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Reese KL, Pantel K, Smit DJ. Multibiomarker panels in liquid biopsy for early detection of pancreatic cancer - a comprehensive review. J Exp Clin Cancer Res 2024; 43:250. [PMID: 39218911 PMCID: PMC11367781 DOI: 10.1186/s13046-024-03166-w] [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: 03/18/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is frequently detected in late stages, which leads to limited therapeutic options and a dismal overall survival rate. To date, no robust method for the detection of early-stage PDAC that can be used for targeted screening approaches is available. Liquid biopsy allows the minimally invasive collection of body fluids (typically peripheral blood) and the subsequent analysis of circulating tumor cells or tumor-associated molecules such as nucleic acids, proteins, or metabolites that may be useful for the early diagnosis of PDAC. Single biomarkers may lack sensitivity and/or specificity to reliably detect PDAC, while combinations of these circulating biomarkers in multimarker panels may improve the sensitivity and specificity of blood test-based diagnosis. In this narrative review, we present an overview of different liquid biopsy biomarkers for the early diagnosis of PDAC and discuss the validity of multimarker panels.
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Affiliation(s)
- Kim-Lea Reese
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | - Klaus Pantel
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany.
| | - Daniel J Smit
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany.
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Chung J, Xiao S, Gao Y, Soung YH. Recent Technologies towards Diagnostic and Therapeutic Applications of Circulating Nucleic Acids in Colorectal Cancers. Int J Mol Sci 2024; 25:8703. [PMID: 39201393 PMCID: PMC11354501 DOI: 10.3390/ijms25168703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 09/02/2024] Open
Abstract
Liquid biopsy has emerged as a promising noninvasive approach for colorectal cancer (CRC) management. This review focuses on technologies detecting circulating nucleic acids, specifically circulating tumor DNA (ctDNA) and circulating RNA (cfRNA), as CRC biomarkers. Recent advancements in molecular technologies have enabled sensitive and specific detection of tumor-derived genetic material in bodily fluids. These include quantitative real-time PCR, digital PCR, next-generation sequencing (NGS), and emerging nanotechnology-based methods. For ctDNA analysis, techniques such as BEAMing and droplet digital PCR offer high sensitivity in detecting rare mutant alleles, while NGS approaches provide comprehensive genomic profiling. cfRNA detection primarily utilizes qRT-PCR arrays, microarray platforms, and RNA sequencing for profiling circulating microRNAs and discovering novel RNA biomarkers. These technologies show potential in early CRC detection, treatment response monitoring, minimal residual disease assessment, and tumor evolution tracking. However, challenges remain in standardizing procedures, optimizing detection limits, and establishing clinical utility across disease stages. This review summarizes current circulating nucleic acid detection technologies, their CRC applications, and discusses future directions for clinical implementation.
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Affiliation(s)
| | | | | | - Young Hwa Soung
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (J.C.); (S.X.); (Y.G.)
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3
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Rackles E, Zaccheroni E, Lopez PH, Faletti S, Bene MD, DiMeco F, Pelicci G, Falcon‐Perez JM. Increased levels of circulating cell-free double-stranded nucleic acids in the plasma of glioblastoma patients. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e168. [PMID: 39100684 PMCID: PMC11294885 DOI: 10.1002/jex2.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
Circulating cell-free nucleic acids are considered a promising source of biomarkers for diseases and cancer. Liquid biopsy biomarkers for brain tumours represent a major, still unmet, clinical need. In plasma, nucleic acids can be free or be associated with extracellular vesicles (EVs). Here we report an easy and reproducible method to analyse cell-free nucleic acids in plasma and EVs by conventional flow cytometry easy to translate into the clinics. Nucleic acids associated with the EVs or present in plasma samples are stained by Pyronin Y, which is a fluorescent dye that is preferably binding double-stranded nucleic acids. Fluorescent staining of EVs isolated from cell-conditioned media is suitable for DNA and RNA detection by flow cytometry. The nucleic acids are partially protected from degradation by the EVs' membrane. Additionally, DNA and RNA can be stained in plasma samples and plasma-derived EVs. Remarkably, analysis of plasma from patients and healthy individuals reveals a difference in their nucleic acid profiles. Taken together, our results indicate that the proposed methodology, which is based on conventional direct flow cytometry, is a promising easy tool for plasma nucleic acid analysis.
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Affiliation(s)
- Elisabeth Rackles
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)DerioSpain
| | - Elena Zaccheroni
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)IRCCSMilanItaly
| | - Patricia Hernandez Lopez
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)DerioSpain
| | - Stefania Faletti
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)IRCCSMilanItaly
| | - Massimiliano Del Bene
- Department of NeurosurgeryFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Francesco DiMeco
- Department of NeurosurgeryFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
- Department of Pathophysiology and TransplantationUniversity of MilanMilanItaly
- Department of Neurological SurgeryJohns Hopkins Medical SchoolBaltimoreMarylandUSA
| | - Giuliana Pelicci
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)IRCCSMilanItaly
- Department of Translational MedicineUniversity of Piemonte OrientaleNovaraItaly
| | - Juan M Falcon‐Perez
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)DerioSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd)MadridSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
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4
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Leo M, Schmitt LI, Mairinger F, Roos A, Hansmann C, Hezel S, Skuljec J, Pul R, Schara-Schmidt U, Kleinschnitz C, Hagenacker T. Analysis of Free Circulating Messenger Ribonucleic Acids in Serum Samples from Late-Onset Spinal Muscular Atrophy Patients Using nCounter NanoString Technology. Cells 2023; 12:2374. [PMID: 37830588 PMCID: PMC10572204 DOI: 10.3390/cells12192374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/11/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
5q-related Spinal muscular atrophy (SMA) is a hereditary multi-systemic disorder leading to progressive muscle atrophy and weakness caused by the degeneration of spinal motor neurons (MNs) in the ventral horn of the spinal cord. Three SMN-enhancing drugs for SMA treatment are available. However, even if these drugs are highly effective when administrated early, several patients do not benefit sufficiently or remain non-responders, e.g., adults suffering from late-onset SMA and starting their therapy at advanced disease stages characterized by long-standing irreversible loss of MNs. Therefore, it is important to identify additional molecular targets to expand therapeutic strategies for SMA treatment and establish prognostic biomarkers related to the treatment response. Using high-throughput nCounter NanoString technology, we analyzed serum samples of late-onset SMA type 2 and type 3 patients before and six months under nusinersen treatment. Four genes (AMIGO1, CA2, CCL5, TLR2) were significantly altered in their transcript counts in the serum of patients, where differential expression patterns were dependent on SMA subtype and treatment response, assessed with outcome scales. No changes in gene expression were observed six months after nusinersen treatment, compared to healthy controls. These alterations in the transcription of four genes in SMA patients qualified those genes as potential SMN-independent therapeutic targets to complement current SMN-enhancing therapies.
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Affiliation(s)
- Markus Leo
- Department of Neurology, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (L.-I.S.); (S.H.); (J.S.); (R.P.); (C.K.); (T.H.)
| | - Linda-Isabell Schmitt
- Department of Neurology, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (L.-I.S.); (S.H.); (J.S.); (R.P.); (C.K.); (T.H.)
| | - Fabian Mairinger
- Institute for Pathology, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany;
| | - Andreas Roos
- Department of Pediatric Neurology, Center for Neuromuscular Disorders, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (A.R.); (U.S.-S.)
| | - Christina Hansmann
- Department of Neurology, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (L.-I.S.); (S.H.); (J.S.); (R.P.); (C.K.); (T.H.)
| | - Stefanie Hezel
- Department of Neurology, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (L.-I.S.); (S.H.); (J.S.); (R.P.); (C.K.); (T.H.)
| | - Jelena Skuljec
- Department of Neurology, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (L.-I.S.); (S.H.); (J.S.); (R.P.); (C.K.); (T.H.)
| | - Refik Pul
- Department of Neurology, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (L.-I.S.); (S.H.); (J.S.); (R.P.); (C.K.); (T.H.)
| | - Ulrike Schara-Schmidt
- Department of Pediatric Neurology, Center for Neuromuscular Disorders, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (A.R.); (U.S.-S.)
| | - Christoph Kleinschnitz
- Department of Neurology, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (L.-I.S.); (S.H.); (J.S.); (R.P.); (C.K.); (T.H.)
| | - Tim Hagenacker
- Department of Neurology, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany; (L.-I.S.); (S.H.); (J.S.); (R.P.); (C.K.); (T.H.)
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Sequeira JP, Barros-Silva D, Ferreira-Torre P, Salta S, Braga I, Carvalho J, Freitas R, Henrique R, Jerónimo C. OncoUroMiR: Circulating miRNAs for Detection and Discrimination of the Main Urological Cancers Using a ddPCR-Based Approach. Int J Mol Sci 2023; 24:13890. [PMID: 37762193 PMCID: PMC10531069 DOI: 10.3390/ijms241813890] [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: 08/14/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The three most common genitourinary malignancies (prostate/kidney/bladder cancers) constitute a substantial proportion of all cancer cases, mainly in the elderly population. Early detection is key to maximizing the patients' survival, but the lack of highly accurate biomarkers that might be used through non-/minimally invasive methods has impaired progress in this domain. Herein, we sought to develop a minimally invasive test to detect and discriminate among those urological cancers based on miRNAs assessment through ddPCR. Plasma samples from 268 patients with renal cell (RCC; n = 119), bladder (BlCa; n = 73), and prostate (PCa; n = 76) carcinomas (UroCancer group), and 74 healthy donors were selected. Hsa-miR-126-3p, hsa-miR-141-3p, hsa-miR-153-5p, hsa-miR-155-5p, hsa-miR-182-5p, hsa-miR-205-5p, and hsa-miR-375-3p levels were assessed. UroCancer cases displayed significantly different circulating hsa-miR-182-5p/hsa-miR-375-3p levels compared to healthy donors. Importantly, the hsa-miR-155-5p/hsa-miR-375-3p panel detected RCC with a high specificity (80.54%) and accuracy (66.04%). Furthermore, the hsa-miR-126-3p/hsa-miR-375-3p panel identified BlCa with a 94.87% specificity and 76.45% NPV whereas higher hsa-miR-126-3p levels were found in PCa patients. We concluded that plasma-derived miRNAs can identify and discriminate among the main genitourinary cancers, with high analytical performance. Although validation in a larger cohort is mandatory, these findings demonstrate that circulating miRNA assessment by ddPCR might provide a new approach for early detection and risk stratification of the most common urological cancers.
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Affiliation(s)
- José Pedro Sequeira
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Doctoral Programme in Biomedical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
| | - Patrícia Ferreira-Torre
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
| | - Sofia Salta
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Doctoral Programme in Molecular Pathology and Genetics, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Isaac Braga
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Urology & Urology Clinics, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Programme in Medical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - João Carvalho
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Urology & Urology Clinics, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Programme in Medical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Freitas
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Urology & Urology Clinics, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Programme in Medical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS–School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS–School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
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Kan CM, Pei XM, Yeung MHY, Jin N, Ng SSM, Tsang HF, Cho WCS, Yim AKY, Yu ACS, Wong SCC. Exploring the Role of Circulating Cell-Free RNA in the Development of Colorectal Cancer. Int J Mol Sci 2023; 24:11026. [PMID: 37446204 DOI: 10.3390/ijms241311026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/25/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
Circulating tumor RNA (ctRNA) has recently emerged as a novel and attractive liquid biomarker. CtRNA is capable of providing important information about the expression of a variety of target genes noninvasively, without the need for biopsies, through the use of circulating RNA sequencing. The overexpression of cancer-specific transcripts increases the tumor-derived RNA signal, which overcomes limitations due to low quantities of circulating tumor DNA (ctDNA). The purpose of this work is to present an up-to-date review of current knowledge regarding ctRNAs and their status as biomarkers to address the diagnosis, prognosis, prediction, and drug resistance of colorectal cancer. The final section of the article discusses the practical aspects involved in analyzing plasma ctRNA, including storage and isolation, detection technologies, and their limitations in clinical applications.
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Affiliation(s)
- Chau-Ming Kan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Martin Ho Yin Yeung
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Nana Jin
- Codex Genetics Limited, Shatin, Hong Kong SAR, China
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong SAR, China
| | | | | | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
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Liu M, Zhang Z, Zhang W, Liu SM. Advances in biomarker discovery using circulating cell-free DNA for early detection of hepatocellular carcinoma. WIREs Mech Dis 2023; 15:e1598. [PMID: 36697374 PMCID: PMC10176863 DOI: 10.1002/wsbm.1598] [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: 08/18/2022] [Revised: 10/21/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023]
Abstract
The past several decades have witnessed unprecedented progress in basic and clinical cancer research, and our understanding of the molecular mechanisms and pathogenesis of cancers have been greatly improved. More recently, with the availability of high-throughput sequencing and profiling platforms as well as sophisticated analytical tools and high-performance computing capacity, there have been tremendous advances in the development of diagnostic approaches in clinical oncology, especially the discovery of novel biomarkers for cancer early detection. Although tissue biopsy-based pathology has been the "gold standard" for cancer diagnosis, notable limitations such as the risk due to invasiveness and the bias due to intra-tumoral heterogeneity have limited its broader applications in oncology (e.g., screening, regular disease monitoring). Liquid biopsy analysis that exploits the genetic and epigenetic information contained in DNA/RNA materials from body fluids, particularly circulating cell-free DNA (cfDNA) in the blood, has been an intriguing alternative approach because of advantageous features such as sampling convenience and minimal invasiveness. Taking advantage of innovative enabling technologies, cfDNA has been demonstrated for its clinical potential in cancer early detection, including hepatocellular carcinoma (HCC), the most common liver cancer that causes serious healthcare burden globally. Hereby, we reviewed the current advances in cfDNA-based approaches for cancer biomarker discovery, with a focus on recent findings of cfDNA-based early detection of HCC. Future clinical investigations and trials are warranted to further validate these approaches for early detection of HCC, which will contribute to more effective prevention, control, and intervention strategies with the ultimate goal of reducing HCC-associated mortality. This article is categorized under: Cancer > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Mingjun Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, China
- Department of Clinical Laboratory, Wuhan Third Hospital and Tongren Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Institute of Precision Medicine, Jining Medical University, Jining, Shandong Province, China
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, China
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8
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Trier Maansson C, Meldgaard P, Stougaard M, Nielsen AL, Sorensen BS. Cell-free chromatin immunoprecipitation can determine tumor gene expression in lung cancer patients. Mol Oncol 2023; 17:722-736. [PMID: 36825535 PMCID: PMC10158780 DOI: 10.1002/1878-0261.13394] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/03/2023] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Cell-free DNA (cfDNA) in blood plasma can be bound to nucleosomes that contain post-translational modifications representing the epigenetic profile of the cell of origin. This includes histone H3 lysine 36 trimethylation (H3K36me3), a marker of active transcription. We hypothesised that cell-free chromatin immunoprecipitation (cfChIP) of H3K36me3-modified nucleosomes present in blood plasma can delineate tumour gene expression levels. H3K36me3 cfChIP followed by targeted NGS (cfChIP-seq) was performed on blood plasma samples from non-small-cell lung cancer (NSCLC) patients (NSCLC, n = 8), small-cell lung cancer (SCLC) patients (SCLC, n = 4) and healthy controls (n = 4). H3K36me3 cfChIP-seq demonstrated increased enrichment of mutated alleles compared with normal alleles in plasma from patients with known somatic cancer mutations. Additionally, genes identified to be differentially expressed in SCLC and NSCLC tumours had concordant H3K36me3 cfChIP enrichment profiles in NSCLC (sensitivity = 0.80) and SCLC blood plasma (sensitivity = 0.86). Findings here expand the utility of cfDNA in liquid biopsies to characterise treatment resistance, cancer subtyping and disease progression.
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Affiliation(s)
- Christoffer Trier Maansson
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
- Department of Biomedicine, Aarhus University, Denmark
| | - Peter Meldgaard
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Denmark
- Department of Oncology, Aarhus University Hospital, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, Denmark
- Department of Pathology, Aarhus University Hospital, Denmark
| | | | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
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Jin N, Kan CM, Pei XM, Cheung WL, Ng SSM, Wong HT, Cheng HYL, Leung WW, Wong YN, Tsang HF, Chan AKC, Wong YKE, Cho WCS, Chan JKC, Tai WCS, Chan TF, Wong SCC, Yim AKY, Yu ACS. Cell-free circulating tumor RNAs in plasma as the potential prognostic biomarkers in colorectal cancer. Front Oncol 2023; 13:1134445. [PMID: 37091184 PMCID: PMC10115432 DOI: 10.3389/fonc.2023.1134445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/24/2023] [Indexed: 04/09/2023] Open
Abstract
BackgroundCell free RNA (cfRNA) contains transcript fragments from multiple cell types, making it useful for cancer detection in clinical settings. However, the pathophysiological origins of cfRNAs in plasma from colorectal cancer (CRC) patients remain unclear.MethodsTo identify the tissue-specific contributions of cfRNAs transcriptomic profile, we used a published single-cell transcriptomics profile to deconvolute cell type abundance among paired plasma samples from CRC patients who underwent tumor-ablative surgery. We further validated the differentially expressed cfRNAs in 5 pairs of CRC tumor samples and adjacent tissue samples as well as 3 additional CRC tumor samples using RNA-sequencing.ResultsThe transcriptomic component from intestinal secretory cells was significantly decreased in the in-house post-surgical cfRNA. The HPGD, PACS1, and TDP2 expression was consistent across cfRNA and tissue samples. Using the Cancer Genome Atlas (TCGA) CRC datasets, we were able to classify the patients into two groups with significantly different survival outcomes.ConclusionsThe three-gene signature holds promise in applying minimal residual disease (MRD) testing, which involves profiling remnants of cancer cells after or during treatment. Biomarkers identified in the present study need to be validated in a larger cohort of samples in order to ascertain their possible use in early diagnosis of CRC.
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Affiliation(s)
- Nana Jin
- R&D, Codex Genetics Limited, Hong Kong, Hong Kong SAR, China
| | - Chau-Ming Kan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | - Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | - Wing Lam Cheung
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Heong Ting Wong
- Department of Pathology, Kiang Wu Hospital, Macau, Macau SAR, China
| | - Hennie Yuk-Lin Cheng
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | - Wing Wa Leung
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yee Ni Wong
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | | | - Yin Kwan Evelyn Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, Hong Kong SAR, China
| | | | - William Chi Shing Tai
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
- *Correspondence: Allen Chi-Shing Yu, ; Aldrin Kay-Yuen Yim, ; Sze Chuen Cesar Wong,
| | - Aldrin Kay-Yuen Yim
- R&D, Codex Genetics Limited, Hong Kong, Hong Kong SAR, China
- *Correspondence: Allen Chi-Shing Yu, ; Aldrin Kay-Yuen Yim, ; Sze Chuen Cesar Wong,
| | - Allen Chi-Shing Yu
- R&D, Codex Genetics Limited, Hong Kong, Hong Kong SAR, China
- *Correspondence: Allen Chi-Shing Yu, ; Aldrin Kay-Yuen Yim, ; Sze Chuen Cesar Wong,
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10
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Chaddha M, Rai H, Gupta R, Thakral D. Integrated analysis of circulating cell free nucleic acids for cancer genotyping and immune phenotyping of tumor microenvironment. Front Genet 2023; 14:1138625. [PMID: 37091783 PMCID: PMC10117686 DOI: 10.3389/fgene.2023.1138625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/15/2023] [Indexed: 04/25/2023] Open
Abstract
The circulating cell-free nucleic acids (ccfNAs) consist of a heterogenous cocktail of both single (ssNA) and double-stranded (dsNA) nucleic acids. These ccfNAs are secreted into the blood circulation by both healthy and malignant cells via various mechanisms including apoptosis, necrosis, and active secretion. The major source of ccfNAs are the cells of hematopoietic system under healthy conditions. These ccfNAs include fragmented circulating cell free DNA (ccfDNA), coding or messenger RNA (mRNA), long non-coding RNA (lncRNA), microRNA (miRNA), and mitochondrial DNA/RNA (mtDNA and mtRNA), that serve as prospective biomarkers in assessment of various clinical conditions. For, e.g., free fetal DNA and RNA migrate into the maternal plasma, whereas circulating tumor DNA (ctDNA) has clinical relevance in diagnostic, prognostic, therapeutic targeting, and disease progression monitoring to improve precision medicine in cancer. The epigenetic modifications of ccfDNA as well as circulating cell-free RNA (ccfRNA) such as miRNA and lncRNA show disease-related variations and hold potential as epigenetic biomarkers. The messenger RNA present in the circulation or the circulating cell free mRNA (ccf-mRNA) and long non-coding RNA (ccf-lncRNA) have gradually become substantial in liquid biopsy by acting as effective biomarkers to assess various aspects of disease diagnosis and prognosis. Conversely, the simultaneous characterization of coding and non-coding RNAs in human biofluids still poses a significant hurdle. Moreover, a comprehensive assessment of ccfRNA that may reflect the tumor microenvironment is being explored. In this review, we focus on the novel approaches for exploring ccfDNA and ccfRNAs, specifically ccf-mRNA as biomarkers in clinical diagnosis and prognosis of cancer. Integrating the detection of circulating tumor DNA (ctDNA) for cancer genotyping in conjunction with ccfRNA both quantitatively and qualitatively, may potentially hold immense promise towards precision medicine. The current challenges and future directions in deciphering the complexity of cancer networks based on the dynamic state of ccfNAs will be discussed.
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Affiliation(s)
| | | | - Ritu Gupta
- *Correspondence: Deepshi Thakral, ; Ritu Gupta,
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11
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Feng F, Zhong YX, Huang JH, Lin FX, Zhao PP, Mai Y, Wei W, Zhu HC, Xu ZP. Identifying stage-associated hub genes in bladder cancer via weighted gene co-expression network and robust rank aggregation analyses. Medicine (Baltimore) 2022; 101:e32318. [PMID: 36595851 PMCID: PMC9794320 DOI: 10.1097/md.0000000000032318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Bladder cancer (BC) is among the most frequent cancers globally. Although substantial efforts have been put to understand its pathogenesis, its underlying molecular mechanisms have not been fully elucidated. METHODS The robust rank aggregation approach was adopted to integrate 4 eligible bladder urothelial carcinoma microarray datasets from the Gene Expression Omnibus. Differentially expressed gene sets were identified between tumor samples and equivalent healthy samples. We constructed gene co-expression networks using weighted gene co-expression network to explore the alleged relationship between BC clinical characteristics and gene sets, as well as to identify hub genes. We also incorporated the weighted gene co-expression network and robust rank aggregation to screen differentially expressed genes. RESULTS CDH11, COL6A3, EDNRA, and SERPINF1 were selected from the key module and validated. Based on the results, significant downregulation of the hub genes occurred during the early stages of BC. Moreover, receiver operating characteristics curves and Kaplan-Meier plots showed that the genes exhibited favorable diagnostic and prognostic value for BC. Based on gene set enrichment analysis for single hub gene, all the genes were closely linked to BC cell proliferation. CONCLUSIONS These results offer unique insight into the pathogenesis of BC and recognize CDH11, COL6A3, EDNRA, and SERPINF1 as potential biomarkers with diagnostic and prognostic roles in BC.
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Affiliation(s)
- Fu Feng
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Yu-Xiang Zhong
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Jian-Hua Huang
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Fu-Xiang Lin
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Peng-Peng Zhao
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Yuan Mai
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Wei Wei
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Hua-Cai Zhu
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Zhan-Ping Xu
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
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12
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Wienert B, Cromer MK. CRISPR nuclease off-target activity and mitigation strategies. Front Genome Ed 2022; 4:1050507. [PMID: 36439866 PMCID: PMC9685173 DOI: 10.3389/fgeed.2022.1050507] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
The discovery of CRISPR has allowed site-specific genomic modification to become a reality and this technology is now being applied in a number of human clinical trials. While this technology has demonstrated impressive efficacy in the clinic to date, there remains the potential for unintended on- and off-target effects of CRISPR nuclease activity. A variety of in silico-based prediction tools and empirically derived experimental methods have been developed to identify the most common unintended effect-small insertions and deletions at genomic sites with homology to the guide RNA. However, large-scale aberrations have recently been reported such as translocations, inversions, deletions, and even chromothripsis. These are more difficult to detect using current workflows indicating a major unmet need in the field. In this review we summarize potential sequencing-based solutions that may be able to detect these large-scale effects even at low frequencies of occurrence. In addition, many of the current clinical trials using CRISPR involve ex vivo isolation of a patient's own stem cells, modification, and re-transplantation. However, there is growing interest in direct, in vivo delivery of genome editing tools. While this strategy has the potential to address disease in cell types that are not amenable to ex vivo manipulation, in vivo editing has only one desired outcome-on-target editing in the cell type of interest. CRISPR activity in unintended cell types (both on- and off-target) is therefore a major safety as well as ethical concern in tissues that could enable germline transmission. In this review, we have summarized the strengths and weaknesses of current editing and delivery tools and potential improvements to off-target and off-tissue CRISPR activity detection. We have also outlined potential mitigation strategies that will ensure that the safety of CRISPR keeps pace with efficacy, a necessary requirement if this technology is to realize its full translational potential.
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Affiliation(s)
- Beeke Wienert
- Graphite Bio, Inc., South San Francisco, CA, United States
| | - M. Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
- Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA, United States
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13
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Gray ER, Mordaka JM, Christoforou ER, von Bargen K, Potts ND, Xyrafaki C, Silva AL, Stolarek-Januszkiewicz M, Anton K, Powalowska PK, Andreazza S, Tomassini A, Palmer RN, Cooke A, Osborne RJ, Balmforth BW. Ultra-sensitive molecular detection of gene fusions from RNA using ASPYRE. BMC Med Genomics 2022; 15:215. [PMID: 36224552 PMCID: PMC9555097 DOI: 10.1186/s12920-022-01363-0] [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: 07/12/2022] [Accepted: 09/23/2022] [Indexed: 12/04/2022] Open
Abstract
Background RNA is a critical analyte for unambiguous detection of actionable mutations used to guide treatment decisions in oncology. Currently available methods for gene fusion detection include molecular or antibody-based assays, which suffer from either being limited to single-gene targeting, lack of sensitivity, or long turnaround time. The sensitivity and predictive value of next generation sequencing DNA-based assays to detect fusions by sequencing intronic regions is variable, due to the extensive size of introns. The required depth of sequencing and input nucleic acid required can be prohibitive; in addition it is not certain that predicted gene fusions are actually expressed. Results Herein we describe a method based on pyrophosphorolysis to include detection of gene fusions from RNA, with identical assay steps and conditions to detect somatic mutations in DNA [1], permitting concurrent assessment of DNA and RNA in a single instrument run. Conclusion The limit of detection was under 6 molecules/ 6 µL target volume. The workflow and instrumentation required are akin to PCR assays, and the entire assay from extracted nucleic acid to sample analysis can be completed within a single day. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01363-0.
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Affiliation(s)
- Eleanor R Gray
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Justyna M Mordaka
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | | | - Kristine von Bargen
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Nicola D Potts
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Christina Xyrafaki
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Ana-Luisa Silva
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | | | - Katarzyna Anton
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Paulina K Powalowska
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Simonetta Andreazza
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Alessandro Tomassini
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Rebecca N Palmer
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Aishling Cooke
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Robert J Osborne
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Barnaby W Balmforth
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England.
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14
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Yonar D, Severcan M, Gurbanov R, Sandal A, Yilmaz U, Emri S, Severcan F. Rapid diagnosis of malignant pleural mesothelioma and its discrimination from lung cancer and benign exudative effusions using blood serum. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166473. [PMID: 35753541 DOI: 10.1016/j.bbadis.2022.166473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 02/01/2023]
Abstract
Malignant pleural mesothelioma (MPM), an aggressive cancer associated with exposure to fibrous minerals, can only be diagnosed in the advanced stage because its early symptoms are also connected with other respiratory diseases. Hence, understanding the molecular mechanism and the discrimination of MPM from other lung diseases at an early stage is important to apply effective treatment strategies and for the increase in survival rate. This study aims to develop a new approach for characterization and diagnosis of MPM among lung diseases from serum by Fourier transform infrared spectroscopy (FTIR) coupled with multivariate analysis. The detailed spectral characterization studies indicated the changes in lipid biosynthesis and nucleic acids levels in the malignant serum samples. Furthermore, the results showed that healthy, benign exudative effusion, lung cancer, and MPM groups were successfully separated from each other by applying principal component analysis (PCA), support vector machine (SVM), and especially linear discriminant analysis (LDA) to infrared spectra.
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Affiliation(s)
- Dilek Yonar
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Yuksek Ihtisas University, Faculty of Medicine, Biophysics Department, Ankara, Turkey
| | - Mete Severcan
- Middle East Technical University, Department of Electrical and Electronics Engineering, Ankara, Turkey
| | - Rafig Gurbanov
- Bilecik Seyh Edebali University, Department of Bioengineering, Bilecik, Turkey
| | - Abdulsamet Sandal
- Hacettepe University, Faculty of Medicine, Department of Chest Diseases, Ankara, Turkey; Ankara Occupational and Environmental Diseases Hospital, Ankara, Turkey
| | - Ulku Yilmaz
- Atatürk Chest Diseases and Chest Surgery Training and Research Hospital, Ankara, Turkey
| | - Salih Emri
- Hacettepe University, Faculty of Medicine, Department of Chest Diseases, Ankara, Turkey; Medicana Hospital, Department of Chest Diseases, Kadikoy, Istanbul, Turkey
| | - Feride Severcan
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Altinbas University, Faculty of Medicine, Biophysics Department, Istanbul, Turkey.
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15
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Kılınç N, Onbaşılar M, Çayır A. Evaluation of circulating cell-free nucleic acids in health workers occupationally exposed to ionizing radiation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:40543-40549. [PMID: 35083692 DOI: 10.1007/s11356-022-18828-5] [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] [Received: 10/29/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Radiology workers might constantly be exposed to low-dose ionizing radiation due to their profession. Low doses of radiation in a short exposure time have the potential to alter the genome, which might potentially lead to diseases. The main objective of this study was to determine whether the amount of cell-free nucleic acids in plasma samples of radiation-exposed workers was different from the general public, in other words, non-exposed individuals. In this context, we investigated the association between radiation exposure and cell-free nucleic acids concentration by using radiation exposure parameters. The study consisted of 40 radiology workers and 40 individuals who were not exposed to ionizing radiation. The plasma concentrations of cell-free DNA, RNA, and miRNA were measured fluorometrically. We found that the ccfRNA concentration of the radiation-exposed group was significantly different from that of the non-exposed group (p = 0.0001). However, there are no differences between both groups in terms of ccfDNA and ccfmiRNA concentration. The concentration of ccfDNA is significantly correlated with working time in the fluoroscopy field (p < 0.05). We found that the concentration of ccfmiRNA was significantly correlated with working time in plain radiography (p < 0.01) and computed tomography (p < 0.05) and with total working time (p < 0.01). Similarly, the concentrations of ccfRNA were significantly correlated with working time in computed tomography (p < 0.01) and with the total working time (p < 0.05) of the workers. We found that imaging number in computed tomography significantly altered the level of ccfRNA (p = 0.006) and that working time in the computed tomography field significantly affected the ccfRNA concentration (p = 0.03, R2 = 0.36 for model). Finally, we determined that total working time was significantly associated with total ccfRNA concentration (p < 0.05, R2 = 0.25 for model). In conclusion, total RNA measured in radiation-exposed workers has the potential to predict the radiation exposure risk. Furthermore, total working time and working time in the tomography field significantly alter the level of free nucleic acids.
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Affiliation(s)
- Nihal Kılınç
- Medical Pathology, Faculty of Medicine, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Mehmet Onbaşılar
- School of Graduate Studies, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Akın Çayır
- Vocational School of Health Services, Canakkale Onsekiz Mart University, Canakkale, Turkey.
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Ginghina O, Hudita A, Zamfir M, Spanu A, Mardare M, Bondoc I, Buburuzan L, Georgescu SE, Costache M, Negrei C, Nitipir C, Galateanu B. Liquid Biopsy and Artificial Intelligence as Tools to Detect Signatures of Colorectal Malignancies: A Modern Approach in Patient's Stratification. Front Oncol 2022; 12:856575. [PMID: 35356214 PMCID: PMC8959149 DOI: 10.3389/fonc.2022.856575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/16/2022] [Indexed: 01/19/2023] Open
Abstract
Colorectal cancer (CRC) is the second most frequently diagnosed type of cancer and a major worldwide public health concern. Despite the global efforts in the development of modern therapeutic strategies, CRC prognosis is strongly correlated with the stage of the disease at diagnosis. Early detection of CRC has a huge impact in decreasing mortality while pre-lesion detection significantly reduces the incidence of the pathology. Even though the management of CRC patients is based on robust diagnostic methods such as serum tumor markers analysis, colonoscopy, histopathological analysis of tumor tissue, and imaging methods (computer tomography or magnetic resonance), these strategies still have many limitations and do not fully satisfy clinical needs due to their lack of sensitivity and/or specificity. Therefore, improvements of the current practice would substantially impact the management of CRC patients. In this view, liquid biopsy is a promising approach that could help clinicians screen for disease, stratify patients to the best treatment, and monitor treatment response and resistance mechanisms in the tumor in a regular and minimally invasive manner. Liquid biopsies allow the detection and analysis of different tumor-derived circulating markers such as cell-free nucleic acids (cfNA), circulating tumor cells (CTCs), and extracellular vesicles (EVs) in the bloodstream. The major advantage of this approach is its ability to trace and monitor the molecular profile of the patient's tumor and to predict personalized treatment in real-time. On the other hand, the prospective use of artificial intelligence (AI) in medicine holds great promise in oncology, for the diagnosis, treatment, and prognosis prediction of disease. AI has two main branches in the medical field: (i) a virtual branch that includes medical imaging, clinical assisted diagnosis, and treatment, as well as drug research, and (ii) a physical branch that includes surgical robots. This review summarizes findings relevant to liquid biopsy and AI in CRC for better management and stratification of CRC patients.
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Affiliation(s)
- Octav Ginghina
- Department II, University of Medicine and Pharmacy “Carol Davila” Bucharest, Bucharest, Romania
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | - Ariana Hudita
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
| | - Marius Zamfir
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | - Andrada Spanu
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | - Mara Mardare
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | - Irina Bondoc
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | | | - Sergiu Emil Georgescu
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
| | - Carolina Negrei
- Department of Toxicology, University of Medicine and Pharmacy “Carol Davila” Bucharest, Bucharest, Romania
| | - Cornelia Nitipir
- Department II, University of Medicine and Pharmacy “Carol Davila” Bucharest, Bucharest, Romania
- Department of Oncology, Elias University Emergency Hospital, Bucharest, Romania
| | - Bianca Galateanu
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
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Mugoni V, Ciani Y, Nardella C, Demichelis F. Circulating RNAs in prostate cancer patients. Cancer Lett 2022; 524:57-69. [PMID: 34656688 DOI: 10.1016/j.canlet.2021.10.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 12/12/2022]
Abstract
Growing bodies of evidence have demonstrated that the identification of prostate cancer (PCa) biomarkers in the patients' blood and urine may remarkably improve PCa diagnosis and progression monitoring. Among diverse cancer-derived circulating materials, extracellular RNA molecules (exRNAs) represent a compelling component to investigate cancer-related alterations. Once outside the intracellular environment, exRNAs circulate in biofluids either in association with protein complexes or encapsulated inside extracellular vesicles (EVs). Notably, EV-associated RNAs (EV-RNAs) were used for the development of several assays (such as the FDA-approved Progensa Prostate Cancer Antigen 3 (PCA3 test) aiming at improving early PCa detection. EV-RNAs encompass a mixture of species, including small non-coding RNAs (e.g. miRNA and circRNA), lncRNAs and mRNAs. Several methods have been proposed to isolate EVs and relevant RNAs, and to perform RNA-Seq studies to identify potential cancer biomarkers. However, EVs in the circulation of a cancer patient include a multitude of diverse populations that are released by both cancer and normal cells from different tissues, thereby leading to a heterogeneous EV-RNA-associated transcriptional signal. Decrypting the complexity of such a composite signal is nowadays the major challenge faced in the identification of specific tumor-associated RNAs. Multiple deconvolution algorithms have been proposed so far to infer the enrichment of cancer-specific signals from gene expression data. However, novel strategies for EVs sorting and sequencing of RNA associated to single EVs populations will remarkably facilitate the identification of cancer-related molecules. Altogether, the studies summarized here demonstrate the high potential of using EV-RNA biomarkers in PCa and highlight the urgent need of improving technologies and computational approaches to characterize specific EVs populations and their relevant RNA cargo.
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Affiliation(s)
- Vera Mugoni
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Caterina Nardella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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18
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Gupta R, Kleinjans J, Caiment F. Identifying novel transcript biomarkers for hepatocellular carcinoma (HCC) using RNA-Seq datasets and machine learning. BMC Cancer 2021; 21:962. [PMID: 34445986 PMCID: PMC8394105 DOI: 10.1186/s12885-021-08704-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/09/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the leading causes of cancer death in the world owing to limitations in its prognosis. The current prognosis approaches include radiological examination and detection of serum biomarkers, however, both have limited efficiency and are ineffective in early prognosis. Due to such limitations, we propose to use RNA-Seq data for evaluating putative higher accuracy biomarkers at the transcript level that could help in early prognosis. METHODS To identify such potential transcript biomarkers, RNA-Seq data for healthy liver and various HCC cell models were subjected to five different machine learning algorithms: random forest, K-nearest neighbor, Naïve Bayes, support vector machine, and neural networks. Various metrics, namely sensitivity, specificity, MCC, informedness, and AUC-ROC (except for support vector machine) were evaluated. The algorithms that produced the highest values for all metrics were chosen to extract the top features that were subjected to recursive feature elimination. Through recursive feature elimination, the least number of features were obtained to differentiate between the healthy and HCC cell models. RESULTS From the metrics used, it is demonstrated that the efficiency of the known protein biomarkers for HCC is comparatively lower than complete transcriptomics data. Among the different machine learning algorithms, random forest and support vector machine demonstrated the best performance. Using recursive feature elimination on top features of random forest and support vector machine three transcripts were selected that had an accuracy of 0.97 and kappa of 0.93. Of the three transcripts, two were protein coding (PARP2-202 and SPON2-203) and one was a non-coding transcript (CYREN-211). Lastly, we demonstrated that these three selected transcripts outperformed randomly taken three transcripts (15,000 combinations), hence were not chance findings, and could then be an interesting candidate for new HCC biomarker development. CONCLUSION Using RNA-Seq data combined with machine learning approaches can aid in finding novel transcript biomarkers. The three biomarkers identified: PARP2-202, SPON2-203, and CYREN-211, presented the highest accuracy among all other transcripts in differentiating the healthy and HCC cell models. The machine learning pipeline developed in this study can be used for any RNA-Seq dataset to find novel transcript biomarkers. Code: www.github.com/rajinder4489/ML_biomarkers.
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Affiliation(s)
- Rajinder Gupta
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.
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Liquid Biopsy in Cervical Cancer: Hopes and Pitfalls. Cancers (Basel) 2021; 13:cancers13163968. [PMID: 34439120 PMCID: PMC8394398 DOI: 10.3390/cancers13163968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Cervical cancer is the fourth most common cancer in women worldwide, and its incidence is variably distributed between developed and less-resourced countries, in which socio-economic issues and religious beliefs often limit the widespread diffusion and the access to screening campaigns. In the “liquid biopsy” era, the application of non-invasive and repeatable techniques to the identification of diagnostic, prognostic, and predictive biomarkers might facilitate the management of this disease and, hopefully, improve its outcome. The purpose of this review is to explore the progress status of liquid biopsy in cervical cancer patients. Several methods are described, which include the analysis of circulating tumor cells, the search for pathogenic mutations on circulating tumor DNA, as well as the identification of circulating RNAs, focusing on their potential clinical applications and current limitations. Abstract Cervical cancer (CC) is the fourth most common cancer in women worldwide, with about 90% of cancer-related deaths occurring in developing countries. The geographical influence on disease evolution reflects differences in the prevalence of human papilloma virus (HPV) infection, which is the main cause of CC, as well as in the access and quality of services for CC prevention and diagnosis. At present, the most diffused screening and diagnostic tools for CC are Papanicolaou test and the more sensitive HPV-DNA test, even if both methods require gynecological practices whose acceptance relies on the woman’s cultural and religious background. An alternative (or complimentary) tool for CC screening, diagnosis, and follow-up might be represented by liquid biopsy. Here, we summarize the main methodologies developed in this context, including circulating tumor cell detection and isolation, cell tumor DNA sequencing, coding and non-coding RNA detection, and exosomal miRNA identification. Moreover, the pros and cons of each method are discussed, and their potential applications in diagnosis and prognosis of CC, as well as their role in treatment monitoring, are explored. In conclusion, it is evident that despite many advances obtained in this field, further effort is needed to validate and standardize the proposed methodologies before any clinical use.
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Ranjan S, Jain S, Bhargava A, Shandilya R, Srivastava RK, Mishra PK. Lateral flow assay-based detection of long non-coding RNAs: A point-of-care platform for cancer diagnosis. J Pharm Biomed Anal 2021; 204:114285. [PMID: 34333453 DOI: 10.1016/j.jpba.2021.114285] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Lateral flow assay (LFA) is a flexible, simple, low-costpoint-of-care platform for rapid detection of disease-specific biomarkers. Importantly, the ability of the assay to capture the circulating bio-molecules has gained significant attention, as it offers a potential minimal invasive system for early disease diagnosis and prognosis. In the present article, we review an innovative concept of LFA-based detection of circulating long non-coding RNAs (lncRNAs), one of the key regulators of fundamental biological processes. In addition, their disease-specific expression pattern and presence in biological fluids at differential levels make them excellent biomarker candidates for cancer detection. Our article also provides an update on the requirements for developing and improving such systems and discusses the key aspects of material selection, operational concepts, principles and conceptual design. We assume that the reviewed points will be helpful to improve the diagnostic applicability of LFA based lncRNA detection in cancer diagnosis.
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Affiliation(s)
- Shashi Ranjan
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Surbhi Jain
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Ruchita Shandilya
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | | | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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21
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Circulating non-coding RNAs as new biomarkers and novel therapeutic targets in colorectal cancer. Clin Transl Oncol 2021; 23:2220-2236. [PMID: 34275108 DOI: 10.1007/s12094-021-02639-0] [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: 10/14/2020] [Accepted: 05/06/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors, and a large number of patients are diagnosed and die every year. Due to the lack of appropriate diagnosis, prediction and treatment, early diagnosis rate of CRC is low and the prognosis is poor. Studies have found that abnormally expressed non-coding RNAs (ncRNAs) (including microRNAs (miRNAs), circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs),etc.) play an important regulatory role in the occurrence and development of CRC. Some studies have shown that they are stable in the blood and can be detected repeatedly. They are expected to be non-invasive biomarkers for early diagnosis, prognosis evaluation, and prediction of drug sensitivity of CRC, as well as potential applications in the treatment of CRC.
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22
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A comprehensive characterization of the cell-free transcriptome reveals tissue- and subtype-specific biomarkers for cancer detection. Nat Commun 2021; 12:2357. [PMID: 33883548 PMCID: PMC8060291 DOI: 10.1038/s41467-021-22444-1] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Cell-free RNA (cfRNA) is a promising analyte for cancer detection. However, a comprehensive assessment of cfRNA in individuals with and without cancer has not been conducted. We perform the first transcriptome-wide characterization of cfRNA in cancer (stage III breast [n = 46], lung [n = 30]) and non-cancer (n = 89) participants from the Circulating Cell-free Genome Atlas (NCT02889978). Of 57,820 annotated genes, 39,564 (68%) are not detected in cfRNA from non-cancer individuals. Within these low-noise regions, we identify tissue- and cancer-specific genes, defined as “dark channel biomarker” (DCB) genes, that are recurrently detected in individuals with cancer. DCB levels in plasma correlate with tumor shedding rate and RNA expression in matched tissue, suggesting that DCBs with high expression in tumor tissue could enhance cancer detection in patients with low levels of circulating tumor DNA. Overall, cfRNA provides a unique opportunity to detect cancer, predict the tumor tissue of origin, and determine the cancer subtype. Cell-free RNA (cfRNA) is a promising analyte for cancer diagnosis. Here, the authors determine the baseline cell-free transcriptome in the absence of cancer and identify tissue- and subtype-specific cfRNA biomarkers in breast and lung cancer patients.
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Khandelwal A, Sharma U, Barwal TS, Seam RK, Gupta M, Rana MK, Vasquez KM, Jain A. Circulating miR-320a Acts as a Tumor Suppressor and Prognostic Factor in Non-small Cell Lung Cancer. Front Oncol 2021; 11:645475. [PMID: 33833996 PMCID: PMC8021852 DOI: 10.3389/fonc.2021.645475] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/22/2021] [Indexed: 12/24/2022] Open
Abstract
Dysregulated expression profiles of microRNAs (miRNAs) have been observed in several types of cancer, including non-small cell lung cancer (NSCLC); however, the diagnostic and prognostic potential of circulating miRNAs in NSCLC remains largely undefined. Here we found that circulating miR-320a was significantly down-regulated (~5.87-fold; p < 0.0001) in NSCLC patients (n = 80) compared to matched control plasma samples from healthy subjects (n = 80). Kaplan-Meier survival analysis revealed that NSCLC patients with lower levels of circulating miR-320a had overall poorer prognosis and survival rates compared to patients with higher levels (p < 0.0001). Moreover, the diagnostic and prognostic potential of miR-320a correlated with clinicopathological characteristics such as tumor size, tumor node metastasis (TNM) stage, and lymph node metastasis. Functionally, depletion of miR-320a in human A549 lung adenocarcinoma cells induced their metastatic potential and reduced apoptosis, which was reversed by exogenous re-expression of miR-320a mimics, indicating that miR-320a has a tumor-suppressive role in NSCLC. These results were further supported by high levels of epithelial-mesenchymal transition (EMT) marker proteins (e.g., Beta-catenin, MMP9, and E-cadherin) in lung cancer cells and tissues via immunoblot and immunohistochemistry experiments. Moreover, through bioinformatics and dual-luciferase reporter assays, we demonstrated that AKT3 was a direct target of miR-320a. In addition, AKT3-associated PI3K/AKT/mTOR protein-signaling pathways were elevated with down-regulated miR-320a levels in NSCLC. These composite data indicate that circulating miR-320a may function as a tumor-suppressor miRNA with potential as a prognostic marker for NSCLC patients.
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Affiliation(s)
- Akanksha Khandelwal
- Department of Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, India
| | - Uttam Sharma
- Department of Zoology, Central University of Punjab, Bathinda, India
| | | | - Rajeev Kumar Seam
- Department of Radiation Oncology, Indira Gandhi Medical College, Shimla, India
| | - Manish Gupta
- Department of Radiation Oncology, Indira Gandhi Medical College, Shimla, India
| | - Manjit Kaur Rana
- Lab Medicine, Department of Pathology, All India Institute of Medical Sciences, Bathinda, India
| | - Karen M. Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, United States
| | - Aklank Jain
- Department of Zoology, Central University of Punjab, Bathinda, India
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24
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Systematic evaluation of multiple qPCR platforms, NanoString and miRNA-Seq for microRNA biomarker discovery in human biofluids. Sci Rep 2021; 11:4435. [PMID: 33627690 PMCID: PMC7904811 DOI: 10.1038/s41598-021-83365-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/02/2021] [Indexed: 02/06/2023] Open
Abstract
Aberrant miRNA expression has been associated with many diseases, and extracellular miRNAs that circulate in the bloodstream are remarkably stable. Recently, there has been growing interest in identifying cell-free circulating miRNAs that can serve as non-invasive biomarkers for early detection of disease or selection of treatment options. However, quantifying miRNA levels in biofluids is technically challenging due to their low abundance. Using reference samples, we performed a cross-platform evaluation in which miRNA profiling was performed on four different qPCR platforms (MiRXES, Qiagen, Applied Biosystems, Exiqon), nCounter technology (NanoString), and miRNA-Seq. Overall, our results suggest that using miRNA-Seq for discovery and targeted qPCR for validation is a rational strategy for miRNA biomarker development in clinical samples that involve limited amounts of biofluids.
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25
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Drag MH, Kilpeläinen TO. Cell-free DNA and RNA-measurement and applications in clinical diagnostics with focus on metabolic disorders. Physiol Genomics 2020; 53:33-46. [PMID: 33346689 DOI: 10.1152/physiolgenomics.00086.2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) and RNA (cfRNA) hold enormous potential as a new class of biomarkers for the development of noninvasive liquid biopsies in many diseases and conditions. In recent years, cfDNA and cfRNA have been studied intensely as tools for noninvasive prenatal testing, solid organ transplantation, cancer screening, and monitoring of tumors. In obesity, higher cfDNA concentration indicates accelerated cellular turnover of adipocytes during expansion of adipose mass and may be directly involved in the development of adipose tissue insulin resistance by inducing inflammation. Furthermore, cfDNA and cfRNA have promising diagnostic value in a range of obesity-related metabolic disorders, such as nonalcoholic fatty liver disease, type 2 diabetes, and diabetic complications. Here, we review the current and future applications of cfDNA and cfRNA within clinical diagnostics, discuss technical and analytical challenges in the field, and summarize the opportunities of using cfDNA and cfRNA in the diagnostics and prognostics of obesity-related metabolic disorders.
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Affiliation(s)
- Markus H Drag
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Yao J, Wu DC, Nottingham RM, Lambowitz AM. Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling. eLife 2020; 9:e60743. [PMID: 32876046 PMCID: PMC7518892 DOI: 10.7554/elife.60743] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Human plasma contains > 40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) combined with peak calling to simultaneously profile all RNA biotypes in apheresis-prepared human plasma pooled from healthy individuals. Extending previous TGIRT-seq analysis, we found that human plasma contains largely fragmented mRNAs from > 19,000 protein-coding genes, abundant full-length, mature tRNAs and other structured small non-coding RNAs, and less abundant tRNA fragments and mature and pre-miRNAs. Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases. Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length excised intron RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons.
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Affiliation(s)
- Jun Yao
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
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27
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Vad-Nielsen J, Meldgaard P, Sorensen BS, Nielsen AL. Cell-free Chromatin Immunoprecipitation (cfChIP) from blood plasma can determine gene-expression in tumors from non-small-cell lung cancer patients. Lung Cancer 2020; 147:244-251. [PMID: 32759018 DOI: 10.1016/j.lungcan.2020.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Lung cancer is the leading cause of cancer related death worldwide. Accurate molecular diagnostics from a tumor biopsy is paramount for correct diagnosis, treatment strategy, and prediction of outcome. However, a tumor biopsy can be misleading due to tumor heterogeneity and consecutive biopsies are rarely achievable. Importantly, tumor-specific genetic information concerning mutations and translocations, can also be obtained from liquid biopsies, e.g. blood plasma, containing cell-free DNA (cfDNA) with both systemic and tumor origin. Tumor-specific gene-expression information can also be determined from liquid biopsies using cfDNA methylation and cell-free RNA analyses. However, supplementary methodologies that can determine gene-expression patterns in lung tumors from liquid biopsies could also have diagnostic impact. MATERIALS AND METHODS We here present the method cell-free chromatin Immunoprecipitation (cfChIP), which for genes having high expression specifically in the tumor, can determine such gene-expression from blood plasma. In cfChIP cell-free nucleosomes modified with histone H3 lysine 36 tri-methylation (H3K36me3), a mark quantitatively correlated with the transcription of the underlying gene, are isolated, and associated cfDNA quantified. RESULTS We demonstrate that cfChIP from lung cancer patient blood plasma can successfully quantify the level of H3K36me3 associated with circulating cell-free nucleosomes and thereby quantify the transcriptional level of genes associated with these nucleosomes. Moreover, as a proof-of-principle we show that in blood plasma from 14 lung cancer patients, H3K36me3 cfChIP can replicate the expected higher expression of KRT6 in lung squamous cell carcinoma relative to adenocarcinoma. CONCLUSION This work shows that for genes with a high expression specifically in tumor, cfChIP can determine this gene-expression pattern from blood plasma. cfChIP is a method that determine gene-expression at the transcriptional level and accordingly can supplement cfDNA methylation and cell-free RNA analyses.
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28
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Cho WCS, Chan LWC, Wong CSC. Editorial: Role of RNA in Molecular Diagnostics of Cancer. Front Genet 2020; 11:435. [PMID: 32435261 PMCID: PMC7218120 DOI: 10.3389/fgene.2020.00435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022] Open
Affiliation(s)
- William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - Lawrence W C Chan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong kong Polytechnic University, Hong Kong, China
| | - Cesar S C Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong kong Polytechnic University, Hong Kong, China
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