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Macias RIR, Kanzaki H, Berasain C, Avila MA, Marin JJG, Hoshida Y. The Search for Risk, Diagnostic and Prognostic Biomarkers of Cholangiocarcinoma and their Biological and Clinicopathological Significance. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00277-3. [PMID: 39103092 DOI: 10.1016/j.ajpath.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/01/2024] [Accepted: 06/20/2024] [Indexed: 08/07/2024]
Abstract
Cholangiocarcinomas (CCAs) are a heterogeneus group of malignant tumors that originate from the biliary tract. They are usually diagnosed in advanced stages, leading to a dismal prognosis for affected patients. As CCA often arises as a sporadic cancer in individuals lacking specific risk factors or with heterogeneous backgrounds, and there are no defined high-risk groups, the implementation of effective surveillance programs for CCA is problematic. The identification and validation of new biomarkers useful for risk stratification, diagnosis, prognosis and prediction of treatment response remains an unmet need for patients with CCA, even though numerous studies have been conducted lately to try to discover and validate CCA biomarkers. In this review, we overview the available information about the different types of biomarkers that have been investigated in recent years using minimally invasive biospecimens (blood, serum/plasma, bile, urine) and their potential usefulness in diagnosis, prognosis and risk stratification. It is widely accepted that early detection of CCA will impact patients' outcomes, by improving survival rates, quality of life, and the possibility of less invasive and/or curative treatments, however, challenges to its translation and clinical application for CCA patients need to be resolved.
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Affiliation(s)
- Rocio I R Macias
- Experimental Hepatology and Drug Targeting (HEVEPHARM) group, University of Salamanca, IBSAL, Salamanca, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain.
| | - Hiroaki Kanzaki
- Division of Digestive and Liver Diseases, Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
| | - Carmen Berasain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain; Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), Cancer Center University of Navarra (CCUN), Pamplona, Spain
| | - Matias A Avila
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain; Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), Cancer Center University of Navarra (CCUN), Pamplona, Spain
| | - Jose J G Marin
- Experimental Hepatology and Drug Targeting (HEVEPHARM) group, University of Salamanca, IBSAL, Salamanca, Spain; Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Yujin Hoshida
- Division of Digestive and Liver Diseases, Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX.
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Choi WJ, Ivanics T, Gravely A, Gallinger S, Sapisochin G, O'Kane GM. Optimizing Circulating Tumour DNA Use in the Perioperative Setting for Intrahepatic Cholangiocarcinoma: Diagnosis, Screening, Minimal Residual Disease Detection and Treatment Response Monitoring. Ann Surg Oncol 2023; 30:3849-3863. [PMID: 36808320 DOI: 10.1245/s10434-023-13126-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023]
Abstract
In this review, we present the current evidence and future perspectives on the use of circulating tumour DNA (ctDNA) in the diagnosis, management and understanding the prognosis of patients with intrahepatic cholangiocarcinoma (iCCA) undergoing surgery. Liquid biopsies or ctDNA maybe utilized to: (1) determine the molecular profile of the tumour and therefore guide the selection of molecular targeted therapy in the neoadjuvant setting, (2) form a surveillance tool for the detection of minimal residual disease or cancer recurrence after surgery, and (3) diagnose and screen for early iCCA detection in high-risk populations. The potential for ctDNA can be tumour-informed or -uninformed depending on the goals of its use. Future studies will require ctDNA extraction technique validations, with standardizations of both the platforms and the timing of ctDNA collections.
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Affiliation(s)
- Woo Jin Choi
- HBP and Multi Organ Transplant Program, Division of General Surgery, Department of Surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,HPB Surgical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Tommy Ivanics
- Department of Surgery, Henry Ford Hospital, Detroit, MI, USA.,Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Annabel Gravely
- HPB Surgical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Steven Gallinger
- HBP and Multi Organ Transplant Program, Division of General Surgery, Department of Surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada.,HPB Surgical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Gonzalo Sapisochin
- HBP and Multi Organ Transplant Program, Division of General Surgery, Department of Surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada. .,HPB Surgical Oncology, University Health Network, Toronto, Ontario, Canada.
| | - Grainne M O'Kane
- Department of Medical Oncology, Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland.
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Abdollahi A, Shokouhmand H. Electrokinetic separation of cfDNA in insulator-based dielectrophoresis systems: a linear model of cfDNA and investigation of effective parameters. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:355101. [PMID: 35381587 DOI: 10.1088/1361-648x/ac6476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
In this study, a comprehensive numerical simulation was done to investigate the electrokinetic translocation of cfDNA molecule as well as the possibility of its detection and separation in insulator based dielectrophoresis (iDEP) systems. Modeling was done for the first time by solving the Poisson equation for the electrical potential, Naiver-Stokes (NS) equation for the fluid flow and energy equation for the heat transfer in the system and considering a coarse-grained bead-spring model to describe the conformational and geometrical changes of cfDNA molecule. The effect of the geometrical parameters of the system, the initial orientation of the molecule, electrical conductivity of the solution and zeta potential of the wall was investigated on the translocation and the minimum voltage required for cfDNA trapping. When the ratio of the inlet height to the constriction zone height is large enough, cfDNA molecules cannot pass through the nanopore and trap in the constriction zone. Also, it was found that the electrical conductivity of the solution is a limiting parameter to directly isolate cfDNA from pure plasma without dilution due to significant increase in the temperature of the system. Our results demonstrate the enormous potential of iDEP systems for rapid detection of cfDNA from diluted plasma under special electrical potential and geometrical parameters of the iDEP systems.
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Affiliation(s)
- Azita Abdollahi
- School of Mechanical Engineering, College of Engineering, University of Tehran, PO Box: 11155-4563, Tehran, Iran
| | - Hossein Shokouhmand
- School of Mechanical Engineering, College of Engineering, University of Tehran, PO Box: 11155-4563, Tehran, Iran
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Carotenuto M, Sacco A, Forgione L, Normanno N. Genomic alterations in cholangiocarcinoma: clinical significance and relevance to therapy. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:200-223. [PMID: 36046845 PMCID: PMC9400790 DOI: 10.37349/etat.2022.00079] [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: 12/18/2021] [Accepted: 02/22/2022] [Indexed: 11/22/2022] Open
Abstract
Improving the survival of patients with cholangiocarcinoma (CCA) has long proved challenging, although the treatment of this disease nowadays is on advancement. The historical invariability of survival outcomes and the limited number of agents known to be effective in the treatment of this disease has increased the number of studies designed to identify genetic targetable hits that can be efficacious for novel therapies. In this respect, the increasing feasibility of molecular profiling starting either from tumor tissue or circulating cell-free DNA (cfDNA) has led to an increased understanding of CCA biology. Intrahepatic CCA (iCCA) and extrahepatic CCA (eCCA) display different and typical patterns of actionable genomic alterations, which offer opportunity for therapeutic intervention. This review article will summarize the current knowledge on the genomic alterations of iCCA and eCCA, provide information on the main technologies for genomic profiling using either tumor tissue or cfDNA, and briefly discuss the main clinical trials with targeted agents in this disease.
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Affiliation(s)
- Marianeve Carotenuto
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Alessandra Sacco
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Laura Forgione
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
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A novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA. Sci Rep 2021; 11:19653. [PMID: 34608196 PMCID: PMC8490367 DOI: 10.1038/s41598-021-98815-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/13/2021] [Indexed: 12/04/2022] Open
Abstract
Low yields of extracted cell-free DNA (cfDNA) from plasma limit continued development of liquid biopsy in cancer, especially in early-stage cancer diagnostics and cancer screening applications. We investigate a novel liquid-phase-based DNA isolation method that utilizes aqueous two-phase systems to purify and concentrate circulating cfDNA. The PHASIFY MAX and PHASIFY ENRICH kits were compared to a commonly employed solid-phase extraction method on their ability to extract cfDNA from a set of 91 frozen plasma samples from cancer patients. Droplet digital PCR (ddPCR) was used as the downstream diagnostic to detect mutant copies. Compared to the QIAamp Circulating Nucleic Acid (QCNA) kit, the PHASIFY MAX method demonstrated 60% increase in DNA yield and 171% increase in mutant copy recovery, and the PHASIFY ENRICH kit demonstrated a 35% decrease in DNA yield with a 153% increase in mutant copy recovery. A follow-up study with PHASIFY ENRICH resulted in the positive conversion of 9 out of 47 plasma samples previously determined negative with QCNA extraction (all with known positive tissue genotyping). Our results indicate that this novel extraction technique offers higher cfDNA recovery resulting in better sensitivity for detection of cfDNA mutations compared to a commonly used solid-phase extraction method.
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Kodali S, Shetty A, Shekhar S, Victor DW, Ghobrial RM. Management of Intrahepatic Cholangiocarcinoma. J Clin Med 2021; 10:jcm10112368. [PMID: 34072277 PMCID: PMC8198953 DOI: 10.3390/jcm10112368] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 01/04/2023] Open
Abstract
Cholangiocarcinoma is a tumor that arises as a result of differentiation of the cholangiocytes and can develop from anywhere in the biliary tree. Subtypes of cholangiocarcinoma are differentiated based on their location in the biliary tree. If diagnosed early these can be resected, but most cases of intrahepatic cholangiocarcinoma present late in the disease course where surgical resection is not an option. In these patients who are poor candidates for resection, a combination of chemotherapy, locoregional therapies like ablation, transarterial chemo and radioembolization, and in very advanced and metastatic disease, external radiation are the available options. These modalities can improve overall disease-free and progression-free survival chances. In this review, we will discuss the risk factors and clinical presentation of intrahepatic cholangiocarcinoma, diagnosis, available therapeutic options, and future directions for management options.
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Affiliation(s)
- Sudha Kodali
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA; (S.K.); (A.S.); (R.M.G.)
- Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Akshay Shetty
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA; (S.K.); (A.S.); (R.M.G.)
- Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Soumya Shekhar
- Texas A&M College of Medicine, Houston Campus, Houston, TX 77030, USA;
| | - David W. Victor
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA; (S.K.); (A.S.); (R.M.G.)
- Houston Methodist Research Institute, Houston, TX 77030, USA
- Correspondence:
| | - Rafik M. Ghobrial
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA; (S.K.); (A.S.); (R.M.G.)
- Houston Methodist Research Institute, Houston, TX 77030, USA
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Chatchawal P, Wongwattanakul M, Tippayawat P, Jearanaikoon N, Jumniansong A, Boonmars T, Jearanaikoon P, Wood BR. Monitoring the Progression of Liver Fluke-Induced Cholangiocarcinoma in a Hamster Model Using Synchrotron FTIR Microspectroscopy and Focal Plane Array Infrared Imaging. Anal Chem 2020; 92:15361-15369. [PMID: 33170647 DOI: 10.1021/acs.analchem.0c02656] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cholangiocarcinoma (CCA) is a bile duct cancer that originates in the bile duct epithelium. Northeastern Thailand has the highest incidence of CCA, and there is a direct correlation with liver fluke (Opisthorchis viverrini) infection. The high mortality rate of CCA is a consequence of delayed diagnosis. Fourier transform infrared (FTIR) spectroscopy is a powerful technique that detects the absorbance of molecular vibrations and is perfectly suited for the interrogation of biological samples. In this study, we applied synchrotron radiation-FTIR (SR-FTIR) microspectroscopy and focal plane array (FPA-FTIR) microspectroscopy to characterize periductal fibrosis and bile duct cells progressing to CCA induced by inoculating O. viverrini metacercariae into hamsters. SR-FTIR and FPA-FTIR measurements were performed in liver sections harvested from 1-, 2-, 3-, and 6-month post-infected hamsters compared to uninfected liver tissues. Principal component analysis (PCA) of the tissue samples showed a clear discrimination among uninfected and early-stage (1 and 2 months) and cancerous-stage (3 and 6 months) tissues. The discrimination is based on intensity changes in the phosphodiester band (1081 cm-1), amino acid residue (∼1396 cm-1), and C═O stretching carboxylic esters (1745 cm-1). Infected tissues also show definitive bands at ∼1280, 1234, and 1201 cm-1 characteristic of the collagen triplet and indicative of fibrosis. Hierarchical cluster analysis (HCA) was performed on the FPA data and showed a classification into specific cell types. Hepatocyte, fibrotic lesion, and bile duct (cancer) were classified and HCA mapping showed similar cellular distribution pattern compared to Sirius red staining. This study was also extended to less invasive sample analysis using attenuated total reflectance-FTIR (ATR-FTIR) spectroscopy. Sera from O. viverrini-infected and uninfected hamsters were analyzed using multivariate analysis, including principal component analysis (PCA), and partial least squares-discriminant analysis (PLS-DA). PCA was able to classify spectra of normal, early-stage CCA, and CCA, while the PLS-DA gave 100% accuracy for the validation. The model was established from 17 samples (11 normal, 6 cancer) in the calibration set and 9 samples in the validation set (4 normal, 2 cancer, 3 precancerous). These results indicate that FTIR-based technology is a potential tool to detect the progression of CCA, especially in the early stages of the disease.
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Affiliation(s)
- Patutong Chatchawal
- Biomedical Sciences, Graduate School, Khon Kaen University, Khon Kaen 40002, Thailand.,Center for Research and Development of Medical Diagnosis Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen40002, Thailand
| | - Molin Wongwattanakul
- Center for Research and Development of Medical Diagnosis Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen40002, Thailand
| | - Patcharaporn Tippayawat
- Center for Research and Development of Medical Diagnosis Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | | | - Amonrat Jumniansong
- Center for Research and Development of Medical Diagnosis Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Thidarat Boonmars
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen40002, Thailand.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Patcharee Jearanaikoon
- Center for Research and Development of Medical Diagnosis Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen40002, Thailand
| | - Bayden R Wood
- Center for Biospectroscopy, School of Chemistry, Faculty of Science, Monash University, Victoria 3800, Australia
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Chen J, Chen J, He F, Huang Y, Lu S, Fan H, Wang M, Xu R. Design of a Targeted Sequencing Assay to Detect Rare Mutations in Circulating Tumor DNA. Genet Test Mol Biomarkers 2019; 23:264-269. [PMID: 30986100 DOI: 10.1089/gtmb.2018.0173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Qualitative and quantitative detection of circulating tumor DNA (ctDNA) is a liquid biopsy technology used for early cancer diagnosis. However, the plasma ctDNA content is extremely low, so it is difficult to detect somatic mutations of tumors using conventional sequencing methods. Target region sequencing (TRS) technology, through enrichment of the target genomic region followed by next generation sequencing, overcomes this challenge and has been widely used in ctDNA sequencing. METHODS We designed a ctDNA sequencing panel to capture 128 tumor genes, and tested the performance of the panel by running TRS for ctDNA of a clear cell renal cell carcinoma (ccRCC) patient and 12 breast cancer patients. RESULTS TRS using the new ctDNA panel at more than 500 × coverage depth achieved almost the same accuracy as traditional whole-exome sequencing (WES). PBRM1 p.L641V was detected in the plasma sample of the ccRCC patient with an allele frequency of 0.2%. The ctDNA of 12 breast cancer patients was sequenced at a depth of 500-fold, achieving 99.89% coverage; 34 genes were detected with mutations, including the drug target genes BRCA2, PTEN, TP53, APC, KDR, and NOTCH2. CONCLUSIONS This TRS new ctDNA panel can be used to detect mutations in cell-free DNA from multiple types of cancer.
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Affiliation(s)
- Jianxia Chen
- 1 Clinical Laboratory, Longgang Central Hospital of Shenzhen, Shenzhen, China
| | - Jun Chen
- 2 Imunobio, Shenzhen, Shenzhen, China
| | | | - Yiqiong Huang
- 3 Department of Breast Thyroid Vascular Surgery, Longgang Central Hospital of Shenzhen, Shenzhen, China
| | - Shan Lu
- 3 Department of Breast Thyroid Vascular Surgery, Longgang Central Hospital of Shenzhen, Shenzhen, China
| | - Haibo Fan
- 4 Division of ultrasonography, Shenzhen People's Hospital, Shenzhen, China
| | - Mingbang Wang
- 5 Xiamen Branch, Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | - Ruihuan Xu
- 1 Clinical Laboratory, Longgang Central Hospital of Shenzhen, Shenzhen, China
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