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Northrop-Albrecht EJ, Wu CW, Berger CK, Taylor WR, Foote PH, Doering KA, Gonser AM, Bhagwate A, Sun Z, Mahoney DW, Burger KN, Boardman LA, Kisiel JB. An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation. PLoS One 2024; 19:e0308711. [PMID: 39146279 PMCID: PMC11326608 DOI: 10.1371/journal.pone.0308711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/29/2024] [Indexed: 08/17/2024] Open
Abstract
Regular screening for colorectal cancer (CRC) is critical for early detection and long-term survival. Despite the current screening options available and advancements in therapies there will be around 53,000 CRC related deaths this year. There is great interest in non-invasive alternatives such as plasma cell-free RNA (cfRNA) for diagnostic, prognostic, and predictive applications. In the current study, our aim was to identify and validate potential cfRNA candidates to improve early CRC diagnosis. In phase 1 (n = 49; 25 controls, 24 cancers), discovery total RNA sequencing was performed. Select exons underwent validation in phase 2 (n = 73; 35 controls, 29 cancers, 9 adenomas) using targeted capture sequencing (n = 10,371 probes). In phase 3 (n = 57; 30 controls, 27 cancers), RT-qPCR was performed on previously identified candidates (n = 99). There were 895 exons that were differentially expressed (325 upregulated, 570 downregulated) among cancers versus controls. In phases 2 and 3, fewer markers were validated than expected in independent sets of patients, most of which were from previously published literature (FGA, FGB, GPR107, CDH3, and RP23AP7). In summary, we optimized laboratory processes and data analysis strategies which can serve as methodological framework for future plasma RNA studies beyond just the scope of CRC detection. Additionally, further exploration is needed in order to determine if the few cfRNA candidates identified in this study have clinical utility for early CRC detection. Over time, advancements in technologies, data analysis, and RNA preservation methods at time of collection may improve the biological and technical reproducibility of cfRNA biomarkers and enhance the feasibility of RNA-based liquid biopsies.
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Affiliation(s)
| | - Chung Wah Wu
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Calise K Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Patrick H Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Karen A Doering
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Anna M Gonser
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Aditya Bhagwate
- Division of Computational Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Zhifu Sun
- Division of Computational Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Douglas W Mahoney
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Kelli N Burger
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
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Islam MS, Gopalan V, Lam AK, Shiddiky MJA. Current advances in detecting genetic and epigenetic biomarkers of colorectal cancer. Biosens Bioelectron 2023; 239:115611. [PMID: 37619478 DOI: 10.1016/j.bios.2023.115611] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Colorectal carcinoma (CRC) is the third most common cancer in terms of diagnosis and the second in terms of mortality. Recent studies have shown that various proteins, extracellular vesicles (i.e., exosomes), specific genetic variants, gene transcripts, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and altered epigenetic patterns, can be used to detect, and assess the prognosis of CRC. Over the last decade, a plethora of conventional methodologies (e.g., polymerase chain reaction [PCR], direct sequencing, enzyme-linked immunosorbent assay [ELISA], microarray, in situ hybridization) as well as advanced analytical methodologies (e.g., microfluidics, electrochemical biosensors, surface-enhanced Raman spectroscopy [SERS]) have been developed for analyzing genetic and epigenetic biomarkers using both optical and non-optical tools. Despite these methodologies, no gold standard detection method has yet been implemented that can analyze CRC with high specificity and sensitivity in an inexpensive, simple, and time-efficient manner. Moreover, until now, no study has critically reviewed the advantages and limitations of these methodologies. Here, an overview of the most used genetic and epigenetic biomarkers for CRC and their detection methods are discussed. Furthermore, a summary of the major biological, technical, and clinical challenges and advantages/limitations of existing techniques is also presented.
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Affiliation(s)
- Md Sajedul Islam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia.
| | - Alfred K Lam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia; Pathology Queensland, Gold Coast University Hospital, Southport, QLD, 4215, Australia
| | - Muhammad J A Shiddiky
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
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Xue VW, Ng SSM, Tsang HF, Wong HT, Leung WW, Wong YN, Wong YKE, Yu ACS, Yim AKY, Cho WCS, Tai WCS, Wong SCC. The non-invasive diagnosis of colorectal cancer via a SOX9-based gene panel. Clin Exp Med 2023; 23:2421-2432. [PMID: 36637582 DOI: 10.1007/s10238-022-00970-6] [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: 10/30/2022] [Accepted: 12/01/2022] [Indexed: 01/14/2023]
Abstract
Colorectal cancer (CRC) threatens human health seriously. Early diagnosis of CRC is critical to improving patient survival. Meanwhile, non-invasive detection through tumor-circulating markers can be an important auxiliary diagnosis. In this study, we performed targeted RNA sequencing in paired tumor and adjacent normal fresh frozen tissues from 68 patients, and we also measured circulating mRNA levels in 4 time-point plasma samples collected before and after operation or chemotherapy. Our results showed that SOX9 (6.73-fold with adjusted p value < 1 × 10-45), MYC (20.59-fold with adjusted p value < 1 × 10-57), and MMP7 (131.94-fold with adjusted p value < 1 × 10-78) highly expressed in tumor compared with adjacent normal tissues. Besides, the circulating mRNA of SOX9 (41.14-fold with adjusted p value < 1 × 10-13) in CRC was significantly higher than in the normal control as well. Moreover, a SOX9-based 9-gene panel (SOX9, GSK3A, FZD4, LEF1, DVL1, FZD7, NFATC1, KRT19, and RUVBL1) showed the non-invasive diagnostic value of CRC (AUC: 0.863 (0.766-0.960), TPR: 0.92, TNR: 0.87). In summary, SOX9 expression consistently increases in tumor and plasma samples from CRC patients, which indicates the important role of SOX9 in CRC progression and its potential in non-invasive diagnosis of CRC.
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Affiliation(s)
- Vivian Weiwen Xue
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Department of Pharmacology, Shenzhen University Health Science Center, Shenzhen, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Heong Ting Wong
- Department of Pathology, Kiang Wu Hospital, Santo António, Macau Special Administrative Region, China
| | - Wing Wa Leung
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Yee Ni Wong
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Yin Kwan Evelyn Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Kowloon, Hong Kong Special Administrative Region, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Kowloon, Hong Kong Special Administrative Region, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - William Chi Shing Tai
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China.
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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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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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Block T, Zezulinski D, Kaplan DE, Lu J, Zanine S, Zhan T, Doria C, Sayeed A. Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma. Front Oncol 2022; 12:963641. [PMID: 36582804 PMCID: PMC9793749 DOI: 10.3389/fonc.2022.963641] [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: 06/07/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
Background and rationale Liver derived messenger ribonucleic acid (mRNA) transcripts were reported to be elevated in the circulation of hepatocellular carcinoma (HCC) patients. We now report the detection of high-risk mRNA variants exclusively in the circulation of HCC patients. Numerous genomic alleles such as single nucleotide polymorphisms (SNPs), nucleotide insertions and deletions (called Indels), splicing variants in many genes, have been associated with elevated risk of cancer. Our findings potentially offer a novel non-invasive platform for HCC surveillance and early detection. Approach RNAseq analysis was carried out in the plasma of 14 individuals with a diagnosis of HCC, 8 with LC and no HCC, and 6 with no liver disease diagnosis. RNA from 6 matching tumors and 5 circulating extracellular vesicle (EV) samples from 14 of those with HCC was also analyzed. Specimens from two cholangiocarcinoma (CCA) patients were also included in our study. HCC specific SNPs and Indels referred as "variants" were identified using GATK HaplotypeCaller and annotated by SnpEff to filter out high risk variants. Results The variant calling on all RNA samples enabled the detection of 5.2 million SNPs, 0.91 million insertions and 0.81 million deletions. RNAseq analyses in tumors, normal liver tissue, plasma, and plasma derived EVs led to the detection of 5480 high-risk tumor specific mRNA variants in the circulation of HCC patients. These variants are concurrently detected in tumors and plasma samples or tumors and EVs from HCC patients, but none of these were detected in normal liver, plasma of LC patients or normal healthy individuals. Our results demonstrate selective detection of concordant high-risk HCC-specific mRNA variants in free plasma, plasma derived EVs and tumors of HCC patients. The variants comprise of splicing, frameshift, fusion and single nucleotide alterations and correspond to cancer and tumor metabolism pathways. Detection of these high-risk variants in matching specimens from same subjects with an enrichment in circulating EVs is remarkable. Validation of these HCC selective ctmRNA variants in larger patient cohorts is likely to identify a predictive set of ctmRNA with high diagnostic performance and thus offer a novel non-invasive serology-based biomarker for HCC.
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Affiliation(s)
- Timothy Block
- Department of Translational Medicine, Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Daniel Zezulinski
- Department of Translational Medicine, Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - David E. Kaplan
- Division of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine and The Corporal Michael J. Crescenz Veterans Administration Hospital, Philadelphia, PA, United States
| | - Jingqiao Lu
- Ray Biotech Life Inc., Peachtree Corners, GA, United States
| | - Samantha Zanine
- Department of Mechanical Engineering, Pennsylvania State University, PA, United States
| | - Tingting Zhan
- Division of Biostatistics, Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia PA, United States
| | - Cataldo Doria
- CHS Liver and Pancreas Centers of Excellence, Capital Health Cancer Center, One Capital Way, Pennington, NJ, United States
| | - Aejaz Sayeed
- Department of Translational Medicine, Baruch S. Blumberg Institute, Doylestown, PA, United States,*Correspondence: Aejaz Sayeed,
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Jia Y, Song G, Wu R, Hong Y, Dou W, Li A. Intravoxel incoherent motion DWI with different mathematical models in predicting rectal adenoma with and without canceration. Eur J Radiol 2022; 155:110496. [PMID: 36030659 DOI: 10.1016/j.ejrad.2022.110496] [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: 04/29/2022] [Revised: 08/06/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022]
Abstract
PURPOSE To evaluate the clinical value of intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) with mono-exponential (ME), bi-exponential (BE), and stretched-exponential (SE) models for predicting rectal adenomas with canceration. MATERIAL AND METHODS Sixty patients with postoperative pathology-confirmed rectal adenoma (n = 31) and adenoma with canceration (n = 29) were enrolled and underwent IVIM-DWI scanning. The ME-derived apparent diffusion coefficient (ADC), BE-derived true diffusion coefficient (D), pseudo-diffusion coefficient (D*), perfusion fraction (f), SE-derived distributed diffusion coefficient (DDC), and water molecular diffusion heterogeneity index (α) were measured. The differences in each parameter between adenoma and canceration were compared. Multivariate binary logistic regression analysis was used to establish models for predicting rectal adenomas with canceration. Receiver operating characteristic curve analysis was applied to evaluate diagnostic performances of each model in terms of sensitivity, specificity, accuracy, and area under the curve (AUC). RESULTS The AUCs of ADC, D, D*, f, DDC and α were 0.851 (95 % confidence interval, CI, 0.735-0.930), 0.895 (95 % CI, 0.789-0.960), 0.720 (95 % CI, 0.589-0.828), 0.791 (95 % CI, 0.667-0.886), 0.841 (95 % CI, 0.724-0.923) and 0.738 (95 % CI, 0.608-0.834), respectively. The AUCs of BE and SE models were 0.927 (95 % CI, 0.829-0.978) and 0.874 (95 % CI, 0.763-0.946), respectively. The AUC, sensitivity, specificity, and accuracy of the derived four values (ADC, D, f, and DDC) from the combination of three models were 0.950, 96.6 % (95 % CI, 95.3-97.6 %), 80.6 % (95 % CI, 78.0-82.9 %), and 88.3 % (95 % CI, 86.2-90.2 %), respectively. CONCLUSION ADC can easily and effectively predict rectal adenomas with canceration. The BE model has a better combination of sensitivity and specificity for the diagnosis of rectal adenoma canceration.
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Affiliation(s)
- Yuping Jia
- Department of Radiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Gesheng Song
- Department of Radiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Rui Wu
- Department of Radiology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014, China
| | - Yu Hong
- Department of Radiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | | | - Aiyin Li
- Department of Radiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China.
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Styk J, Buglyó G, Pös O, Csók Á, Soltész B, Lukasz P, Repiská V, Nagy B, Szemes T. Extracellular Nucleic Acids in the Diagnosis and Progression of Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14153712. [PMID: 35954375 PMCID: PMC9367600 DOI: 10.3390/cancers14153712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is a disease that usually shows no evident clinical symptoms in the early stages, often leading to late diagnosis. Over the past few years, a new approach based on liquid biopsy has gained far-reaching applications in less-invasive CRC diagnosis and management, allowing for the use of extracellular nucleic acids as promising biomarkers to detect CRC at an early stage and monitor disease recurrence. That is why an up-to-date review and discussion of in-depth liquid biopsy-derived DNA and RNA biomarkers is essential. We hereby offer an overview of known predisposing genetic factors for developing sporadic and hereditary CRC, and an extensive repertoire of available extracellular DNA/RNA molecules with their potential clinical applications and shortcomings. Our review may be of value to experts dealing with CRC at the molecular level as well as to clinical professionals aiming for a better understanding of state-of-the-art techniques in CRC diagnosis and management. Abstract Colorectal cancer (CRC) is the 3rd most common malignant neoplasm worldwide, with more than two million new cases diagnosed yearly. Despite increasing efforts in screening, many cases are still diagnosed at a late stage, when mortality is high. This paper briefly reviews known genetic causes of CRC (distinguishing between sporadic and familial forms) and discusses potential and confirmed nucleic acid biomarkers obtainable from liquid biopsies, classified by their molecular features, focusing on clinical relevance. We comment on advantageous aspects such as better patient compliance due to blood sampling being minimally invasive, the possibility to monitor mutation characteristics of sporadic and hereditary CRC in a disease showing genetic heterogeneity, and using up- or down-regulated circulating RNA markers to reveal metastasis or disease recurrence. Current difficulties and thoughts on some possible future directions are also discussed. We explore current evidence in the field pointing towards the introduction of personalized CRC management.
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Affiliation(s)
- Jakub Styk
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Correspondence:
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Ondrej Pös
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Ádám Csók
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Beáta Soltész
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Peter Lukasz
- Department of Surgery, Transplantation and Gastroenterology, Semmelweis University, 1082 Budapest, Hungary;
| | - Vanda Repiská
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
- Medirex Group Academy, n.p.o., 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Tomáš Szemes
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 05 Bratislava, Slovakia
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Sattar RSA, Verma R, Nimisha, Kumar A, Dar GM, Apurva, Sharma AK, Kumari I, Ahmad E, Ali A, Mahajan B, Saluja SS. Diagnostic and prognostic biomarkers in colorectal cancer and the potential role of exosomes in drug delivery. Cell Signal 2022; 99:110413. [PMID: 35907519 DOI: 10.1016/j.cellsig.2022.110413] [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: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/03/2022]
Abstract
Colorectal cancer (CRC) is third most common cancer with second most common cause of death worldwide. One fourth to one fifth of the CRC cases are detected at advance stage. Early detection of colorectal cancer might help in decreasing mortality and morbidity worldwide. CRC being a heterogeneous disease, new non-invasive approaches are needed to complement and improve the screening and management of CRC. Reliable and early detectable biomarkers would improve diagnosis, prognosis, therapeutic responses, and will enable the prediction of drug response and recurrence risk. Over the past decades molecular research has demonstrated the potentials of CTCs, ctDNAs, circulating mRNA, ncRNAs, and exosomes as tumor biomarkers. Non-invasive screening approaches using fecal samples for identification of altered gut microbes in CRC is also gaining attention. Exosomes can be potential candidates that can be employed in the drug delivery system. Further, the integration of in vitro, in vivo and in silico models that involve CRC biomarkers will help to understand the interactions occurring at the cellular level. This review summarizes recent update on CRC biomarkers and their application along with the nanoparticles followed by the application of organoid culture in CRC.
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Affiliation(s)
- Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Renu Verma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ghulam Mehdi Dar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Abhay Kumar Sharma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Indu Kumari
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ejaj Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Asgar Ali
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of Biochemistry, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
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10
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Apurva, Kumar A, Dar GM, Sumayya Abdul Sattar R, Verma R, Mahajan B, Singh Saluja S. Molecular markers in cancer. Clin Chim Acta 2022; 532:95-114. [DOI: https:/doi.org/10.1016/j.cca.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
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11
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Apurva, Kumar A, Mehdi G, Sumayya Abdul Sattar R, Verma R, Mahajan B, Singh Saluja S. Molecular markers in cancer. Clin Chim Acta 2022; 532:95-114. [DOI: 10.1016/j.cca.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 12/01/2022]
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12
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Kim HJ, Rames MJ, Tassi Yunga S, Armstrong R, Morita M, Ngo ATP, McCarty OJT, Civitci F, Morgan TK, Ngo TTM. Irreversible alteration of extracellular vesicle and cell-free messenger RNA profiles in human plasma associated with blood processing and storage. Sci Rep 2022; 12:2099. [PMID: 35136102 PMCID: PMC8827089 DOI: 10.1038/s41598-022-06088-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/19/2022] [Indexed: 12/31/2022] Open
Abstract
The discovery and utility of clinically relevant circulating biomarkers depend on standardized methods that minimize preanalytical errors. Despite growing interest in studying extracellular vesicles (EVs) and cell-free messenger RNA (cf-mRNA) as potential biomarkers, how blood processing and freeze/thaw impacts the profiles of these analytes in plasma was not thoroughly understood. We utilized flow cytometric analysis to examine the effect of differential centrifugation and a freeze/thaw cycle on EV profiles. Utilizing flow cytometry postacquisition analysis software (FCMpass) to calibrate light scattering and fluorescence, we revealed how differential centrifugation and post-freeze/thaw processing removes and retains EV subpopulations. Additionally, cf-mRNA levels measured by RT-qPCR profiles from a panel of housekeeping, platelet, and tissue-specific genes were preferentially affected by differential centrifugation and post-freeze/thaw processing. Critically, freezing plasma containing residual platelets yielded irreversible ex vivo generation of EV subpopulations and cf-mRNA transcripts, which were not removable by additional processing after freeze/thaw. Our findings suggest the importance of minimizing confounding variation attributed to plasma processing and platelet contamination.
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Affiliation(s)
- Hyun Ji Kim
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute (CEDAR), Oregon Health and Science University, 2720 SW Moody Ave, KR-CEDR, Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Matthew J Rames
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute (CEDAR), Oregon Health and Science University, 2720 SW Moody Ave, KR-CEDR, Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Samuel Tassi Yunga
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute (CEDAR), Oregon Health and Science University, 2720 SW Moody Ave, KR-CEDR, Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Randall Armstrong
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute (CEDAR), Oregon Health and Science University, 2720 SW Moody Ave, KR-CEDR, Portland, OR, 97201, USA
| | - Mayu Morita
- Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Anh T P Ngo
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Owen J T McCarty
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Fehmi Civitci
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute (CEDAR), Oregon Health and Science University, 2720 SW Moody Ave, KR-CEDR, Portland, OR, 97201, USA
| | - Terry K Morgan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute (CEDAR), Oregon Health and Science University, 2720 SW Moody Ave, KR-CEDR, Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Thuy T M Ngo
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute (CEDAR), Oregon Health and Science University, 2720 SW Moody Ave, KR-CEDR, Portland, OR, 97201, USA.
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
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13
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Wang S, Zhou H, Zhang R, Zhang Y. Integrated Analysis of Mutations, miRNA and mRNA Expression in Glioblastoma. Int J Gen Med 2021; 14:8281-8292. [PMID: 34815700 PMCID: PMC8605868 DOI: 10.2147/ijgm.s336421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/02/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is a common, malignant brain tumor in adults, with a median survival of only 15-23 months. Organisms respond to disease stress through sophisticated mechanisms at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks responsible for occurrence, progression and recurrence of glioma have yet to be elucidated. METHODS In this study, we sought to determine the cause of gliomas by developing an RNA-seq technique that analyzes mRNA and small RNA (sRNA) with the aim of discovering potential methods for precisely blocking key signaling pathways in occurrence, progression, and recurrence. The explication of mechanisms leading to GBM formation has become a feasible and promising new therapeutic method. RESULTS GBM-associated genes were identified based on their expression during the disease stress response. Analysis of the inverse correlations between microRNAs (miRNAs) and target mRNAs revealed 43 mRNA-miRNA interactions during disease progression. BOC-SMO and BOC-RAS were found to promote the malignant progression of glioma. A total of 3088 differentially expressed genes were identified as involved in several biological processes, such as amino acid metabolism, protein transport associated with immune response, cell proliferation, and cell apoptosis. Fifteen miRNAs were also identified as being differentially expressed in GBM and control groups. CONCLUSION The results of this study provide an important foundation for understanding the pathogenesis of glioma and discovering new therapeutic targets.
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Affiliation(s)
- ShiChao Wang
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, People’s Republic of China
| | - HuanMin Zhou
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, People’s Republic of China
| | - RuiJian Zhang
- Department of Neurosurgery, The People’s Hospital of Inner Mongolia, Hohhot, Inner Mongolia, 010017, People’s Republic of China
| | - YanRu Zhang
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, People’s Republic of China
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14
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Ita MI, Wang JH, Fanning N, Kaar G, Lim C, Redmond HP. Plasma circulating cell free messenger RNA as a potential biomarker of melanoma. Acta Oncol 2021; 60:1201-1209. [PMID: 34086522 DOI: 10.1080/0284186x.2021.1928749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND Blood borne cell free nucleic acids are increasingly emerging as significant non-invasive adjuncts to current methods of disease status evaluation in cancer patients. In this study, we sought to examine whether significant differences exist in the plasma transcriptomic profile of advanced melanoma patients with a high disease burden compared to patients with a low disease burden or therapeutic response. METHODS Pathway focussed gene expression analysis was performed using cDNA derived from the plasma circulating cell free messenger ribonucleic acid (ccfmRNA) samples of twenty-two patients with advanced melanoma. Patients were assessed with paired blood sample collection and CT scan assessments at baseline and at 3 months follow up. RESULTS We identified several genes which were significantly over-expressed in patients with a low disease burden or therapeutic response; BCL2L1, CXCL9, IDO1, IL13, MIF, MYD88 and TLR4 (p ≤ 0.001, versus high disease burden). There was an increase in the magnitude of fold change (2^ (-dd CT)) of BCL2L1 (p = 0.031), CCL4 (p = 0.001), CCL5 (p = 0.043), CXCL9 (p = 0.012), GZMB (p = 0.023) and TNFSF10 (p = 0.039) genes in patients with therapeutic response at 3 months follow up assessment relative to baseline assessment. Moreover, in stage IV melanoma patients with brain metastases, CCL18, CCR1, CCR4, CD274, CSF2, EGF, and PTGS2 genes were significantly over-expressed (p < 0.001, versus patients without melanoma brain metastasis). CONCLUSION Significant differences were observed in the plasma transcriptomic profile between the various melanoma patient groups, and we postulate that these differences may be exploited to identify novel therapeutic targets or biomarkers relevant to melanoma.
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Affiliation(s)
- Michael Itak Ita
- Department of Academic Surgery, University College Cork, Cork, Ireland
- Department of Neurosurgery, University College Cork, Cork, Ireland
| | - Jiang Huai Wang
- Department of Academic Surgery, University College Cork, Cork, Ireland
| | - Noel Fanning
- Department of Radiology, University College Cork, Cork, Ireland
| | - George Kaar
- Department of Neurosurgery, University College Cork, Cork, Ireland
| | - Chris Lim
- Department of Neurosurgery, University College Cork, Cork, Ireland
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15
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Zhang Y, Wu Q, Xu L, Wang H, Liu X, Li S, Hu T, Liu Y, Peng Q, Chen Z, Wu X, Fan JB. Sensitive detection of colorectal cancer in peripheral blood by a novel methylation assay. Clin Epigenetics 2021; 13:90. [PMID: 33892797 PMCID: PMC8066866 DOI: 10.1186/s13148-021-01076-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Early detection of CRC can significantly reduce its mortality rate. Current method of CRC diagnosis relies on the invasive endoscopy. Non-invasive assays including fecal occult blood testing (FOBT) and fecal immunological test (FIT) are compromised by low sensitivity and specificity, especially at early stages. Thus, a non-invasive and accurate approach for CRC screening would be highly desirable. RESULTS A new qPCR-based assay combining the simultaneous detection of the DNA methylation status of ten candidate genes was used to examine plasma samples from 56 normal controls, 6 hyperplastic polys, 9 non-advanced adenomas (NAAs), 22 advanced adenomas (AAs) and 175 CRC patients, using 10 ng of cfDNA. We further built a logistic regression model for CRC diagnosis. We tested ten candidate methylation markers including twist1, vav3-as1, fbn1, c9orf50, sfmbt2, kcnq5, fam72c, itga4, kcnj12 and znf132. All markers showed moderate diagnostic performance with AUCs ranging from 0.726 to 0.815. Moreover, a 4-marker model, comprised of two previously reported markers (c9orf50 and twist1) and two novel ones (kcnj12 and znf132), demonstrated high performance for detecting colorectal cancer in an independent validation set (N = 69) with an overall AUC of 0.911 [95% confidence interval (CI) 0.834-0.988], sensitivity of 0.800 [95% CI 0.667-0.933] and specificity of 0.971 [95% CI 0.914-1.000]. The stage-stratified sensitivity of the model was 0.455 [95% CI 0.227-0.682], 0.667 [95% CI 0.289-1.000], 0.800 [95% CI 0.449-1.000], 0.800 [95% CI 0.449-1.000] and 0.842 [95% CI 0.678-1.000] for advanced adenoma and CRC stage I-IV, respectively. CONCLUSION kcnj12 and znf132 are two novel methylation biomarkers for CRC diagnosis. The 4-marker methylation model provides a new non-invasive choice for CRC screening and interception.
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Affiliation(s)
- Yunfeng Zhang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Qian Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Linhao Xu
- AnchorDx Medical Co., Ltd, Unit 502, 3rd Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Hong Wang
- AnchorDx Medical Co., Ltd, Unit 502, 3rd Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Xin Liu
- AnchorDx Inc., 6305 Landing Pkwy, Fremont, CA, 94538, USA
| | - Sihui Li
- AnchorDx Medical Co., Ltd, Unit 502, 3rd Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Tianliang Hu
- AnchorDx Medical Co., Ltd, Unit 502, 3rd Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Yanying Liu
- AnchorDx Medical Co., Ltd, Unit 502, 3rd Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Quanzhou Peng
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Zhiwei Chen
- AnchorDx Medical Co., Ltd, Unit 502, 3rd Luoxuan Road, International Bio-Island, Guangzhou, 510300, China. .,AnchorDx Inc., 6305 Landing Pkwy, Fremont, CA, 94538, USA.
| | - Xianrui Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China. .,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
| | - Jian-Bing Fan
- AnchorDx Medical Co., Ltd, Unit 502, 3rd Luoxuan Road, International Bio-Island, Guangzhou, 510300, China. .,Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China.
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Multiparametric MRI-based machine learning models for preoperatively predicting rectal adenoma with canceration. MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2021; 34:707-716. [PMID: 33646452 DOI: 10.1007/s10334-021-00915-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To propose multiparametric MRI-based machine learning models and assess their ability to preoperatively predict rectal adenoma with canceration. MATERIALS AND METHODS A total of 53 patients with postoperative pathology confirming rectal adenoma (n = 29) and adenoma with canceration (n = 24) were enrolled in this retrospective study. All patients were divided into a training cohort (n = 42) and a test cohort (n = 11). All patients underwent preoperative pelvic MR examination, including high-resolution T2-weighted imaging (HR-T2WI) and diffusion-weighted imaging (DWI). A total of 1396 radiomics features were extracted from the HR-T2WI and DWI sequences, respectively. The least absolute shrinkage and selection operator (LASSO) was utilized for feature selection from the radiomics feature sets from the HR-T2WI and DWI sequences and from the combined feature set with 2792 radiomics features incorporating two sequences. Five-fold cross-validation and two machine learning algorithms (logistic regression, LR; support vector machine, SVM) were utilized for model construction in the training cohort. The diagnostic performance of the models was evaluated by sensitivity, specificity and area under the curve (AUC) and compared with the Delong's test. RESULTS Ten, 8, and 25 optimal features were selected from 1396 HR-T2WI, 1396 DWI and 2792 combined features, respectively. Three group models were constructed using the selected features from HR-T2WI (ModelT2), DWI (ModelDWI) and the two sequences combined (Modelcombined). Modelcombined showed better prediction performance than ModelT2 and ModelDWI. In Modelcombined, there was no significant difference between the LR and SVM algorithms (p = 0.4795), with AUCs in the test cohort of 0.867 and 0.900, respectively. CONCLUSIONS Multiparametric MRI-based machine learning models have the potential to predict rectal adenoma with canceration. Compared with ModelT2 and ModelDWI, Modelcombined showed the best performance. Moreover, both LR and SVM have equal excellent performance for model construction.
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Decruyenaere P, Offner F, Vandesompele J. Circulating RNA biomarkers in diffuse large B-cell lymphoma: a systematic review. Exp Hematol Oncol 2021; 10:13. [PMID: 33593440 PMCID: PMC7885416 DOI: 10.1186/s40164-021-00208-3] [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: 12/30/2020] [Accepted: 02/06/2021] [Indexed: 12/31/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common histological subtype of non-Hodgkin's lymphomas (NHL). DLBCL is an aggressive malignancy that displays a great heterogeneity in terms of morphology, genetics and biological behavior. While a sustained complete remission is obtained in the majority of patients with standard immunochemotherapy, patients with refractory of relapsed disease after first-line treatment have a poor prognosis. This patient group represents an important unmet need in lymphoma treatment. In recent years, improved understanding of the underlying molecular pathogenesis had led to new classification and prognostication tools, including the development of cell-free biomarkers in liquid biopsies. Although the majority of studies have focused on the use of cell-free fragments of DNA (cfDNA), there has been an increased interest in circulating-free coding and non-coding RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA), as well as RNA encapsulated in extracellular vesicles or tumor-educated platelets (TEPs). We performed a systematic search in PubMed to identify articles that evaluated circulating RNA as diagnostic, subtype, treatment response or prognostic biomarkers in a human DLBCL population. A total of 35 articles met the inclusion criteria. The aim of this systematic review is to present the current understanding of circulating RNA molecules as biomarker in DLBCL and to discuss their future potential.
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Affiliation(s)
- Philippe Decruyenaere
- Department of Hematology, Ghent University Hospital, 9K12, Campus UZ Ghent, Corneel Heymanslaan 10, 9000 Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Fritz Offner
- Department of Hematology, Ghent University Hospital, 9K12, Campus UZ Ghent, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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Gallardo-Gómez M, De Chiara L, Álvarez-Chaver P, Cubiella J. Colorectal cancer screening and diagnosis: omics-based technologies for development of a non-invasive blood-based method. Expert Rev Anticancer Ther 2021; 21:723-738. [PMID: 33507120 DOI: 10.1080/14737140.2021.1882858] [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] [Indexed: 02/07/2023]
Abstract
Introduction: Colorectal cancer (CRC) is one of the most important health problems in the Western world. In order to reduce the burden of the disease, two strategies are proposed: screening and prompt detection in symptomatic patients. Although diagnosis and prevention are mainly based on colonoscopy, fecal hemoglobin detection has been widely implemented as a noninvasive strategy. Various studies aiming to discover blood-based biomarkers have recently emerged.Areas covered: The burgeoning omics field provides diverse high-throughput approaches for CRC blood-based biomarker discovery. In this review, we appraise the most robust and commonly used technologies within the fields of genomics, transcriptomics, epigenomics, proteomics, and metabolomics, together with their targeted validation approaches. We summarize the transference process from the discovery phase until clinical translation. Finally, we review the best candidate biomarkers and their potential clinical applicability.Expert opinion: Some available biomarkers are promising, especially in the field of epigenomics: DNA methylation and microRNA. Transference requires the joint collaboration of basic researchers, intellectual property experts, technology transfer officers and clinicians. Blood-based biomarkers will be selected not only based on their diagnostic accuracy and cost but also on their reliability, applicability to clinical analysis laboratories and their acceptance by the population.
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Affiliation(s)
- María Gallardo-Gómez
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Loretta De Chiara
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Paula Álvarez-Chaver
- Proteomics Unit, Service of Structural Determination, Proteomics and Genomics, Center for Scientific and Technological Research Support (CACTI), University of Vigo, Vigo, Spain
| | - Joaquin Cubiella
- Department of Gastroenterology, Hospital Universitario De Ourense, Ourense, Spain.,Instituto De Investigación Sanitaria Galicia Sur, Ourense, Spain.,Centro De Investigación Biomédica En Red Enfermedades Hepáticas Y Digestivas, Ourense, Spain
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Circulating Cell-Free Nucleic Acids: Main Characteristics and Clinical Application. Int J Mol Sci 2020; 21:ijms21186827. [PMID: 32957662 PMCID: PMC7555669 DOI: 10.3390/ijms21186827] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Liquid biopsy recently became a very promising diagnostic method that has several advantages over conventional invasive methods. Liquid biopsy may serve as a source of several important biomarkers including cell-free nucleic acids (cf-NAs). Cf-DNA is widely used in prenatal testing in order to characterize fetal genetic disorders. Analysis of cf-DNA may provide information about the mutation profile of tumor cells, while cell-free non-coding RNAs are promising biomarker candidates in the diagnosis and prognosis of cancer. Many of these markers have the potential to help clinicians in therapy selection and in the follow-up of patients. Thus, cf-NA-based diagnostics represent a new path in personalized medicine. Although several reviews are available in the field, most of them focus on a limited number of cf-NA types. In this review, we give an overview about all known cf-NAs including cf-DNA, cf-mtDNA and cell-free non-coding RNA (miRNA, lncRNA, circRNA, piRNA, YRNA, and vtRNA) by discussing their biogenesis, biological function and potential as biomarker candidates in liquid biopsy. We also outline possible future directions in the field.
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20
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Matsuyama T, Kandimalla R, Ishikawa T, Takahashi N, Yamada Y, Yasuno M, Kinugasa Y, Hansen TF, Fakih M, Uetake H, Győrffy B, Goel A. A novel mesenchymal-associated transcriptomic signature for risk-stratification and therapeutic response prediction in colorectal cancer. Int J Cancer 2020; 147:3250-3261. [PMID: 32657428 DOI: 10.1002/ijc.33129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/25/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Risk stratification in Stage II and III colorectal cancer (CRC) patients is critical, as it allows patient selection for adjuvant chemotherapy. In view of the inadequacy of current clinicopathological features for risk-stratification, we undertook a systematic and comprehensive biomarker discovery effort to develop a risk-assessment signature in CRC patients. The biomarker discovery phase examined 853 CRC patients, and identified a gene signature for predicting recurrence-free survival (RFS). This signature was validated in a meta-analysis of 1212 patients from nine independent datasets, and its performance was compared against established prognostic signatures and consensus molecular subtypes (CMS). In addition, a risk-prediction model was trained (n = 142), and subsequently validated in an independent clinical cohort (n = 286). As a result, this mesenchymal-associated transcriptomic signature (MATS) identified high-risk CRC patients with poor RFS in the discovery (hazard ratio [HR]: 1.79), and nine validation cohorts (HR: 1.86). In multivariate analysis, MATS was the most significant predictor of RFS compared to established prognostic signatures and CMS subtypes. Intriguingly, MATS robustly identified CMS4-subtype in multiple CRC cohorts (AUC = 0.92-0.99). In the two clinical cohorts, MATS stratified low and high-risk groups with a 5-year RFS in the training (HR: 4.11) and validation cohorts (HR: 2.55), as well as predicted response to adjuvant therapy in Stage II and III CRC patients. We report a novel prognostic and predictive biomarker signature in CRC, which is superior to currently used approaches and have the potential for clinical translation in near future.
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Affiliation(s)
- Takatoshi Matsuyama
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA.,Department of Gastrointestinal Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Raju Kandimalla
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
| | - Toshiaki Ishikawa
- Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Naoki Takahashi
- Department of Gastroenterology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuhide Yamada
- Department of Gastroenterology, National Cancer Center Hospital, Tokyo, Japan
| | - Masamichi Yasuno
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Yusuke Kinugasa
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | | | - Marwan Fakih
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California, USA
| | - Hiroyuki Uetake
- Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary.,2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA.,Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, California, USA
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21
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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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