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Dai L, Johnson-Buck A, Laird PW, Tewari M, Walter NG. Ultrasensitive amplification-free quantification of a methyl CpG-rich cancer biomarker by single-molecule kinetic fingerprinting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.587997. [PMID: 38645159 PMCID: PMC11030368 DOI: 10.1101/2024.04.06.587997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The most well-studied epigenetic marker in humans is the 5-methyl modification of cytosine in DNA, which has great potential as a disease biomarker in liquid biopsies of cell-free DNA. Currently, quantification of DNA methylation relies heavily on bisulfite conversion followed by PCR amplification and NGS or microarray analysis. PCR is subject to potential bias in differential amplification of bisulfite-converted methylated versus unmethylated sequences. Here, we combine bisulfite conversion with single-molecule kinetic fingerprinting to develop an amplification-free assay for DNA methylation at the branched-chain amino acid transaminase 1 (BCAT1) promoter. Our assay selectively responds to methylated sequences with a limit of detection below 1 fM and a specificity of 99.9999%. Evaluating complex genomic DNA matrices, we reliably distinguish 2-5% DNA methylation at the BCAT1 promoter in whole blood DNA from completely unmethylated whole-genome amplified DNA. Taken together, these results demonstrate the feasibility and sensitivity of our amplification-free, single-molecule quantification approach to improve the early detection of methylated cancer DNA biomarkers.
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Affiliation(s)
- Liuhan Dai
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Muneesh Tewari
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
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van Toledo DEFWM, Bleijenberg AGC, Venema A, de Wit MJ, van Eeden S, Meijer GA, Carvalho B, Dekker E, Henneman P, IJspeert JEG, van Noesel CJM. Aberrant PRDM2 methylation as an early event in serrated lesions destined to evolve into microsatellite-instable colorectal cancers. J Pathol Clin Res 2024; 10:e348. [PMID: 38380944 PMCID: PMC10880511 DOI: 10.1002/cjp2.348] [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: 05/31/2023] [Revised: 08/17/2023] [Accepted: 10/15/2023] [Indexed: 02/22/2024]
Abstract
Up to 30% of colorectal cancers (CRCs) develop from sessile serrated lesions (SSLs). Within the serrated neoplasia pathway, at least two principally distinct oncogenetic routes exist generating microsatellite-stable and microsatellite-instable CRCs, respectively. Aberrant DNA methylation (DNAm) is found early in the serrated pathway and might play a role in both oncogenetic routes. We studied a cohort of 23 SSLs with a small focus (<10 mm) of dysplasia or cancer, 10 of which were MLH1 deficient and 13 MLH1 proficient. By comparing, for each SSL, the methylation status of (1) the region of dysplasia or cancer (SSL-D), (2) the nondysplastic SSL (SSL), and (3) adjacent normal mucosa, differentially methylated probes (DMPs) and regions (DMRs) were assessed both genome-wide as well as in a tumor-suppressor gene-focused approach. By comparing DNAm of MLH1-deficient SSL-Ds with their corresponding SSLs, we identified five DMRs, including those annotating for PRDM2 and, not unexpectedly, MLH1. PRDM2 gene promotor methylation was associated with MLH1 expression status, as it was largely hypermethylated in MLH1-deficient SSL-Ds and hypomethylated in MLH1-proficient SSL-Ds. Significantly increased DNAm levels of PRDM2 and MLH1, in particular at 'critical' MLH1 probe sites, were to some extent already visible in SSLs as compared to normal mucosa (p = 0.02, p = 0.01, p < 0.0001, respectively). No DMRs, nor DMPs, were identified for SSLs destined to evolve into MLH1-proficient SSL-Ds. Our data indicate that, within both arms of the serrated CRC pathway, the majority of the epigenetic alterations are introduced early during SSL formation. Promoter hypermethylation of PRDM2 and MLH1 on the other hand specifically initiates in SSLs destined to transform into MLH1-deficient CRCs suggesting that the fate of SSLs may not necessarily result from a stochastic process but possibly is already imprinted and predisposed.
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Affiliation(s)
- David EFWM van Toledo
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Arne GC Bleijenberg
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Andrea Venema
- Department of Human Genetics, Epigenetics of disease, Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Mireille J de Wit
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
| | - Susanne van Eeden
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
| | - Gerrit A Meijer
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Beatrice Carvalho
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Peter Henneman
- Department of Human Genetics, Epigenetics of disease, Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Joep EG IJspeert
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Carel JM van Noesel
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
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Xu K, Yu AR, Pan SB, He J. Diagnostic value of methylated branched chain amino acid transaminase 1/IKAROS family zinc finger 1 for colorectal cancer. World J Gastroenterol 2023; 29:5240-5253. [PMID: 37901447 PMCID: PMC10600955 DOI: 10.3748/wjg.v29.i36.5240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND The diagnostic value of combined methylated branched chain amino acid transaminase 1 (BCAT1)/IKAROS family zinc finger 1 (IKZF1) in plasma for colorectal cancer (CRC) has been explored since 2015. Recently, several related studies have published their results and showed its diagnostic efficacy. AIM To analyze the diagnostic value of methylated BCAT1/IKZF1 in plasma for screening and postoperative follow-up of CRC. METHODS The candidate studies were identified by searching the PubMed, Embase, Cochrane Library, CNKI, and Wanfang databases from May 31, 2003 to June 1, 2023. Sensitivity, specificity, and diagnostic accuracy were calculated by merging ratios or means. RESULTS Twelve eligible studies were included in the analysis, involving 6561 participants. The sensitivity of methylated BCAT1/IKZF1 in plasma for CRC diagnosis was 60% [95% confidence interval (CI) 53-67] and specificity was 92% (95%CI: 90-94). The positive and negative likelihood ratios were 8.0 (95%CI: 5.8-11.0) and 0.43 (95%CI: 0.36-0.52), respectively. Diagnostic odds ratio was 19 (95%CI: 11-30) and area under the curve was 0.88 (95%CI: 0.85-0.91). The sensitivity and specificity for CRC screening were 64% (95%CI: 59-69) and 92% (95%CI: 91-93), respectively. The sensitivity and specificity for recurrence detection during follow-up were 54% (95%CI: 42-67) and 93% (95%CI: 88-96), respectively. CONCLUSION The detection of methylated BCAT1/IKZF1 in plasma, as a non-invasive detection method of circulating tumor DNA, has potential CRC diagnosis, but the clinical application prospect needs to be further explored.
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Affiliation(s)
- Ke Xu
- Clinical Medical College, Chengdu Medical College, Chengdu 610500, Sichuan Province, China
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| | - Ai-Ru Yu
- Clinical Medical College, Chengdu Medical College, Chengdu 610500, Sichuan Province, China
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| | - Shen-Bin Pan
- Clinical Medical College, Chengdu Medical College, Chengdu 610500, Sichuan Province, China
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| | - Jie He
- Clinical Medical College, Chengdu Medical College, Chengdu 610500, Sichuan Province, China
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
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Kresse SH, Brandt-Winge S, Pharo H, Flatin BTB, Jeanmougin M, Vedeld HM, Lind GE. Evaluation of commercial kits for isolation and bisulfite conversion of circulating cell-free tumor DNA from blood. Clin Epigenetics 2023; 15:151. [PMID: 37710283 PMCID: PMC10503171 DOI: 10.1186/s13148-023-01563-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND DNA methylation biomarkers in circulating cell-free DNA (cfDNA) have great clinical potential for cancer management. Most methods for DNA methylation analysis require bisulfite conversion, causing DNA degradation and loss. This is particularly challenging for cfDNA, which is naturally fragmented and normally present in low amounts. The aim of the present study was to identify an optimal combination of cfDNA isolation and bisulfite conversion kits for downstream analysis of DNA methylation biomarkers in plasma. RESULTS Of the five tested bisulfite conversion kits (EpiJET Bisulfite Conversion Kit, EpiTect Plus DNA Bisulfite Kit (EpiTect), EZ DNA Methylation-Direct Kit, Imprint DNA Modification Kit (Imprint) and Premium Bisulfite Kit), the highest and lowest DNA yield and recovery were achieved using the EpiTect kit and the Imprint kit, respectively, with more than double the amount of DNA for the EpiTect kit. Of the three tested cfDNA isolation kits (Maxwell RSC ccfDNA Plasma Kit, QIAamp Circulating Nucleic Acid Kit (CNA) and QIAamp MinElute ccfDNA Mini Kit), the CNA kit yielded around twice as much cfDNA compared to the two others kits, although with more high molecular weight DNA present. When comparing various combinations of cfDNA isolation kits and bisulfite conversion kits, the CNA kit and the EpiTect kit were identified as the best-performing combination, resulting in the highest yield of bisulfite converted cfDNA from normal plasma, as measured by droplet digital PCR (ddPCR). As a proof of principle, this kit combination was used to process plasma samples from 13 colorectal cancer patients for subsequent ddPCR methylation analysis of BCAT1 and IKZF1. Methylation of BCAT1 and/or IKZF1 was identified in 6/10 (60%) stage IV patients and 1/3 (33%) stage III patients. CONCLUSIONS Based on a thorough evaluation of five bisulfite conversion kits and three cfDNA isolation kits, both individually and in combination, the CNA kit and the EpiTect kit were identified as the best-performing kit combination, with highest DNA yield and recovery across a range of DNA input amounts. The combination was successfully used for detection of clinically relevant DNA methylation biomarkers in plasma from cancer patients.
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Affiliation(s)
- Stine H Kresse
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Sara Brandt-Winge
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Heidi Pharo
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Bjørnar T B Flatin
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway.
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
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Dawood ZS, Hamad A, Moazzam Z, Alaimo L, Lima HA, Shaikh C, Munir MM, Endo Y, Pawlik TM. Colonoscopy, imaging, and carcinoembryonic antigen: Comparison of guideline adherence to surveillance strategies in patients who underwent resection of colorectal cancer - A systematic review and meta-analysis. Surg Oncol 2023; 47:101910. [PMID: 36806402 DOI: 10.1016/j.suronc.2023.101910] [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: 11/01/2022] [Revised: 01/22/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023]
Abstract
INTRODUCTION Almost one-third of patients with colorectal cancer (CRC) experience recurrence after resection. Adherence to surveillance guidelines largely dictates efficacy in early detection of recurrence. We sought to assess and compare adherence to postoperative surveillance guidelines for colonoscopy, imaging, and Carcinoembryonic Antigen (CEA). METHODS PubMed, Medline, Embase, Scopus, Cochrane, Web of Science, and CINAHL were systematically searched. Random-effects meta-analysis was performed and pooled adherence to each surveillance strategy was assessed for CEA, imaging, and colonoscopy. RESULTS Overall 14 studies (55,895 patients) met the inclusion criteria. Adherence to colonoscopy guidelines was the highest (70%, 95%CI 67-73), followed by imaging (63%, 95%CI 47-80), and CEA (54%; 95%CI 42-66). Among 7 (50%) studies that examined adherence to the American Society of Clinical Oncology guidelines, compliance with colonoscopy was the highest (73%; 95% CI 70-76), followed by imaging (58%; 95% CI 37-78), and CEA (45%; 95%CI 37-52). Of note, guideline adherence to CEA testing was much lower than colonoscopy among patients with colon (OR 0.21; 95%CI 0.20-0.22) and rectal cancer (OR 0.25; 95%CI 0.23-0.28) (both p < 0.05). This was also noted when compared with imaging recommendations among older patients (OR = 0.62; 95%CI 0.42-0.93) and patients with stage II, (OR = 0.80; 95%CI 0.76-0.84) and stage III disease (OR = 0.88; 95%CI 0.82-0.94) (all p < 0.05). CONCLUSION While guideline adherence to postoperative surveillance with colonoscopy was high, adherence to CEA testing and imaging surveillance strategies was markedly lower following CRC resection. Future studies should investigate avenues to improve compliance with surveillance guidelines among health care providers and patients to optimize postoperative follow-up for CRC.
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Affiliation(s)
- Zaiba Shafik Dawood
- Medical College, The Aga Khan University Hospital, Stadium Road, Karachi, 74800, Pakistan
| | - Ahmad Hamad
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Zorays Moazzam
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Laura Alaimo
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Henrique A Lima
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Chanza Shaikh
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Muhammad Musaab Munir
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Yutaka Endo
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Timothy M Pawlik
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA.
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Dawood ZS, Alaimo L, Lima HA, Moazzam Z, Shaikh C, Ahmed AS, Munir MM, Endo Y, Pawlik TM. Circulating Tumor DNA, Imaging, and Carcinoembryonic Antigen: Comparison of Surveillance Strategies Among Patients Who Underwent Resection of Colorectal Cancer-A Systematic Review and Meta-analysis. Ann Surg Oncol 2023; 30:259-274. [PMID: 36219278 DOI: 10.1245/s10434-022-12641-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/22/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Almost one-third of colorectal cancer (CRC) patients experience recurrence after resection; nevertheless, follow-up strategies remain controversial. We sought to systematically assess and compare the accuracy of carcinoembryonic antigen (CEA), imaging [positron emission tomography (PET) and computed tomography (CT) scans], and circulating tumor DNA (CtDNA) as surveillance strategies. PATIENTS AND METHODS PubMed, Medline, Embase, Scopus, Cochrane, Web of Science, and CINAHL were systematically searched. The Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) was used to assess methodological quality. We performed a bivariate random-effects meta-analysis and reported pooled sensitivity, specificity, and diagnostic odds ratio (DOR) values for each surveillance strategy. RESULTS Thirty studies were included in the analysis. PET scans had the highest sensitivity to detect recurrence (0.95; 95%CI 0.91-0.97), followed by CT scans (0.77; 95%CI 0.67-0.85). CtDNA positivity had the highest specificity to detect recurrence (0.95; 95%CI 0.91-0.97), followed by increased CEA levels (0.88; 95%CI 0.82-0.92). Furthermore, PET scans had the highest DOR to detect recurrence (DOR 120.7; 95%CI 48.9-297.9) followed by CtDNA (DOR 37.6; 95%CI 20.8-68.0). CONCLUSION PET scans had the highest sensitivity and DOR to detect recurrence, while CtDNA had the highest specificity and second highest DOR. Combinations of traditional cross-sectional/functional imaging and newer platforms such as CtDNA may result in optimized surveillance of patients following resection of CRC.
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Affiliation(s)
- Zaiba Shafik Dawood
- Medical College, The Aga Khan University Hospital, Stadium Road, Karachi, 74800, Pakistan
| | - Laura Alaimo
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Henrique A Lima
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Zorays Moazzam
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Chanza Shaikh
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Muhammad Musaab Munir
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Yutaka Endo
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Timothy M Pawlik
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA.
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Exploitation and Verification of a Stroma- and Metastasis-Associated Risk Prognostic Signature in Pancreatic Adenocarcinoma. Pharmaceuticals (Basel) 2022; 15:ph15111336. [DOI: 10.3390/ph15111336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic adenocarcinoma (PAAD), one of the most malignant tumors, not only has abundant mesenchymal components, but is also characterized by an extremely high metastatic risk. The purpose of this study was to construct a model of stroma- and metastasis-associated prognostic signature, aiming to benefit the existing clinical staging system and predict the prognosis of patients. First, stroma-associated genes were screened from the TCGA database with the ESTIMATE algorithm. Subsequently, transcriptomic data from clinical tissues in the RenJi cohort were screened for metastasis-associated genes. Integrating the two sets of genes, we constructed a risk prognostic signature by Cox and LASSO regression analysis. We then obtained a risk score by a quantitative formula and divided all samples into high- and low-risk groups based on the scores. The results demonstrated that patients with high-risk scores have a worse prognosis than those with low-risk scores, both in the TCGA database and in the RenJi cohort. In addition, tumor mutation burden, chemotherapeutic drug sensitivity and immune infiltration analysis also exhibited significant differences between the two groups. In exploring the potential mechanisms of how stromal components affect tumor metastasis, we simulated different matrix stiffness in vitro to explore its effect on EMT key genes in PAAD cells. We found that cancer cells stimulated by high matrix stiffness may trigger EMT and promote PAAD metastasis.
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Pedersen SK, Symonds EL, Roy AC, Cornthwaite KJ, LaPointe LC, Young GP. Detection of methylated BCAT1 and IKZF1 after curative-intent treatment as a prognostic indicator for colorectal cancer recurrence. Cancer Med 2022; 12:1319-1329. [PMID: 35822405 PMCID: PMC9883422 DOI: 10.1002/cam4.5008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The risk of recurrence after completion of curative-intent treatment of colorectal cancer (CRC) is hard to predict. Post-treatment assaying for circulating tumor DNA (ctDNA) is an encouraging approach for stratifying patients for therapy, but the prognostic value of this approach is less explored. This study aimed to determine if detection of methylated BCAT1 and IKZF1 following completion of initial treatment identified patients with a poorer recurrence-free survival (RFS). METHODS 142 CRC stage I-III cases with at least 2 years of follow up (unless recurrence was evident sooner) and a methylated BCAT1/IKZF1 test result between 2 weeks and 12 months after completion of initial treatment were eligible for study inclusion. The association between BCAT1/IKZF1 and RFS was assessed by the log-rank (Mantel-Cox) method. Cox proportional hazard regression analysis was used for multivariable survival analysis. RESULTS Thirty-three (23.2%) had recurrence at a median 1.6y (interquartile range: 0.8-2.4). Methylated BCAT1/IKZF1 was detected in 19 of the 142 patients (13.4%) and was associated with a significant risk of recurrence (hazard ratio [HR] 5.7, 95%CI: 1.9-17.3, p = 0.002). Three-year RFS for patients with or without detectable methylated BCAT1/IKZF1 was 56.5% and 83.3%, respectively. Multivariable analysis showed that detection of methylated BCAT1/IKZF1 (HR = 2.6, p = 0.049) and site of the primary tumor (HR = 4.2, p = 0.002) were the only significant prognostic indicators of poor RFS. CONCLUSIONS BCAT1/IKZF1 methylation testing after curative-intent treatment is an independent prognostic indicator for RFS and identifies a subgroup at high risk. Personalized surveillance is warranted for patients with these ctDNA biomarkers detectable after curative-intent treatment.
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Affiliation(s)
- Susanne K. Pedersen
- Flinders Health and Medical Research InstituteFlinders UniversitySouth AustraliaAustralia,Clinical Genomics IncNew JerseyUSA
| | - Erin L. Symonds
- Flinders Health and Medical Research InstituteFlinders UniversitySouth AustraliaAustralia,Bowel Health ServiceFlinders Medical CentreSouth AustraliaAustralia
| | - Amitesh C. Roy
- Flinders Health and Medical Research InstituteFlinders UniversitySouth AustraliaAustralia,Department of Medical OncologyFlinders Medical CentreSouth AustraliaAustralia
| | - Kathryn J. Cornthwaite
- Flinders Health and Medical Research InstituteFlinders UniversitySouth AustraliaAustralia
| | | | - Graeme P. Young
- Flinders Health and Medical Research InstituteFlinders UniversitySouth AustraliaAustralia
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