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O'Sullivan NJ, Temperley HC, Kyle ET, Sweeney KJ, O'Neill M, Gilham C, O'Sullivan J, O'Kane G, Mehigan B, O'Toole S, Larkin J, Gallagher D, McCormick P, Kelly ME. Assessing circulating tumour DNA (ctDNA) as a prognostic biomarker in locally advanced rectal cancer: a systematic review and meta-analysis. Int J Colorectal Dis 2024; 39:82. [PMID: 38809315 PMCID: PMC11136793 DOI: 10.1007/s00384-024-04656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/23/2024] [Indexed: 05/30/2024]
Abstract
INTRODUCTION Circulating tumour DNA (ctDNA) has emerged as a promising biomarker in various cancer types, including locally advanced rectal cancer (LARC), offering potential insights into disease progression, treatment response and recurrence. This review aims to comprehensively evaluate the utility of ctDNA as a prognostic biomarker in LARC. METHODS PubMed, EMBASE and Web of Science were searched as part of our review. Studies investigating the utility of ctDNA in locally advanced rectal cancer (LARC) were assessed for eligibility. Quality assessment of included studies was performed using the Newcastle Ottawa Scale (NOS) risk of bias tool. Outcomes extracted included basic participant characteristics, ctDNA details and survival data. A meta-analysis was performed on eligible studies to determine pooled recurrence-free survival (RFS). RESULTS Twenty-two studies involving 1676 participants were included in our analysis. Methodological quality categorised by the Newcastle Ottawa Scale was generally satisfactory across included studies. ctDNA detected at various time intervals was generally associated with poor outcomes across included studies. Meta-analysis demonstrated a pooled hazard ratio of 8.87 (95% CI 4.91-16.03) and 15.15 (95% CI 8.21-27.95), indicating an increased risk of recurrence with ctDNA positivity in the post-neoadjuvant and post-operative periods respectively. CONCLUSION Our systematic review provides evidence supporting the prognostic utility of ctDNA in patients with LARC, particularly in identifying patients at higher risk of disease recurrence in the post-neoadjuvant and post-operative periods.
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Affiliation(s)
- Niall J O'Sullivan
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland.
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Hugo C Temperley
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Eimear T Kyle
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Kevin J Sweeney
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Maeve O'Neill
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Charles Gilham
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Department of Radiation Oncology, St. James's Hospital, Dublin 8, Ireland
| | - Jacintha O'Sullivan
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Trinity Translational Medicine Institute, Trinity St. James's Cancer Institute, Trinity College, St. James's Hospital, Dublin, Ireland
| | - Grainne O'Kane
- Department of Medical Oncology, St. James's Hospital, Dublin 8, Ireland
| | - Brian Mehigan
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Sharon O'Toole
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Trinity Translational Medicine Institute, Trinity St. James's Cancer Institute, Trinity College, St. James's Hospital, Dublin, Ireland
| | - John Larkin
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - David Gallagher
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Department of Medical Oncology, St. James's Hospital, Dublin 8, Ireland
- Department of Genetics, St. James's Hospital, Dublin 8, Ireland
| | - Paul McCormick
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Michael E Kelly
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Trinity St. James's Cancer Institute, St. James's Hospital, Dublin 8, Ireland
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Zhao H, Su Y, Wang Y, Lyu Z, Xu P, Gu W, Tian L, Fu P. Using tumor habitat-derived radiomic analysis during pretreatment 18F-FDG PET for predicting KRAS/NRAS/BRAF mutations in colorectal cancer. Cancer Imaging 2024; 24:26. [PMID: 38342905 PMCID: PMC10860234 DOI: 10.1186/s40644-024-00670-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/29/2024] [Indexed: 02/13/2024] Open
Abstract
BACKGROUND To investigate the association between Kirsten rat sarcoma viral oncogene homolog (KRAS) / neuroblastoma rat sarcoma viral oncogene homolog (NRAS) /v-raf murine sarcoma viral oncogene homolog B (BRAF) mutations and the tumor habitat-derived radiomic features obtained during pretreatment 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) in patients with colorectal cancer (CRC). METHODS We retrospectively enrolled 62 patients with CRC who had undergone 18F-FDG PET/computed tomography from January 2017 to July 2022 before the initiation of therapy. The patients were randomly split into training and validation cohorts with a ratio of 6:4. The whole tumor region radiomic features, habitat-derived radiomic features, and metabolic parameters were extracted from 18F-FDG PET images. After reducing the feature dimension and selecting meaningful features, we constructed a hierarchical model of KRAS/NRAS/BRAF mutations by using the support vector machine. The convergence of the model was evaluated by using learning curve, and its performance was assessed based on the area under the receiver operating characteristic curve (AUC), calibration curve, and decision curve analysis. The SHapley Additive exPlanation was used to interpret the contributions of various features to predictions of the model. RESULTS The model constructed by using habitat-derived radiomic features had adequate predictive power with respect to KRAS/NRAS/BRAF mutations, with an AUC of 0.759 (95% CI: 0.585-0.909) on the training cohort and that of 0.701 (95% CI: 0.468-0.916) on the validation cohort. The model exhibited good convergence, suitable calibration, and clinical application value. The results of the SHapley Additive explanation showed that the peritumoral habitat and a high_metabolism habitat had the greatest impact on predictions of the model. No meaningful whole tumor region radiomic features or metabolic parameters were retained during feature selection. CONCLUSION The habitat-derived radiomic features were found to be helpful in stratifying the status of KRAS/NRAS/BRAF in CRC patients. The approach proposed here has significant implications for adjuvant treatment decisions in patients with CRC, and needs to be further validated on a larger prospective cohort.
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Affiliation(s)
- Hongyue Zhao
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yexin Su
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yan Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhehao Lyu
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Peng Xu
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Wenchao Gu
- Department of Diagnostic and Interventional Radiology, University of Tsukuba, Ibaraki, Japan
| | - Lin Tian
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
| | - Peng Fu
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
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Mi J, Wang R, Han X, Ma R, Zhao D. Treatment stratification and prognosis assessment using circulating tumor DNA in locally advanced rectal cancer: A systematic review and meta-analysis. Cancer Med 2023; 12:17934-17944. [PMID: 37553845 PMCID: PMC10523996 DOI: 10.1002/cam4.6434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/10/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) is an emerging biomarker for locally advanced rectal cancer (LARC), giving hope for stratified treatment. As the completed studies have small sample sizes and different experimental methods, systematic review and meta-analysis were performed to explore their role in predicting pathological complete response (pCR), tumor recurrence, and prognosis. METHODS PubMed, Embase, and the Web of Science were searched for potentially eligible studies published up to September 6, 2022. Pooled relative risk (RR) was calculated to predict pCR and tumor recurrence, and pooled hazard ratio (HR) was calculated to evaluate the prognosis of overall survival (OS), recurrence-free survival (RFS), and metastasis-free survival (MRS). RESULTS Twelve studies published between 2018 and 2022 included 931 patients, and 2544 serum samples were eventually included in the meta-analysis. The pooled revealed that ctDNA-negative patients were more likely to have a pCR (RR = 1.64, 95% confidence interval [CI]: 1.26-2.12). The pooled revealed that ctDNA-positive patients were at high risk of recurrence (RR = 3.37, 95% CI: 2.34-4.85) and had a poorer prognosis for OS (HR = 3.03, 95% CI: 1.86-4.95), RFS (HR = 7.08, 95% CI: 4.12-12.14), and MRS (HR = 2.77, 95% CI: 2.01-3.83). CONCLUSION ctDNA may be useful for stratifying treatment and assessing prognosis in patients with LARC, but its clinical application still needs to be confirmed in a prospective multicenter study with large samples.
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Affiliation(s)
- Junjie Mi
- Department of GastroenterologyShanxi Provincial People's Hospital (The Fifth Hospital of Shanxi Medical University)TaiyuanChina
| | - Rong Wang
- Department of GastroenterologyShanxi Provincial People's Hospital (The Fifth Hospital of Shanxi Medical University)TaiyuanChina
| | - Xiaofang Han
- Core LaboratoryShanxi Provincial People's Hospital (The Fifth Hospital of Shanxi Medical University)TaiyuanChina
| | - Ruijun Ma
- Department of GastroenterologyShanxi Provincial People's Hospital (The Fifth Hospital of Shanxi Medical University)TaiyuanChina
| | - Danyu Zhao
- Department of GastroenterologyShanxi Provincial People's Hospital (The Fifth Hospital of Shanxi Medical University)TaiyuanChina
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Cohen R, Platell CF, McCoy MJ, Meehan K, Fuller K. Circulating tumour DNA in colorectal cancer management. Br J Surg 2023; 110:773-783. [PMID: 37190784 PMCID: PMC10364542 DOI: 10.1093/bjs/znad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/17/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
Circulating tumour DNA analysis can be performed using two opposing paradigms: tumour-informed and tumour-agnostic approaches. The first requires sequencing data from the primary tumour sample to identify tumour DNA in circulation, whereas the latter occurs without previous primary tumour genetic profiling.
Several preanalytical and laboratory considerations need to be taken into account before proceeding with in-house circulating tumour DNA analysis.
Detection of circulating tumour DNA after curative resection is associated with a significant risk of recurrence. For those with stage II disease and detectable postoperative circulating tumour DNA, administration of adjuvant chemotherapy results in a reduction in the number of patients receiving chemotherapy while providing non-inferior recurrence-free survival compared with standard histopathological decision-making algorithms.
Monitoring circulating tumour DNA during post-treatment surveillance may provide a significantly earlier diagnosis of recurrence.
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Affiliation(s)
- Ryan Cohen
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
| | - Cameron F Platell
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Melanie J McCoy
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Katie Meehan
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kathy Fuller
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
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Sayagués JM, Montero JC, Jiménez-Pérez A, Del Carmen S, Rodríguez M, Vidal Tocino R, Montero E, Sanz J, Abad M. Analysis of Circulating Tumor DNA in Synchronous Metastatic Colorectal Cancer at Diagnosis Predicts Overall Patient Survival. Int J Mol Sci 2023; 24:ijms24098438. [PMID: 37176143 PMCID: PMC10179090 DOI: 10.3390/ijms24098438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Sporadic colorectal cancer (sCRC) initially presents as metastatic tumors in 25-30% of patients. The 5-year overall survival (OS) in patients with metastatic sCRC is 50%, falling to 10% in patients presenting with synchronous metastatic disease (stage IV). In this study, we systematically analyzed the mutations of RAS, PIK3CA and BRAF genes in circulating tumor DNA (ctDNA) and tumoral tissue DNA (ttDNA) from 51 synchronous metastatic colorectal carcinoma (SMCC) patients by real-time PCR, and their relationship with the clinical, biological and histological features of disease at diagnosis. The highest frequency of mutations detected was in the KRAS gene, in tumor biopsies and plasma samples, followed by mutations of the PIK3CA, NRAS and BRAF genes. Overall, plasma systematically contained those genetic abnormalities observed in the tumor biopsy sample from the same subject, the largest discrepancies detected between the tumor biopsy and plasma from the same patient being for mutations in the KRAS and PIK3CA genes, with concordances of genotyping results between ttDNA and ctDNA at diagnosis of 75% and 84%, respectively. Of the 51 SMCC patients in the study, 25 (49%) showed mutations in at least 1 of the 4 genes analyzed in patient plasma. From the prognostic point of view, the presence and number of the most common mutations in the RAS, PIK3CA and BRAF genes in plasma from SMCC patients are independent prognostic factors for OS. Determination of the mutational status of ctDNA in SMCC could be a key tool for the clinical management of patients.
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Affiliation(s)
- José María Sayagués
- Department of Pathology and IBSAL, University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain
- Biomedical Research Networking Centers-Oncology (CIBERONC), 28029 Madrid, Spain
| | - Juan Carlos Montero
- Department of Pathology and IBSAL, University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain
- Biomedical Research Networking Centers-Oncology (CIBERONC), 28029 Madrid, Spain
| | - Andrea Jiménez-Pérez
- Department of Pathology and IBSAL, University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain
- Biomedical Research Networking Centers-Oncology (CIBERONC), 28029 Madrid, Spain
| | - Sofía Del Carmen
- Department of Pathology, University Hospital of Marqués de Valdecilla, 39008 Santander, Spain
| | - Marta Rodríguez
- Department of Pathology and IBSAL, University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain
- Biomedical Research Networking Centers-Oncology (CIBERONC), 28029 Madrid, Spain
| | - Rosario Vidal Tocino
- Department of Oncology and IBSAL, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Enrique Montero
- Department of Pathology, University Hospital of Zamora, 49071 Zamora, Spain
| | - Julia Sanz
- Department of Pathology, Puerto Real University Hospital, 11510 Cadiz, Spain
| | - Mar Abad
- Department of Pathology and IBSAL, University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain
- Biomedical Research Networking Centers-Oncology (CIBERONC), 28029 Madrid, Spain
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van Rees JM, Wullaert L, Grüter AAJ, Derraze Y, Tanis PJ, Verheul HMW, Martens JWM, Wilting SM, Vink G, van Vugt JLA, Beije N, Verhoef C. Circulating tumour DNA as biomarker for rectal cancer: A systematic review and meta-analyses. Front Oncol 2023; 13:1083285. [PMID: 36793616 PMCID: PMC9922989 DOI: 10.3389/fonc.2023.1083285] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
Background Circulating tumour DNA (ctDNA) has been established as a promising (prognostic) biomarker with the potential to personalise treatment in cancer patients. The objective of this systematic review is to provide an overview of the current literature and the future perspectives of ctDNA in non-metastatic rectal cancer. Methods A comprehensive search for studies published prior to the 4th of October 2022 was conducted in Embase, Medline, Cochrane, Google scholar, and Web of Science. Only peer-reviewed original articles and ongoing clinical trials investigating the association between ctDNA and oncological outcomes in non-metastatic rectal cancer patients were included. Meta-analyses were performed to pool hazard ratios (HR) for recurrence-free survival (RFS). Results A total of 291 unique records were screened, of which 261 were original publications and 30 ongoing trials. Nineteen original publications were reviewed and discussed, of which seven provided sufficient data for meta-analyses on the association between the presence of post-treatment ctDNA and RFS. Results of the meta-analyses demonstrated that ctDNA analysis can be used to stratify patients into very high and low risk groups for recurrence, especially when detected after neoadjuvant treatment (HR for RFS: 9.3 [4.6 - 18.8]) and after surgery (HR for RFS: 15.5 [8.2 - 29.3]). Studies investigated different types of assays and used various techniques for the detection and quantification of ctDNA. Conclusions This literature overview and meta-analyses provide evidence for the strong association between ctDNA and recurrent disease. Future research should focus on the feasibility of ctDNA-guided treatment and follow-up strategies in rectal cancer. A blueprint for agreed-upon timing, preprocessing, and assay techniques is needed to empower adaptation of ctDNA into daily practice.
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Affiliation(s)
- Jan M van Rees
- Department of Surgical Oncology and Gastrointestinal Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Lissa Wullaert
- Department of Surgical Oncology and Gastrointestinal Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Alexander A J Grüter
- Department of Surgery, Amsterdam University Medical Centres (UMC), Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Yassmina Derraze
- Department of Surgery, Amsterdam University Medical Centres (UMC), Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Pieter J Tanis
- Department of Surgical Oncology and Gastrointestinal Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Geraldine Vink
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Research and Development, Netherlands Comprehensive Cancer Organisation, Utrecht, Netherlands
| | - Jeroen L A van Vugt
- Department of Surgical Oncology and Gastrointestinal Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Nick Beije
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Cornelis Verhoef
- Department of Surgical Oncology and Gastrointestinal Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
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Bádon ES, Mokánszki A, Mónus A, András C, Méhes G. Clonal diversity in KRAS mutant colorectal adenocarcinoma under treatment: Monitoring of cfDNA using reverse hybridization and DNA sequencing platforms. Mol Cell Probes 2023; 67:101891. [PMID: 36586518 DOI: 10.1016/j.mcp.2022.101891] [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: 10/12/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Biological heterogeneity is a key feature of malignancies that significantly contributes to disease progression and therapy resistance. Residual/relapsed tumor foci may represent genetically divergent subclones, which remain uncovered as repeated and multiple tumor sampling is usually limited. The analysis of circulating free DNA (cfDNA) from the peripheral blood plasma (also called a liquid biopsy, LB) is a new achievement that provides an effective tool for follow-up monitoring of cancer-related genetic status. The present study highlights the phenomenon of mutational variability observed in patients with metastatic KRAS mutant colorectal cancer (mCRC) during treatment with bevacizumab in combination in a longitudinal fashion. The prospective study included 490 mCRC patients evaluated between 2020 and 2022 in our institution. Out of the 211 KRAS mutant cases (43.06%) 12 tumors were identified with multiple KRAS gene variants (5.68%). Detailed follow-up investigations were possible in 3 of these patients including the genotyping of the primary and available metastatic tumors, and the peripheral blood cfDNA. cfDNA was collected from three different time points before and between cycles of combined treatment with bevacizumab chemotherapy. KRAS gene variants were identified using reverse-hybridization strips, and next-generation sequencing (NGS), and confirmed by conventional Sanger sequencing. Interestingly, surgery and multiple treatment cycles reorganized the mutational profiles in the selected cases. The effect of the treatments resulted either in the overrepresentation of one of the pre-existing gene variants or in the appearance of new KRAS variants absent in the primary sample, according to the plasma cfDNA findings. Besides the KRAS variants demonstrated by targeted analysis, NGS mutational profiling identified some additional pathogenic variants from the cfDNA samples (including NRAS and MET alterations). In conclusion, plasma cfDNA sampling enables the monitoring of mutational heterogeneity and subclonal dynamics of the actual metastatic tumor mass in mCRC. The pattern of molecular profile potentially reflects a differential drug response determining further progression.
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Affiliation(s)
- Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Csilla András
- Department of Oncology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary.
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Promises and Challenges of Predictive Blood Biomarkers for Locally Advanced Rectal Cancer Treated with Neoadjuvant Chemoradiotherapy. Cells 2023; 12:cells12030413. [PMID: 36766755 PMCID: PMC9913546 DOI: 10.3390/cells12030413] [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: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
The treatment of locally advanced rectal cancer (LARC) requires a multimodal approach combining neoadjuvant radiotherapy or chemoradiotherapy (CRT) and surgery. Predicting tumor response to CRT can guide clinical decision making and improve patient care while avoiding unnecessary toxicity and morbidity. Circulating biomarkers offer both the advantage to be easily accessed and followed over time. In recent years, biomarkers such as proteins, blood cells, or nucleic acids have been investigated for their predictive value in oncology. We conducted a comprehensive literature review with the aim to summarize the status of circulating biomarkers predicting response to CRT in LARC. Forty-nine publications, of which forty-seven full-text articles, one review and one systematic review, were retrieved. These studies evaluated circulating markers (CEA and CA 19-9), inflammatory biomarkers (CRP, albumin, and lymphocytes), hematologic markers (hemoglobin and thrombocytes), lipids and circulating nucleic acids (cell-free DNA [cfDNA], circulating tumor DNA [ctDNA], and microRNA [miRNA]). Post-CRT CEA levels had the most consistent association with tumor response, while cfDNA integrity index, MGMT promoter methylation, ERCC-1, miRNAs, and miRNA-related SNPs were identified as potential predictive markers. Although circulating biomarkers hold great promise, inconsistent results, low statistical power, and low specificity and sensibility prevent them from reliably predicting tumor response following CRT. Validation and standardization of methods and technologies are further required to confirm results.
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Mirza S, Bhadresha K, Mughal MJ, McCabe M, Shahbazi R, Ruff P, Penny C. Liquid biopsy approaches and immunotherapy in colorectal cancer for precision medicine: Are we there yet? Front Oncol 2023; 12:1023565. [PMID: 36686736 PMCID: PMC9853908 DOI: 10.3389/fonc.2022.1023565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related deaths globally, with nearly half of patients detected in the advanced stages. This is due to the fact that symptoms associated with CRC often do not appear until the cancer has reached an advanced stage. This suggests that CRC is a cancer with a slow progression, making it curable and preventive if detected in its early stage. Therefore, there is an urgent clinical need to improve CRC early detection and personalize therapy for patients with this cancer. Recently, liquid biopsy as a non-invasive or nominally invasive approach has attracted considerable interest for its real-time disease monitoring capability through repeated sample analysis. Several studies in CRC have revealed the potential for liquid biopsy application in a real clinical setting using circulating RNA/miRNA, circulating tumor cells (CTCs), exosomes, etc. However, Liquid biopsy still remains a challenge since there are currently no promising results with high specificity and specificity that might be employed as optimal circulatory biomarkers. Therefore, in this review, we conferred the plausible role of less explored liquid biopsy components like mitochondrial DNA (mtDNA), organoid model of CTCs, and circulating cancer-associated fibroblasts (cCAFs); which may allow researchers to develop improved strategies to unravel unfulfilled clinical requirements in CRC patients. Moreover, we have also discussed immunotherapy approaches to improve the prognosis of MSI (Microsatellite Instability) CRC patients using neoantigens and immune cells in the tumor microenvironment (TME) as a liquid biopsy approach in detail.
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Affiliation(s)
- Sheefa Mirza
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Department of Internal Medicine, Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kinjal Bhadresha
- Hematology/Oncology Division, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Muhammed Jameel Mughal
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Science, The George Washington University, Washington, DC, United States
| | - Michelle McCabe
- Department of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown, Johannesburg, South Africa
| | - Reza Shahbazi
- Hematology/Oncology Division, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Paul Ruff
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Department of Internal Medicine, Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clement Penny
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Department of Internal Medicine, Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,*Correspondence: Clement Penny,
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Piercey O, Tie J. Circulating tumour DNA in the evolving treatment landscape of locally advanced rectal cancer: where does it fit in? Ther Adv Med Oncol 2023; 15:17588359231160138. [PMID: 36936200 PMCID: PMC10017954 DOI: 10.1177/17588359231160138] [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: 10/02/2022] [Accepted: 02/03/2023] [Indexed: 03/16/2023] Open
Abstract
The management of locally advanced rectal cancer (LARC) requires multimodality treatment, typically with neoadjuvant chemoradiotherapy (CRT) followed by total mesorectal excision. However, the treatment landscape is rapidly evolving with total neoadjuvant therapy and non-operative management for selected patients emerging as other novel treatment approaches. With so many treatment options, there is a need for biomarkers to direct a more personalised treatment strategy for patients with LARC. In this review, we summarise the available data regarding the use of circulating tumour DNA (ctDNA) in patients with LARC, as both a marker of treatment response to neoadjuvant therapy and as a marker of minimal residual disease (MRD) after patients have completed definitive local treatment. To date, the ability of ctDNA status to predict for pathologic complete response at any timepoint during multimodality treatment has been variably reported. The most consistent finding across available studies is the ability of ctDNA to detect MRD after CRT and surgery, the presence of which confers a significantly poor prognosis, with increased risk of cancer recurrence and worse overall survival. It is yet to be determined if providing additional therapies to patients with MRD improves outcomes. The available studies assessing the potential utility of ctDNA in LARC are limited by significant heterogeneity in the choice of ctDNA assay, timepoint at which ctDNA was collected, treatment that patients received and length of follow-up, leading to uncertainties about how to implement it into daily clinical practice. As the treatment landscape evolves, larger randomised trials assessing the role of ctDNA in LARC are needed.
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Affiliation(s)
- Oliver Piercey
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
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11
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Bregni G, Pretta A, Senti C, Acedo Reina E, Vandeputte C, Trevisi E, Gkolfakis P, Kehagias P, Deleporte A, Van Laethem JL, Vergauwe P, Van den Eynde M, Deboever G, Janssens J, Demolin G, Holbrechts S, Clausse M, De Grez T, Peeters M, D'Hondt L, Geboes K, Besse-Hammer T, Rothé F, Flamen P, Hendlisz A, Sclafani F. Circulating DNA in the neoadjuvant setting of early stage colon cancer. Acta Oncol 2022; 61:1223-1229. [PMID: 35866544 DOI: 10.1080/0284186x.2022.2101023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND While circulating tumour (ct)DNA is an indicator of minimal residual disease and negative prognostic factor in stage II-III colon cancer, no study has ever analysed the value of this biomarker in colon cancer patients treated with neoadjuvant chemotherapy. We sought to fill this gap by using prospectively collected plasma samples from 80 stage III colon cancer patients, receiving one cycle of neoadjuvant FOLFOX followed by surgery +/- adjuvant FOLFOX in the PePiTA trial. MATERIAL AND METHODS Samples were collected at baseline, 2 weeks and surgery. NPY and WIF1 were selected as universal methylation markers for ctDNA, and analysed with ddPCR technology. ROC curves were applied for cut-off points, and outcome measures included 5-year disease-free survival (DFS) and 6-year overall survival (OS). RESULTS After a median follow-up of 52.5 months, baseline circulating-free (cf) DNA was an independent prognostic factor for DFS (HR 3.35, 95% CI: 1.15-9.77, p = .03), and a trend towards a similar association was observed for relative cfDNA changes between baseline and surgery (HR 2.57, 95% CI: 0.94-7.05, p = .07). Among 60 ctDNA assessable patients, 25 (42%) had detectable ctDNA at baseline. While detection of ctDNA at any pre-operative timepoint was not associated with outcome, patients with ctDNA increase (change of the worst trending methylation marker ≥11%, or mean ctDNA change of NPY and WIF1 ≥ 0%) between baseline and surgery showed a trend towards worse 5-year DFS (HR 3.66, 95% CI: 0.81-16.44, p = .09). CONCLUSION This is the first study of ctDNA in the neoadjuvant setting of early-stage colon cancer. Results are hypothesis-generating and should be confirmed in larger series.
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Dizdarevic E, Hansen TF, Jakobsen A. The Prognostic Importance of ctDNA in Rectal Cancer: A Critical Reappraisal. Cancers (Basel) 2022; 14:cancers14092252. [PMID: 35565381 PMCID: PMC9101261 DOI: 10.3390/cancers14092252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 01/04/2023] Open
Abstract
Simple Summary An individualized treatment approach is necessary to improve survival and quality of life in rectal cancer. Tools to stratify patients are missing, but ctDNA seems to be a good candidate. Current results are sparse, conflicting and characterized by lack of a uniform approach. As the interpretation of results is dependent on the quality of reporting, we aimed to address this issue in our paper. Our results indicate an association between ctDNA status and outcome. In six out of nine papers, bias was low. However, a conclusion is dubious because of the heterogeneity among the studies and lack of standardized methods. Studies addressing these issues are warranted. Abstract The treatment of locally advanced rectal cancer (LARC) has evolved during the last decades, but recurrence remains a problem. Circulating tumor DNA (ctDNA) may result in an individualized treatment approach with improved survival and quality of life, but diverging results impede further development. In this systematic review, we addressed the quality of reporting and its impact on the interpretation of ctDNA results. We performed a systematic literature search using subject headings and search terms related to ctDNA and rectal cancer. The Quality of Prognostic Studies (QUIPS) tool was used to assess bias. Nine studies, with substantial heterogeneity, were included in the analysis. Three out of nine articles had moderate or high risk of bias. No association was found between treatment response and ctDNA status at baseline. There was a negative association between ctDNA positivity at baseline, before and after surgery and survival. The ctDNA status may be of importance to the long-term prognosis, but the area of research is new and is short of dedicated studies. There is an obvious need for standardization in ctDNA research, and the issue should be addressed in future research.
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Affiliation(s)
- Edina Dizdarevic
- Danish Colorectal Cancer Center South, Department of Oncology, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (T.F.H.); (A.J.)
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
- Correspondence:
| | - Torben Frøstrup Hansen
- Danish Colorectal Cancer Center South, Department of Oncology, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (T.F.H.); (A.J.)
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Anders Jakobsen
- Danish Colorectal Cancer Center South, Department of Oncology, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (T.F.H.); (A.J.)
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
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Hayashi T, Yoshida Y, Yamada T, Tanaka K, Shimaoka H, Kajitani R, Munechika T, Nagano H, Matsumoto Y, Komono A, Sakamoto R, Aisu N, Yoshimatsu G, Yoshimura F, Hasegawa S. Relationship between perioperative oncological evaluation and recurrence using circulating tumor DNA with KRAS mutation in patients with colorectal cancer. Cancer Med 2022; 11:3126-3135. [PMID: 35312176 PMCID: PMC9385586 DOI: 10.1002/cam4.4677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022] Open
Abstract
Background The detection of circulating tumor DNA (ctDNA) in colorectal cancer (CRC) by liquid biopsy may have prognostic information. In this perioperative study, we evaluate if there is a relationship between mutant allele frequency (MAF) of Kirsten rat sarcoma viral oncogene homolog (KRAS) and tumor recurrence and how that could be useful in the early detection of recurrence. Methods Among 304 cases of colorectal cancer surgery, ctDNA was sampled from the perioperative blood of 84 patients with CRC with KRAS mutation (exon 4 p.A146T, exon 4 p.A146V, exon 2 p.G12A, exon 2 p.G12C, exon 2 p.G12D, exon 2 p.G12S, exon 2 p.G12V, exon 2 p.G13D, exon 3 p.Q61H) and analyzed using the digital polymerase chain reaction system. The median observation period was 26 months. Results Although the relationship between the perioperative MAF of KRAS and recurrence was not proved, tumor diameter, tumor depth, and stage were correlated with the preoperative MAF of KRAS (p = 0.034, p = 0.002, p = 0.008). However, tumor diameter, tumor depth, and stage did not correlate with MAF of KRAS at postoperative day 30. Conclusions In this study, pathological tumor size, tumor depth, and stage were correlated with preoperative MAF of KRAS, but it was unreliable to predict recurrence by detection of ctDNA with KRAS mutation in the perioperative period of colorectal surgery.
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Affiliation(s)
- Takaomi Hayashi
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Yoichiro Yoshida
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Teppei Yamada
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Keita Tanaka
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Hideki Shimaoka
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Ryuji Kajitani
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Taro Munechika
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Hideki Nagano
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Yoshiko Matsumoto
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Akira Komono
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Ryohei Sakamoto
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Naoya Aisu
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Gumpei Yoshimatsu
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Fumihiro Yoshimura
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Suguru Hasegawa
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
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The potential of PIK3CA, KRAS, BRAF, and APC hotspot mutations as a non-invasive detection method for colorectal cancer. Mol Cell Probes 2022; 63:101807. [DOI: 10.1016/j.mcp.2022.101807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 02/07/2023]
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Kuligina E, Moiseyenko F, Belukhin S, Stepanova E, Zakharova M, Chernobrivtseva V, Aliev I, Sharabura T, Moiseyenko V, Aleksakhina S, Laidus T, Martianov A, Kholmatov M, Whitehead A, Yanus G, Imyanitov E. Tumor irradiation may facilitate the detection of tumor-specific mutations in plasma. World J Clin Oncol 2021; 12:1215-1226. [PMID: 35070740 PMCID: PMC8716992 DOI: 10.5306/wjco.v12.i12.1215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/26/2021] [Accepted: 11/28/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The mutation-based analysis of circulating tumor DNA (ctDNA) is a promising diagnostic tool for clinical oncology. However, it has low success rate because many cancer patients do not have detectable ctDNA in the bloodstream.
AIM To evaluate whether preoperative tumor irradiation results in a transient increase of plasma ctDNA concentration due to the induction of apoptosis in radiation-exposed cells.
METHODS This study focused on patients with locally advanced rectal cancer, because preoperative tumor irradiation is a part of their standard treatment plan. Nine subjects, whose tumors contained KRAS, NRAS or BRAF mutations, donated serial blood samples 1 h prior to the first fraction of irradiation (at baseline), immediately after the first fraction (time 0), and 1, 3, 6, 12, 24, 36, 48, 72 and 96 h after the first fraction. The amount of mutated gene copies was measured by droplet digital PCR.
RESULTS Five out of nine patients were mutation-negative by ctDNA test at baseline; two of these subjects demonstrated an emergence of the mutated DNA copies in the bloodstream within the follow-up period. There were 4 patients, who had detectable ctDNA in the plasma at the start of the experiment; three of them showed an evident treatment-induced increase of the content of mutated RAS/RAF alleles.
CONCLUSION Local tumor irradiation may facilitate the detection of tumor-specific DNA in the bloodstream. These data justify further assessment of the clinical feasibility of irradiation-assisted liquid biopsy.
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Affiliation(s)
- Ekaterina Kuligina
- Department of Tumor Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Fedor Moiseyenko
- Department of Therapy, City Cancer Center, St.-Petersburg 197758, Russia
| | - Sergey Belukhin
- Department of Surgery, City Cancer Center, St.-Petersburg 197758, Russia
| | | | - Maria Zakharova
- Department of Radiology, City Cancer Center, St.-Petersburg 197758, Russia
| | | | - Ikram Aliev
- Department of Surgery, City Cancer Center, St.-Petersburg 197758, Russia
| | - Tatiana Sharabura
- Department of Radiology, City Cancer Center, St.-Petersburg 197758, Russia
| | | | - Svetlana Aleksakhina
- Department of Tumor Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Tatiana Laidus
- Department of Tumor Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
| | - Aleksandr Martianov
- Department of Tumor Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Maksim Kholmatov
- Department of Tumor Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
| | - Aldon Whitehead
- Internal Medicine Residency Program, The University of Illinois College of Medicine, Chicago, IL 60612, United States
| | - Grigoriy Yanus
- Department of Tumor Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny Imyanitov
- Department of Tumor Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
- Department of Oncology, I.I. Mechnikov Northwestern Medical University, St.-Petersburg 191015, Russia
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Ye P, Cai P, Xie J, Zhang J. Reliability of BRAF mutation detection using plasma sample: A systematic review and meta-analysis. Medicine (Baltimore) 2021; 100:e28382. [PMID: 34941166 PMCID: PMC8701458 DOI: 10.1097/md.0000000000028382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/10/2021] [Accepted: 12/01/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Testing of B-Raf proto-oncogene (BRAF) mutation in tumor is necessary before targeted therapies are given. When tumor samples are not available, plasma samples are commonly used for the testing of BRAF mutation. The aim of this study was to investigate the diagnostic accuracy of BRAF mutation testing using plasma sample of cancer patients. METHODS Databases of Pubmed, Embase, and Cochrane Library were searched for eligible studies investigating BRAF mutation in paired tissue and plasma samples of cancer patients. A total of 798 publications were identified after database searching. After removing 229 duplicated publications, 569 studies were screened using the following exclusion criteria: (1) BRAF mutation not measured in plasma or in tumor sample; (2) lacking BRAF-wildtype or BRAF-mutated samples; (3) tissue and plasma samples not paired; (4) lacking tumor or plasma samples; (5) not plasma sample; (6) not cancer; (7) un-interpretable data. Accuracy data and relevant information were extracted from each eligible study by 2 independent researchers and analyzed using statistical software. RESULTS After pooling the accuracy data from 3943 patients of the 53 eligible studies, the pooled sensitivity, specificity, and diagnostic odds ratio of BRAF mutation testing using plasma sample were 69%, 98%, and 55.78, respectively. Area under curve of summary receiver operating characteristic curve was 0.9435. Subgroup analysis indicated that BRAF mutation testing using plasma had overall higher accuracy (diagnostic odds ratio of 89.17) in colorectal cancer, compared to melanoma and thyroid carcinoma. In addition, next-generation sequencing had an overall higher accuracy in detecting BRAF mutation using plasma sample (diagnostic odds ratio of 63.90), compared to digital polymerase chain reaction (PCR) and conventional PCR, while digital PCR showed the highest sensitivity (74%) among the 3 techniques. CONCLUSION BRAF testing using plasma sample showed an overall high accuracy compared to paired tumor tissue sample, which could be used for cancer genotyping when tissue sample is not available. Large prospective studies are needed to further investigate the accuracy of BRAF mutation testing in plasma sample.
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Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, P.R. China
| | - Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, P.R. China
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People's Hospital, Chengdu, P.R. China
| | - Jie Zhang
- Adverse Drug Reaction Monitoring Center, Chengdu, P.R. China
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Sahu S, Gupta P, Dey P. Molecular testing on serous effusion: An update. Cytojournal 2021; 18:35. [PMID: 35126613 PMCID: PMC8813628 DOI: 10.25259/cytojournal_55_2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 06/07/2021] [Indexed: 01/15/2023] Open
Abstract
Cytological examination of the effusion fluid provides valuable information regarding the presence of malignancy. At times, it is challenging to diagnose malignant cells in serous effusion. The various ancillary techniques are available to solve the problem including immunocytochemistry, DNA ploidy, and multicolored flow cytometry. At present, the molecular tests on the effusion sample are of growing interest. The effusion sample is rich in cells and cell-free fluid that contains free DNA, cytokines, and extracellular vesicles. Molecular tests in effusion sample not only provide a diagnosis of malignancy but can also give valuable information that may be essential for the individualized therapy, management, and prognostic assessment. In this paper, we reviewed the application of the different molecular tests in the effusion sample.
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Affiliation(s)
- Saumya Sahu
- Department of Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India,
| | - Parikshaa Gupta
- Department of Cytology, Postgraduate Institute of Medical Education and Research, Chandigarh, India,
| | - Pranab Dey
- Department of Cytology, Postgraduate Institute of Medical Education and Research, Chandigarh, India,
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Morais M, Pinto DM, Machado JC, Carneiro S. ctDNA on liquid biopsy for predicting response and prognosis in locally advanced rectal cancer: A systematic review. Eur J Surg Oncol 2021; 48:218-227. [PMID: 34511270 DOI: 10.1016/j.ejso.2021.08.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 08/31/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The management of locally advanced rectal cancer (LARC) requires a multidisciplinary approach, with an increasing interest for non-operative strategies. Liquid biopsy for obtaining circulating tumor DNA (ctDNA) can provide information on neoadjuvant chemoradiotherapy (nCRT) pathological response and cancer-specific prognosis, and therefore might be a promising guide for these treatments. METHODS A systematic review of the studies available in literature has been performed to assess the role of ctDNA as a predictive and prognostic biomarker in LARC patients. RESULTS We retrieved 21 publications, of which 17 full-text articles and 4 abstracts. Results have been labelled into two groups: predictive and prognostic. Data about the usefulness of liquid biopsy in this setting is still inconclusive. However, baseline higher levels of longer fragments of cell-free DNA and integrity index, tumor-specific mutations and certain methylated genes could predict non-responders. Also, undetectable baseline ctDNA and decrease of common rectal cancer mutations throughout treatment (dynamic monitoring) were predictive factors of pathological complete response. The continuous detection of ctDNA in different timepoints of treatment (minimal residual disease) was consistently associated with worse prognosis. CONCLUSIONS ctDNA is a promising biomarker that could assist predicting treatment response to nCRT and prognosis in patients with LARC. The ideal methods and timings for the liquid biopsy still have to be defined.
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Affiliation(s)
- Marina Morais
- Surgery Department, Hospital Pedro Hispano, Matosinhos, Portugal; Surgery Department, Faculty of Medicine, University of Porto, Porto, Portugal.
| | - Diogo Melo Pinto
- Surgery Department, Hospital Pedro Hispano, Matosinhos, Portugal
| | - José Carlos Machado
- I3S - Institute for Research and Innovation in Health and IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; Pathology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Silvestre Carneiro
- Surgery Department, Faculty of Medicine, University of Porto, Porto, Portugal; Surgery Department, Centro Hospitalar de São João, Porto, Portugal
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Ma Y, Wang J, Song K, Qiang Y, Jiao X, Zhao J. Spatial-Frequency dual-branch attention model for determining KRAS mutation status in colorectal cancer with T2-weighted MRI. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2021; 209:106311. [PMID: 34352652 DOI: 10.1016/j.cmpb.2021.106311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND OBJECTIVE Identifying the KRAS mutation status accurately in medical images is very important for the diagnosis and treatment of colorectal cancer. Despite the substantial progress achieved by existing methods, it remains challenging due to limited annotated dataset, large intra-class variances, and a high degree of inter-class similarities. METHODS To tackle these challenges, we propose a spatial-frequency dual-branch attention model (SF-DBAM) to determine the KRAS mutation status of colorectal cancer patients using a limited T2-weighted MRI dataset. The dataset contains 169 wild-type patients (2151 images) and 137 mutation-type patients (1666 images). The first branch utilizes part of the pre-trained Xception model to capture spatial-domain information and alleviate the small-scale dataset problem. The second branch builds frequency-domain information into cube columns using block-based discrete cosine transform and channel rearrangement. Then the cube columns are fed into convolutional long short-term memory (convLSTM) to explore the effective information between the reconstructed frequency-domain channels. Also, we design a channel enhanced attention module (CEAM) at the end of each branch to make them focus on the lesion areas. Finally, we concatenate the two branches and output the classified results through fully connected layers. RESULTS The proposed method achieves 88.03% overall accuracy with AUC of 94.27% and specificity of 90.75% in 10-fold cross-validation, which is better than the current non-invasive methods for determining KRAS mutation status. CONCLUSIONS We believe that the proposed method can assist physicians to diagnose the KRAS mutation status in patients with colorectal cancer, and other medical problems can benefit from the spatial and frequency domains information.
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Affiliation(s)
- Yulan Ma
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Jiawen Wang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
| | - Kai Song
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
| | - Yan Qiang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China.
| | - Xiong Jiao
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China.
| | - Juanjuan Zhao
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
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Zhang G, Chen L, Liu A, Pan X, Shu J, Han Y, Huan Y, Zhang J. Comparable Performance of Deep Learning-Based to Manual-Based Tumor Segmentation in KRAS/NRAS/BRAF Mutation Prediction With MR-Based Radiomics in Rectal Cancer. Front Oncol 2021; 11:696706. [PMID: 34395262 PMCID: PMC8358773 DOI: 10.3389/fonc.2021.696706] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/15/2021] [Indexed: 12/22/2022] Open
Abstract
Radiomic features extracted from segmented tumor regions have shown great power in gene mutation prediction, while deep learning–based (DL-based) segmentation helps to address the inherent limitations of manual segmentation. We therefore investigated whether deep learning–based segmentation is feasible in predicting KRAS/NRAS/BRAF mutations of rectal cancer using MR-based radiomics. In this study, we proposed DL-based segmentation models with 3D V-net architecture. One hundred and eight patients’ images (T2WI and DWI) were collected for training, and another 94 patients’ images were collected for validation. We evaluated the DL-based segmentation manner and compared it with the manual-based segmentation manner through comparing the gene prediction performance of six radiomics-based models on the test set. The performance of the DL-based segmentation was evaluated by Dice coefficients, which are 0.878 ± 0.214 and 0.955 ± 0.055 for T2WI and DWI, respectively. The performance of the radiomics-based model in gene prediction based on DL-segmented VOI was evaluated by AUCs (0.714 for T2WI, 0.816 for DWI, and 0.887 for T2WI+DWI), which were comparable to that of corresponding manual-based VOI (0.637 for T2WI, P=0.188; 0.872 for DWI, P=0.181; and 0.906 for T2WI+DWI, P=0.676). The results showed that 3D V-Net architecture could conduct reliable rectal cancer segmentation on T2WI and DWI images. All-relevant radiomics-based models presented similar performances in KRAS/NRAS/BRAF prediction between the two segmentation manners.
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Affiliation(s)
- Guangwen Zhang
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Lei Chen
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Aie Liu
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Xianpan Pan
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Jun Shu
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Ye Han
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yi Huan
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jinsong Zhang
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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Ye P, Cai P, Xie J, Wei Y. The diagnostic accuracy of digital PCR, ARMS and NGS for detecting KRAS mutation in cell-free DNA of patients with colorectal cancer: A systematic review and meta-analysis. PLoS One 2021; 16:e0248775. [PMID: 33770081 PMCID: PMC7997033 DOI: 10.1371/journal.pone.0248775] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Introduction Before anti-EGFR therapy is given to patients with colorectal cancer, it is required to determine KRAS mutation status in tumor. When tumor tissue is not available, cell-free DNA (liquid biopsy) is commonly used as an alternative. Due to the low abundance of tumor-derived DNA in cell-free DNA samples, methods with high sensitivity were preferred, including digital polymerase chain reaction, amplification refractory mutation system and next-generation sequencing. The aim of this systemic review and meta-analysis was to investigate the accuracy of those methods in detecting KRAS mutation in cell-free DNA sample from patients with colorectal cancer. Methods Literature search was performed in Pubmed, Embase, and Cochrane Library. After removing duplicates from the 170 publications found by literature search, eligible studies were identified using pre-defined criteria. Quality of the publications and relevant data were assessed and extracted thereafter. Meta-DiSc and STATA softwares were used to pool the accuracy parameters from the extracted data. Results A total of 33 eligible studies were identified for this systemic review and meta-analysis. After pooling, the overall sensitivity, specificity, and diagnostic odds ratio were 0.77 (95%CI: 0.74–0.79), 0.87 (95%CI: 0.85–0.89), and 23.96 (95%CI: 13.72–41.84), respectively. The overall positive and negative likelihood ratios were 5.55 (95%CI: 3.76–8.19) and 0.29 (95%CI: 0.21–0.38), respectively. Area under curve of the summarized ROC curve was 0.8992. Conclusion Digital polymerase chain reaction, amplification refractory mutation system, and next-generation sequencing had overall high accuracy in detecting KRAS mutation in cell-free DNA sample. Large prospective randomized clinical trials are needed to further convince the accuracy and usefulness of KRAS mutation detection using cfDNA/liquid biopsy samples in clinical practice. Trial registration PROSPERO CRD42020176682; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=176682.
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Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
| | - Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People’s Hospital, Chengdu, Sichuan Province, People’s Republic of China
| | - Yuanyuan Wei
- Department of Physiology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
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22
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Applications of liquid biopsy in the Pharmacological Audit Trail for anticancer drug development. Nat Rev Clin Oncol 2021; 18:454-467. [PMID: 33762744 DOI: 10.1038/s41571-021-00489-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 02/06/2023]
Abstract
Anticancer drug development is a costly and protracted activity, and failure at late phases of clinical testing is common. We have previously proposed the Pharmacological Audit Trail (PhAT) intended to improve the efficiency of drug development, with a focus on the use of tumour tissue-based biomarkers. Blood-based 'liquid biopsy' approaches, such as targeted or whole-genome sequencing studies of plasma circulating cell-free tumour DNA (ctDNA) and circulating tumour cells (CTCs), are of increasing relevance to this drug development paradigm. Liquid biopsy assays can provide quantitative and qualitative data on prognostic, predictive, pharmacodynamic and clinical response biomarkers, and can also enable the characterization of disease evolution and resistance mechanisms. In this Perspective, we examine the promise of integrating liquid biopsy analyses into the PhAT, focusing on the current evidence, advances, limitations and challenges. We emphasize the continued importance of analytical validation and clinical qualification of circulating tumour biomarkers through prospective clinical trials.
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23
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Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients. Genes (Basel) 2021; 12:genes12020289. [PMID: 33669856 PMCID: PMC7923234 DOI: 10.3390/genes12020289] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 02/07/2023] Open
Abstract
Liquid biopsy and cell-free DNA (cfDNA) show great promise in cancer diagnostics. In this study, we designed a custom droplet digital PCR (ddPCR) assay for the quantification and quality control of cfDNA isolated from serum. The assay was validated on a group of locally advanced colorectal cancer (CRC) patients and two control groups-patients with hemorrhoids and healthy individuals. The assay shows a high correlation with Qubit measurement (r = 0.976) but offers a higher dynamic range. Mean concentrations of cfDNA were 12.36 ng/µL, 5.17 ng/µL, and 0.29 ng/µL for CRC, hemorrhoid patients, and healthy controls, respectively. The quality of cfDNA was assessed with the measurement of B-cell DNA contamination. On a subset of CRC patients, we compared the mutation status on KRAS (G12A, G12D, G12V, G13D) and BRAF (V600E) genes in the primary tumor and cfDNA isolated from the serum. A total of 70.6% of primary tumor samples were mutated, and the mean fractional abundance of mutations was 9.50%. The matching serum samples were mutated in 38% cases with an average fractional abundance of 0.23%. We conclude that any decisions based solely on the amount of cfDNA present in patient serum must be interpreted carefully and in the context of co-morbidities. This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management.
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24
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Preoperative detection of KRAS mutated circulating tumor DNA is an independent risk factor for recurrence in colorectal cancer. Sci Rep 2021; 11:441. [PMID: 33432066 PMCID: PMC7801374 DOI: 10.1038/s41598-020-79909-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
Preoperative ctDNA status in relation to recurrence in cases of CRC remains unclear. We examined preoperative ctDNA detection by targeting KRAS gene mutations as a predictive marker for recurrence after CRC surgery. We measured the preoperative KRAS mutated ctDNA status and analyzed the correlation with clinicopathologic features of 180 patients that underwent surgery for CRC. We studied the association between preoperative KRAS mutated ctDNA and postoperative recurrence in patients (n = 150) that underwent radical surgery. KRAS mutated ctDNA was detected in 59 patients (32.8%). Median mutant allele frequency of KRAS in ctDNA was 0.20%. KRAS status in ctDNA and lymph node metastasis and distant metastasis were not significantly different. Among patients that underwent radical resection, recurrence occurred in 21 (14.0%, median follow-up 24 months). In Kaplan-Meier analysis, preoperative detection of KRAS mutated ctDNA was associated with inferior recurrence-free interval (RFI) (p = 0.002) and recurrence-free survival (RFS) (p = 0.025). In a multivariate Cox proportional hazards model, preoperative detection of KRAS mutated ctDNA was an independent factor related to both RFI (HR = 3.08; p = 0.012) and RFS (HR = 2.18; p = 0.044). Preoperative measurement of KRAS mutated ctDNA could be useful to decide postoperative treatment.
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25
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Qiu CX, Bai XF, Shen Y, Zhou Z, Pan LQ, Xu YC, Zhao WB, Chen SQ. Specific Inhibition of Tumor Growth by T Cell Receptor-Drug Conjugates Targeting Intracellular Cancer-Testis Antigen NY-ESO-1/LAGE-1. Bioconjug Chem 2020; 31:2767-2778. [PMID: 33237767 DOI: 10.1021/acs.bioconjchem.0c00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the significant therapeutic advances in T-cell immunotherapy, many malignancies remain unresponsive, which might be because of the negative regulation of T cells by the tumor microenvironment (TME). T cells discriminate tumor cells and normal cells through T-cell receptors (TCRs); therefore, we generated a novel type of TCR-drug conjugates (TDCs) by referring antibody-drug conjugations (ADCs) to overcome the effects of the TME on T cells while preserving the specificity of TCR for tumor recognition. We selected HLA-A2/NY-ESO-1157-165 (peptide NY-ESO-1157-165 in complex with human leukocyte antigen serotype HLA-A*02:01) as the antigen and the antigen-specific TCR (1G4113) as the carrier. By sortase A-mediated ligation, we obtained three NY-TCR-vcMMAEs and further studied their properties, antitumor activity, and toxicity in vitro and in vivo. We found that all the NY-TCR-vcMMAEs had high endocytosis efficiency and specifically killed HLA-A2/NY-ESO-1157-165 positive tumor cells. In xenograft models, one of the TDCs, NY-TCR-2M, was effectively and specifically distributed into tumor tissues and inhibited tumor growth without inducing obvious toxicity. Our results demonstrated that TCRs can be carriers of toxic payloads and that the TDCs thus formed can specifically inhibit tumor growth, neglecting the immune microenvironment.
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Affiliation(s)
- Chi-Xiao Qiu
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xue-Fei Bai
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Li-Qiang Pan
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying-Chun Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wen-Bin Zhao
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shu-Qing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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26
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Nguyen HT, Le DT, Duong QH, Tatipamula VB, Van Nguyen B. High frequency of microsatellite instability and its substantial co-existence with KRAS and BRAF mutations in Vietnamese patients with colorectal cancer. Oncol Lett 2020; 21:41. [PMID: 33262833 PMCID: PMC7693389 DOI: 10.3892/ol.2020.12302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Tumor heterogeneity and resistance to chemotherapy have been recognized as two major obstacles in the diagnosis and treatment of colorectal cancer (CRC). Microsatellite instability (MSI) and KRAS and BRAF mutations are common diagnostic factors that have been widely used to classify CRC for therapeutics. In the present study, 151 patients with CRC were analyzed from the two most populous ethnic groups of Vietnam, Kinh and Muong, for their MSI status, frequency of KRAS and BRAF mutations, and their clinical implications. MSI-high (MSI-H) was detected in 45.0% (68/151), while mutated KRAS and BRAF were identified in 37.1% (56/151) and 2.6% (4/151) of the cases, respectively. There was a substantial co-existence of MSI-H with KRAS (27/56; 48.2%) and BRAF (3/4; 75.0%) mutations. Statistical analysis showed that MSI-H tumors were significantly associated with colon location (P=0.011) and more advanced T stages (P=0.016). KRAS exon 2 mutations were significantly more likely to be detected in patients who belonged to the Muong ethnic group (P=0.013) or those with no/fewer lymph node metastasis (P=0.048) as compared with their counterparts. In summary, the data revealed typical molecular features of Vietnamese patients with CRC, including a strikingly high rate of MSI-H and its high co-existence with KRAS and BRAF mutations, which should be carefully considered in the future therapeutics for this type of cancer.
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Affiliation(s)
- Ha Thi Nguyen
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam.,Faculty of Medicine, Duy Tan University, Danang 550000, Vietnam
| | - Do Thanh Le
- Institute for Global Health Innovations, Duy Tan University, Danang 550000, Vietnam.,Faculty of Pharmacy, Duy Tan University, Danang 550000, Vietnam
| | - Quan Hong Duong
- Laboratory Center, Hanoi University of Public Heath, Hanoi 100000, Vietnam
| | - Vinay Bharadwaj Tatipamula
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam.,Faculty of Pharmacy, Duy Tan University, Danang 550000, Vietnam
| | - Bang Van Nguyen
- Anapathology Department, Hue Central Hospital, Hue 530000, Vietnam
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27
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Germetaki T, Nicholls C, Adams RA, Braun M, Rogan J, Moghadam S, Lenfert E, Lukas A, Edelstein DL, Jones FS, Saunders MP. Blood-based RAS mutation testing: concordance with tissue-based RAS testing and mutational changes on progression. Future Oncol 2020; 16:2177-2189. [PMID: 32716216 DOI: 10.2217/fon-2020-0523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Aim: To determine the concordance between plasma and tissue RAS mutation status in metastatic colorectal cancer patients to gauge whether blood-based testing is a viable alternative. We also evaluated the change in mutation status on progression. Materials/methods: RAS testing was performed on plasma from patients commencing first-line therapy (OncoBEAM™ RAS CEIVD kit). Results were then compared with formalin-fixed paraffin embedded tumor samples. Results: The overall percentage agreement (concordance) was 86.0% (86/100), which demonstrates that blood-based testing is an alternative to tissue-based testing. Reproducibility was 100% between three laboratories and 20% showed changes in their RAS mutational status on progression. Conclusion: These results show good concordance between tissue and plasma samples and suggest the need for longitudinal plasma testing during treatment to guide management decisions.
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Affiliation(s)
- Theodora Germetaki
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Camille Nicholls
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Richard A Adams
- Department of Medical Oncology, Velindre Hospital, Velindre Road, Cardiff, Wales CF14 2TL, UK
| | - Michael Braun
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Jane Rogan
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Sharzad Moghadam
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Eva Lenfert
- Sysmex Inostics GmbH, Falkenried 88, Hamburg 20251, Germany
| | - Antje Lukas
- Sysmex Inostics GmbH, Falkenried 88, Hamburg 20251, Germany
| | | | | | - Mark P Saunders
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
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28
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Lee J, Kim JH, Kang SH, Yoo HM. Improvement of digital PCR conditions for direct detection of KRAS mutations. J Clin Lab Anal 2020; 34:e23344. [PMID: 32329932 PMCID: PMC7439326 DOI: 10.1002/jcla.23344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 03/05/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In standard analytical conditions, an isolation step is essential for circulating tumor DNA (ctDNA) analysis. The necessity of this step becomes unclear with the development of highly sensitive detection methods. The aim of this study was to evaluate ctDNA mimetic nDNA detection as reference materials (RMs) using dPCR technologies either directly from serum or without serum. METHODS To determine an absolute count of both mutation and wild-type bearing DNA molecules, genomic DNA (gDNA) and nucleosomal DNA (nDNA), which are similar in size to cell-free DNA, were evaluated. We tested 3 KRAS mutations in colorectal cancer cell lines. RESULTS We describe the recent progress in RMs. The short DNA fragments, such as sDNA and nDNA, exhibited higher quantitative values of dPCR compared to gDNA. The efficiency between Atlantis dsDNase (AD) and Micrococcal Nuclease (MN) affects DNA quantification. Moreover, there was a significant difference in dPCR output when spiking gDNA or nDNA containing KRAS mutations into FBS compared to the dPCR output under non-FBS conditions. CONCLUSION The matrix effect crucially affects the accuracy of gDNA and nDNA level estimation in the direct detection of mimic of patient samples. The form of reference material we proposed should be optimized for various conditions to develop reference materials that can accurately measure copy number and verify the detection of KRAS mutations in the matrix.
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Affiliation(s)
- Jina Lee
- Center for BioanalysisKorea Research Institute of Standards and Science (KRISS)DaejeonKorea
- College of PharmacyChungnam National UniversityDaejeonKorea
| | - Ji Hyun Kim
- Center for BioanalysisKorea Research Institute of Standards and Science (KRISS)DaejeonKorea
| | - Sun Hyung Kang
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineChungnam National University School of MedicineDaejeonKorea
| | - Hee Min Yoo
- Center for BioanalysisKorea Research Institute of Standards and Science (KRISS)DaejeonKorea
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29
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Circulating Tumor DNA in KRAS positive colorectal cancer patients as a prognostic factor - a systematic review and meta-analysis. Crit Rev Oncol Hematol 2020; 154:103065. [PMID: 32763752 DOI: 10.1016/j.critrevonc.2020.103065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/13/2020] [Accepted: 07/20/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Liquid biopsy is a novel tool in oncology. It provides minimally invasive detection of tumor specific DNA. This review summarizes data on presence of circulating tumor DNA in serum or plasma of CRC patients as a potential negative prognostic factor. MATERIALS AND METHODS The systematic review was performed according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). The search was performed using PubMed, Web of Science and Scopus. RESULTS In total 18 articles with a total of 1779 patients met the inclusion criteria. Six out of 8 studies found that presence of ctDNA in plasma/serum was associated with inferior overall survival. All 6 studies found that high concentrations of ctDNA in plasma/serum was associated with inferior overall survival. CONCLUSIONS Presence or high concentrations of KRAS mutation in plasma or serum were associated with inferior prognosis. Establishing cut-off concentrations is warranted for further clinical implementation of liquid biopsy.
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30
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Circulating Tumour DNAs and Non-Coding RNAs as Liquid Biopsies for the Management of Colorectal Cancer Patients. GASTROINTESTINAL DISORDERS 2020. [DOI: 10.3390/gidisord2030022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circulating tumour DNAs and non-coding RNAs present in body fluids have been under investigation as tools for cancer diagnosis, disease monitoring, and prognosis for many years. These so-called liquid biopsies offer the opportunity to obtain information about the molecular make-up of a cancer in a minimal invasive way and offer the possibility to implement theranostics for precision oncology. Furthermore, liquid biopsies could overcome the limitations of tissue biopsies in capturing the complexity of tumour heterogeneity within the primary cancer and among different metastatic sites. Liquid biopsies may also be implemented to detect early tumour formation or to monitor cancer relapse of response to therapy with greater sensitivity compared with the currently available protein-based blood biomarkers. Most colorectal cancers are often diagnosed at late stages and have a high mortality rate. Hence, biomolecules as nucleic acids present in liquid biopsies might have prognostic potential and could serve as predictive biomarkers for chemotherapeutic regimens. This review will focus on the role of circulating tumour DNAs and non-coding RNAs as diagnostic, prognostic, and predictive biomarkers in the context of colorectal cancer.
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31
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Leick KM, Kazarian AG, Rajput M, Tomanek-Chalkley A, Miller A, Shrader HR, McCarthy A, Coleman KL, Kasi PM, Chan CHF. Peritoneal Cell-Free Tumor DNA as Biomarker for Peritoneal Surface Malignancies. Ann Surg Oncol 2020; 27:5065-5071. [PMID: 32648179 DOI: 10.1245/s10434-020-08832-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/27/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Disease burden in patients with peritoneal carcinomatosis (PC) is difficult to estimate. We evaluate whether peritoneal cell-free tumor DNA can be used as a measure of disease burden. PATIENTS AND METHODS Malignant ascites or peritoneal lavage fluids were collected from patients with PC under approved IRB protocol. Cell-free DNA was extracted from peritoneal fluid. Droplet digital PCR (ddPCR) was performed using a commercially available KRAS G12/G13 screening kit. Mutant allele frequency (MAF) was calculated based on the numbers of KRAS wild-type and mutant droplets. Clinicopathological, treatment and outcome data were abstracted and correlated with MAF of cell-free KRAS mutant DNA. RESULTS Cell-free KRAS mutant DNA was detected in 15/37 (40%) malignant peritoneal fluids with a MAF of 0.1% to 26.2%. While peritoneal cell-free KRAS mutant DNA was detected in all the patients with KRAS mutant tumors (N = 10), 3/16 (19%) patients with KRAS wild-type tumors also had peritoneal cell-free KRAS mutant DNA. We also found that 71% (5/7) of patients with disease amenable to cytoreductive surgery (CRS) had a MAF of < 1% (median: 0.5%, range: 0.1-4.7%), while 75% (6/8) of patients with unresectable disease had a MAF of > 1% (median: 4.4%, range: 0.1-26.2%). CONCLUSIONS This pilot proof-of-principle study suggests that peritoneal cell-free tumor DNA detected by ddPCR may enable prediction of disease burden and a measure of disease amenable to CRS in patients with PC.
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Affiliation(s)
- Katie M Leick
- Department of Surgery, University of Iowa, Iowa City, IA, USA
| | | | - Maheen Rajput
- Department of Radiology, University of Iowa, Iowa City, IA, USA
| | | | - Ann Miller
- Department of Surgery, University of Iowa, Iowa City, IA, USA
| | | | - Ashley McCarthy
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Kristen L Coleman
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Pashtoon M Kasi
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA.,Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Carlos H F Chan
- Department of Surgery, University of Iowa, Iowa City, IA, USA. .,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA.
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32
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Shinjo K, Hara K, Nagae G, Umeda T, Katsushima K, Suzuki M, Murofushi Y, Umezu Y, Takeuchi I, Takahashi S, Okuno Y, Matsuo K, Ito H, Tajima S, Aburatani H, Yamao K, Kondo Y. A novel sensitive detection method for DNA methylation in circulating free DNA of pancreatic cancer. PLoS One 2020; 15:e0233782. [PMID: 32520974 PMCID: PMC7286528 DOI: 10.1371/journal.pone.0233782] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 12/26/2022] Open
Abstract
Despite recent advances in clinical treatment, pancreatic cancer remains a highly lethal malignancy. In order to improve the survival rate of patients with pancreatic cancer, the development of non-invasive diagnostic methods using effective biomarkers is urgently needed. Here, we developed a highly sensitive method to detect DNA methylation in cell-free (cf)DNA samples based on the enrichment of methyl-CpG binding (MBD) protein coupled with a digital PCR method (MBD–ddPCR). Five DNA methylation markers for the diagnosis of pancreatic cancer were identified through DNA methylation microarray analysis in 37 pancreatic cancers. The sensitivity and specificity of the five markers were validated in another independent cohort of pancreatic cancers (100% and 100%, respectively; n = 46) as well as in The Cancer Genome Atlas data set (96% and 90%, respectively; n = 137). MBD–ddPCR analysis revealed that DNA methylation in at least one of the five markers was detected in 23 (49%) samples of cfDNA from 47 patients with pancreatic cancer. Further, a combination of DNA methylation markers and the KRAS mutation status improved the diagnostic capability of this method (sensitivity and specificity, 68% and 86%, respectively). Genome-wide MBD-sequencing analysis in cancer tissues and corresponding cfDNA revealed that more than 80% of methylated regions were overlapping; DNA methylation profiles of cancerous tissues and cfDNA significantly correlated with each other (R = 0.97). Our data indicate that newly developed MBD–ddPCR is a sensitive method to detect cfDNA methylation and that using five marker genes plus KRAS mutations may be useful for the detection of pancreatic cancers.
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Affiliation(s)
- Keiko Shinjo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuo Hara
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Genta Nagae
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Umeda
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Keisuke Katsushima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miho Suzuki
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiteru Murofushi
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuta Umezu
- Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan.,School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Ichiro Takeuchi
- Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan.,RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hiroyuki Aburatani
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kenji Yamao
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya, Japan.,Department of Gastroenterology, Narita Memorial Hospital, Toyohashi, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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33
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Casiraghi N, Orlando F, Ciani Y, Xiang J, Sboner A, Elemento O, Attard G, Beltran H, Demichelis F, Romanel A. ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA. Bioinformatics 2020; 36:2665-2674. [PMID: 31922552 PMCID: PMC7203757 DOI: 10.1093/bioinformatics/btaa016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/04/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION The use of liquid biopsies for cancer patients enables the non-invasive tracking of treatment response and tumor dynamics through single or serial blood drawn tests. Next-generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single-nucleotide variants (SNVs) in circulating cell-free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs. RESULTS We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic SNVs in cfDNA. We tested the capability of our method to analyze data generated using different platforms with distinct sequencing error properties and we compared ABEMUS performances with other popular SNV callers on both synthetic and real cancer patients sequencing data. Results show that ABEMUS performs better in most of the tested conditions proving its reliability in calling low variant allele frequencies somatic SNVs in low ctDNA levels plasma samples. AVAILABILITY AND IMPLEMENTATION ABEMUS is cross-platform and can be installed as R package. The source code is maintained on Github at http://github.com/cibiobcg/abemus, and it is also available at CRAN official R repository. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicola Casiraghi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| | - Francesco Orlando
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| | - Jenny Xiang
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Genomics and Epigenomics Core Facility
| | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Gerhardt Attard
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Himisha Beltran
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
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Prognostic Value of Serum NPY Hypermethylation in Neoadjuvant Chemoradiotherapy for Rectal Cancer: Secondary Analysis of a Randomized Trial. Am J Clin Oncol 2020; 43:9-13. [PMID: 31569168 DOI: 10.1097/coc.0000000000000609] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Long-term prevention of metastatic disease remains a challenge in locally advanced rectal cancer, and robust pretreatment prognostic factors for metastatic progression are lacking. We hypothesized that detecting circulating tumor-specific DNA (ctDNA) based on hypermethylation of the neuropeptide Y gene (meth-ctDNA) could be a prognostic marker in the neoadjuvant setting; we examined this in a secondary, explorative analysis of a prospective trial. MATERIALS AND METHODS Serum samples were prospectively collected in a phase III trial for locally advanced rectal cancer. Positivity for and fractional abundance of meth-ctDNA in baseline samples were estimated. Overall survival (OS) and the rate of distant metastases were compared between meth-ctDNA positive and negative patients; other prognostic factors were controlled for in multivariate Cox regression. Importance of quantitative load was examined by considering the fractional abundance of meth-ctDNA relative to total circulating DNA. RESULTS Baseline serum samples were available for 146 patients. In total, 30 patients had presence of meth-ctDNA, with no correlation with cT (P=0.8) or cN (P=0.6) stages. Median follow-up was 10.6 years for OS and 5.1 years for freedom from distant metastases. Patients with meth-ctDNA had significantly worse 5-year OS (47% vs. 69%), even when controlling for other prognostic factors (hazard ratio=2.08; 95% confidence interval, 1.23-1.51). This seemed mainly driven by disparity in the rate of distant metastases (55% vs. 72% at 5 y, P=0.01); hazard ratio=2.20 (95% confidence interval, 1.19-4.07, P=0.01) in multivariate analysis. Increased quantitative load was highly significant for worse outcomes. CONCLUSIONS Meth-ctDNA could be a potential prognostic marker in the neoadjuvant setting and may, if validated, identify patients at increased risk of distant metastases.
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Abstract
PURPOSE OF REVIEW To summarise diagnostic clinical/laboratory findings and highlight differences between classical hairy cell leukaemia (HCLc) and hairy cell leukaemia variant (HCLv). Discussion of prognosis and current treatment indications including novel therapies, linked to understanding of the underlying molecular pathogenesis. RECENT FINDINGS Improved understanding of the underlying pathogenesis of HCLc, particularly the causative mutation BRAF V600E, leading to constitutive activation of the MEK/ERK signalling pathway and increased cell proliferation. HCLc is caused by BRAF V600E mutation in most cases. Purine nucleoside analogue (PNA) therapy is the mainstay of treatment, with the addition of rituximab, improving response and minimal residual disease (MRD) clearance. Despite excellent responses to PNAs, many patients will eventually relapse, requiring further therapy. Rarely, patients are refractory to PNA therapy. In relapsed/refractory patients, novel targeted therapies include BRAF inhibitors (BRAFi), anti-CD22 immunoconjugate moxetumomab and Bruton tyrosine kinase inhibitors (BTKi). HCLv has a worse prognosis with median overall survival (OS), only 7-9 years, despite the combination of PNA/rituximab improving front-line response. Moxetumomab or ibrutinib may be a viable treatment but lacks substantial evidence.
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Affiliation(s)
- Matthew Cross
- The Royal Marsden Hospital and the Institute of Cancer Research, Sutton, UK
| | - Claire Dearden
- The Royal Marsden Hospital and the Institute of Cancer Research, Sutton, UK.
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Khatami F, Larijani B, Heshmat R, Nasiri S, Haddadi-Aghdam M, Teimoori-Toolabi L, Tavangar SM. Hypermethylated RASSF1 and SLC5A8 promoters alongside BRAF V600E mutation as biomarkers for papillary thyroid carcinoma. J Cell Physiol 2020; 235:6954-6968. [PMID: 32017063 DOI: 10.1002/jcp.29591] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022]
Abstract
Circulating cell-free DNA (cfDNA) has been considered as a diagnostic source to track genetic and epigenetic alterations in cancer. We aimed to study mutation in addition to the methylation status in the promoter regions of RASSF1 and SLC5A8 genes in tissues and circulating free DNA samples of patients affected with papillary thyroid carcinoma (PTC) and thyroid nodules as controls. BRAFV600E mutation was studied by ARMS-scorpion real-time polymerase chain reaction method in 57 PTC and 45 thyroid nodule cases. Methylation status of RASSF1 and SLC5A8 promoter regions was analyzed by methylation-specific high-resolution melting curve analysis. BRAFV600E mutation was found in 39 (68.4%) out of 57 PTC tissue samples, while in 33 (49.1%) cases of cfDNA, this mutation was detected. The frequency of BRAFV600E mutation in cfDNA was significantly different between metastatic and nonmetastatic PTC cases (22 of 33 PTC cases vs. 5 of 34 thyroid nodule samples). Methylation levels of three promoter regions of SLC5A8 and proximal promoter region of RASSF1 was significantly different between PTC and thyroid nodule cases in both cfDNA and tissue DNA. In addition, the methylation status of these two genes in tissue DNA was reflected in methylation status observed in cfDNA. This study confirmed that BRAFV600E mutation is better for discrimination between papillary thyroid carcinoma and thyroid nodules. On the other hand, hypermethylation in the more proximal promoter regions to RASSF1 and SLC5A8 genes showed higher sensitivity and more acceptable specificity for this discrimination.
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Affiliation(s)
- Fatemeh Khatami
- Urology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Heshmat
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirzad Nasiri
- Departments of Surgery, Dr. Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Haddadi-Aghdam
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Teimoori-Toolabi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed M Tavangar
- Department of Pathology, Dr. Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Mardinian K, Okamura R, Kato S, Kurzrock R. Temporal and spatial effects and survival outcomes associated with concordance between tissue and blood KRAS alterations in the pan-cancer setting. Int J Cancer 2020; 146:566-576. [PMID: 31199507 PMCID: PMC6874714 DOI: 10.1002/ijc.32510] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/29/2019] [Accepted: 06/05/2019] [Indexed: 12/11/2022]
Abstract
We investigated the impact of time interval, primary vs. metastatic biopsy site, variant allele fraction (VAF) and histology on concordance of KRAS alterations in tissue vs. circulating tumor DNA (ctDNA), and association of concordance with survival. Blood and tissue were evaluated by next-generation sequencing in 433 patients with diverse cancers. Altogether, 101 patients (23.3%) had KRAS alterations: 56, ctDNA (12.9%); 81, tissue (18.7%); and 36, both (8.3%). The overall blood and tissue concordance rate for KRAS alterations was 85%, but was mainly driven by the large negative/negative subset. Therefore, specificity of one test for the other was high (88.1-94.3%), while sensitivity was not high (44.4-64.3%) and was lower still in patients with >6 vs. ≤2 months between blood and tissue sampling (31.0-40.9% vs. 51.2-84.0%; p = 0.14 time interval-dependent sensitivity of blood for tissue; p = 0.003, tissue for blood). Positive concordance rate for KRAS alterations was 57.1% vs. 27.4% (colorectal vs. noncolorectal cancer; p = 0.01), but site of biopsy (primary vs. metastatic) and VAF (%ctDNA) was not impactful. The presence of KRAS alterations in both tests was independently associated with shorter survival from diagnosis (hazard ratio, 1.72; 95% confidence interval, 1.04-2.86) and from recurrent/metastatic disease (1.70; 1.03-2.81). Positive concordance of KRAS alterations between ctDNA and tissue was negatively affected by a longer time period between blood and tissue sampling and was higher in colorectal cancer than in other malignancies. The presence of KRAS alterations in both tests was an independent prognostic factor for poor survival.
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Di Liello R, Cimmino F, Simón S, Giunta EF, De Falco V, Martín-Martorell P. Role of liquid biopsy for thoracic cancers immunotherapy. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:183-199. [PMID: 36046196 PMCID: PMC9400760 DOI: 10.37349/etat.2020.00012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/11/2020] [Indexed: 01/09/2023] Open
Abstract
Immunotherapy has shifted the therapeutic landscape in thoracic cancers. However, assessment of biomarkers for patient selection and disease monitoring remain challenging, especially considering the lack of tissue sample availability for clinical and research purposes. In this scenario, liquid biopsy (LB), defined as the study and characterization of biomarkers in body fluids, represents a useful alternative strategy. In other malignancies such as colorectal cancer, breast cancer or melanoma, the potential of LB has been more extensively explored for monitoring minimal residual disease or response to treatment, and to investigate mechanisms of resistance to targeted agents. Even if various experiences have already been published about the applications of LB in immunotherapy in thoracic cancers, the standardization of methodology and assessment of its clinical utility is still pending. In this review, the authors will focus on the applications of LB in immunotherapy in non-small cell lung cancer, small cell lung cancer, and malignant pleural mesothelioma, describing available data and future perspectives.
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Affiliation(s)
- Raimondo Di Liello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy,Medical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain,Correspondence: Raimondo Di Liello, Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy.
| | | | - Soraya Simón
- Medical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - Emilio Francesco Giunta
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy
| | - Vincenzo De Falco
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy
| | - Paloma Martín-Martorell
- Medical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
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Khakoo S, Carter PD, Brown G, Valeri N, Picchia S, Bali MA, Shaikh R, Jones T, Begum R, Rana I, Wotherspoon A, Terlizzo M, von Loga K, Kalaitzaki E, Saffery C, Watkins D, Tait D, Chau I, Starling N, Hubank M, Cunningham D. MRI Tumor Regression Grade and Circulating Tumor DNA as Complementary Tools to Assess Response and Guide Therapy Adaptation in Rectal Cancer. Clin Cancer Res 2020; 26:183-192. [PMID: 31852830 DOI: 10.1158/1078-0432.ccr-19-1996] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/30/2019] [Accepted: 10/21/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Response to preoperative chemo-radiotherapy (CRT) varies. We assessed whether circulating tumor DNA (ctDNA) might be an early indicator of tumor response or progression to guide therapy adaptation in rectal cancer. EXPERIMENTAL DESIGN A total of 243 serial plasma samples were analyzed from 47 patients with localized rectal cancer undergoing CRT. Up to three somatic variants were tracked in plasma using droplet digital PCR. RECIST and MRI tumor regression grade (mrTRG) evaluated response. Survival analyses applied Kaplan-Meier method and Cox regression. RESULTS ctDNA detection rates were: 74% (n = 35/47) pretreatment, 21% (n = 10/47) mid CRT, 21% (n = 10/47) after completing CRT, and 13% (n = 3/23) after surgery. ctDNA status after CRT was associated with primary tumor response by mrTRG (P = 0.03). With a median follow-up of 26.4 months, metastases-free survival was shorter in patients with detectable ctDNA after completing CRT [HR 7.1; 95% confidence interval (CI), 2.4-21.5; P < 0.001], persistently detectable ctDNA pre and mid CRT (HR 3.8; 95% CI, 1.2-11.7; P = 0.02), and pre, mid, and after CRT (HR 11.5; 95% CI, 3.3-40.4; P < 0.001) compared with patients with undetectable or nonpersistent ctDNA. In patients with detectable ctDNA, a fractional abundance threshold of ≥0.07% mid CRT or ≥0.13% after completing CRT predicted for metastases with 100% sensitivity and 83.3% specificity for mid CRT and 66.7% for CRT completion. All 3 patients with detectable ctDNA post-surgery relapsed compared with none of the 20 patients with undetectable ctDNA (P = 0.001). CONCLUSIONS ctDNA identified patients at risk of developing metastases during the neoadjuvant period and post-surgery, and could be used to tailor treatment.
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Affiliation(s)
- Shelize Khakoo
- Department of Medicine, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Paul David Carter
- Clinical Genomics, The Royal Marsden Hospital NHS Foundation Trust, Sutton, United Kingdom
| | - Gina Brown
- Department of Radiology, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Nicola Valeri
- Molecular Pathology, The Institute of Cancer Research/The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Simona Picchia
- Department of Radiology, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Maria Antonietta Bali
- Department of Radiology, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Ridwan Shaikh
- Clinical Genomics, The Royal Marsden Hospital NHS Foundation Trust, Sutton, United Kingdom
| | - Thomas Jones
- Clinical Genomics, The Royal Marsden Hospital NHS Foundation Trust, Sutton, United Kingdom
| | - Ruwaida Begum
- Department of Medicine, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Isma Rana
- Department of Medicine, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Andrew Wotherspoon
- Department of Histopathology, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Monica Terlizzo
- Department of Histopathology, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Katharina von Loga
- Department of Histopathology, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Eleftheria Kalaitzaki
- Clinical Research and Development, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Claire Saffery
- Department of Medicine, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - David Watkins
- Department of Medicine, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Diana Tait
- Department of Medicine, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Ian Chau
- Department of Medicine, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Naureen Starling
- Department of Medicine, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom
| | - Michael Hubank
- Clinical Genomics, The Royal Marsden Hospital NHS Foundation Trust, Sutton, United Kingdom
| | - David Cunningham
- Department of Medicine, The Royal Marsden Hospital NHS Foundation Trust, London and Surrey, United Kingdom.
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Machackova T, Prochazka V, Kala Z, Slaby O. Translational Potential of MicroRNAs for Preoperative Staging and Prediction of Chemoradiotherapy Response in Rectal Cancer. Cancers (Basel) 2019; 11:cancers11101545. [PMID: 31614848 PMCID: PMC6827048 DOI: 10.3390/cancers11101545] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer is the third most common cancer and the second cause of cancer-related deaths. Rectal cancer presents roughly one-third of all colorectal cancer cases and differs from it on both anatomical and molecular levels. While standard treatment of colon cancer patients is radical surgery, rectal cancer is usually treated with pre-operative chemoradiotherapy followed by total mesorectal excision, which requires precise estimation of TNM staging. Unfortunately, stage evaluation is based solely on imaging modalities, and they often do not correlate with postoperative pathological findings. Moreover, approximately half of rectal cancer patients do not respond to such pre-operative therapy, so they are exposed to its toxic effects without any clinical benefit. Thus, biomarkers that could precisely predict pre-operative TNM staging, and especially response to therapy, would significantly advance rectal cancer treatment—but till now, no such biomarker has been identified. In cancer research, microRNAs are emerging biomarkers due to their connection with carcinogenesis and exceptional stability. Circulating miRNAs are promising non-invasive biomarkers that could allow monitoring of a patient throughout the whole therapeutic process. This mini-review aims to summarize the current knowledge on miRNAs and circulating miRNAs involved in the prediction of response to treatment and pre-operative staging in rectal cancer patients.
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Affiliation(s)
- Tana Machackova
- Department of Molecular Medicine, European Institute of Technology, 625 00 Brno, Czech Republic.
| | - Vladimir Prochazka
- Department of Surgery, University Hospital Brno, 625 00 Brno, Czech Republic.
| | - Zdenek Kala
- Department of Surgery, University Hospital Brno, 625 00 Brno, Czech Republic.
| | - Ondrej Slaby
- Department of Molecular Medicine, European Institute of Technology, 625 00 Brno, Czech Republic.
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Artyuhov AS, Dashinimaev EB, Mescheryakova NV, Ashikhmina AA, Vorotelyak EA, Vasiliev AV. Detection of small numbers of iPSCs in different heterogeneous cell mixtures with highly sensitive droplet digital PCR. Mol Biol Rep 2019; 46:6675-6683. [PMID: 31578676 DOI: 10.1007/s11033-019-05100-2] [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] [Received: 01/28/2019] [Accepted: 09/24/2019] [Indexed: 11/25/2022]
Abstract
Induced pluripotent stem cells (iPS cells) are a prospective resource for regenerative biomedicine. iPS cells can differentiate into any type of stem, progenitor and somatic cells to help replace structures within damaged organs or tissues. However, iPS cells themselves, can produce malignant tumors if they are injected into the body of an immunocompatible or immunodeficient recipient. Thus, it is necessary to detect any residual iPS cells content in biomedical cell products obtained from iPS cells and destined for transplantation. In this article we describe searches for iPS cells in heterogeneous cell mixtures, using two different methods-quantitative RT-PCR and droplet digital PCR (ddPCR). In experiments with various heterogeneous mixtures, including mixtures with neural stem cells, we found that the OCT4, TDGF1 and LIN28 genes are the best markers for such a search, and droplet digital PCR provides the greatest measurement accuracy, which is 0.002%. Thus, we have confirmed the advantage of using droplet digital PCR in the search for pluripotent stem cells in heterogeneous cell mixtures. We hope that this data can be useful for biosafety control in regenerative biomedicine.
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Affiliation(s)
- A S Artyuhov
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, Moscow, Russia, 117997. .,Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, Moscow Region, Russia, 141701.
| | - E B Dashinimaev
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, Moscow, Russia, 117997.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova str. 26, Moscow, Russia, 119334
| | | | - A A Ashikhmina
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, Moscow, Russia, 117997
| | - E A Vorotelyak
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, Moscow, Russia, 117997.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova str. 26, Moscow, Russia, 119334.,Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, Russia, 119991
| | - A V Vasiliev
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, Moscow, Russia, 117997.,Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, Russia, 119991
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Rice A, Del Rio Hernandez A. The Mutational Landscape of Pancreatic and Liver Cancers, as Represented by Circulating Tumor DNA. Front Oncol 2019; 9:952. [PMID: 31608239 PMCID: PMC6769086 DOI: 10.3389/fonc.2019.00952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
The mutational landscapes of pancreatic and liver cancers share many common genetic alterations which drive cancer progression. However, these mutations do not occur in all cases of these diseases, and this tumoral heterogeneity impedes diagnosis, prognosis, and therapeutic development. One minimally invasive method for the evaluation of tumor mutations is the analysis of circulating tumor DNA (ctDNA), released through apoptosis, necrosis, and active secretion by tumor cells into various body fluids. By observing mutations in those genes which promote transformation by controlling the cell cycle and oncogenic signaling pathways, a representation of the mutational profile of the tumor is revealed. The analysis of ctDNA is a promising technique for investigating these two gastrointestinal cancers, as many studies have reported on the accuracy of ctDNA assessment for diagnosis and prognosis using a variety of techniques.
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Affiliation(s)
- Alistair Rice
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Armando Del Rio Hernandez
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Faculty of Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
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Wilson K, Narasimhan V, Pham T, Das A, Ramsay R, Heriot A. Precision medicine in colorectal surgery: coming to a hospital near you. ANZ J Surg 2019; 89:995-996. [PMID: 31522479 DOI: 10.1111/ans.15391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/01/2019] [Accepted: 07/07/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Kasmira Wilson
- Department of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Vignesh Narasimhan
- Department of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Toan Pham
- Department of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Atandrila Das
- Department of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Robert Ramsay
- Department of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alexander Heriot
- Department of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
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44
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Massihnia D, Pizzutilo EG, Amatu A, Tosi F, Ghezzi S, Bencardino K, Di Masi P, Righetti E, Patelli G, Scaglione F, Vanzulli A, Siena S, Sartore-Bianchi A. Liquid biopsy for rectal cancer: A systematic review. Cancer Treat Rev 2019; 79:101893. [PMID: 31499407 DOI: 10.1016/j.ctrv.2019.101893] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND The management of locally advanced rectal cancer (RC) is an evolving clinical field where the multidisciplinary approach can reach its best, and liquid biopsy for obtaining tumor-derived component such as circulating tumor DNA (ctDNA) might provide complementary informations. METHODS A systematic review of studies available in literature of liquid biopsy in non-metastatic RC has been performed according to PRISMA criteria to assess the role of ctDNA as a diagnostic, predictive and prognostic biomarker in this setting. RESULTS Twenty-five publications have been retrieved, of which 8 full-text articles, 7 abstracts and 10 clinical trials. Results have been categorized into three groups: diagnostic, predictive and prognostic. Few but promising data are available about the use of liquid biopsy for early diagnosis of RC, with the main limitation of sensitivity due to low concentrations of ctDNA in this setting. In terms of prediction of response to chemoradiation, still inconclusive data are available about the utility of a pre-treatment liquid biopsy, whereas some studies report a positive correlation with a dynamic (pre/post-treatment) monitoring. The presence of minimal residual disease by ctDNA was consistently associated with worse prognosis across studies. CONCLUSIONS The use of liquid biopsy for monitoring response to chemoradiation and assess the risk of disease recurrence are the most advanced potential applications for liquid biopsy in RC, with implications also in the context of non-operative management strategies.
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Affiliation(s)
- Daniela Massihnia
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy
| | - Elio Gregory Pizzutilo
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy
| | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Federica Tosi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy
| | - Silvia Ghezzi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Katia Bencardino
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Pietro Di Masi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy
| | - Elena Righetti
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy
| | - Giorgio Patelli
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy
| | - Francesco Scaglione
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy
| | - Angelo Vanzulli
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy; Università degli Studi di Milano, Department of Oncology and Hemato-Oncology, Milan, Italy.
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Jacobson RA, Munding E, Hayden DM, Levy M, Kuzel TM, Pappas SG, Masood A. Evolving Clinical Utility of Liquid Biopsy in Gastrointestinal Cancers. Cancers (Basel) 2019; 11:E1164. [PMID: 31412682 PMCID: PMC6721625 DOI: 10.3390/cancers11081164] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 12/13/2022] Open
Abstract
Room for improvement exists regarding recommendations for screening, staging, therapy selection, and frequency of surveillance of gastrointestinal cancers. Screening is costly and invasive, improved staging demands increased sensitivity and specificity to better guide therapy selection. Surveillance requires increased sensitivity for earlier detection and precise management of recurrences. Peripherally collected blood-based liquid biopsies enrich and analyze circulating tumor cells and/or somatic genomic material, including circulating tumor DNA along with various subclasses of RNA. Such assays have the potential to impact clinical practice at multiple stages of management in gastrointestinal cancers. This review summarizes current basic and clinical evidence for the utilization of liquid biopsy in cancers of the esophagus, pancreas, stomach, colon, and rectum. Technical aspects of various liquid biopsy methodologies and targets are reviewed and evidence supporting current commercially available assays is examined. Finally, current clinical applicability, potential future uses, and pitfalls of applying liquid biopsy to the screening, staging and therapeutic management of these diseases are discussed.
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Affiliation(s)
- Richard A Jacobson
- Department of Surgery, Rush University Medical Center, Chicago, IL 60612, USA
| | - Emily Munding
- Department of Surgery, Rush University Medical Center, Chicago, IL 60612, USA
| | - Dana M Hayden
- Department of Surgery, Rush University Medical Center, Chicago, IL 60612, USA
| | - Mia Levy
- Division of Hematology/Oncology and Cell Therapy, Rush University Medical Center, Chicago, IL 60612, USA
- Rush Precision Oncology Program, Rush University Medical Center, Chicago, IL 60612, USA
| | - Timothy M Kuzel
- Division of Hematology/Oncology and Cell Therapy, Rush University Medical Center, Chicago, IL 60612, USA
- Rush Precision Oncology Program, Rush University Medical Center, Chicago, IL 60612, USA
| | - Sam G Pappas
- Department of Surgery, Rush University Medical Center, Chicago, IL 60612, USA
| | - Ashiq Masood
- Division of Hematology/Oncology and Cell Therapy, Rush University Medical Center, Chicago, IL 60612, USA.
- Rush Precision Oncology Program, Rush University Medical Center, Chicago, IL 60612, USA.
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Sclafani F, Wilson SH, Cunningham D, Gonzalez De Castro D, Kalaitzaki E, Begum R, Wotherspoon A, Capdevila J, Glimelius B, Roselló S, Thomas J, Tait D, Brown G, Oates J, Chau I. Analysis of KRAS, NRAS, BRAF, PIK3CA and TP53 mutations in a large prospective series of locally advanced rectal cancer patients. Int J Cancer 2019; 146:94-102. [PMID: 31199501 DOI: 10.1002/ijc.32507] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/06/2019] [Accepted: 05/21/2019] [Indexed: 12/18/2022]
Abstract
Little information is available on the clinical significance of cancer-related genes such as KRAS, NRAS, BRAF, PIK3CA and TP53 in nonmetastatic rectal cancer. We investigated mutations of these genes in a large prospective series of locally advanced rectal cancer (LARC) patients who were recruited into two phase II trials. Mutational analyses were performed with diagnostically validated methods including polymerase chain reaction, capillary electrophoresis single-strand conformational analysis, Sanger sequencing and next-generation sequencing. Associations between single or multiple gene mutations and clinicopathological characteristics and treatment outcomes were explored. Of these 269, 210 (78%) patients were assessable. Mutations of KRAS, NRAS, BRAF, PIK3CA and TP53 occurred in 43, 9, 4, 9 and 60% of patients, respectively. Concordance between paired biopsy and resection specimens was 82% for KRAS, 95% for NRAS, 99% for BRAF, 96% for PIK3CA and 63% for TP53. TP53 mutations were associated with extramural venous invasion on baseline MRI (78% vs. 65%, p = 0.04), poor pathological tumour regression (23% vs. 36%, p = 0.05) and a trend toward a worse 5-year progression-free survival (PFS; 60% vs. 74%, HR 1.59, p = 0.06). Patients with tumours harbouring mutation of TP53 and either KRAS or NRAS (32%) had a worse 5-year PFS than those with TP53/KRAS/NRAS wild-type tumours (54% vs. 72%, HR 1.75, p = 0.02). In univariate analysis, BRAF mutation predicted poor 5-year overall survival only among patients treated without cetuximab (20% vs. 73%, HR 3.29, p = 0.03). This is one of the largest biomarker studies in a prospective, largely homogeneous, LARC population. Our findings are hypothesis generating and require validation in independent series.
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Affiliation(s)
- Francesco Sclafani
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sanna Hulkki Wilson
- Department of Molecular Diagnostics, Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - David Cunningham
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - David Gonzalez De Castro
- Department of Molecular Diagnostics, Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Eleftheria Kalaitzaki
- Department of Clinical Research & Development, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Ruwaida Begum
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Andrew Wotherspoon
- Department of Histopathology, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jaume Capdevila
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Section of Experimental and Clinical Oncology, University of Uppsala, Uppsala, Sweden
| | - Susana Roselló
- Department of Haematology and Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Janet Thomas
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Daina Tait
- Department of Radiotherapy, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Gina Brown
- Department of Radiology, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jacqui Oates
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Ian Chau
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
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Bach S, Sluiter NR, Beagan JJ, Mekke JM, Ket JCF, van Grieken NCT, Steenbergen RDM, Ylstra B, Kazemier G, Tuynman JB. Circulating Tumor DNA Analysis: Clinical Implications for Colorectal Cancer Patients. A Systematic Review. JNCI Cancer Spectr 2019; 3:pkz042. [PMID: 32328554 PMCID: PMC7050033 DOI: 10.1093/jncics/pkz042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/21/2019] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
Background Liquid biopsies could improve diagnosis, prognostication, and monitoring of colorectal cancer (CRC). Mutation, chromosomal copy number alteration, and methylation analysis in circulating tumor DNA (ctDNA) from plasma or serum has gained great interest. However, the literature is inconsistent on preferred candidate markers, hampering a clear direction for further studies and clinical translation. This review assessed the potential of ctDNA analysis for clinical utility. Methods A systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines was conducted up to December 3, 2018, followed by methodological quality assessment. Primary endpoints were accuracy for detection, prognostication, and monitoring. Results Eighty-four studies were included. For CRC detection, sensitivity was 75% using ctDNA mutation analysis and up to 96% using copy number analysis. Septin 9 (SEPT9) hypermethylation analysis showed sensitivities of 100% and specificities of 97%. Regarding prognostication, ctDNA KRAS mutations were associated with oncological outcome and could predict response to anti-epidermal growth factor receptor therapy. For monitoring, sequential ctDNA KRAS mutation analysis showed promise for detection of relapses or therapy resistance. Conclusions This comprehensive overview of ctDNA candidate markers demonstrates SEPT9 methylation analysis to be promising for CRC detection, and KRAS mutation analysis could assist in prognostication and monitoring. Prospective evaluation of marker panels in clinical decision making should bring ctDNA analysis into practice.
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Affiliation(s)
- Sander Bach
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Nina R Sluiter
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Jamie J Beagan
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Joost M Mekke
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Johannes C F Ket
- Medical Information Specialist/Literature Researcher Medical Library, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Nicole C T van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Geert Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Jurriaan B Tuynman
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
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48
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Ghosh RK, Pandey T, Dey P. Liquid biopsy: A new avenue in pathology. Cytopathology 2019; 30:138-143. [DOI: 10.1111/cyt.12661] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/07/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Ratan Kumar Ghosh
- Department of Nephrology Post Graduate Institute of Medical Education and Research Chandigarh India
| | - Tushar Pandey
- Department of Pathology Post Graduate Institute of Medical Education and Research Chandigarh India
| | - Pranab Dey
- Department of Cytology and Gynaec Pathology Post Graduate Institute of Medical Education and Research Chandigarh India
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49
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Yamashita K, Matsuda T, Hasegawa H, Mukohyama J, Arimoto A, Tanaka T, Yamamoto M, Matsuda Y, Kanaji S, Nakamura T, Sumi Y, Suzuki S, Kakeji Y. Recent advances of neoadjuvant chemoradiotherapy in rectal cancer: Future treatment perspectives. Ann Gastroenterol Surg 2019; 3:24-33. [PMID: 30697607 PMCID: PMC6345659 DOI: 10.1002/ags3.12213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/16/2018] [Accepted: 09/05/2018] [Indexed: 02/06/2023] Open
Abstract
Neoadjuvant chemoradiotherapy (nCRT) has been widely used as a multidisciplinary approach for stage II/III rectal cancer. However, its safety and efficacy are controversial because previous studies have shown conflicting outcomes. The present review aimed to elucidate the benefits and limitations of nCRT for patients with rectal cancer. Future perspectives of nCRT are also described. No recent randomized trials have been able to show a survival benefit, although many studies have demonstrated good local control with the use of fluoropyrimidine (e.g. 5-fluorouracil [FU] or capecitabine)-based nCRT. Addition of oxaliplatin (OX) to FU-based nCRT might improve overall survival by preventing distant metastasis, as shown in recent meta-analyses. However, control of adverse effects is an important concern with this treatment. New treatment strategies such as nonoperative management (watch and wait policy) and total neoadjuvant therapy (TNT) are promising, but the establishment of reliable diagnostic methods of metastasis is essential. Development of new biomarkers is also necessary to select patients who are more likely to benefit from nCRT.
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Affiliation(s)
- Kimihiro Yamashita
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Takeru Matsuda
- Division of Minimally Invasive SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Hiroshi Hasegawa
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Junko Mukohyama
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Akira Arimoto
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Tomoko Tanaka
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Masashi Yamamoto
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Yoshiko Matsuda
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Shingo Kanaji
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Tetsu Nakamura
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Yasuo Sumi
- Division of International Clinical Cancer ResearchDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Satoshi Suzuki
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
| | - Yoshihiro Kakeji
- Division of Gastrointestinal SurgeryDepartment of SurgeryKobe University Graduate School of MedicineKobeJapan
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50
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Boysen AK, Schou JV, Spindler KLG. Cell-free DNA and preoperative chemoradiotherapy for rectal cancer: a systematic review. Clin Transl Oncol 2018; 21:874-880. [PMID: 30506526 DOI: 10.1007/s12094-018-1997-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/17/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Preoperative chemoradiotherapy is the standard of care for patients with locally advanced rectal cancer, yet valid circulating biomarkers are lacking. We aimed at systematically reviewing the literature of cell-free DNA and locally advanced rectal cancer. METHODS A systematic literature search was performed. We retrieved papers reporting a correlation between a clinical outcome and cell-free DNA for patients receiving chemoradiotherapy for locally advanced rectal cancer. RESULTS We included nine studies of a total of 615 patients. Only single-arm studies were identified, analyzing either the total level of cell-free DNA or tumor-specific DNA. Despite differences in the methodology and outcomes, eight of the nine studies showed a correlation between cell-free DNA and a clinical outcome. CONCLUSIONS Cell-free DNA might hold prognostic and predictive information for patients with locally advanced rectal cancer receiving preoperative chemoradiotherapy; although, firm conclusions are limited by the heterogeneity in this field.
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Affiliation(s)
- Anders Kindberg Boysen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Nørrebrogade 44, 8000, Aarhus, Denmark. .,Department of Oncology, Aarhus University Hospital, Nørrebrogade 44, 8000, Aarhus, Denmark.
| | - Jakob Vasehus Schou
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Hellerup, Denmark
| | - Karen-Lise Garm Spindler
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Nørrebrogade 44, 8000, Aarhus, Denmark.,Department of Oncology, Aarhus University Hospital, Nørrebrogade 44, 8000, Aarhus, Denmark
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