitro. Additionally, we assessed their expression in tumour tissues from Egyptian HCC patients. METHODS MET and L1-MET expressions were assessed by qRT-PCR in six liver cancer cell lines (SNU-387, SNU-475, SK-HEP-1, PLC/PRF/5, SNU-449 and SNU-423) and 47 HCC tumour tissues. MET protein expression was measured by western blot in cell lines and immunohistochemistry in the tumours. Cell proliferation assay was used to assess the effect of crizotinib and tivantinib on the six liver cancer cell lines in correlation with the expression of MET, L1-MET and MET. RESULTS The antitumor effect of crizotinib and tivantinib correlated with MET gene expression but not with L1-MET transcript or MET protein expressions. No significant difference was observed between HCC tumours and non-tumour samples in MET and L1-MET transcripts expression. There were no significant correlations between the 2-year overall survival rate and the MET, L1-MET transcripts and the MET protein expression. CONCLUSION MET RNA expression could be useful biomarker for tivantinib and crizotinib targeted therapy in HCC. The value of assessment of MET protein expression is limited.
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Affiliation(s)
- Wafaa M Rashed
- Department of Research, Children's Cancer Hospital, Egypt, Cairo, Egypt
| | - Mohamed A Kandeil
- Department of Biochemistry, Faculty of Veterinary Medicine, Beni-Suef University, Beni Suef, Egypt
| | - Mohamed O Mahmoud
- Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni Suef, Egypt
| | - Doha Maher
- Department of Pathology, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Sameera Ezzat
- Department of Epidemiology and Prevention Medicine, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Mohamed H Abdel-Rahman
- Department of Pathology, National Liver Institute, Menoufia University, Menoufia, Egypt.
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.
- Department of Ophthalmology, The Ohio State University, 400 W 12th Ave, Room 202 Wiseman Hall, Columbus, OH, 43210, USA.
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Moon J, Lim J, Lee S, Son HY, Rho HW, Kim H, Kang H, Jeong J, Lim EK, Jung J, Huh YM, Park HG, Kang T. Urinary exosomal mRNA detection using novel isothermal gene amplification method based on three-way junction. Biosens Bioelectron 2020; 167:112474. [PMID: 32798804 DOI: 10.1016/j.bios.2020.112474] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022]
Abstract
Exosomal messenger RNA (mRNA) has emerged as a valuable biomarker for liquid biopsy-based disease diagnosis and prognosis due to its stability in body fluids and its biological regulatory function. Here, we report a rapid one-step isothermal gene amplification reaction based on three-way junction (3WJ) formation and the successful detection of urinary exosomal mRNA from tumor-bearing mice. The 3WJ structure can be formed by the association of 3WJ probes (3WJ-template and 3WJ-primer) in the presence of target RNA. After 3WJ structure formation, the 3WJ primer is repeatedly extended and cleaved by a combination of DNA polymerase and nicking endonuclease, producing multiple signal primers. Subsequently, the signal primers promote a specially designed network reaction pathway to produce G-quadruplex probes under isothermal conditions. Finally, G-quadruplex structure produces highly enhanced fluorescence signal upon binding to thioflavin T. This method provides a detection limit of 1.23 pM (24.6 amol) with high selectivity for the target RNA. More importantly, this method can be useful for the sensing of various kinds of mRNA, including breast cancer cellular mRNA, breast cancer exosomal mRNA, and even urinary exosomal mRNA from breast cancer mice. We anticipate that the developed RNA detection assay can be used for various biomedical applications, such as disease diagnosis, prognosis, and treatment monitoring.
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Affiliation(s)
- Jeong Moon
- Bionanotechnology Research Center, KRIBB, Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daejeon, 34141, Republic of Korea
| | - Jaewoo Lim
- Bionanotechnology Research Center, KRIBB, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daejeon, 34141, Republic of Korea
| | - Hye Young Son
- Department of Radiology, College of Medicine, Yonsei University, Seoul, 03772, Republic of Korea; YUHS-KRIBB Medical Convergence Research Institute, Seoul, 03722, Republic of Korea
| | - Hyun Wook Rho
- Department of Radiology, College of Medicine, Yonsei University, Seoul, 03772, Republic of Korea
| | - Hongki Kim
- Bionanotechnology Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Hyunju Kang
- Bionanotechnology Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Jinyoung Jeong
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea; Environmental Disease Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, KRIBB, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, KRIBB, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University, Seoul, 03772, Republic of Korea; Severance Biomedical Science Institute, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daejeon, 34141, Republic of Korea.
| | - Taejoon Kang
- Bionanotechnology Research Center, KRIBB, Daejeon, 34141, Republic of Korea.
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Zhang R, Wang J, Liu B, Wang W, Fan X, Zheng B, Yuan Q, Xue M, Xu F, Guo P, Chen Y. Differentially expressed lncRNAs, miRNAs and mRNAs with associated ceRNA networks in a mouse model of myocardial ischemia/reperfusion injury. Mol Med Rep 2020; 22:2487-2495. [PMID: 32705277 PMCID: PMC7411395 DOI: 10.3892/mmr.2020.11300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
Non‑coding RNAs, including long non‑coding RNAs (lncRNAs) and microRNAs (miRNAs/miRs), have significant regulatory effects on a number of biological processes in myocardial ischemia/reperfusion (I/R) injury, including cell differentiation, proliferation and apoptosis. In the present study, the expression levels of lncRNAs, miRNAs and mRNAs were evaluated in a mouse model of myocardial I/R injury. The potential functions of these differentially expressed genes were then analyzed via Gene Ontology and pathway analyses. Additionally, the interactions between lncRNA‑miRNA‑mRNA were predicted by constructing a competing endogenous RNA regulatory network. It was found that 14,366 lncRNAs, 151 miRNAs and 9,377 mRNAs were differentially expressed in mice hearts after I/R compared with the Sham group (fold change >2; P<0.05). The results indicated that these differentially expressed genes were involved in multiple molecular functions, including 'guanosine diphosphate binding', 'RNA polymerase II carboxy‑terminal domain kinase activity', 'TATA‑binding protein‑class protein binding', 'nicotinamide adenine dinucleotide binding' and 'protein phosphatase type 2A regulator activity'. The interactions between lncRNA‑miRNA‑mRNA, including five lncRNAs, 38 miRNAs and 196 mRNAs, were predicted, specifically Gm12040‑mmu‑miR‑125a‑5p‑decapping mRNA 1B, Rpl7l1‑ps1‑mmu‑miR‑124‑3p‑G protein‑coupled receptor 146, Gm11407‑mmu‑miR‑190a‑5p‑homeobox and leucine zipper encoding (HOMEZ), 1600029O15Rik‑mmu‑miR‑132‑3p‑HOMEZ and AK155692‑mmu‑miR‑1224‑3p‑activating transcription factor 6β. Collectively, these findings provided novel insights for future research on lncRNAs, miRNAs and mRNAs in myocardial I/R injury.
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Affiliation(s)
- Rui Zhang
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Jiali Wang
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Baoshan Liu
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Wenjun Wang
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Xinhui Fan
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Boyuan Zheng
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Qiuhuan Yuan
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Mengyang Xue
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Feng Xu
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Ping Guo
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Yuguo Chen
- Department of Emergency Medicine, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
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Zhu L, Nazeri A, Pacia CP, Yue Y, Chen H. Focused ultrasound for safe and effective release of brain tumor biomarkers into the peripheral circulation. PLoS One 2020; 15:e0234182. [PMID: 32492056 PMCID: PMC7269259 DOI: 10.1371/journal.pone.0234182] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
The development of noninvasive approaches for brain tumor diagnosis and monitoring continues to be a major medical challenge. Although blood-based liquid biopsy has received considerable attention in various cancers, limited progress has been made for brain tumors, at least partly due to the hindrance of tumor biomarker release into the peripheral circulation by the blood-brain barrier. Focused ultrasound (FUS) combined with microbubbles induced BBB disruption has been established as a promising technique for noninvasive and localized brain drug delivery. Building on this established technique, we propose to develop FUS-enabled liquid biopsy technique (FUS-LBx) to enhance the release of brain tumor biomarkers (e.g., DNA, RNA, and proteins) into the circulation. The objective of this study was to demonstrate that FUS-LBx could sufficiently increase plasma levels of brain tumor biomarkers without causing hemorrhage in the brain. Mice with orthotopic implantation of enhanced green fluorescent protein (eGFP)-transfected murine glioma cells were treated using magnetic resonance (MR)-guided FUS system in the presence of systemically injected microbubbles at three peak negative pressure levels (0.59, 1.29, and 1.58 MPa). Plasma eGFP mRNA levels were quantified with the quantitative polymerase chain reaction (qPCR). Contrast-enhanced MR images were acquired before and after the FUS sonication. FUS at 0.59 MPa resulted in an increased plasma eGFP mRNA level, comparable to those at higher acoustic pressures (1.29 MPa and 1.58 MPa). Microhemorrhage density associated with FUS at 0.59 MPa was significantly lower than that at higher acoustic pressures and not significantly different from the control group. MRI analysis revealed that post-sonication intratumoral and peritumoral hyperenhancement had strong correlations with the level of FUS-induced biomarker release and the extent of hemorrhage. This study suggests that FUS-LBx could be a safe and effective brain-tumor biomarker release technique, and MRI could be used to develop image-guided FUS-LBx.
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Affiliation(s)
- Lifei Zhu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Arash Nazeri
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Christopher Pham Pacia
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Yimei Yue
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Hong Chen
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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49
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Ayakannu T, Taylor AH, Konje JC. Selection of Endogenous Control Reference Genes for Studies on Type 1 or Type 2 Endometrial Cancer. Sci Rep 2020; 10:8468. [PMID: 32439920 PMCID: PMC7242460 DOI: 10.1038/s41598-020-64663-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/02/2020] [Indexed: 02/02/2023] Open
Abstract
A panel of 32 candidate reference genes was used to identify the most stable genes for gene normalisation in quantitative RT-PCR studies using endometrial biopsies obtained from women with endometrial cancer (type 1 or type 2) and without cancer (controls). RNA from the biopsies was isolated, examined for purity and quality, and then reverse transcribed into cDNA before being subjected to real-time qRT-PCR analysis in triplicate within the TaqMan gene Expression Assay kit. The most 'stable' endogenous control genes were then identified using the geNorm qbase + 2 and NormFinder software packages. PSMC4, PUM1 and IPO8 were identified as the best reference genes combination for type 1 endometrial cancer (grades 1, 2 and 3), whereas for type 2 endometrial cancer (serous and carcinosarcoma), UBC, MRPL19, PGK1 and PPIA were the best reference genes combination. We conclude that the use of these normaliser combinations should provide accurate interpretation of gene expression at the transcript level in endometrial cancer studies especially for types 1 and 2 cancers.
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Affiliation(s)
- Thangesweran Ayakannu
- Faculty of Health and Life Sciences, University of Liverpool, Thompson Yates Brownlow Hill, Liverpool, L69 3GB, UK.
- Reproductive Sciences Section, Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, UK.
- Gynaecology Oncology Cancer Centre, Liverpool Women's NHS Foundation Trust, Liverpool Women's Hospital, Liverpool, UK.
| | - Anthony H Taylor
- Faculty of Health and Life Sciences, University of Liverpool, Thompson Yates Brownlow Hill, Liverpool, L69 3GB, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, Leicestershire, UK
| | - Justin C Konje
- Faculty of Health and Life Sciences, University of Liverpool, Thompson Yates Brownlow Hill, Liverpool, L69 3GB, UK
- Department of Obstetrics and Gynaecology, Sidra Medicine, Women's Wellness and Research Center, HMC, Doha, Qatar
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50
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Ishikawa T, Haino A, Seki M, Kurihara T, Hirose T, Imai Y, Ishiguro T, Chou T, Toshima M, Terada H, Nashimoto M. The 31-nucleotide Y4-RNA fragment in plasma is a potential novel biomarker. Noncoding RNA Res 2020; 5:37-40. [PMID: 32206739 PMCID: PMC7078377 DOI: 10.1016/j.ncrna.2019.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/13/2019] [Accepted: 12/14/2019] [Indexed: 11/17/2022] Open
Abstract
The 31- and 32-nt 5′-fragment of Y4-RNA (Y4RNAfr) exists abundantly in human peripheral blood plasma. Although physiological roles of the plasma Y4RNAfr are not well established, its potential utility as a diagnostic/prognostic marker for acute coronary syndrome was suggested. In this paper, to establish a normal range of the Y4RNAfr level in plasma, we measured plasma Y4RNAfr levels of 40 healthy persons using the method we have developed, and compared them with other blood test data. From the obtained data, we tentatively regarded <0.1 fmol/ng as normal for the Y4RNAfr level in peripheral blood plasma. And the white blood cell count (WBC) and the C-reactive protein (CRP) level showed moderate positive correlations with the Y4RNAfr level, suggesting that Y4RNAfr could be a potential novel inflammatory marker. We also measured the Y4RNAfr level in peripheral blood plasma from four multiple myeloma patients. The plasma Y4RNAfr level was abnormal in all four myeloma patients, and the levels for two patients were far beyond the normal level. The WBC for each patient was normal and the CRP levels for two patients were normal. These observations together suggest that a high level of Y4RNAfr in peripheral blood plasma and a normal WBC could be indicative of multiple myeloma.
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Affiliation(s)
- Tatsuya Ishikawa
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Arisa Haino
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Taro Kurihara
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Takayuki Hirose
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Yosuke Imai
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Takuro Ishiguro
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Takaaki Chou
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Muneatsu Toshima
- Niitsu Medical Center Hospital, Niigata, Niigata, 956-0025, Japan
| | - Hiroshi Terada
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
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