51
|
Song D, Wang F, Ju Y, He Q, Sun T, Deng W, Ding R, Zhang C, Xu Q, Qi C, Bao J. Application and development of noninvasive biomarkers for colorectal cancer screening: a systematic review. Int J Surg 2023; 109:925-935. [PMID: 36974713 PMCID: PMC10389553 DOI: 10.1097/js9.0000000000000260] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/22/2023] [Indexed: 03/29/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is the second most common cause of cancer-related death (9.4% of the 9.9 million cancer deaths). However, CRC develops slowly, and early detection and intervention can effectively improve the survival rate and quality of life. Although colonoscopy can detect and diagnose CRC, it is unsuitable for CRC screening in average-risk populations. Some commercial kits based on DNA mutation or methylation are approved for screening, but the low sensitivity for advanced adenoma or early-stage CRC would limit the applications. MAIN RESULTS Recently, researchers have focused on developing noninvasive or minimally invasive, easily accessible biomarkers with higher sensitivity and accuracy for CRC screening. Numerous reports describe advances in biomarkers, including DNA mutations and methylation, mRNA and miRNA, gut microbes, and metabolites, as well as low-throughput multiomics panels. In small cohorts, the specificity and sensitivity improved when fecal immunochemical testing combined with other biomarkers; further verification in large cohorts is expected. In addition, the continuous improvement of laboratory technology has also improved the sensitivity of detection technology, such as PCR, and the application of CRISPR/Cas technology. Besides, artificial intelligence has extensively promoted the mining of biomarkers. Machine learning was performed to construct a diagnosis model for CRC screening based on the cfDNA fragment features from whole-genome sequencing data. In another study, multiomics markers, including cfDNA, epigenetic, and protein signals, were also discovered by machine learning. Finally, advancements in sensor technology promote the applicability of volatile organic compounds in CRC early detection. CONCLUSION Here, the authors review advances in early detection and screening of CRC based on different biomarker types. Most studies reported optimistic findings based on preliminary research, and prospective clinical studies are ongoing. These promising biomarkers are expected to more accurately identify early-stage patients with CRC and be applied in the future.
Collapse
Affiliation(s)
| | - Fei Wang
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd, Nanjing Simcere Medical Laboratory Science Co. Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co. Ltd, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Yongzhi Ju
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd, Nanjing Simcere Medical Laboratory Science Co. Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co. Ltd, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Qianru He
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd, Nanjing Simcere Medical Laboratory Science Co. Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co. Ltd, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Tingting Sun
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd, Nanjing Simcere Medical Laboratory Science Co. Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co. Ltd, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Wanglong Deng
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd, Nanjing Simcere Medical Laboratory Science Co. Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co. Ltd, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Ran Ding
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd, Nanjing Simcere Medical Laboratory Science Co. Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co. Ltd, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Chao Zhang
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd, Nanjing Simcere Medical Laboratory Science Co. Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co. Ltd, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Qing Xu
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd, Nanjing Simcere Medical Laboratory Science Co. Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co. Ltd, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Chuang Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd, Nanjing Simcere Medical Laboratory Science Co. Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co. Ltd, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Jun Bao
- Medical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting
| |
Collapse
|
52
|
Lak NSM, Seijger A, van Zogchel LMJ, Gelineau NU, Javadi A, Zappeij-Kannegieter L, Bongiovanni L, Andriessen A, Stutterheim J, van der Schoot CE, de Bruin A, Tytgat GAM. Cell-Free RNA from Plasma in Patients with Neuroblastoma: Exploring the Technical and Clinical Potential. Cancers (Basel) 2023; 15:cancers15072108. [PMID: 37046768 PMCID: PMC10093559 DOI: 10.3390/cancers15072108] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/17/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Neuroblastoma affects mostly young children, bearing a high morbidity and mortality. Liquid biopsies, e.g., molecular analysis of circulating tumor-derived nucleic acids in blood, offer a minimally invasive diagnostic modality. Cell-free RNA (cfRNA) is released by all cells, especially cancer. It circulates in blood packed in extracellular vesicles (EV) or attached to proteins. We studied the feasibility of analyzing cfRNA and EV, isolated by size exclusion chromatography (SEC), from platelet-poor plasma from healthy controls (n = 40) and neuroblastoma patients with localized (n = 10) and metastatic disease (n = 30). The mRNA content was determined using several multiplex droplet digital PCR (ddPCR) assays for a neuroblastoma-specific gene panel (PHOX2B, TH, CHRNA3) and a cell cycle regulation panel (E2F1, CDC6, ATAD2, H2AFZ, MCM2, DHFR). We applied corrections for the presence of platelets. We demonstrated that neuroblastoma-specific markers were present in plasma from 14/30 patients with metastatic disease and not in healthy controls and patients with localized disease. Most cell cycle markers had a higher expression in patients. The mRNA markers were mostly present in the EV-enriched SEC fractions. In conclusion, cfRNA can be isolated from plasma and EV and analyzed using multiplex ddPCR. cfRNA is an interesting novel liquid biopsy-based target to explore further.
Collapse
|
53
|
Brito-Rocha T, Constâncio V, Henrique R, Jerónimo C. Shifting the Cancer Screening Paradigm: The Rising Potential of Blood-Based Multi-Cancer Early Detection Tests. Cells 2023; 12:cells12060935. [PMID: 36980276 PMCID: PMC10047029 DOI: 10.3390/cells12060935] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer remains a leading cause of death worldwide, partly owing to late detection which entails limited and often ineffective therapeutic options. Most cancers lack validated screening procedures, and the ones available disclose several drawbacks, leading to low patient compliance and unnecessary workups, adding up the costs to healthcare systems. Hence, there is a great need for innovative, accurate, and minimally invasive tools for early cancer detection. In recent years, multi-cancer early detection (MCED) tests emerged as a promising screening tool, combining molecular analysis of tumor-related markers present in body fluids with artificial intelligence to simultaneously detect a variety of cancers and further discriminate the underlying cancer type. Herein, we aim to provide a highlight of the variety of strategies currently under development concerning MCED, as well as the major factors which are preventing clinical implementation. Although MCED tests depict great potential for clinical application, large-scale clinical validation studies are still lacking.
Collapse
Affiliation(s)
- Tiago Brito-Rocha
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Master Program in Oncology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Vera Constâncio
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Program in Biomedical Sciences, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| |
Collapse
|
54
|
Tan WY, Sharma A, Das P, Ahuja N. Early Detection of Cancers in the Era of Precision Oncology. Curr Opin Oncol 2023; 35:115-124. [PMID: 36721896 DOI: 10.1097/cco.0000000000000931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
PURPOSE OF REVIEW The increasing global incidence of cancer demands innovative cancer detection modalities. The current population-based early cancer detection approaches focus on several major types of cancers (breast, prostate, cervical, lung and colon) at their early stages, however, they generally do not target high-risk individuals at precancerous stages. RECENT FINDINGS Some cancers, such as pancreatic cancer, are challenging to detect in their early stages. Therefore, there is a pressing need for improved, accessible, noninvasive, and cost-effective early detection methods. Harnessing cell-free-based biomarker-driven strategies paves a new era of precision diagnosis for multicancer early detection. The majority of these tests are in the early stages and expensive, but these approaches are expected to become cost sensitive in the near future. SUMMARY This review provides an overview of early cancer detection strategies, highlighting the methods, challenges, and issues to be addressed to revolutionize and improve global early cancer detection.
Collapse
Affiliation(s)
| | - Anup Sharma
- Yale School of Medicine, Department of Surgery
| | | | - Nita Ahuja
- Yale School of Medicine, Department of Surgery
- Yale School of Medicine, Department of Pathology
- Yale School of Medicine, Biological and Biomedical Sciences Program (BBS), Yale University, New Haven, Connecticut, USA
| |
Collapse
|
55
|
Aggarwal N, Liang Y, Foo JL, Ling H, Hwang IY, Chang MW. FELICX: A robust nucleic acid detection method using flap endonuclease and CRISPR-Cas12. Biosens Bioelectron 2023; 222:115002. [PMID: 36527830 DOI: 10.1016/j.bios.2022.115002] [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: 10/11/2022] [Revised: 11/26/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Nucleic acid detection is crucial for monitoring diseases for which rapid, sensitive, and easy-to-deploy diagnostic tools are needed. CRISPR-based technologies can potentially fulfill this need for nucleic acid detection. However, their widespread use has been restricted by the requirement of a protospacer adjacent motif in the target and extensive guide RNA optimization. In this study, we developed FELICX, a technique that can overcome these limitations and provide a useful alternative to existing technologies. FELICX comprises flap endonuclease, Taq ligase and CRISPR-Cas for diagnostics (X) and can be used for detecting nucleic acids and single-nucleotide polymorphisms. This method can be deployed as a point-of-care test, as only two temperatures are needed without thermocycling for its functionality, with the result generated on lateral flow strips. As a proof-of-concept, we showed that up to 0.6 copies/μL of DNA and RNA could be detected by FELICX in 60 min and 90 min, respectively, using simulated samples. Additionally, FELICX could be used to probe any base pair, unlike other CRISPR-based technologies. Finally, we demonstrated the versatility of FELICX by employing it for virus detection in infected human cells, the identification of antibiotic-resistant bacteria, and cancer diagnostics using simulated samples. Based on its unique advantages, we envision the use of FELICX as a next-generation CRISPR-based technology in nucleic acid diagnostics.
Collapse
Affiliation(s)
- Nikhil Aggarwal
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yuanmei Liang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jee Loon Foo
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - In Young Hwang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| |
Collapse
|
56
|
A straightforward method to quantify circulating mRNAs as biomarkers of colorectal cancer. Sci Rep 2023; 13:2739. [PMID: 36792801 PMCID: PMC9932139 DOI: 10.1038/s41598-023-29948-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Optimizing the biomarker combination to be analyzed in liquid biopsies should improve personalized medicine. We developed a method to purify circulating cell-free mRNAs from plasma samples and to quantify them by RT-qPCR. We selected three candidate colorectal cancer biomarkers (B2M, TIMP-1, and CLU). Their mRNA levels were significantly higher in plasma of patients with metastatic colorectal cancer patients (mCRC) (n = 107) than in healthy individuals (HI) (n = 53). To increase the discriminating performance of our method, we analyzed the sum of the three mRNA levels (BTC index). The area under the ROC curve (AUC) to estimate the BTC index capacity to discriminate between mCRC and HI plasma was 0.903. We also determined the optimal BTC index cut-off to distinguish between plasma samples, with 82% of sensitivity and 93% of specificity. By using mRNA as a novel liquid biopsy analytical parameter, our method has the potential to facilitate rapid screening of CRCm.
Collapse
|
57
|
Chen G, Zhang J, Fu Q, Taly V, Tan F. Integrative analysis of multi-omics data for liquid biopsy. Br J Cancer 2023; 128:505-518. [PMID: 36357703 PMCID: PMC9938261 DOI: 10.1038/s41416-022-02048-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
The innovation of liquid biopsy holds great potential to revolutionise cancer management through early diagnosis and timely treatment of cancer. Integrative analysis of different tumour-derived omics data (such as genomics, epigenetics, fragmentomics, and proteomics) from body fluids for cancer detection and monitoring could outperform the analysis of single modality data alone. In this review, we focussed on the discussion of early cancer detection and molecular residual disease surveillance based on multi-omics data of blood. We summarised diverse types of tumour-derived components, current popular platforms for profiling cancer-associated signals, machine learning approaches for joint analysis of liquid biopsy data, as well as multi-omics-based early detection of cancers, molecular residual disease monitoring, and treatment response surveillance. We also discussed the challenges and future directions of multi-omics-based liquid biopsy. With the development of both experimental protocols and computational methods dedicated to liquid biopsy, the implementation of multi-omics strategies into the clinical workflow will likely benefit the clinical management of cancers including decision-making guidance and patient outcome improvement.
Collapse
Affiliation(s)
- Geng Chen
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China.
- Center for Bioinformatics and Computational Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China.
| | - Jing Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China
| | - Qiaoting Fu
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, 200443, Shanghai, China
| | - Valerie Taly
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe labélisée Ligue Nationale contre le cancer, Centre de Recherche des Cordeliers, Paris, France.
| | - Fei Tan
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China.
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, 200443, Shanghai, China.
| |
Collapse
|
58
|
Zhu W, Love K, Gray SW, Raz DJ. Liquid Biopsy Screening for Early Detection of Lung Cancer: Current State and Future Directions. Clin Lung Cancer 2023; 24:209-217. [PMID: 36797152 DOI: 10.1016/j.cllc.2023.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/06/2023] [Accepted: 01/17/2023] [Indexed: 01/28/2023]
Abstract
Liquid biopsy (LB) is clinically utilized to detect minute amounts of genetic material or protein shed by cancer cells, most commonly cell free DNA (cfDNA), as a noninvasive precision oncology tool to assess genomic alterations to guide cancer therapy or to detect the persistence of tumor cells after therapy. LB is also being developed as a multi-cancer screening assay. The use of LB holds great promise as a tool to detect lung cancer early. Although lung cancer screening (LCS) with low-dose computed tomography (LDCT) substantially reduces lung cancer mortality in high-risk individuals, the ability of current LCS guidelines to reduce the public health burden of advanced lung cancer through early detection has been limited. LB may be an important tool to improve early lung cancer detection among all populations at risk for lung cancer. In this systematic review, we summarize the test characteristics, including sensitivity and specificity of individual tests, as they pertain to the detection of lung cancer. We also address critical questions in the use of liquid biopsy for early detection of lung cancer including: 1. How might liquid biopsy be used to detect lung cancer early; 2. How accurate is liquid biopsy in detecting lung cancer early; and 3. Does liquid biopsy perform as well in never and light-smokers compared with current and former smokers.
Collapse
Affiliation(s)
- William Zhu
- Department of Surgery, City of Hope, Duarte, CA
| | - Kyra Love
- Library Services, City of Hope, Duarte, CA
| | - Stacy W Gray
- Department of Medical Oncology and Therapeutics Research/ Department of Population Sciences, City of Hope, Duarte, CA
| | - Dan J Raz
- Department of Surgery, City of Hope, Duarte, CA.
| |
Collapse
|
59
|
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.
Collapse
Affiliation(s)
| | | | - Ritu Gupta
- *Correspondence: Deepshi Thakral, ; Ritu Gupta,
| | | |
Collapse
|
60
|
Zhang L, Liu X, Wang C, Li X, Tian G, Wang W. Cell-Free RNA Sequencing from Biofluid Samples. Methods Mol Biol 2023; 2695:9-25. [PMID: 37450109 DOI: 10.1007/978-1-0716-3346-5_2] [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] [Indexed: 07/18/2023]
Abstract
Liquid biopsy has obvious advantages over invasive sampling methods. Cell-free DNA is now widely used in prenatal and cancer diagnosis. Cell-free RNA is relatively unstable but could contain potential biomarkers, and some studies have demonstrated that cfRNA sequencing may be developed to be a promising diagnostic assay for disease detection. In this chapter, we introduce a modified protocol for the detection of cfRNA based on next-generation sequencing (NGS). This protocol has been specifically optimized for low-input, fragmented cfRNA samples.
Collapse
|
61
|
Hamza E, Cosandey J, Gerber V, Koch C, Unger L. The potential of three whole blood microRNAs to predict outcome and monitor treatment response in sarcoid-bearing equids. Vet Res Commun 2023; 47:87-98. [PMID: 35484337 PMCID: PMC9873782 DOI: 10.1007/s11259-022-09930-7] [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: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 01/28/2023]
Abstract
MicroRNAs (miRNAs) have been proposed as biomarkers for equine sarcoid (ES) disease. In this study, the suitability of three whole blood miRNAs to diagnose ES and to predict and monitor the outcome of therapy was explored. Using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), expression levels of eca-miR-127, eca-miR-379, and eca-miR-432 in whole blood of ES-affected equids before and at least one year after therapy were compared to those of unaffected control equids. Associations of age, sex, species, diagnosis, and therapy outcome with miRNA expression levels were examined using general linear models. In total, 48 ES-affected equids and 47 control equids were recruited. From the affected animals, 31 responded favorably to treatment, and 17 demonstrated a failure of therapy. None of the tested miRNAs were influenced by age. Male equids showed increased expression of eca-miR-127 compared to females and horses showed higher expression levels of eca-miR-379 and eca-miR-432 than donkeys. Eca-miR-127 was confirmed as a diagnostic discriminator between ES-affected and control equids. No difference in miRNA profiles before therapy was found when comparing ES-affected equids with success vs. failure of therapy. Eca-miR-379 and eca-miR-432 decreased over time in horses where therapy was successful, but not in those cases where it failed. Biological variables influence equine whole blood miRNA expression, which may complicate biomarker validation. While none of the tested miRNAs could predict the response to therapy in ES-affected equids and eca-miR-127 showed poor diagnostic accuracy for ES, eca-miR-379 and eca-miR-432 miRNAs might allow refinement of monitoring of success of ES therapy.
Collapse
Affiliation(s)
- E. Hamza
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland ,Departement of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - J. Cosandey
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - V. Gerber
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - C. Koch
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - L. Unger
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| |
Collapse
|
62
|
Deleu J, Schoofs K, Decock A, Verniers K, Roelandt S, Denolf A, Verreth J, De Wilde B, Van Maerken T, De Preter K, Vandesompele J. Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA. Hum Genomics 2022; 16:73. [PMID: 36587211 PMCID: PMC9805675 DOI: 10.1186/s40246-022-00446-4] [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: 10/06/2022] [Accepted: 12/19/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Blood plasma, one of the most studied liquid biopsies, contains various molecules that have biomarker potential for cancer detection, including cell-free DNA (cfDNA) and cell-free RNA (cfRNA). As the vast majority of cell-free nucleic acids in circulation are non-cancerous, a laboratory workflow with a high detection sensitivity of tumor-derived nucleic acids is a prerequisite for precision oncology. One way to meet this requirement is by the combined analysis of cfDNA and cfRNA from the same liquid biopsy sample. So far, no study has systematically compared the performance of cfDNA and cfRNA co-purification to increase sensitivity. RESULTS First, we set up a framework using digital PCR (dPCR) technology to quantify cfDNA and cfRNA from human blood plasma in order to compare cfDNA/cfRNA co-purification kit performance. To that end, we optimized two dPCR duplex assays, designed to quantify both cfDNA and cfRNA with the same assays, by ensuring that primers and probes are located within a highly abundant exon. Next, we applied our optimized workflow to evaluate the co-purification performance of two manual and two semi-automated methods over a range of plasma input volumes (0.06-4 mL). Some kits result in higher nucleic acid concentrations in the eluate, while consuming only half of the plasma volume. The combined nucleic acid quantification systematically results in higher nucleic acid concentrations as compared to a parallel quantification of cfDNA and cfRNA in the eluate. CONCLUSIONS We provide a framework to evaluate the performance of cfDNA/cfRNA co-purification kits and have tested two manual and two semi-automated co-purification kits in function of the available plasma input amount and the intended use of the nucleic acid eluate. We demonstrate that the combined quantification of cfDNA and cfRNA has a benefit compared to separate quantification. We foresee that the results of this study are instrumental for clinical applications to help increase mutation detection sensitivity, allowing improved disease detection and monitoring.
Collapse
Affiliation(s)
- Jill Deleu
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kathleen Schoofs
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.510942.bTranslational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Anneleen Decock
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kimberly Verniers
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sofie Roelandt
- grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.510942.bTranslational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Angie Denolf
- grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.510942.bTranslational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Joke Verreth
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bram De Wilde
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.410566.00000 0004 0626 3303Department of Paediatric Haematology Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Tom Van Maerken
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.420028.c0000 0004 0626 4023Department of Laboratory Medicine, AZ Groeninge, Kortrijk, Belgium
| | - Katleen De Preter
- grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium ,grid.510942.bTranslational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Jo Vandesompele
- grid.510942.bOncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| |
Collapse
|
63
|
Wen X, Pu H, Liu Q, Guo Z, Luo D. Circulating Tumor DNA-A Novel Biomarker of Tumor Progression and Its Favorable Detection Techniques. Cancers (Basel) 2022; 14:6025. [PMID: 36551512 PMCID: PMC9775401 DOI: 10.3390/cancers14246025] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/20/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Cancer is the second leading cause of death in the world and seriously affects the quality of life of patients. The diagnostic techniques for tumors mainly include tumor biomarker detection, instrumental examination, and tissue biopsy. In recent years, liquid technology represented by circulating tumor DNA (ctDNA) has gradually replaced traditional technology with its advantages of being non-invasive and accurate, its high specificity, and its high sensitivity. ctDNA may carry throughout the circulatory system through tumor cell necrosis, apoptosis, circulating exosome secretion, etc., carrying the characteristic changes in tumors, such as mutation, methylation, microsatellite instability, gene rearrangement, etc. In this paper, ctDNA mutation and methylation, as the objects to describe the preparation process before ctDNA analysis, and the detection methods of two gene-level changes, including a series of enrichment detection techniques derived from PCR, sequencing-based detection techniques, and comprehensive detection techniques, are combined with new materials. In addition, the role of ctDNA in various stages of cancer development is summarized, such as early screening, diagnosis, molecular typing, prognosis prediction, recurrence monitoring, and drug guidance. In summary, ctDNA is an ideal biomarker involved in the whole process of tumor development.
Collapse
Affiliation(s)
- Xiaosha Wen
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, China
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Huijie Pu
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, China
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Quan Liu
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Zifen Guo
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Dixian Luo
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| |
Collapse
|
64
|
Doebley AL, Ko M, Liao H, Cruikshank AE, Santos K, Kikawa C, Hiatt JB, Patton RD, De Sarkar N, Collier KA, Hoge ACH, Chen K, Zimmer A, Weber ZT, Adil M, Reichel JB, Polak P, Adalsteinsson VA, Nelson PS, MacPherson D, Parsons HA, Stover DG, Ha G. A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA. Nat Commun 2022; 13:7475. [PMID: 36463275 PMCID: PMC9719521 DOI: 10.1038/s41467-022-35076-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Cell-free DNA (cfDNA) has the potential to inform tumor subtype classification and help guide clinical precision oncology. Here we develop Griffin, a framework for profiling nucleosome protection and accessibility from cfDNA to study the phenotype of tumors using as low as 0.1x coverage whole genome sequencing data. Griffin employs a GC correction procedure tailored to variable cfDNA fragment sizes, which generates a better representation of chromatin accessibility and improves the accuracy of cancer detection and tumor subtype classification. We demonstrate estrogen receptor subtyping from cfDNA in metastatic breast cancer. We predict estrogen receptor subtype in 139 patients with at least 5% detectable circulating tumor DNA with an area under the receive operator characteristic curve (AUC) of 0.89 and validate performance in independent cohorts (AUC = 0.96). In summary, Griffin is a framework for accurate tumor subtyping and can be generalizable to other cancer types for precision oncology applications.
Collapse
Affiliation(s)
- Anna-Lisa Doebley
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Minjeong Ko
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hanna Liao
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - A Eden Cruikshank
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Caroline Kikawa
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Joseph B Hiatt
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Robert D Patton
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Anna C H Hoge
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Katharine Chen
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Anat Zimmer
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zachary T Weber
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Mohamed Adil
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jonathan B Reichel
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paz Polak
- Department of Oncological Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | | | - Peter S Nelson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - David MacPherson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Daniel G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Gavin Ha
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
| |
Collapse
|
65
|
Seneviratne C, Shetty AC, Geng X, McCracken C, Cornell J, Mullins K, Jiang F, Stass S. A Pilot Analysis of Circulating cfRNA Transcripts for the Detection of Lung Cancer. Diagnostics (Basel) 2022; 12:2897. [PMID: 36552904 PMCID: PMC9776862 DOI: 10.3390/diagnostics12122897] [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: 06/13/2022] [Revised: 09/20/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
Lung cancers are the leading cause of cancer-related deaths worldwide. Studies have shown that non-small cell lung cancer (NSCLC), which constitutes the majority of lung cancers, is significantly more responsive to early-stage interventions. However, the early stages are often asymptomatic, and current diagnostic methods are limited in their precision and safety. The cell-free RNAs (cfRNAs) circulating in plasma (liquid biopsies) offer a non-invasive detection of spatial and temporal changes occurring in primary tumors since the early stages. To address gaps in the current cfRNA knowledge base, we conducted a pilot study for the comprehensive analysis of transcriptome-wide changes in plasma cfRNA in NSCLC patients. Total cfRNA was extracted from archived plasma collected from NSCLC patients (N = 12), cancer-free former smokers (N = 12), and non-smoking healthy volunteers (N = 12). Plasma cfRNA expression levels were quantified by using a tagmentation-based library preparation and sequencing. The comparisons of cfRNA expression levels between patients and the two control groups revealed a total of 2357 differentially expressed cfRNAs enriched in 123 pathways. Of these, 251 transcripts were previously reported in primary NSCLCs. A small subset of genes (N = 5) was validated in an independent sample (N = 50) using qRT-PCR. Our study provides a framework for developing blood-based assays for the early detection of NSCLC and warrants further validation.
Collapse
Affiliation(s)
- Chamindi Seneviratne
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Amol Carl Shetty
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Xinyan Geng
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carrie McCracken
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jessica Cornell
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kristin Mullins
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD 21201, USA
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sanford Stass
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD 21201, USA
| |
Collapse
|
66
|
Stankunaite R, Marshall LV, Carceller F, Chesler L, Hubank M, George SL. Liquid biopsy for children with central nervous system tumours: Clinical integration and technical considerations. Front Pediatr 2022; 10:957944. [PMID: 36467471 PMCID: PMC9709284 DOI: 10.3389/fped.2022.957944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) analysis has the potential to revolutionise the care of patients with cancer and is already moving towards standard of care in some adult malignancies. Evidence for the utility of cfDNA analysis in paediatric cancer patients is also accumulating. In this review we discuss the limitations of blood-based assays in patients with brain tumours and describe the evidence supporting cerebrospinal fluid (CSF) cfDNA analysis. We make recommendations for CSF cfDNA processing to aid the standardisation and technical validation of future assays. We discuss the considerations for interpretation of cfDNA analysis and highlight promising future directions. Overall, cfDNA profiling shows great potential as an adjunct to the analysis of biopsy tissue in paediatric cancer patients, with the potential to provide a genetic molecular profile of the tumour when tissue biopsy is not feasible. However, to fully realise the potential of cfDNA analysis for children with brain tumours larger prospective studies incorporating serial CSF sampling are required.
Collapse
Affiliation(s)
- Reda Stankunaite
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Clinical Genomics, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Evolutionary Genomics and Modelling, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Lynley V. Marshall
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Fernando Carceller
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Michael Hubank
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Clinical Genomics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sally L. George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| |
Collapse
|
67
|
Punzón-Jiménez P, Lago V, Domingo S, Simón C, Mas A. Molecular Management of High-Grade Serous Ovarian Carcinoma. Int J Mol Sci 2022; 23:13777. [PMID: 36430255 PMCID: PMC9692799 DOI: 10.3390/ijms232213777] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) represents the most common form of epithelial ovarian carcinoma. The absence of specific symptoms leads to late-stage diagnosis, making HGSOC one of the gynecological cancers with the worst prognosis. The cellular origin of HGSOC and the role of reproductive hormones, genetic traits (such as alterations in P53 and DNA-repair mechanisms), chromosomal instability, or dysregulation of crucial signaling pathways have been considered when evaluating prognosis and response to therapy in HGSOC patients. However, the detection of HGSOC is still based on traditional methods such as carbohydrate antigen 125 (CA125) detection and ultrasound, and the combined use of these methods has yet to support significant reductions in overall mortality rates. The current paradigm for HGSOC management has moved towards early diagnosis via the non-invasive detection of molecular markers through liquid biopsies. This review presents an integrated view of the relevant cellular and molecular aspects involved in the etiopathogenesis of HGSOC and brings together studies that consider new horizons for the possible early detection of this gynecological cancer.
Collapse
Affiliation(s)
- Paula Punzón-Jiménez
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
| | - Victor Lago
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Obstetrics and Gynecology, CEU Cardenal Herrera University, 46115 Valencia, Spain
| | - Santiago Domingo
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
| | - Carlos Simón
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Harvard University, Boston, MA 02215, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aymara Mas
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
| |
Collapse
|
68
|
Gray KJ, Hemberg M, Karumanchi SA. Cell-Free RNA Transcriptome and Prediction of Adverse Pregnancy Outcomes. Clin Chem 2022; 68:1358-1360. [PMID: 35929553 PMCID: PMC9990094 DOI: 10.1093/clinchem/hvac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022]
Affiliation(s)
- Kathryn J Gray
- Department of Obstetrics & Gynecology, Brigham and Women's Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Martin Hemberg
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - S Ananth Karumanchi
- Harvard Medical School, Boston, MA, USA.,Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| |
Collapse
|
69
|
Albrecht LJ, Höwner A, Griewank K, Lueong SS, von Neuhoff N, Horn PA, Sucker A, Paschen A, Livingstone E, Ugurel S, Zimmer L, Horn S, Siveke JT, Schadendorf D, Váraljai R, Roesch A. Circulating cell-free messenger RNA enables non-invasive pan-tumour monitoring of melanoma therapy independent of the mutational genotype. Clin Transl Med 2022; 12:e1090. [PMID: 36320118 PMCID: PMC9626658 DOI: 10.1002/ctm2.1090] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/09/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Plasma-derived tumour-specific cell-free nucleic acids are increasingly utilized as a minimally invasive, real-time biomarker approach in many solid tumours. Circulating tumour DNA of melanoma-specific mutations is currently the best studied liquid biopsy biomarker for melanoma. However, the combination of hotspot genetic alterations covers only around 80% of all melanoma patients. Therefore, alternative approaches are needed to enable the follow-up of all genotypes, including wild-type. METHODS We identified KPNA2, DTL, BACE2 and DTYMK messenger RNA (mRNA) upregulated in melanoma versus nevi tissues by unsupervised data mining (N = 175 melanoma, N = 20 normal skin, N = 6 benign nevi) and experimentally confirmed differential mRNA expression in vitro (N = 18 melanoma, N = 8 benign nevi). Circulating cell-free RNA (cfRNA) was analysed in 361 plasma samples (collected before and during therapy) from 100 melanoma patients and 18 healthy donors. Absolute cfRNA copies were quantified on droplet digital PCR. RESULTS KPNA2, DTL, BACE2 and DTYMK cfRNA demonstrated high diagnostic accuracy between melanoma patients' and healthy donors' plasma (AUC > 86%, p < .0001). cfRNA copies increased proportionally with increasing tumour burden independently of demographic variables and even remained elevated in individuals with radiological absence of disease. Re-analysis of single-cell transcriptomes revealed a pan-tumour origin of cfRNA, including endothelial, cancer-associated fibroblasts, macrophages and B cells beyond melanoma cells as cellular sources. Low baseline cfRNA levels were associated with significantly longer progression-free survival (PFS) (KPNA2 HR = .54, p = .0362; DTL HR = .60, p = .0349) and overall survival (KPNA2 HR = .52, p = .0237; BACE2 HR = .55, p = .0419; DTYMK HR = .43, p = .0393). Lastly, we found that cfRNA copies significantly increased during therapy in non-responders compared to responders regardless of therapy and mutational subtypes and that the increase of KPNA2 (HR = 1.73, p = .0441) and DTYMK (HR = 1.82, p = .018) cfRNA during therapy was predictive of shorter PFS. CONCLUSIONS In sum, we identified a new panel of cfRNAs for a pan-tumour liquid biopsy approach and demonstrated its utility as a prognostic, therapy-monitoring tool independent of the melanoma mutational genotype.
Collapse
Affiliation(s)
- Lea Jessica Albrecht
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Anna Höwner
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Klaus Griewank
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Smiths S. Lueong
- Bridge Institute of Experimental Tumor TherapyWest German Cancer CenterUniversity Hospital of EssenUniversity of Duisburg‐EssenEssenGermany
- Division of Solid Tumor Translational OncologyGerman Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research CenterDKFZHeidelbergGermany
| | - Nils von Neuhoff
- Department of Pediatric Hematology and OncologyDepartment for Pediatrics IIIUniversity Hospital of EssenEssenGermany
| | - Peter A. Horn
- Institute for Transfusion MedicineUniversity Hospital of EssenEssenGermany
| | - Antje Sucker
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Annette Paschen
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Elisabeth Livingstone
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Selma Ugurel
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Lisa Zimmer
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Susanne Horn
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
- Faculty Rudolf‐Schönheimer‐Institute for BiochemistryUniversity of LeipzigLeipzigGermany
| | - Jens T. Siveke
- Bridge Institute of Experimental Tumor TherapyWest German Cancer CenterUniversity Hospital of EssenUniversity of Duisburg‐EssenEssenGermany
- Division of Solid Tumor Translational OncologyGerman Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research CenterDKFZHeidelbergGermany
| | - Dirk Schadendorf
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Renáta Váraljai
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Alexander Roesch
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| |
Collapse
|
70
|
Circulating biomarkers in the diagnosis and management of hepatocellular carcinoma. Nat Rev Gastroenterol Hepatol 2022; 19:670-681. [PMID: 35676420 DOI: 10.1038/s41575-022-00620-y] [Citation(s) in RCA: 111] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/20/2022] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal causes of cancer-related death worldwide. The treatment of HCC remains challenging and is largely predicated on early diagnosis. Surveillance of high-risk groups using abdominal ultrasonography, with or without serum analysis of α-fetoprotein (AFP), can permit detection of early, potentially curable tumours, but is limited by its insensitivity. Reviewed here are two current approaches that aim to address this limitation. The first is to use old re-emerged empirically derived biomarkers such as AFP, now applied within statistical models. The second is to use circulating nucleic acid biomarkers, which include cell-free DNA (for example, circulating tumour DNA, cell-free mitochondrial DNA and cell-free viral DNA) and cell-free RNA, applying modern molecular biology-based technologies and machine learning techniques closely allied to the underlying biology of cancer. Taken together, these approaches are likely to be complementary. Both hold considerable promise for achieving earlier diagnosis as well as offering additional functionalities including improved monitoring of therapy and prediction of response thereto.
Collapse
|
71
|
Hill BT, Kahl B. Upfront therapy for diffuse large B-cell lymphoma: looking beyond R-CHOP. Expert Rev Hematol 2022; 15:805-812. [DOI: 10.1080/17474086.2022.2124156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Brian T. Hill
- Taussig Cancer Institute Cleveland Clinic, Cleveland, OH, USA
| | - Brad Kahl
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| |
Collapse
|
72
|
Berchuck JE, Facchinetti F, DiToro DF, Baiev I, Majeed U, Reyes S, Chen C, Zhang K, Sharman R, Junior PLSU, Maurer J, Shroff RT, Pritchard CC, Wu MJ, Catenacci DVT, Javle M, Friboulet L, Hollebecque A, Bardeesy N, Zhu AX, Lennerz JK, Tan B, Borad M, Parikh AR, Kiedrowski LA, Kelley RK, Mody K, Juric D, Goyal L. The Clinical Landscape of Cell-Free DNA Alterations in 1,671 Patients with Advanced Biliary Tract Cancer. Ann Oncol 2022; 33:1269-1283. [PMID: 36089135 DOI: 10.1016/j.annonc.2022.09.150] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/18/2022] [Accepted: 09/01/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Targeted therapies have transformed clinical management of advanced biliary tract cancer (BTC). Cell-free DNA (cfDNA) analysis is an attractive approach for cancer genomic profiling that overcomes many limitations of traditional tissue-based analysis. We examined cfDNA as a tool to inform clinical management of patients with advanced BTC and generate novel insights into BTC tumor biology. PATIENTS AND METHODS We analyzed next-generation sequencing data of 2,068 cfDNA samples from 1,671 patients with advanced BTC generated with Guardant360. We performed clinical annotation on a multi-institutional subset (n=225) to assess intra-patient cfDNA-tumor concordance and the association of cfDNA variant allele fraction (VAF) with clinical outcomes. RESULTS Genetic alterations were detected in cfDNA in 84% of patients, with targetable alterations detected in 44% of patients. FGFR2 fusions, IDH1 mutations, and BRAF V600E were clonal in majority of cases, affirming these targetable alterations as early driver events in BTC. Concordance between cfDNA and tissue for mutation detection was high for IDH1 mutations (87%) and BRAF V600E (100%), and low for FGFR2 fusions (18%). cfDNA analysis uncovered novel putative mechanisms of resistance to targeted therapies, including mutation of the cysteine residue (FGFR2 C492F) to which covalent FGFR inhibitors bind. High pre-treatment cfDNA VAF associated with poor prognosis and shorter response to chemotherapy and targeted therapy. Finally, we report the frequency of promising targets in advanced BTC currently under investigation in other advanced solid tumors, including KRAS G12C (1.0%), KRAS G12D (5.1%), PIK3CA mutations (6.8%), and ERBB2 amplifications (4.9%). CONCLUSIONS These findings from the largest and most comprehensive study to date of cfDNA from patients with advanced BTC highlight the utility of cfDNA analysis in current management of this disease. Characterization of oncogenic drivers and mechanisms of therapeutic resistance in this study will inform drug development efforts to reduce mortality for patients with BTC.
Collapse
Affiliation(s)
- Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Francesco Facchinetti
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Daniel F DiToro
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Islam Baiev
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | - Umair Majeed
- Division of Hematology/Oncology, Mayo Clinic, Jacksonville, FL
| | | | - Christopher Chen
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
| | - Karen Zhang
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Reya Sharman
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ
| | | | - Jordan Maurer
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | - Rachna T Shroff
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Meng-Ju Wu
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | | | - Milind Javle
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luc Friboulet
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Antoine Hollebecque
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Nabeel Bardeesy
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | - Andrew X Zhu
- Jiahui International Cancer Center, Jihaui Health, Shanghai, China; I-Mab Biopharma, Shanghai, China
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Benjamin Tan
- Department of Medicine, Washington University, St. Louis, MO
| | - Mitesh Borad
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ
| | - Aparna R Parikh
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | | | - Robin Kate Kelley
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Kabir Mody
- Division of Hematology/Oncology, Mayo Clinic, Jacksonville, FL
| | - Dejan Juric
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | - Lipika Goyal
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA.
| |
Collapse
|
73
|
Choi EJ, Kim YJ. Liquid biopsy for early detection and therapeutic monitoring of hepatocellular carcinoma. JOURNAL OF LIVER CANCER 2022; 22:103-114. [PMID: 37383403 PMCID: PMC10035729 DOI: 10.17998/jlc.2022.09.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 06/30/2023]
Abstract
Advances in our knowledge of the molecular characteristics of hepatocellular carcinoma (HCC) have enabled significant progress in the detection and therapeutic prediction of HCC. As a non-invasive alternative to tissue biopsy, liquid biopsy examines circulating cellular components such as exosomes, nucleic acids, and cell-free DNA found in body fluids (e.g., urine, saliva, ascites, and pleural effusions) and provides information about tumor characteristics. Technical advances in liquid biopsy have led to the increasing adoption of diagnostic and monitoring applications for HCC. This review summarizes the various analytes, ongoing clinical trials, and case studies of United States Food and Drug Administrationapproved in vitro diagnostic applications for liquid biopsy, and provides insight into its implementation in managing HCC.
Collapse
Affiliation(s)
| | - Young-Joon Kim
- LepiDyne Co., Ltd., Seoul, Korea
- Department of Biochemistry, Yonsei University, Seoul, Korea
| |
Collapse
|
74
|
Fjelstrup S, Dupont DM, Bus C, Enghild J, Jensen J, Birkenkamp-Demtröder K, Dyrskjøt L, Kjems J. Differential RNA aptamer affinity profiling on plasma as a potential diagnostic tool for bladder cancer. NAR Cancer 2022; 4:zcac025. [PMID: 36004048 PMCID: PMC9394167 DOI: 10.1093/narcan/zcac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/08/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The molecular composition of blood is a signature of human health, reflected in the thousands of blood biomarkers known for human diseases. However, establishing robust disease markers is challenging due to the diversity of individual samples. New sequencing methods have simplified biomarker discovery for circulating DNA and RNA while protein profiling is still laborious and costly. To harness the power of high-throughput sequencing to profile the protein content of a biological sample, we developed a method termed APTASHAPE that uses oligonucleotide aptamers to recognize proteins in complex biofluids. We selected a large pool of 2'Fluoro protected RNA sequences to recognize proteins in human plasma and identified a set of 33 cancer-specific aptamers. Differential enrichment of these aptamers after selection against 1 μl of plasma from individual patients allowed us to differentiate between healthy controls and bladder cancer-diagnosed patients (91% accuracy) and between early non-invasive tumors and late stage tumors (83% accuracy). Affinity purification and mass spectrometry of proteins bound to the predictive aptamers showed the main target proteins to be C4b-binding protein, Complement C3, Fibrinogen, Complement factor H and IgG. The APTASHAPE method thus provides a general, automated and highly sensitive platform for discovering potential new disease biomarkers.
Collapse
Affiliation(s)
- Søren Fjelstrup
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Claus Bus
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
| | - Jørgen B Jensen
- Department of Urology, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical medicine, Aarhus University, Aarhus, Denmark
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical medicine, Aarhus University, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical medicine, Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
| |
Collapse
|
75
|
Laser empowered ‘chemo-free’ phytotherapy: Newer approach in anticancer therapeutics delivery. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
76
|
Safrastyan A, Wollny D. Network analysis of hepatocellular carcinoma liquid biopsies augmented by single-cell sequencing data. Front Genet 2022; 13:921195. [PMID: 36092896 PMCID: PMC9452847 DOI: 10.3389/fgene.2022.921195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
Liquid biopsy, the analysis of body fluids, represents a promising approach for disease diagnosis and prognosis with minimal intervention. Sequencing cell-free RNA derived from liquid biopsies has been very promising for the diagnosis of several diseases. Cancer research, in particular, has emerged as a prominent candidate since early diagnosis has been shown to be a critical determinant of disease prognosis. Although high-throughput analysis of liquid biopsies has uncovered many differentially expressed genes in the context of cancer, the functional connection between these genes is not investigated in depth. An important approach to remedy this issue is the construction of gene networks which describes the correlation patterns between different genes, thereby allowing to infer their functional organization. In this study, we aimed at characterizing extracellular transcriptome gene networks of hepatocellular carcinoma patients compared to healthy controls. Our analysis revealed a number of genes previously associated with hepatocellular carcinoma and uncovered their association network in the blood. Our study thus demonstrates the feasibility of performing gene co-expression network analysis from cell-free RNA data and its utility in studying hepatocellular carcinoma. Furthermore, we augmented cell-free RNA network analysis with single-cell RNA sequencing data which enables the contextualization of the identified network modules with cell-type specific transcriptomes from the liver.
Collapse
Affiliation(s)
- Aram Safrastyan
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Damian Wollny
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- *Correspondence: Damian Wollny,
| |
Collapse
|
77
|
Holohan C, Feely N, Li P, Curran G, Lee GU. Role of detergents and nuclease inhibitors in the extraction of RNA from eukaryotic cells in complex matrices. NANOSCALE 2022; 14:12153-12161. [PMID: 35968721 DOI: 10.1039/d2nr02850f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The potential for liquid biopsy samples to be used in place of more invasive tissue biopsies has become increasingly revalent as it has been found that nucleic acids (NAs) present in the blood of cancer patients originate from tumors. Nanomagnetic extraction has proven to be a highly effective means to rapidly prepare NA from clinical samples for molecular diagnostics. In this article, the lysis reaction used to extract RNA from the human epithelial melanoma cells have been optimized using silica coated superparamagnetic nanoparticles (SPM NP). The lysis buffer (LB) is composed of several agents that denature cells, i.e., surfactant and guanidinium isothiocyanate (GITC), and agents that inhibit the degradation of circulated nucleic acids (cfNAs). The surfactant Triton X-100 has been widely used in LB but has been placed on the European Union REACH list. We have compared the qRT-PCR sensitivity resulting from LBs composed of Triton X-100 to several sustainable surfactants, i.e., Tergitol 15-S-7, Tergitol 15-S-9 and Tween-20. Surprisingly, the inclusion of these surfactants in the LB was not found to significantly improve cell lysis, and subsequently the sensitivity of qRT-PCR. The role of the sample matrix was also examined by performing extractions from solutions containing up to 30 mg mL-1 serum albumin. The qRT-PCR sensitivity was found to decrease as the concentration of this protein was increased; however, this was linked to an increased RNase activity and not the concentration of the protein itself. These results lead us to recommend a reformulation of LB for clinical samples, and to conclude that sensitive qRT-PCR RNA analysis can be performed in serum with the timely addition of an RNase inhibitor.
Collapse
Affiliation(s)
- Cian Holohan
- Conway Institute for Biomedical Research and School of Chemistry, University College Dublin, Ireland.
| | - Nathan Feely
- Conway Institute for Biomedical Research and School of Chemistry, University College Dublin, Ireland.
| | - Peng Li
- Magnostics Ltd, 2 Clifton Lane, Monkstown, Co Dublin, Ireland
| | - Gerard Curran
- Magnostics Ltd, 2 Clifton Lane, Monkstown, Co Dublin, Ireland
| | - Gil U Lee
- Conway Institute for Biomedical Research and School of Chemistry, University College Dublin, Ireland.
| |
Collapse
|
78
|
Morales RTT, Ko J. Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles. ACS NANO 2022; 16:11619-11645. [PMID: 35904433 PMCID: PMC10174080 DOI: 10.1021/acsnano.2c04337] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Extracellular vesicles (EVs) are complex lipid membrane vehicles with variable expressions of molecular cargo, composed of diverse subpopulations that participate in the intercellular signaling of biological responses in disease. EV-based liquid biopsies demonstrate invaluable clinical potential for overhauling current practices of disease management. Yet, EV heterogeneity is a major needle-in-a-haystack challenge to translate their use into clinical practice. In this review, existing digital assays will be discussed to analyze EVs at a single vesicle resolution, and future opportunities to optimize the throughput, multiplexing, and sensitivity of current digital EV assays will be highlighted. Furthermore, this review will outline the challenges and opportunities that impact the clinical translation of single EV technologies for disease diagnostics and treatment monitoring.
Collapse
Affiliation(s)
- Renee-Tyler T Morales
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jina Ko
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
79
|
Vidal AC, Moylan CA, Wilder J, Grant DJ, Murphy SK, Hoyo C. Racial disparities in liver cancer: Evidence for a role of environmental contaminants and the epigenome. Front Oncol 2022; 12:959852. [PMID: 36072796 PMCID: PMC9441658 DOI: 10.3389/fonc.2022.959852] [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: 06/02/2022] [Accepted: 07/21/2022] [Indexed: 01/09/2023] Open
Abstract
Liver cancer incidence has tripled since the early 1980s, making this disease one of the fastest rising types of cancer and the third leading cause of cancer-related deaths worldwide. In the US, incidence varies by geographic location and race, with the highest incidence in the southwestern and southeastern states and among racial minorities such as Hispanic and Black individuals. Prognosis is also poorer among these populations. The observed ethnic disparities do not fully reflect differences in the prevalence of risk factors, e.g., for cirrhosis that may progress to liver cancer or from genetic predisposition. Likely substantial contributors to risk are environmental factors, including chemical and non-chemical stressors; yet, the paucity of mechanistic insights impedes prevention efforts. Here, we review the current literature and evaluate challenges to reducing liver cancer disparities. We also discuss the hypothesis that epigenetic mediators may provide biomarkers for early detection to support interventions that reduce disparities.
Collapse
Affiliation(s)
- Adriana C. Vidal
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Cynthia A. Moylan
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Duke University, Durham, NC, United States
| | - Julius Wilder
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Duke University, Durham, NC, United States
| | - Delores J. Grant
- Department of Biomedical and Biological Sciences, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, United States
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Division of Research, School of Medicine, Duke University, Durham, NC, United States
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
80
|
Hassan S, Shehzad A, Khan SA, Miran W, Khan S, Lee YS. Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management. Biomedicines 2022; 10:2047. [PMID: 36009594 PMCID: PMC9405989 DOI: 10.3390/biomedicines10082047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 11/20/2022] Open
Abstract
Over time, molecular biology and genomics techniques have been developed to speed up the early diagnosis and clinical management of cancer. These therapies are often most effective when administered to the subset of malignancies harboring the target identified by molecular testing. Important advances in applying molecular testing involve circulating-free DNA (cfDNA)- and cell-free RNA (cfRNA)-based liquid biopsies for the diagnosis, prognosis, prediction, and treatment of cancer. Both cfDNA and cfRNA are sensitive and specific biomarkers for cancer detection, which have been clinically proven through multiple randomized and prospective trials. These help in cancer management based on the noninvasive evaluation of size, quantity, and point mutations, as well as copy number alterations at the tumor site. Moreover, personalized detection of ctDNA helps in adjuvant therapeutics and predicts the chances of recurrence of cancer and resistance to cancer therapy. Despite the controversial diagnostic values of cfDNA and cfRNA, many clinical trials have been completed, and the Food and Drug Administration has approved many multigene assays to detect genetic alterations in the cfDNA of cancer patients. In this review, we underpin the recent advances in the physiological roles of cfDNA and cfRNA, as well as their roles in cancer detection by highlighting recent clinical trials and their roles as prognostic and predictive markers in cancer management.
Collapse
Affiliation(s)
- Sadia Hassan
- Department of Biomedical Engineering and Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Adeeb Shehzad
- Department of Biomedical Engineering and Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Shahid Ali Khan
- Department of Chemistry, School of Natural Sciences (SNS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Waheed Miran
- Department of Chemical Engineering, School of Chemical and Materials Engineering National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Salman Khan
- Department of pharmacy, Quaid-i-Azam University, Islamabad 44000, Pakistan
| | - Young-Sup Lee
- School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea
| |
Collapse
|
81
|
Cabús L, Lagarde J, Curado J, Lizano E, Pérez-Boza J. Current challenges and best practices for cell-free long RNA biomarker discovery. Biomark Res 2022; 10:62. [PMID: 35978416 PMCID: PMC9385245 DOI: 10.1186/s40364-022-00409-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
The analysis of biomarkers in biological fluids, also known as liquid biopsies, is seen with great potential to diagnose complex diseases such as cancer with a high sensitivity and minimal invasiveness. Although it can target any biomolecule, most liquid biopsy studies have focused on circulating nucleic acids. Historically, studies have aimed at the detection of specific mutations on cell-free DNA (cfDNA), but recently, the study of cell-free RNA (cfRNA) has gained traction. Since 2020, a handful of cfDNA tests have been approved for therapy selection by the FDA, however, no cfRNA tests are approved to date. One of the main drawbacks in the field of RNA-based liquid biopsies is the low reproducibility of the results, often caused by technical and biological variability, a lack of standardized protocols and insufficient cohorts. In this review, we will identify the main challenges and biases introduced during the different stages of biomarker discovery in liquid biopsies with cfRNA and propose solutions to minimize them.
Collapse
Affiliation(s)
- Lluc Cabús
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain
- Flomics Biotech, Barcelona, Spain
| | | | | | - Esther Lizano
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain
| | | |
Collapse
|
82
|
Feng Z, Li K, Qin K, Liang J, Shi M, Ma Y, Zhao S, Liang H, Han D, Shen B, Peng C, Chen H, Jiang L. The LINC00623/NAT10 signaling axis promotes pancreatic cancer progression by remodeling ac4C modification of mRNA. J Hematol Oncol 2022; 15:112. [PMID: 35978332 PMCID: PMC9387035 DOI: 10.1186/s13045-022-01338-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although a substantial increase in the survival of patients with other cancers has been observed in recent decades, pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest diseases. No effective screening approach exists. METHODS Differential exosomal long noncoding RNAs (lncRNAs) isolated from the serum of patients with PDAC and healthy individuals were profiled to screen for potential markers in liquid biopsies. The functions of LINC00623 in PDAC cell proliferation, migration and invasion were confirmed through in vivo and in vitro assays. RNA pulldown, RNA immunoprecipitation (RIP) and coimmunoprecipitation (Co-IP) assays and rescue experiments were performed to explore the molecular mechanisms of the LINC00623/NAT10 signaling axis in PDAC progression. RESULTS A novel lncRNA, LINC00623, was identified, and its diagnostic value was confirmed, as it could discriminate patients with PDAC from patients with benign pancreatic neoplasms and healthy individuals. Moreover, LINC00623 was shown to promote the tumorigenicity and migratory capacity of PDAC cells in vitro and in vivo. Mechanistically, LINC00623 bound to N-acetyltransferase 10 (NAT10) and blocked its ubiquitination-dependent degradation by recruiting the deubiquitinase USP39. As a key regulator of N4-acetylcytidine (ac4C) modification of mRNA, NAT10 was demonstrated to maintain the stability of oncogenic mRNAs and promote their translation efficiency through ac4C modification. CONCLUSIONS Our data revealed the role of LINC00623/NAT10 signaling axis in PDAC progression, showing that it is a potential biomarker and therapeutic target for PDAC.
Collapse
Affiliation(s)
- Zengyu Feng
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
- Department of General Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Kexian Li
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Kai Qin
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Juyong Liang
- Otolaryngology and Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, People's Republic of China
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Minmin Shi
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Yang Ma
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Shiwei Zhao
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Huaiyu Liang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Dongni Han
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
- Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai, People's Republic of China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Chenghong Peng
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
- Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai, People's Republic of China.
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
- Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai, People's Republic of China.
| | - Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
- Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai, People's Republic of China.
| |
Collapse
|
83
|
Sohail AM, Khawar MB, Afzal A, Hassan A, Shahzaman S, Ali A. Multifaceted roles of extracellular RNAs in different diseases. Mil Med Res 2022; 9:43. [PMID: 35948986 PMCID: PMC9367134 DOI: 10.1186/s40779-022-00405-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
Extracellular RNAs (exRNAs) are novel circulating factors that can be used as biomarkers in various diseases. Their unique and diverse kinds, as well as their role as biomarkers, make them significant biomarkers. There has been immense work carried out since the discovery of exRNAs in circulation and other biological fluids to catalog and determine whether exRNAs may be utilized as indicators for health and illness. In this review, we aim to understand the current state of exRNAs in relation to various diseases and their potential as biomarkers. We will also review current issues and challenges faced in using exRNAs, with clinical and lab trials, that can be used as viable markers for different diseases.
Collapse
Affiliation(s)
- Abdullah Muhammad Sohail
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Babar Khawar
- Applied Molecular Biology and Biomedicine Lab, Department of Zoology, University of Narowal, Narowal, Pakistan.
| | - Ali Afzal
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| | - Ali Hassan
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| | - Sara Shahzaman
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| | - Ahmed Ali
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| |
Collapse
|
84
|
Carmona-Ule N, Gal N, Abuín Redondo C, De La Fuente Freire M, López López R, Dávila-Ibáñez AB. Peptide-Functionalized Nanoemulsions as a Promising Tool for Isolation and Ex Vivo Culture of Circulating Tumor Cells. Bioengineering (Basel) 2022; 9:380. [PMID: 36004905 PMCID: PMC9405120 DOI: 10.3390/bioengineering9080380] [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: 07/04/2022] [Revised: 07/26/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Circulating Tumor Cells (CTCs) are shed from primary tumors and travel through the blood, generating metastases. CTCs represents a useful tool to understand the biology of metastasis in cancer disease. However, there is a lack of standardized protocols to isolate and culture them. In our previous work, we presented oil-in-water nanoemulsions (NEs) composed of lipids and fatty acids, which showed a benefit in supporting CTC cultures from metastatic breast cancer patients. Here, we present Peptide-Functionalized Nanoemulsions (Pept-NEs), with the aim of using them as a tool for CTC isolation and culture in situ. Therefore, NEs from our previous work were surface-decorated with the peptides Pep10 and GE11, which act as ligands towards the specific cell membrane proteins EpCAM and EGFR, respectively. We selected the best surface to deposit a layer of these Pept-NEs through a Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D) method. Next, we validated the specific recognition of Pept-NEs for their protein targets EpCAM and EGFR by QCM-D and fluorescence microscopy. Finally, a layer of Pept-NEs was deposited in a culture well-plate, and cells were cultured on for 9 days in order to confirm the feasibility of the Pept-NEs as a cell growth support. This work presents peptide-functionalized nanoemulsions as a basis for the development of devices for the isolation and culture of CTCs in situ due to their ability to specifically interact with membrane proteins expressed in CTCs, and because cells are capable of growing on top of them.
Collapse
Affiliation(s)
- Nuria Carmona-Ule
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), Hospital Gil Casares, 15706 Santiago de Compostela, Spain
| | - Noga Gal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Carmen Abuín Redondo
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), Hospital Gil Casares, 15706 Santiago de Compostela, Spain
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (SERGAS), 15706 Santiago de Compostela, Spain
| | - María De La Fuente Freire
- Cancer Network Research (CIBERONC), 28029 Madrid, Spain
- Nano-Oncology Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (SERGAS), 15706 Santiago de Compostela, Spain
- DIVERSA Technologies S.L., 15782 Santiago de Compostela, Spain
| | - Rafael López López
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), Hospital Gil Casares, 15706 Santiago de Compostela, Spain
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (SERGAS), 15706 Santiago de Compostela, Spain
- Cancer Network Research (CIBERONC), 28029 Madrid, Spain
- DIVERSA Technologies S.L., 15782 Santiago de Compostela, Spain
| | - Ana Belén Dávila-Ibáñez
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), Hospital Gil Casares, 15706 Santiago de Compostela, Spain
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (SERGAS), 15706 Santiago de Compostela, Spain
- Cancer Network Research (CIBERONC), 28029 Madrid, Spain
| |
Collapse
|
85
|
Sarhadi VK, Armengol G. Molecular Biomarkers in Cancer. Biomolecules 2022; 12:1021. [PMID: 35892331 PMCID: PMC9331210 DOI: 10.3390/biom12081021] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Molecular cancer biomarkers are any measurable molecular indicator of risk of cancer, occurrence of cancer, or patient outcome. They may include germline or somatic genetic variants, epigenetic signatures, transcriptional changes, and proteomic signatures. These indicators are based on biomolecules, such as nucleic acids and proteins, that can be detected in samples obtained from tissues through tumor biopsy or, more easily and non-invasively, from blood (or serum or plasma), saliva, buccal swabs, stool, urine, etc. Detection technologies have advanced tremendously over the last decades, including techniques such as next-generation sequencing, nanotechnology, or methods to study circulating tumor DNA/RNA or exosomes. Clinical applications of biomarkers are extensive. They can be used as tools for cancer risk assessment, screening and early detection of cancer, accurate diagnosis, patient prognosis, prediction of response to therapy, and cancer surveillance and monitoring response. Therefore, they can help to optimize making decisions in clinical practice. Moreover, precision oncology is needed for newly developed targeted therapies, as they are functional only in patients with specific cancer genetic mutations, and biomarkers are the tools used for the identification of these subsets of patients. Improvement in the field of cancer biomarkers is, however, needed to overcome the scientific challenge of developing new biomarkers with greater sensitivity, specificity, and positive predictive value.
Collapse
Affiliation(s)
- Virinder Kaur Sarhadi
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland;
| | - Gemma Armengol
- Department of Animal Biology, Plant Biology, and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Barcelona, Catalonia, Spain
| |
Collapse
|
86
|
Expert opinion on NSCLC small specimen biomarker testing - Part 2: Analysis, reporting, and quality assessment. Virchows Arch 2022; 481:351-366. [PMID: 35857103 PMCID: PMC9297263 DOI: 10.1007/s00428-022-03344-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 10/31/2022]
Abstract
The diagnostic work-up for non-small cell lung cancer (NSCLC) requires biomarker testing to guide therapy choices. This article is the second of a two-part series. In Part 1, we summarised evidence-based recommendations for obtaining and processing small specimen samples (i.e. pre-analytical steps) from patients with advanced NSCLC. Here, in Part 2, we summarise evidence-based recommendations relating to analytical steps of biomarker testing (and associated reporting and quality assessment) of small specimen samples in NSCLC. As the number of biomarkers for actionable (genetic) targets and approved targeted therapies continues to increase, simultaneous testing of multiple actionable oncogenic drivers using next-generation sequencing (NGS) becomes imperative, as set forth in European Society for Medical Oncology guidelines. This is particularly relevant in advanced NSCLC, where tissue specimens are typically limited and NGS may help avoid tissue exhaustion compared with sequential biomarker testing. Despite guideline recommendations, significant discrepancies in access to NGS persist across Europe, primarily due to reimbursement constraints. The use of increasingly complex testing methods also has implications for the reporting of results. Molecular testing reports should include clinical interpretation with additional commentary on sample adequacy as appropriate. Molecular tumour boards are recommended to facilitate the interpretation of complex genetic information arising from NGS, and to collaboratively determine the optimal treatment for patients with NSCLC. Finally, whichever testing modality is employed, it is essential that adequate internal and external validation and quality control measures are implemented.
Collapse
|
87
|
Chen S, Jin Y, Wang S, Xing S, Wu Y, Tao Y, Ma Y, Zuo S, Liu X, Hu Y, Chen H, Luo Y, Xia F, Xie C, Yin J, Wang X, Liu Z, Zhang N, Zech Xu Z, Lu ZJ, Wang P. Cancer type classification using plasma cell-free RNAs derived from human and microbes. eLife 2022; 11:e75181. [PMID: 35816095 PMCID: PMC9273212 DOI: 10.7554/elife.75181] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/26/2022] [Indexed: 11/23/2022] Open
Abstract
The utility of cell-free nucleic acids in monitoring cancer has been recognized by both scientists and clinicians. In addition to human transcripts, a fraction of cell-free nucleic acids in human plasma were proven to be derived from microbes and reported to have relevance to cancer. To obtain a better understanding of plasma cell-free RNAs (cfRNAs) in cancer patients, we profiled cfRNAs in ~300 plasma samples of 5 cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer, and esophageal cancer) and healthy donors (HDs) with RNA-seq. Microbe-derived cfRNAs were consistently detected by different computational methods when potential contaminations were carefully filtered. Clinically relevant signals were identified from human and microbial reads, and enriched Kyoto Encyclopedia of Genes and Genomes pathways of downregulated human genes and higher prevalence torque teno viruses both suggest that a fraction of cancer patients were immunosuppressed. Our data support the diagnostic value of human and microbe-derived plasma cfRNAs for cancer detection, as an area under the ROC curve of approximately 0.9 for distinguishing cancer patients from HDs was achieved. Moreover, human and microbial cfRNAs both have cancer type specificity, and combining two types of features could distinguish tumors of five different primary locations with an average recall of 60.4%. Compared to using human features alone, adding microbial features improved the average recall by approximately 8%. In summary, this work provides evidence for the clinical relevance of human and microbe-derived plasma cfRNAs and their potential utilities in cancer detection as well as the determination of tumor sites.
Collapse
Affiliation(s)
- Shanwen Chen
- Division of General Surgery, Peking University First HospitalBeijingChina
- Translational Cancer Research Center, Peking University First HospitalBeijingChina
| | - Yunfan Jin
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua UniversityBeijingChina
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua UniversityBeijingChina
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua UniversityBeijingChina
| | - Yingchao Wu
- Division of General Surgery, Peking University First HospitalBeijingChina
| | - Yuhuan Tao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua UniversityBeijingChina
| | - Yongchen Ma
- Division of General Surgery, Peking University First HospitalBeijingChina
| | - Shuai Zuo
- Division of General Surgery, Peking University First HospitalBeijingChina
| | - Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua UniversityBeijingChina
| | - Yichen Hu
- State Key Laboratory of Food Science and Technology, Nanchang UniversityNanchangChina
| | - Hongyan Chen
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yuandeng Luo
- Institute of Hepatobiliary Surgery, The First Hospital Affiliated to Army Medical UniversityChongqingChina
| | - Feng Xia
- Institute of Hepatobiliary Surgery, The First Hospital Affiliated to Army Medical UniversityChongqingChina
| | - Chuanming Xie
- Institute of Hepatobiliary Surgery, The First Hospital Affiliated to Army Medical UniversityChongqingChina
| | - Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical UniversityShanghaiChina
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer /Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ning Zhang
- Translational Cancer Research Center, Peking University First HospitalBeijingChina
| | - Zhenjiang Zech Xu
- State Key Laboratory of Food Science and Technology, Nanchang UniversityNanchangChina
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical UniversityShenzhenChina
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical UniversityGuangzhouChina
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua UniversityBeijingChina
| | - Pengyuan Wang
- Division of General Surgery, Peking University First HospitalBeijingChina
| |
Collapse
|
88
|
Abstract
Cancer cells shed naked DNA molecules into the circulation. This circulating tumor DNA (ctDNA) has become the predominant analyte for liquid biopsies to understand the mutational landscape of cancer. Coupled with next-generation sequencing, ctDNA can serve as an alternative substrate to tumor tissues for mutation detection and companion diagnostic purposes. In fact, recent advances in precision medicine have rapidly enabled the use of ctDNA to guide treatment decisions for predicting response and resistance to targeted therapies and immunotherapies. An advantage of using ctDNA over conventional tissue biopsies is the relatively noninvasive approach of obtaining peripheral blood, allowing for simple repeated and serial assessments. Most current clinical practice using ctDNA has endeavored to identify druggable and resistance mutations for guiding systemic therapy decisions, albeit mostly in metastatic disease. However, newer research is evaluating potential for ctDNA as a marker of minimal residual disease in the curative setting and as a useful screening tool to detect cancer in the general population. Here we review the history of ctDNA and liquid biopsies, technologies to detect ctDNA, and some of the current challenges and limitations in using ctDNA as a marker of minimal residual disease and as a general blood-based cancer screening tool. We also discuss the need to develop rigorous clinical studies to prove the clinical utility of ctDNA for future applications in oncology.
Collapse
|
89
|
Vasseur D, Sassi H, Bayle A, Tagliamento M, Besse B, Marzac C, Arbab A, Auger N, Cotteret S, Aldea M, Blanc-Durand F, Géraud A, Gazzah A, Loriot Y, Hollebecque A, Martín-Romano P, Ngo-Camus M, Nicotra C, Ponce S, Sakkal M, Caron O, Smolenschi C, Micol JB, Italiano A, Rouleau E, Lacroix L. Next-Generation Sequencing on Circulating Tumor DNA in Advanced Solid Cancer: Swiss Army Knife for the Molecular Tumor Board? A Review of the Literature Focused on FDA Approved Test. Cells 2022; 11:cells11121901. [PMID: 35741030 PMCID: PMC9221453 DOI: 10.3390/cells11121901] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022] Open
Abstract
FDA-approved next-generation sequencing assays based on cell-free DNA offers new opportunities in a molecular-tumor-board context thanks to the noninvasiveness of liquid biopsy, the diversity of analyzed parameters and the short turnaround time. It gives the opportunity to study the heterogeneity of the tumor, to elucidate complex resistance mechanisms and to adapt treatment strategies. However, lowering the limit of detection and increasing the panels' size raise new questions in terms of detection of incidental germline alterations, occult malignancies and clonal hematopoiesis of indeterminate potential mutations. In this review, after a technological discussion and description of the common problematics encountered, we establish recommendations in properly using these FDA-approved tests in a molecular-tumor-board context.
Collapse
Affiliation(s)
- Damien Vasseur
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
- AMMICa UAR3655/US23, Gustave Roussy, F-94805 Villejuif, France
- Correspondence:
| | - Hela Sassi
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Arnaud Bayle
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
- Oncostat U1018, Inserm, Université Paris-Saclay, Équipe Labellisée Ligue Contre le Cancer, F-94805 Villejuif, France
| | - Marco Tagliamento
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Benjamin Besse
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Christophe Marzac
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Ahmadreza Arbab
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Nathalie Auger
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Sophie Cotteret
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Mihaela Aldea
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Félix Blanc-Durand
- Gynecological Cancer Unit, Department of Medicine, Gustave Roussy, F-94805 Villejuif, France;
| | - Arthur Géraud
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Anas Gazzah
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Yohann Loriot
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Antoine Hollebecque
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Patricia Martín-Romano
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Maud Ngo-Camus
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Claudio Nicotra
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Santiago Ponce
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Madona Sakkal
- Dermatology Unit, Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.S.); (C.S.)
| | - Olivier Caron
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Cristina Smolenschi
- Dermatology Unit, Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.S.); (C.S.)
| | | | - Antoine Italiano
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Etienne Rouleau
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
- AMMICa UAR3655/US23, Gustave Roussy, F-94805 Villejuif, France
| | - Ludovic Lacroix
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
- AMMICa UAR3655/US23, Gustave Roussy, F-94805 Villejuif, France
| |
Collapse
|
90
|
Vorperian SK, Moufarrej MN, Quake SR. Cell types of origin of the cell-free transcriptome. Nat Biotechnol 2022; 40:855-861. [PMID: 35132263 PMCID: PMC9200634 DOI: 10.1038/s41587-021-01188-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022]
Abstract
Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases.
Collapse
Affiliation(s)
- Sevahn K Vorperian
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - Mira N Moufarrej
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
91
|
Guelman S, Zhou Y, Brady A, Peng K. A Fit-for-Purpose Method to Measure Circulating Levels of the mRNA Component of a Liposomal-Formulated Individualized Neoantigen-Specific Therapy for Cancer. AAPS J 2022; 24:64. [PMID: 35501406 DOI: 10.1208/s12248-022-00709-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Autogene cevumeran is an individualized neoantigen-specific therapy (iNeST) under development for the treatment of various solid tumors. It consists of an RNA-Lipoplex (RNA-LPX) in which the encapsulated mRNA molecule encodes up to ten neoepitopes identified from each individual patient. In association with major histocompatibility complex (MHC) class I and MHC class II, these neoantigens can potentially stimulate and expand neoantigen-specific CD4+ and CD8+ T cells, leading to antitumor responses. As part of the pharmacokinetic (PK) property assessment of Autogene cevumeran in patients, both the lipid and mRNA content in circulation are measured. This work focused on our efforts to establish a sensitive and robust method for the measurement of mRNA levels of RNA-LPX in plasma. Due to the chemical characteristics of mRNA, extra precautions are required in order to effectively preserve mRNA integrity in human plasma during sample collection, handling and storage. To this end, a number of sample collection tubes and storage conditions were evaluated in order to inform the most optimal and operationally feasible conditions by which to preserve mRNA integrity during sample collection and upon freeze-thaw. PAXgene Blood ccfDNA tubes successfully prevented mRNA degradation and were subsequently selected for patient sample collection in the clinical trial. A branched DNA (bDNA)-based mRNA PK assay was developed to achieve the desired assay performance. Here, we discuss the evaluation of various sample collection and processing conditions as well as the optimization of the work flow during bDNA PK method development.
Collapse
Affiliation(s)
- Sebastian Guelman
- Department of BioAnalytical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, California, 94080-4990, USA.
| | - Ying Zhou
- Department of BioAnalytical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, California, 94080-4990, USA
| | - Ann Brady
- Department of BioAnalytical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, California, 94080-4990, USA
| | - Kun Peng
- Department of BioAnalytical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, California, 94080-4990, USA
| |
Collapse
|
92
|
Poellmann MJ, Rawding P, Kim D, Bu J, Kim Y, Hong S. Branched, dendritic, and hyperbranched polymers in liquid biopsy device design. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1770. [PMID: 34984833 PMCID: PMC9480505 DOI: 10.1002/wnan.1770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022]
Abstract
The development of minimally invasive tests for cancer diagnosis and prognosis will aid in the research of new treatments and improve survival rates. Liquid biopsies seek to derive actionable information from tumor material found in routine blood samples. The relative scarcity of tumor material in this complex mixture makes isolating and detecting cancerous material such as proteins, circulating tumor DNA, exosomes, and whole circulating tumor cells a challenge for device engineers. This review describes the chemistry and applications of branched and hyperbranched to improve the performance of liquid biopsy devices. These polymers can improve the performance of a liquid biopsy through several mechanisms. For example, polymers designed to increase the affinity of capture enhance device sensitivity. On the other hand, polymers designed to increase binding avidity or repel nonspecific adsorption enhance device specificity. Branched and hyperbranched polymers can also be used to amplify the signal from small amounts of detected material. The further development of hyperbranched polymers in liquid biopsy applications will enhance device capabilities and help these critical technologies reach the oncology clinic where they are sorely needed. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.
Collapse
Affiliation(s)
- Michael J Poellmann
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
- Capio Biosciences, Madison, Wisconsin, USA
| | - Piper Rawding
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - DaWon Kim
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Jiyoon Bu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - YoungSoo Kim
- Department of Pharmacy, Yonsei University, Incheon, South Korea
| | - Seungpyo Hong
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
- Capio Biosciences, Madison, Wisconsin, USA
- Department of Pharmacy, Yonsei University, Incheon, South Korea
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Center for NanoBioSystems, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
93
|
A TRIzol-based method for high recovery of plasma sncRNAs approximately 30 to 60 nucleotides. Sci Rep 2022; 12:6778. [PMID: 35474236 PMCID: PMC9042852 DOI: 10.1038/s41598-022-10800-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/13/2022] [Indexed: 11/08/2022] Open
Abstract
Protein functional effector sncRNAs (pfeRNAs) are approximately 30–60 nucleotides (nt), of which the extraction method from plasma has not yet been reported. Silver staining in a high-resolution polyacrylamide gel suggested that the majority of plasma sncRNAs extracted by some broadly used commercial kits were sncRNAs from 100 nt upwards. Additionally, TRIzol’s protocol is for long RNA but not sncRNA recovery. Here, we report a TRIzol-based frozen precipitation method (TFP method), which shows rigor and reproducibility in high yield and quality for plasma sncRNAs approximately 30–60 nt. In contrast to the yields by the commercial kit, plasma sncRNAs extracted by the TFP method enriched more sncRNAs. We used four different pfeRNAs of 34 nt, 45 nt, 53 nt, and 58 nt to represent typical sizes of sncRNAs from 30 to 60 nt and compared their levels in the recovered sncRNAs by the TFP method and by the commercial kit. The TFP method showed lower cycle threshold (CT) values by 2.01–9.17 cycles in 38 plasma samples from 38 patients, including Caucasian, Asian, African American, Latin, Mexican, and those who were a mix of more than one race. In addition, pfeRNAs extracted by two organic-based extraction methods and four commercial kits were undetermined in 22 of 38 samples. Thus, the quick and unbiased TFP method enriches plasma sncRNA ranging from 30 to 60 nt.
Collapse
|
94
|
Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies. NPJ Precis Oncol 2022; 6:28. [PMID: 35468987 PMCID: PMC9038724 DOI: 10.1038/s41698-022-00270-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/16/2022] [Indexed: 01/23/2023] Open
Abstract
Cell-free RNA (cfRNA) in plasma reflects phenotypic alterations of both localized sites of cancer and the systemic host response. Here we report that cfRNA sequencing enables the discovery of messenger RNA (mRNA) biomarkers in plasma with the tissue of origin-specific to cancer types and precancerous conditions in both solid and hematologic malignancies. To explore the diagnostic potential of total cfRNA from blood, we sequenced plasma samples of eight hepatocellular carcinoma (HCC) and ten multiple myeloma (MM) patients, 12 patients of their respective precancerous conditions, and 20 non-cancer (NC) donors. We identified distinct gene sets and built classification models using Random Forest and linear discriminant analysis algorithms that could distinguish cancer patients from premalignant conditions and NC individuals with high accuracy. Plasma cfRNA biomarkers of HCC are liver-specific genes and biomarkers of MM are highly expressed in the bone marrow compared to other tissues and are related to cell cycle processes. The cfRNA level of these biomarkers displayed a gradual transition from noncancerous states through precancerous conditions and cancer. Sequencing data were cross-validated by quantitative reverse transcription PCR and cfRNA biomarkers were validated in an independent sample set (20 HCC, 9 MM, and 10 NC) with AUC greater than 0.86. cfRNA results observed in precancerous conditions require further validation. This work demonstrates a proof of principle for using mRNA transcripts in plasma with a small panel of genes to distinguish between cancers, noncancerous states, and precancerous conditions.
Collapse
|
95
|
Chen K, Zhang F, Yu X, Huang Z, Gong L, Xu Y, Li H, Yu S, Fan Y. A molecular approach integrating genomic and DNA methylation profiling for tissue of origin identification in lung-specific cancer of unknown primary. J Transl Med 2022; 20:158. [PMID: 35382836 PMCID: PMC8981640 DOI: 10.1186/s12967-022-03362-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 03/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Determining the tissue of origin (TOO) is essential for managing cancer of unknown primary (CUP). In this study, we evaluated the concordance between genome profiling and DNA methylation analysis in determining TOO for lung-specific CUP and assessed their performance by comparing the clinical responses and survival outcomes of patients predicted with multiple primary or with metastatic cancer. METHODS We started by retrospectively screening for CUP patients who presented with both intra- and extrathoracic tumors. Tumor samples from included patients were analyzed with targeted sequencing with a 520-gene panel and targeted bisulfite sequencing. TOO inferences were made in parallel via an algorithm using genome profiles and time interval between tumors and via machine learning-based classification of DNA methylation profiles. RESULTS Four hundred patients were screened retrospectively. Excluding patients definitively diagnosed with conventional diagnostic work-up or without available samples, 16 CUP patients were included. Both molecular approaches alone enabled inference of clonality for all analyzed patients. Genome profile enabled TOO inference for 43.8% (7/16) patients, and the percentage rose to 68.8% (11/16) after considering inter-tumor time lag. On the other hand, DNA methylation analysis was conclusive for TOO prediction for 100% (14/14) patients with available samples. The two approaches gave 100% (9/9) concordant inferences regarding clonality and TOO identity. Moreover, patients predicted with metastatic disease showed significantly shorter overall survival than those with multiple primary tumors. CONCLUSIONS Genome and DNA methylation profiling have shown promise as individual analysis for TOO identification. This study demonstrated the feasibility of incorporating the two methods and proposes an integrative scheme to facilitate diagnosing and treating lung-specific CUPs.
Collapse
Affiliation(s)
- Kaiyan Chen
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Fanrong Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Xiaoqing Yu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,Department of Clinical Trial, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Zhiyu Huang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Lei Gong
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Yanjun Xu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Hui Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Sizhe Yu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Yun Fan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China. .,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China. .,Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China. .,Department of Thoracic Medical Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, China.
| |
Collapse
|
96
|
Wang Y, Li J, Zhang L, Sun HX, Zhang Z, Xu J, Xu Y, Lin Y, Zhu A, Luo Y, Zhou H, Wu Y, Lin S, Sun Y, Xiao F, Chen R, Wen L, Chen W, Li F, Ou R, Zhang Y, Kuo T, Li Y, Li L, Sun J, Sun K, Zhuang Z, Lu H, Chen Z, Mai G, Zhuo J, Qian P, Chen J, Yang H, Wang J, Xu X, Zhong N, Zhao J, Li J, Zhao J, Jin X. Plasma cell-free RNA characteristics in COVID-19 patients. Genome Res 2022; 32:228-241. [PMID: 35064006 PMCID: PMC8805721 DOI: 10.1101/gr.276175.121] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022]
Abstract
The pathogenesis of COVID-19 is still elusive, which impedes disease progression prediction, differential diagnosis, and targeted therapy. Plasma cell-free RNAs (cfRNAs) carry unique information from human tissue and thus could point to resourceful solutions for pathogenesis and host-pathogen interactions. Here, we performed a comparative analysis of cfRNA profiles between COVID-19 patients and healthy donors using serial plasma. Analyses of the cfRNA landscape, potential gene regulatory mechanisms, dynamic changes in tRNA pools upon infection, and microbial communities were performed. A total of 380 cfRNA molecules were up-regulated in all COVID-19 patients, of which seven could serve as potential biomarkers (AUC > 0.85) with great sensitivity and specificity. Antiviral (NFKB1A, IFITM3, and IFI27) and neutrophil activation (S100A8, CD68, and CD63)–related genes exhibited decreased expression levels during treatment in COVID-19 patients, which is in accordance with the dynamically enhanced inflammatory response in COVID-19 patients. Noncoding RNAs, including some microRNAs (let 7 family) and long noncoding RNAs (GJA9-MYCBP) targeting interleukin (IL6/IL6R), were differentially expressed between COVID-19 patients and healthy donors, which accounts for the potential core mechanism of cytokine storm syndromes; the tRNA pools change significantly between the COVID-19 and healthy group, leading to the accumulation of SARS-CoV-2 biased codons, which facilitate SARS-CoV-2 replication. Finally, several pneumonia-related microorganisms were detected in the plasma of COVID-19 patients, raising the possibility of simultaneously monitoring immune response regulation and microbial communities using cfRNA analysis. This study fills the knowledge gap in the plasma cfRNA landscape of COVID-19 patients and offers insight into the potential mechanisms of cfRNAs to explain COVID-19 pathogenesis.
Collapse
|
97
|
Sadovska L, Auders J, Keiša L, Romanchikova N, Silamiķele L, Kreišmane M, Zayakin P, Takahashi S, Kalniņa Z, Linē A. Exercise-Induced Extracellular Vesicles Delay the Progression of Prostate Cancer. Front Mol Biosci 2022; 8:784080. [PMID: 35087866 PMCID: PMC8787363 DOI: 10.3389/fmolb.2021.784080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Increasing evidence suggests that regular physical exercise not only reduces the risk of cancer but also improves functional capacity, treatment efficacy and disease outcome in cancer patients. At least partially, these effects are mediated by the secretome of the tissues responding to exercise. The secreted molecules can be released in a carrier-free form or enclosed into extracellular vesicles (EVs). Several recent studies have shown that EVs are actively released into circulation during physical exercise. Here, we for the first time investigated the effects of exercise-induced EVs on the progression of cancer in an F344 rat model of metastatic prostate cancer. Although we did not observe a consistent increase in the circulating EV levels, RNA sequencing analysis demonstrated substantial changes in the RNA content of EVs collected before and immediately after forced wheel running exercise as well as differences between EVs from runners at resting state and sedentary rats. The major RNA biotype in EVs was mRNA, followed by miRNA and rRNA. Molecular functions of differentially expressed RNAs reflected various physiological processes including protein folding, metabolism and regulation of immune responses triggered by the exercise in the parental cells. Intravenous administration of exercise-induced EVs into F344 rats with orthotopically injected syngeneic prostate cancer cells PLS10, demonstrated reduction of the primary tumor volume by 35% and possibly—attenuation of lung metastases. Hence, our data provide the first evidence that exercise-induced EVs may modulate tumor physiology and delay the progression of cancer.
Collapse
Affiliation(s)
- Lilite Sadovska
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Jānis Auders
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Laura Keiša
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | | | - Laila Silamiķele
- Laboratory Animal Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Madara Kreišmane
- Laboratory Animal Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Zane Kalniņa
- Laboratory Animal Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Aija Linē
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Biology, University of Latvia, Riga, Latvia
- *Correspondence: Aija Linē,
| |
Collapse
|
98
|
Halasz H, Carpenter S. Challenges and Future Directions for LncRNAs and Inflammation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:179-183. [DOI: 10.1007/978-3-030-92034-0_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
99
|
Irofei Zamfir MA, Buburuzan L, Hudiţă A, Gălăţeanu B, Ginghină O, Ion D, Motaş N, Ardeleanu CM, Costache M. Liquid biopsy in lung cancer management. ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY = REVUE ROUMAINE DE MORPHOLOGIE ET EMBRYOLOGIE 2022; 63:31-38. [PMID: 36074665 PMCID: PMC9593132 DOI: 10.47162/rjme.63.1.02] [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: 08/12/2021] [Accepted: 08/23/2022] [Indexed: 05/31/2023]
Abstract
Liquid biopsy is a promising tool for a better cancer management and currently opens perspectives for several clinical applications, such as detection of mutations when the analysis from tissue is not available, monitoring tumor mutational burden and prediction of targeted therapy response. These characteristics validate liquid biopsy analysis as a strong cancer biomarkers source with high potential for improving cancer patient's evolution. Compared to classical biopsy, liquid biopsy is a minimal invasive procedure, and it allows the real-time monitoring of treatment response. Considering that lung cancer is the most common cause of cancer-associated death worldwide and that only 15-19% of the lung cancer patients survive five years after diagnosis, there is an important interest in improving its management. Like in other types of solid cancers, lung cancer could benefit from liquid biopsy through a simple peripheral blood sample as tumor-related biomarkers, such as circulating tumor cells (CTCs), cell-free nucleic acids (cfNA) [cell-free ribonucleic acid (cfRNA) and cell-free deoxyribonucleic acid (cfDNA)], exosomes and tumor-educated platelets (TEPs) may shed into circulation because of necrosis or in an active manner. More, the detection and analysis of these biomarkers could lead to a better understanding of oncological diseases like lung cancer. The better the tumor profile is established; the better management is possible. However, this approach has currently some limitations, such as low cfNA concentration or low count of CTCs that might be overcome by improving the actual methods and technologies.
Collapse
|
100
|
Kiat Whye K, ShyongTai E, Shabbir A, Khoo CM, Koh W. Non-Invasive Characterization of the Pancreas During Bariatric Surgery via Circulating Pancreatic Specific Cell-free Messenger RNA. Front Genet 2021; 12:742496. [PMID: 34707641 PMCID: PMC8542674 DOI: 10.3389/fgene.2021.742496] [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: 07/16/2021] [Accepted: 09/10/2021] [Indexed: 11/30/2022] Open
Abstract
Bariatric surgery results in sustained weight loss and improvement in glucose homeostasis. However, the lack of accessible non-invasive tools to examine molecular alterations occurring in the pancreas limits our understanding of the causes and recovery of glucose homeostasis. Here, we describe the use of a circulating cell free mRNA (cfmRNA) based multiplex qPCR assay to selectively amplify and quantify circulating pancreatic specific transcripts levels within plasma. We applied this assay to a cohort of 58 plasma samples consisting of 10 patients that tracks multiple time points including pre and post-bariatric surgery. In our targeted multiplex screen of 14 selected pancreatic specific circulating transcripts, we identified 13 pancreatic specific transcripts that can be amplified from plasma. Furthermore, when quantifying the amplicons obtained in the short-term post-surgery (2 weeks–1 month) and long-term (3–12 months), we observed a consistent reduction of circulating GCG transcripts during short term post-surgery. Across the cohort, GCG cfmRNA levels correlated significantly with common metrics of improvement following bariatric surgery such as: haemoglobin A1c levels (R: −0.41, p-value: 0.0039) and percentage of excess weight loss (R: 0.29, p-value: 0.046).
Collapse
Affiliation(s)
- Kong Kiat Whye
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - E ShyongTai
- Division of Endocrinology, Department of Medicine, National University Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Asim Shabbir
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Surgery, National University Hospital, Singapore, Singapore
| | - Chin Meng Khoo
- Division of Endocrinology, Department of Medicine, National University Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Winston Koh
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| |
Collapse
|