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Zhang W, Dong C, Li Z, Shi H, Xu Y, Zhu M. Serum targeted metabolomics uncovering specific amino acid signature for diagnosis of intrahepatic cholangiocarcinoma. J Pharm Biomed Anal 2024; 252:116457. [PMID: 39241676 DOI: 10.1016/j.jpba.2024.116457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 08/25/2024] [Accepted: 08/31/2024] [Indexed: 09/09/2024]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a hepatobiliary malignancy which accounts for approximately 5-10 % of primary liver cancers and has a high mortality rate. The diagnosis of iCCA remains significant challenges owing to the lack of specific and sensitive diagnostic tests available. Hence, improved methods are needed to detect iCCA with high accuracy. In this study, we evaluated the efficacy of serum amino acid profiling combined with machine learning modeling for the diagnosis of iCCA. A comprehensive analysis of 28 circulating amino acids was conducted in a total of 140 blood samples from patients with iCCA and normal individuals. We screened out 6 differentially expressed amino acids with the criteria of |Log2(Fold Change, FC)| > 0.585, P-value < 0.05, variable importance in projection (VIP) > 1.0 and area under the curve (AUC) > 0.8, in which amino acids L-Asparagine and Kynurenine showed an increasing tendency as the disease progressed. Five frequently used machine learning algorithms (Logistic Regression, Random Forest, Supporting Vector Machine, Neural Network and Naïve Bayes) for diagnosis of iCCA based on the 6 circulating amino acids were established and validated with high sensitivity and good overall accuracy. The resulting models were further improved by introducing a clinical indicator, gamma-glutamyl transferase (GGT). This study introduces a new approach for identifying potential serum biomarkers for the diagnosis of iCCA with high accuracy.
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Affiliation(s)
- Wenjun Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, China
| | - Chuntao Dong
- Nanjing High-Tech Precision Medicine Technology Co., Ltd, Nanjing 210061, China
| | - Zhaosheng Li
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Huina Shi
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Yijun Xu
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Mingchen Zhu
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing 210009, China.
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Li TH, Zhao BB, Qin C, Wang YY, Li ZR, Cao HT, Yang XY, Zhou XT, Wang WB. IFIT1 modulates the proliferation, migration and invasion of pancreatic cancer cells via Wnt/β-catenin signaling. Cell Oncol (Dordr) 2024; 47:1253-1265. [PMID: 38536650 DOI: 10.1007/s13402-024-00925-x] [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] [Accepted: 02/08/2024] [Indexed: 09/26/2024] Open
Abstract
OBJECTIVES Previously, Interferon-induced Protein with Tetratricopeptide Repeats 1 (IFIT1) has been shown to promote cancer development. Here, we aimed to explore the role of IFIT1 in the development and progression of pancreatic cancer, including the underlying mechanisms. METHODS We explored IFIT1 expression in pancreatic cancer samples using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Cell Counting Kit-8 (CCK8), colony formation, scratch wound-healing and Transwell assays were performed to assess the proliferation, migration and invasion abilities of pancreatic cancer cells. Gene Set Enrichment Analysis (GSEA) and Western blotting were performed to assess the regulatory effect of IFIT1 on the Wnt/β-catenin pathway. RESULTS We found that upregulation of IFIT1 expression is common in pancreatic cancer and is negatively associated with overall patient survival. Knockdown of IFIT1 expression led to decreased proliferation, migration and invasion of pancreatic cancer cells. We also found that IFIT1 could regulate Wnt/β-catenin signaling, and that a Wnt/β-catenin agonist could reverse this effect. In addition, we found that IFIT1 can promote epithelial-mesenchymal transition (EMT) of pancreatic cancer cells. CONCLUSIONS Our data indicate that IFIT1 increases pancreatic cancer cell proliferation, migration and invasion by activating the Wnt/β-catenin pathway. In addition, we found that EMT could be regulated by IFIT1. IFIT1 may serve as a potential therapeutic target for pancreatic cancer.
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Affiliation(s)
- Tian-Hao Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Bang-Bo Zhao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Cheng Qin
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yuan-Yang Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ze-Ru Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hong-Tao Cao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiao-Ying Yang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xing-Tong Zhou
- Department of Breast Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wei-Bin Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
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3
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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [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: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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Sullivan BA, Lieberman DA. Colon Polyp Surveillance: Separating the Wheat From the Chaff. Gastroenterology 2024; 166:743-757. [PMID: 38224860 DOI: 10.1053/j.gastro.2023.11.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 01/17/2024]
Abstract
One goal of colorectal cancer (CRC) screening is to prevent CRC incidence by removing precancerous colonic polyps, which are detected in up to 50% of screening examinations. Yet, the lifetime risk of CRC is 3.9%-4.3%, so it is clear that most of these individuals with polyps would not develop CRC in their lifetime. It is, therefore, a challenge to determine which individuals with polyps will benefit from follow-up, and at what intervals. There is some evidence that individuals with advanced polyps, based on size and histology, benefit from intensive surveillance. However, a large proportion of individuals will have small polyps without advanced histologic features (ie, "nonadvanced"), where the benefits of surveillance are uncertain and controversial. Demand for surveillance will further increase as more polyps are detected due to increased screening uptake, recent United States recommendations to expand screening to younger individuals, and emergence of polyp detection technology. We review the current understanding and clinical implications of the natural history, biology, and outcomes associated with various categories of colon polyps based on size, histology, and number. Our aims are to highlight key knowledge gaps, specifically focusing on certain categories of polyps that may not be associated with future CRC risk, and to provide insights to inform research priorities and potential management strategies. Optimization of CRC prevention programs based on updated knowledge about the future risks associated with various colon polyps is essential to ensure cost-effective screening and surveillance, wise use of resources, and inform efforts to personalize recommendations.
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Affiliation(s)
- Brian A Sullivan
- Cooperative Studies Program Epidemiology Center-Durham, Durham VA Health Care System, Durham, North Carolina; Division of Gastroenterology, Department of Medicine, Duke University Medical Center, Durham, North Carolina.
| | - David A Lieberman
- Portland Veteran Affairs Medical Center, Portland, Oregon; Division of Gastroenterology and Hepatology, School of Medicine, Oregon Health and Science University, Portland, Oregon
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Pan P, Li J, Wang B, Tan X, Yin H, Han Y, Wang H, Shi X, Li X, Xie C, Chen L, Chen L, Bai Y, Li Z, Tian G. Molecular characterization of colorectal adenoma and colorectal cancer via integrated genomic transcriptomic analysis. Front Oncol 2023; 13:1067849. [PMID: 37546388 PMCID: PMC10401844 DOI: 10.3389/fonc.2023.1067849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 06/21/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction Colorectal adenoma can develop into colorectal cancer. Determining the risk of tumorigenesis in colorectal adenoma would be critical for avoiding the development of colorectal cancer; however, genomic features that could help predict the risk of tumorigenesis remain uncertain. Methods In this work, DNA and RNA parallel capture sequencing data covering 519 genes from colorectal adenoma and colorectal cancer samples were collected. The somatic mutation profiles were obtained from DNA sequencing data, and the expression profiles were obtained from RNA sequencing data. Results Despite some similarities between the adenoma samples and the cancer samples, different mutation frequencies, co-occurrences, and mutually exclusive patterns were detected in the mutation profiles of patients with colorectal adenoma and colorectal cancer. Differentially expressed genes were also detected between the two patient groups using RNA sequencing. Finally, two random forest classification models were built, one based on mutation profiles and one based on expression profiles. The models distinguished adenoma and cancer samples with accuracy levels of 81.48% and 100.00%, respectively, showing the potential of the 519-gene panel for monitoring adenoma patients in clinical practice. Conclusion This study revealed molecular characteristics and correlations between colorectal adenoma and colorectal cancer, and it demonstrated that the 519-gene panel may be used for early monitoring of the progression of colorectal adenoma to cancer.
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Affiliation(s)
- Peng Pan
- Department of Gastroenterology, Shanghai Changhai Hospital, Shanghai, China
| | - Jingnan Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Beijing, China
| | - Bo Wang
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
| | - Xiaoyan Tan
- Department of Gastroenterology, Maoming People's Hospital, Maoming, China
| | - Hekun Yin
- Department of Gastroenterology, Jiangmen Central Hospital, Jiangmen, China
| | - Yingmin Han
- Department of Bioinformatics, Boke Biotech Co., Ltd., Wuxi, China
| | - Haobin Wang
- Department of Bioinformatics, Boke Biotech Co., Ltd., Wuxi, China
| | - Xiaoli Shi
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
| | - Xiaoshuang Li
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
| | - Cuinan Xie
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
| | - Longfei Chen
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
| | - Lanyou Chen
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
| | - Yu Bai
- Department of Gastroenterology, Shanghai Changhai Hospital, Shanghai, China
| | - Zhaoshen Li
- Department of Gastroenterology, Shanghai Changhai Hospital, Shanghai, China
| | - Geng Tian
- Department of Bioinformatics, Boke Biotech Co., Ltd., Wuxi, China
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6
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Shi L, Liao F, Liao W, Zhu Y, Chen Y, Shu X. Risk factors for inadequate bowel preparation before colonoscopy: a retrospective cohort study. BMC Gastroenterol 2023; 23:204. [PMID: 37312029 DOI: 10.1186/s12876-023-02796-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 05/03/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Colonoscopy is the standard and most effective screening tool for colonic diseases and the accuracy of colonoscopy depends on the quality of bowel preparation. The aim of this study was to analyze the risk factors for inadequate bowel preparation before colonoscopy. METHODS In this retrospective study, patients who underwent colonoscopy in 2018 and received 3 L of Polyethylene Glycol Electrolytes powder were included. They were instructed to drink 1.5 L the night before the colonoscopy and 1.5 L 4-6 h before the procedure given in doses of 250 ml every 10 min with 30 ml of simethicone given 4-6 h before the colonoscopy. Patient- and procedure-related parameters were recorded. An adequate bowel preparation was defined as all 3 segments rated 2 or 3 on the Boston Bowel Preparation scale. Risk factors for inadequate bowel preparation were identified using multivariate logistic regression analysis. RESULTS A total of 6720 patients were included in the present study. The mean age of these patients was 49.7 ± 13.0 years old. Inadequate bowel preparation was found in 233 (12.4%), 139 (6.4%), 131 (7%), 68 (8.6%) patients in spring, summer, autumn and winter respectively. On the multivariate analysis, male gender (OR: 1.295; 95% CI: 1.088-1.542; P = 0.005), inpatient status (OR: 1.377; 95% CI: 1.040-1.822; P = 0.025) and season (spring vs. winter, OR: 1.514; 95% CI: 1.139-2.012; P = 0.004) were the independent risk factors for inadequate bowel preparation. CONCLUSIONS Male gender, inpatient status and spring season were the independent risk factors for inadequate bowel preparation. For patients with risk factors for inadequate bowel preparation, enhanced bowel preparation and instructions may help to optimize the quality of bowel preparation.
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Affiliation(s)
- Liu Shi
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
- Department of Gastroenterology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, 341000, Jiangxi, China
| | - Foqiang Liao
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Wangdi Liao
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yin Zhu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Youxiang Chen
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xu Shu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
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Patterns of Somatic Variants in Colorectal Adenoma and Carcinoma Tissue and Matched Plasma Samples from the Hungarian Oncogenome Program. Cancers (Basel) 2023; 15:cancers15030907. [PMID: 36765865 PMCID: PMC9913259 DOI: 10.3390/cancers15030907] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
Analysis of circulating cell-free DNA (cfDNA) of colorectal adenoma (AD) and cancer (CRC) patients provides a minimally invasive approach that is able to explore genetic alterations. It is unknown whether there are specific genetic variants that could explain the high prevalence of CRC in Hungary. Whole-exome sequencing (WES) was performed on colon tissues (27 AD, 51 CRC) and matched cfDNAs (17 AD, 33 CRC); furthermore, targeted panel sequencing was performed on a subset of cfDNA samples. The most frequently mutated genes were APC, KRAS, and FBN3 in AD, while APC, TP53, TTN, and KRAS were the most frequently mutated in CRC tissue. Variants in KRAS codons 12 (AD: 8/27, CRC: 11/51 (0.216)) and 13 (CRC: 3/51 (0.06)) were the most frequent in our sample set, with G12V (5/27) dominance in ADs and G12D (5/51 (0.098)) in CRCs. In terms of the cfDNA WES results, tumor somatic variants were found in 6/33 of CRC cases. Panel sequencing revealed somatic variants in 8 out of the 12 enrolled patients, identifying 12/20 tumor somatic variants falling on its targeted regions, while WES recovered only 20% in the respective regions in cfDNA of the same patients. In liquid biopsy analyses, WES is less efficient compared to the targeted panel sequencing with a higher coverage depth that can hold a relevant clinical potential to be applied in everyday practice in the future.
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Heide T, Househam J, Cresswell GD, Spiteri I, Lynn C, Mossner M, Kimberley C, Fernandez-Mateos J, Chen B, Zapata L, James C, Barozzi I, Chkhaidze K, Nichol D, Gunasri V, Berner A, Schmidt M, Lakatos E, Baker AM, Costa H, Mitchinson M, Piazza R, Jansen M, Caravagna G, Ramazzotti D, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Graham TA, Sottoriva A. The co-evolution of the genome and epigenome in colorectal cancer. Nature 2022; 611:733-743. [PMID: 36289335 PMCID: PMC9684080 DOI: 10.1038/s41586-022-05202-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/05/2022] [Indexed: 12/13/2022]
Abstract
Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.
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Affiliation(s)
- Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - George D Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Claire Lynn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Chris Kimberley
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Bingjie Chen
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chela James
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK
- Centre for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Ketevan Chkhaidze
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Vinaya Gunasri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alison Berner
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Melissa Schmidt
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Helena Costa
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Miriam Mitchinson
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Marnix Jansen
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Mathematics and Geosciences, University of Triest, Triest, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Darryl Shibata
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | | | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
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Zhou M, Lv S, Hou Y, Zhang R, Wang W, Yan Z, Li T, Gan W, Zeng Z, Zhang F, Yang M. Characterization of sialylation-related long noncoding RNAs to develop a novel signature for predicting prognosis, immune landscape, and chemotherapy response in colorectal cancer. Front Immunol 2022; 13:994874. [PMID: 36330513 PMCID: PMC9623420 DOI: 10.3389/fimmu.2022.994874] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/03/2022] [Indexed: 08/22/2023] Open
Abstract
Aberrant sialylation plays a key biological role in tumorigenesis and metastasis, including tumor cell survival and invasion, immune evasion, angiogenesis, and resistance to therapy. It has been proposed as a possible cancer biomarker and a potential therapeutic target of tumors. Nevertheless, the prognostic significance and biological features of sialylation-related long noncoding RNAs (lncRNAs) in colorectal cancer (CRC) remain unclear. This study aimed to develop a novel sialylation-related lncRNA signature to accurately evaluate the prognosis of patients with CRC and explore the potential molecular mechanisms of the sialylation-related lncRNAs. Here, we identified sialylation-related lncRNAs using the Pearson correlation analysis on The Cancer Genome Atlas (TCGA) dataset. Univariate and stepwise multivariable Cox analysis were used to establish a signature based on seven sialylation-related lncRNAs in the TCGA dataset, and the risk model was validated in the Gene Expression Omnibus dataset. Kaplan-Meier curve analysis revealed that CRC patients in the low-risk subgroup had a better survival outcome than those in the high-risk subgroup in the training set, testing set, and overall set. Multivariate analysis demonstrated that the sialylation-related lncRNA signature was an independent prognostic factor for overall survival, progression-free survival, and disease-specific survival prediction. The sialylation lncRNA signature-based nomogram exhibited a robust prognostic performance. Furthermore, enrichment analysis showed that cancer hallmarks and oncogenic signaling were enriched in the high-risk group, while inflammatory responses and immune-related pathways were enriched in the low-risk group. The comprehensive analysis suggested that low-risk patients had higher activity of immune response pathways, greater immune cell infiltration, and higher expression of immune stimulators. In addition, we determined the sialylation level in normal colonic cells and CRC cell lines by flow cytometry combined with immunofluorescence, and verified the expression levels of seven lncRNAs using real-time quantitative polymerase chain reaction. Finally, combined drug sensitivity analysis using the Genomics of Drug Sensitivity in Cancer, Cancer Therapeutics Response Portal, and Profiling Relative Inhibition Simultaneously in Mixtures indicated that the sialylation-related lncRNA signature could serve as a potential predictor for chemosensitivity. Collectively, this is the first sialylation lncRNA-based signature for predicting the prognosis, immune landscape, and chemotherapeutic response in CRC, and may provide vital guidance to facilitate risk stratification and optimize individualized therapy for CRC patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Min Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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10
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Lee HW, Song B, Kim K. Colorectal cancers with a residual adenoma component: Clinicopathologic features and KRAS mutation. PLoS One 2022; 17:e0273723. [PMID: 36083889 PMCID: PMC9462729 DOI: 10.1371/journal.pone.0273723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/22/2022] [Indexed: 11/19/2022] Open
Abstract
Background/Aim
Colorectal cancer is well known for its “adenoma-carcinoma” sequential carcinogenesis. Some colorectal cancers demonstrate a residual adenoma component during progression from adenoma to invasive carcinoma. However, the clinicopathological significance of residual adenoma component remains unclear. In this study, we aimed to investigate the clinicopathologic and molecular characteristics including the KRAS mutation in colorectal cancers containing a residual adenoma component.
Materials and methods
In this study, 498 surgically resected colorectal cancer patients were enrolled. Their detailed clinicopathologic features and results of molecular study including KRAS mutation test and microsatellite instability were analyzed.
Results
A residual adenoma component was identified in 42 (8.4%) patients with colorectal cancer. The presence of a residual adenoma component was associated with a high frequency of the KRAS mutation (65%, p = 0.031) as well as indolent clinicopathological features, including polypoid gross type (p < 0.001), well-differentiated histology (p < 0.001), low pT (p < 0.001) and pN stage (p = 0.003), absence of vascular invasion (p = 0.005), and a better progression-free prognosis (p = 0.029). The cases with an adenoma component had a 35.7% discordance rate on the KRAS mutation tests in their adenoma and carcinoma regions.
Conclusion
In conclusion, colorectal cancer with a residual adenoma component showed indolent clinicopathologic features and frequent KRAS mutations. Due to the discordance in the incidence of the KRAS mutation between the adenoma and carcinoma components, the adenoma component should be documented in the pathology report, and care should be taken not to include the adenoma component when collecting samples for molecular testing.
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Affiliation(s)
- Hyoun Wook Lee
- Department of Pathology, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Republic of Korea
| | - Boram Song
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyungneun Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- * E-mail:
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11
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Parmar S, Easwaran H. Genetic and epigenetic dependencies in colorectal cancer development. Gastroenterol Rep (Oxf) 2022; 10:goac035. [PMID: 35975243 PMCID: PMC9373935 DOI: 10.1093/gastro/goac035] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/24/2022] [Accepted: 05/22/2022] [Indexed: 11/12/2022] Open
Abstract
Recent studies have mapped key genetic changes in colorectal cancer (CRC) that impact important pathways contributing to the multistep models for CRC initiation and development. In parallel with genetic changes, normal and cancer tissues harbor epigenetic alterations impacting regulation of critical genes that have been shown to play profound roles in the tumor initiation. Cumulatively, these molecular changes are only loosely associated with heterogenous transcriptional programs, reflecting the heterogeneity in the various CRC molecular subtypes and the paths to CRC development. Studies from mapping molecular alterations in early CRC lesions and use of experimental models suggest that the intricate dependencies of various genetic and epigenetic hits shape the early development of CRC via different pathways and its manifestation into various CRC subtypes. We highlight the dependency of epigenetic and genetic changes in driving CRC development and discuss factors affecting epigenetic alterations over time and, by extension, risk for cancer.
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Affiliation(s)
- Sehej Parmar
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hariharan Easwaran
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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12
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Robinson PS, Thomas LE, Abascal F, Jung H, Harvey LMR, West HD, Olafsson S, Lee BCH, Coorens THH, Lee-Six H, Butlin L, Lander N, Truscott R, Sanders MA, Lensing SV, Buczacki SJA, Ten Hoopen R, Coleman N, Brunton-Sim R, Rushbrook S, Saeb-Parsy K, Lalloo F, Campbell PJ, Martincorena I, Sampson JR, Stratton MR. Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells. Nat Commun 2022; 13:3949. [PMID: 35803914 PMCID: PMC9270427 DOI: 10.1038/s41467-022-31341-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 06/14/2022] [Indexed: 12/21/2022] Open
Abstract
Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequence normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 4-fold in all individuals, except for one showing a 31-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C > A changes. Different mutation rates and signatures between individuals are likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing.
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Affiliation(s)
- Philip S Robinson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Laura E Thomas
- Institute of Life Science, Swansea University, Swansea, SA28PP, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Hyunchul Jung
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Luke M R Harvey
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Hannah D West
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Sigurgeir Olafsson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Bernard C H Lee
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Henry Lee-Six
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Laura Butlin
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Nicola Lander
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Rebekah Truscott
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Haematology, Erasmus University Medical Centre, 3015 CN, Rotterdam, The Netherlands
| | - Stefanie V Lensing
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Simon J A Buczacki
- Nuffield Department of Surgical Sciences, Medical Sciences Division, University of Oxford, Oxford, UK
| | | | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Simon Rushbrook
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
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13
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dos Santos W, dos Reis MB, Porto J, de Carvalho AC, Matsushita M, Oliveira G, Syrjänen K, Reis RM, Guimarães DP. Somatic targeted mutation profiling of colorectal cancer precursor lesions. BMC Med Genomics 2022; 15:143. [PMID: 35761395 PMCID: PMC9238170 DOI: 10.1186/s12920-022-01294-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Most colorectal cancers (CRC) arise from precursor lesions. This study aimed to characterize the mutation profile of colorectal cancer precursor lesions in a Brazilian population.
Methods
In total, 90 formalin-fixed paraffin-embedded colorectal precursor lesions, including 67 adenomas, 7 sessile serrated lesions, and 16 hyperplastic polyps, were analyzed by next-generation sequencing using a panel of 50 oncogenes and tumor suppressor genes. The genetic ancestry of the patients was estimated.
Results
Somatic driver mutations were identified in 66.7% of cases, including alterations in APC (32.2%), TP53 (20.0%), KRAS (18.9%), BRAF (13.3%) and EGFR (7.8%). Adenomas displayed a higher number of mutations, mainly in APC, compared to serrated polyps (73.1% vs. 47.8%, p = 0.026). Advanced adenomas had a significantly higher frequency of mutation in KRAS and a high overall mutation rate than early adenomas (92.9% vs. 59%, p = 0.006). A high degree of ancestry admixture was observed in the population studied, with a predominance of European components (mean of 73%) followed by African (mean of 11.3%). No association between genetic ancestry and type of lesions was found. The mutation profile of Brazilian colorectal precursor lesions exhibits alteration in APC, KRAS, TP53, and BRAF at different frequencies according to lesion type.
Conclusions
These results bestow the knowledge of CRC's biologic history and support the potential of these biomarkers for precursor lesions detection in CRC screening of the Brazilian population.
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14
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Hálková T, Ptáčková R, Semyakina A, Suchánek Š, Traboulsi E, Ngo O, Hejcmanová K, Májek O, Bureš J, Zavoral M, Minárik M, Benešová L. Somatic Mutations in Exon 7 of the TP53 Gene in Index Colorectal Lesions Are Associated with the Early Occurrence of Metachronous Adenoma. Cancers (Basel) 2022; 14:cancers14122823. [PMID: 35740488 PMCID: PMC9221022 DOI: 10.3390/cancers14122823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Identifying patients with an increased risk of early recurrence of colorectal lesions is still a problem. In our study, we focused on improving this identification by determining the mutation profile of index lesions. We found a statistically significant association between the mutation in exon 7 of the TP53 gene in the index lesion and the risk of early metachronous adenoma. Abstract (1) Background: this prospective study was focused on detailed analysis of the mutation heterogeneity in colorectal lesions removed during baseline (index) colonoscopy to identify patients at high risk of early occurrence of metachronous adenomas. (2) Methods: a total of 120 patients after endoscopic therapy of advanced colorectal neoplasia size ≥10 mm (index lesion) with subsequent surveillance colonoscopy after 10–18 months were included. In total, 143 index lesions and 84 synchronous lesions in paraffin blocks were divided into up to 30 samples. In each of them, the detection of somatic mutations in 11 hot spot gene loci was performed. Statistical analysis to correlate the mutation profiles and the degree of heterogeneity of the lesions with the risk of metachronous adenoma occurrence was undertaken. (3) Results: mutation in exon 7 of the TP53 gene found in the index lesion significantly correlated with the early occurrence of metachronous adenoma (log-rank test p = 0.003, hazard ratio 2.73, 95% confidence interval 1.14–6.56). We did not find an association between the risk of metachronous adenomas and other markers monitored. (4) Conclusions: the findings of this study could lead to an adjustment of existing recommendations for surveillance colonoscopies in a specific group of patients with mutations in exon 7 of the TP53 gene in an index lesion, where a shortening of surveillance interval may be warranted.
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Affiliation(s)
- Tereza Hálková
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
| | - Renata Ptáčková
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
| | - Anastasiya Semyakina
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
| | - Štěpán Suchánek
- Department of Medicine, 1st Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
- Department of Gastrointestinal Oncology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
- Correspondence:
| | - Eva Traboulsi
- Department of Pathology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
| | - Ondřej Ngo
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic; (O.N.); (K.H.); (O.M.)
| | - Kateřina Hejcmanová
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic; (O.N.); (K.H.); (O.M.)
| | - Ondřej Májek
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic; (O.N.); (K.H.); (O.M.)
| | - Jan Bureš
- Department of Gastrointestinal Oncology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
| | - Miroslav Zavoral
- Department of Medicine, 1st Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
- Department of Gastrointestinal Oncology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
| | - Marek Minárik
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
- Elphogene, Drnovská 1112/60, 161 00 Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 00 Prague, Czech Republic
| | - Lucie Benešová
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
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15
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Chen X, Hu M, Chen Y, Li A, Hua Y, Jiang H, Li H, Lin M. Targeted deep sequencing reveals APC mutations as predictors of overall survival in Chinese colorectal patients receiving adjuvant chemotherapy. Scand J Gastroenterol 2022; 57:465-472. [PMID: 34978498 DOI: 10.1080/00365521.2021.2022189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objective: Targeted deep sequencing was used to characterize the mutational spectrum of APC in Chinese colorectal tumors in comparison to that in Caucasians from The Cancer Genome Atlas (TCGA) and to investigate whether APC mutations can predict overall survival in CRC patients receiving adjuvant chemotherapy.Methods: A total of 315 Chinese CRC patients including 241 stage II/III patients receiving fluorouracil-based adjuvant chemotherapy were included in this study. Next generation sequencing was carried out to detect somatic mutations on all APC exons. The associations between APC mutations and overall survival were determined by the Cox proportional hazards model.Results:APC was mutated in 221 of 315 colorectal tumors (70.2%). Chinese CRC had a much higher frequency of missense mutations (16.2% vs. 2.4%), but a lower frequency of nonsense (41.0% vs. 54.2%) and frameshift mutations (10.5% vs. 18.4%) than Caucasian CRC. Among stage II/III patients receiving fluorouracil-based adjuvant chemotherapy, APC mutations showed a significant association with worse survival (HR = 1.69; 95% CI, 1.10-2.62; p = .0179). Of the mutation types, frameshift mutations conferred the highest risk of death (HR = 2.88; 95% CI, 1.54-5.37; p =.0009). Among individual mutation sites, Arg232Ter, the most frequent mutation in Chinese CRC, exhibited the strongest negative impact on survival (HR = 2.65; 95% CI, 1.16-6.03; p =.0202).Conclusion:APC overall mutation was an independent predictor for overall survival of stage II/III CRC patients receiving fluorouracil-based chemotherapy.
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Affiliation(s)
- Xin Chen
- Department of General Surgery, Yangpu Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Mengjun Hu
- Department of Pathology, Zhuji People's Hospital, Shaoxing, China
| | - Ying Chen
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai, China
| | - Ajian Li
- Department of General Surgery, Yangpu Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Yutong Hua
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai, China
| | - Huihong Jiang
- Department of General Surgery, Yangpu Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Huaguang Li
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai, China
| | - Moubin Lin
- Department of General Surgery, Yangpu Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China.,Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai, China
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16
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Wang QW, Wang XY, Zhang QW, Chen JN, Zhou YJ, Tang ZR, Wang RL, Chen H, Chen H, Li XB. ERBB2 Mutations as Potential Predictors for Recurrence in Colorectal Serrated Polyps by Targeted Next-Generation Sequencing. Front Oncol 2022; 12:769709. [PMID: 35402217 PMCID: PMC8984468 DOI: 10.3389/fonc.2022.769709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundFollow-up guidelines for serrated polyps (SPs) are mainly based on factors such as histology and size with limited evidence. The underlying genomic mechanism of SPs in relation to recurrence risks is utterly unknown.MethodsWe applied targeted next-generation sequencing (NGS) approach on two groups of SPs [polyp-relapsed SPs (PRSPs) vs. polyp-free SPs (PFSPs)] based on the surveillance outcomes to compare differences of DNA variants in 71 colorectal cancer-associated genes. A multicenter validation cohort was established longitudinally from 2016 to 2019 to confirm the relevant results.ResultsAmong the 96 NGS samples, at least one mutant after filtration was detected in 90 samples (94%). Molecular profiling presented BRAF, KRAS, and APC as top 3 mutated genes. FBXW7, MSH2, and ERBB2 might be recurrence-relevant, while DMD, BRCA1, and BRCA2 might be negatively correlated with recurrence. Notably, ERBB2 mutants (R678Q and V842I) (n = 5) had higher risks of polyp recurrence than the wild types (n = 85), with a median polyp-free interval of 15 months compared to 26 months [P < 0.001; hazard ratio (HR) = 4.9; 95% confidence interval (CI) = 1.9–12.8]. Furthermore, a multicenter cohort composed by 321 SPs verified that ERBB2-mutated SPs had increased risks of polyp recurrence (P < 0.001; HR = 3.7; 95% CI = 2.3–6.0) and advanced neoplastic lesion (ANL) recurrence (P < 0.001; HR = 10.0; 95% CI = 2.7–36.9) compared with wild-type SPs, respectively.ConclusionsOur results are emphasizing that SP individuals with ERBB2 mutants are at higher risks of subsequent colorectal neoplasms. ERBB2 mutants might work as facilitated markers for prediction of high-risk SPs and might implicate a potential mechanism in the serrated pathway to colorectal carcinoma (CRC).
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Affiliation(s)
- Qi-Wen Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Xin-Yuan Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qing-Wei Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jin-Nan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yu-Jie Zhou
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zhao-Rong Tang
- Department of Gastroenterology and Hepatology, Chongqing Traditional Chinese Medicine Hospital, Chongqing, China
| | - Rui-Lan Wang
- Department of Gastroenterology and Hepatology, Sichuan Provincial Corps Hospital of Chinese People’s Armed Forces, Leshan, China
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huimin Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
- *Correspondence: Xiao-Bo Li, ; Huimin Chen,
| | - Xiao-Bo Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
- *Correspondence: Xiao-Bo Li, ; Huimin Chen,
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17
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Muthamilselvan S, Raghavendran A, Palaniappan A. Stage-differentiated ensemble modeling of DNA methylation landscapes uncovers salient biomarkers and prognostic signatures in colorectal cancer progression. PLoS One 2022; 17:e0249151. [PMID: 35202405 PMCID: PMC8870460 DOI: 10.1371/journal.pone.0249151] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Background Aberrant DNA methylation acts epigenetically to skew the gene transcription rate up or down, contributing to cancer etiology. A gap in our understanding concerns the epigenomics of stagewise cancer progression. In this study, we have developed a comprehensive computational framework for the stage-differentiated modelling of DNA methylation landscapes in colorectal cancer (CRC). Methods The methylation β-matrix was derived from the public-domain TCGA data, converted into M-value matrix, annotated with AJCC stages, and analysed for stage-salient genes using an ensemble of approaches involving stage-differentiated modelling of methylation patterns and/or expression patterns. Differentially methylated genes (DMGs) were identified using a contrast against controls (adjusted p-value <0.001 and |log fold-change of M-value| >2), and then filtered using a series of all possible pairwise stage contrasts (p-value <0.05) to obtain stage-salient DMGs. These were then subjected to a consensus analysis, followed by matching with clinical data and performing Kaplan–Meier survival analysis to evaluate the impact of methylation patterns of consensus stage-salient biomarkers on disease prognosis. Results We found significant genome-wide changes in methylation patterns in cancer cases relative to controls agnostic of stage. The stage-differentiated models yielded the following consensus salient genes: one stage-I gene (FBN1), one stage-II gene (FOXG1), one stage-III gene (HCN1) and four stage-IV genes (NELL1, ZNF135, FAM123A, LAMA1). All the biomarkers were significantly hypermethylated in the promoter regions, indicating down-regulation of expression and implying a putative CpG island Methylator Phenotype (CIMP) manifestation. A prognostic signature consisting of FBN1 and FOXG1 survived all the analytical filters, and represents a novel early-stage epigenetic biomarker / target. Conclusions We have designed and executed a workflow for stage-differentiated epigenomic analysis of colorectal cancer progression, and identified several stage-salient diagnostic biomarkers, and an early-stage prognostic biomarker panel. The study has led to the discovery of an alternative CIMP-like signature in colorectal cancer, reinforcing the role of CIMP drivers in tumor pathophysiology.
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Affiliation(s)
- Sangeetha Muthamilselvan
- Department of Bioinformatics, School of Chemical and BioTechnology, SASTRA Deemed University, Thanjavur, India
| | - Abirami Raghavendran
- Department of Bioinformatics, School of Chemical and BioTechnology, SASTRA Deemed University, Thanjavur, India
| | - Ashok Palaniappan
- Department of Bioinformatics, School of Chemical and BioTechnology, SASTRA Deemed University, Thanjavur, India
- * E-mail:
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18
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Li TH, Zhao BB, Qin C, Wang YY, Li ZR, Cao HT, Yang XY, Zhou XT, Wang WB. IFIT1 modulates the proliferation, migration and invasion of pancreatic cancer cells via Wnt/β-catenin signaling. Cell Oncol (Dordr) 2021; 44:1425-1437. [PMID: 34791638 PMCID: PMC8648688 DOI: 10.1007/s13402-021-00651-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES Previously, Interferon-induced Protein with Tetratricopeptide Repeats 1 (IFIT1) has been shown to promote cancer development. Here, we aimed to explore the role of IFIT1 in the development and progression of pancreatic cancer, including the underlying mechanisms. METHODS We explored IFIT1 expression in pancreatic cancer samples using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Cell Counting Kit-8 (CCK8), colony formation, scratch wound-healing and Transwell assays were performed to assess the proliferation, migration and invasion abilities of pancreatic cancer cells. Gene Set Enrichment Analysis (GSEA) and Western blotting were performed to assess the regulatory effect of IFIT1 on the Wnt/β-catenin pathway. RESULTS We found that upregulation of IFIT1 expression is common in pancreatic cancer and is negatively associated with overall patient survival. Knockdown of IFIT1 expression led to decreased proliferation, migration and invasion of pancreatic cancer cells. We also found that IFIT1 could regulate Wnt/β-catenin signaling, and that a Wnt/β-catenin agonist could reverse this effect. In addition, we found that IFIT1 can promote epithelial-mesenchymal transition (EMT) of pancreatic cancer cells. CONCLUSIONS Our data indicate that IFIT1 increases pancreatic cancer cell proliferation, migration and invasion by activating the Wnt/β-catenin pathway. In addition, we found that EMT could be regulated by IFIT1. IFIT1 may serve as a potential therapeutic target for pancreatic cancer.
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Affiliation(s)
- Tian-Hao Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Bang-Bo Zhao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Cheng Qin
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yuan-Yang Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ze-Ru Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hong-Tao Cao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiao-Ying Yang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xing-Tong Zhou
- Department of Breast Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wei-Bin Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
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19
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Perne C, Peters S, Cartolano M, Horpaopan S, Grimm C, Altmüller J, Sommer AK, Hillmer AM, Thiele H, Odenthal M, Möslein G, Adam R, Sivalingam S, Kirfel J, Schweiger MR, Peifer M, Spier I, Aretz S. Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis. PLoS One 2021; 16:e0259185. [PMID: 34843512 PMCID: PMC8629245 DOI: 10.1371/journal.pone.0259185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
The spectrum of somatic genetic variation in colorectal adenomas caused by biallelic pathogenic germline variants in the MSH3 gene, was comprehensively analysed to characterise mutational signatures and identify potential driver genes and pathways of MSH3-related tumourigenesis. Three patients from two families with MSH3-associated polyposis were included. Whole exome sequencing of nine adenomas and matched normal tissue was performed. The amount of somatic variants in the MSH3-deficient adenomas and the pattern of single nucleotide variants (SNVs) was similar to sporadic adenomas, whereas the fraction of small insertions/deletions (indels) (21-42% of all small variants) was significantly higher. Interestingly, pathogenic somatic APC variants were found in all but one adenoma. The vast majority (12/13) of these were di-, tetra-, or penta-base pair (bp) deletions. The fraction of APC indels was significantly higher than that reported in patients with familial adenomatous polyposis (FAP) (p < 0.01) or in sporadic adenomas (p < 0.0001). In MSH3-deficient adenomas, the occurrence of APC indels in a repetitive sequence context was significantly higher than in FAP patients (p < 0.01). In addition, the MSH3-deficient adenomas harboured one to five (recurrent) somatic variants in 13 established or candidate driver genes for early colorectal carcinogenesis, including ACVR2A and ARID genes. Our data suggest that MSH3-related colorectal carcinogenesis seems to follow the classical APC-driven pathway. In line with the specific function of MSH3 in the mismatch repair (MMR) system, we identified a characteristic APC mutational pattern in MSH3-deficient adenomas, and confirmed further driver genes for colorectal tumourigenesis.
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Affiliation(s)
- Claudia Perne
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Maria Cartolano
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sukanya Horpaopan
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Christina Grimm
- Institute for Translational Epigenetics, Medical Faculty and University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
- Berlin Institute of Health at Charité, Core Facility Genomics, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anna K. Sommer
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Axel M. Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Margarete Odenthal
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Gabriela Möslein
- Zentrum für Hereditäre Tumore, BETHESDA Khs. Duisburg, Duisburg, Germany
| | - Ronja Adam
- Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Sugirthan Sivalingam
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jutta Kirfel
- Institute of Pathology, University of Lübeck, Lübeck, Germany
| | - Michal R. Schweiger
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Translational Epigenetics, Medical Faculty and University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Martin Peifer
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
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20
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Li H, Lin J, Xiao Y, Zheng W, Zhao L, Yang X, Zhong M, Liu H. Colorectal Cancer Detected by Machine Learning Models Using Conventional Laboratory Test Data. Technol Cancer Res Treat 2021; 20:15330338211058352. [PMID: 34806496 PMCID: PMC8606732 DOI: 10.1177/15330338211058352] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background: Current diagnostic methods for colorectal cancer (CRC) are colonoscopy and sigmoidoscopy, which are invasive and complex procedures with possible complications. This study aimed to determine models for CRC identification that involve minimally invasive, affordable, portable, and accurate screening variables. Methods: This was a retrospective study that used data from electronic medical records of patients with CRC and healthy individuals between July 2017 and June 2018. Laboratory data, including liver enzymes, lipid profiles, complete blood counts, and tumor biomarkers, were extracted from the electronic medical records. Five machine learning models (logistic regression, random forest, k-nearest neighbors, support vector machine [SVM], and naïve Bayes) were used to identify CRC. The performances were evaluated using the areas under the curve (AUCs), sensitivity, specificity, positive predictive values (PPV), and negative predictive values (NPV). Results: A total of 1164 electronic medical records (CRC patients: 582; healthy controls: 582) were included. The logistic regression model achieved the highest performance in identifying CRC (AUC: 0.865, sensitivity: 89.5%, specificity: 83.5%, PPV: 84.4%, NPV: 88.9%). The first four weighted features in the model were carcinoembryonic antigen (CEA), hemoglobin (HGB), lipoprotein (a) (Lp(a)), and high-density lipoprotein (HDL). A diagnostic model for CRC was established based on the four indicators, with an AUC of 0.849 (0.840-0.860) for identifying all CRC patients, and it performed best in discriminating patients with late colon cancer from healthy individuals with an AUC of 0.905 (0.889-0.929). Conclusions: The logistic regression model based on CEA, HGB, Lp(a), and HDL might be a powerful, noninvasive, and cost-effective method to identify CRC.
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Affiliation(s)
- Hui Li
- 373651Department of Clinical Laboratory, The Sixth Affiliated Hospital, 26469Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jianmei Lin
- 373651Department of Clinical Laboratory, The Sixth Affiliated Hospital, 26469Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanhong Xiao
- 373651Department of Clinical Laboratory, The Sixth Affiliated Hospital, 26469Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenwen Zheng
- 373651Department of Clinical Laboratory, The Sixth Affiliated Hospital, 26469Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lu Zhao
- 373651Department of Clinical Laboratory, The Sixth Affiliated Hospital, 26469Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiangling Yang
- 373651Department of Clinical Laboratory, The Sixth Affiliated Hospital, 26469Sun Yat-sen University, Guangzhou, Guangdong, China.,373651Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, 26469Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Minsheng Zhong
- Department of Artificial Intelligence Laboratory, Xuanwu Technology, Guangzhou, Guangdong, China
| | - Huanliang Liu
- 373651Department of Clinical Laboratory, The Sixth Affiliated Hospital, 26469Sun Yat-sen University, Guangzhou, Guangdong, China.,373651Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, 26469Sun Yat-sen University, Guangzhou, Guangdong, China
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21
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Norollahi SE, Foumani MG, Pishkhan MK, Shafaghi A, Alipour M, Jamkhaneh VB, Marghoob MN, Vahidi S. DNA Methylation Profiling of MYC, SMAD2/3 and DNMT3A in Colorectal Cancer. Oman Med J 2021; 36:e315. [PMID: 34804598 PMCID: PMC8581152 DOI: 10.5001/omj.2020.93] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/04/2020] [Indexed: 11/18/2022] Open
Abstract
Epigenetic modifications, particularly DNA methylation, is commonplace and a remarkable factor in carcinogenesis transformation. Conspicuously, previous findings have presented a cluster of irregular promoter methylation alterations related with silencing of tumor suppressor genes, little is accepted regarding their sequential DNA methylation (hypo and hyper) modifications during the cancer progression. In this way, fluctuations of DNA methylation of many genes, especially MYC, SMAD2/3, and DNMT3A, have an impressive central key role in many different cancers, including colorectal cancer (CRC). CRC is distinguished by DNA methylation, which is related to tumorigenesis and also genomic instability. Importantly, molecular heterogeneity between multiple adenomas in different patients with CRC may show diverse developmental phenotypes for these kinds of tumors. Conclusively, studying factors that are involved in CRC carcinogenesis, especially the alterations in epigenetic elements, such as DNA methylation besides RNA remodeling, and histone modification, acetylation and phosphorylation, can be influential to find new therapeutic and diagnostic biomarkers in this type of malignancy. In this account, we discuss and address the potential significant methylated modifications of these genes and their importance during the development of CRC carcinogenesis.
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Affiliation(s)
- Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | | | | | - Afshin Shafaghi
- Faculty of Medicine, Department of Gastroenterology, Guilan University of Medical Sciences, Rasht, Iran
| | - Majid Alipour
- Department of Biology, Islamic Azad University of Babol Branch, Babol, Iran
| | - Vida Baloui Jamkhaneh
- Department of Veterinary Medicine, Islamic Azad University of Babol Branch, Babol, Iran
| | - Mohammad Namayan Marghoob
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran.,Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sogand Vahidi
- Clinical Research Development Unit of Poursina Hospital, Guilan University of Medical Sciences, Rasht, Iran
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22
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Tornillo L, Lehmann FS, Garofoli A, Paradiso V, Ng CKY, Piscuoglio S. The Genomic Landscape of Serrated Lesion of the Colorectum: Similarities and Differences With Tubular and Tubulovillous Adenomas. Front Oncol 2021; 11:668466. [PMID: 34712603 PMCID: PMC8546104 DOI: 10.3389/fonc.2021.668466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/15/2021] [Indexed: 01/06/2023] Open
Abstract
Serrated lesions of the colorectum are the precursors of 15-30% of colorectal cancers (CRCs). These lesions have a peculiar morphological appearance, and they are more difficult to detect than conventional adenomatous polyps. In this study, we sought to define the genomic landscape of these lesions using high-depth targeted sequencing. Eight sessile serrated lesions without dysplasia (SSL), three sessile serrated lesions with dysplasia (SSL/D), two traditional serrated adenomas (TSA), and three tubular adenomas (TA) were retrieved from the files of the Institute of Pathology of the University Hospital Basel and from the GILAB AG, Allschwil, Switzerland. Samples were microdissected together with the matched normal counterpart, and DNA was extracted for library preparation. Library preparation was performed using the Oncomine Comprehensive Assay targeting 161 common cancer driver genes. Somatic genetic alterations were defined using state-of-the-art bioinformatic analysis. Most SSLs, as well as all SSL/Ds and TSAs, showed the classical BRAF p.V600E mutation. The BRAF-mutant TSAs showed additional alterations in CTNNB1, NF1, TP53, NRAS, PIK3CA, while TA showed a consistently different profile, with mutations in ARID1A (two cases), SMAD4, CDK12, ERBB3, and KRAS. In conclusion, our results provide evidence that SSL/D and TSA are similar in somatic mutations with the BRAF hotspot somatic mutation as a major driver of the disease. On the other hand, TAs show a different constellation of somatic mutations such as ARID1A loss of function.
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Affiliation(s)
- Luigi Tornillo
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- GILAB AG, Labor für Gastrointestinale Pathologie, Allschwil, Switzerland
| | - Frank Serge Lehmann
- Division of Gastroenterology and Hepatology, University Hospital of Basel, Basel, Switzerland
| | - Andrea Garofoli
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Visceral Surgery and Precision Medicine Research Laboratory, Basel, Switzerland
| | - Viola Paradiso
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Salvatore Piscuoglio
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Visceral Surgery and Precision Medicine Research Laboratory, Basel, Switzerland
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23
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Robinson PS, Coorens THH, Palles C, Mitchell E, Abascal F, Olafsson S, Lee BCH, Lawson ARJ, Lee-Six H, Moore L, Sanders MA, Hewinson J, Martin L, Pinna CMA, Galavotti S, Rahbari R, Campbell PJ, Martincorena I, Tomlinson I, Stratton MR. Increased somatic mutation burdens in normal human cells due to defective DNA polymerases. Nat Genet 2021; 53:1434-1442. [PMID: 34594041 PMCID: PMC8492474 DOI: 10.1038/s41588-021-00930-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Mutation accumulation in somatic cells contributes to cancer development and is proposed as a cause of aging. DNA polymerases Pol ε and Pol δ replicate DNA during cell division. However, in some cancers, defective proofreading due to acquired POLE/POLD1 exonuclease domain mutations causes markedly elevated somatic mutation burdens with distinctive mutational signatures. Germline POLE/POLD1 mutations cause familial cancer predisposition. Here, we sequenced normal tissue and tumor DNA from individuals with germline POLE/POLD1 mutations. Increased mutation burdens with characteristic mutational signatures were found in normal adult somatic cell types, during early embryogenesis and in sperm. Thus human physiology can tolerate ubiquitously elevated mutation burdens. Except for increased cancer risk, individuals with germline POLE/POLD1 mutations do not exhibit overt features of premature aging. These results do not support a model in which all features of aging are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.
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Affiliation(s)
- Philip S Robinson
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | | | | | - Bernard C H Lee
- Wellcome Sanger Institute, Hinxton, UK
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | | | | | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | | | - Lynn Martin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Claudia M A Pinna
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sara Galavotti
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | | | | | - Ian Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK.
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Genomic, Microbial and Immunological Microenvironment of Colorectal Polyps. Cancers (Basel) 2021; 13:cancers13143382. [PMID: 34298598 PMCID: PMC8303543 DOI: 10.3390/cancers13143382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Colorectal cancers (CRC) initiate from small cell clusters known as polyps. Colonoscopic surveillance and removal of polyps is an important strategy to prevent CRC progression. Recent advances in sequencing technologies have highlighted genetic mutations in polyps that potentially contribute to CRC development. However, CRC might be considered more than a genetic disease, as emerging evidence describes early changes to immune surveillance and gut microbiota in people with polyps. Here, we review the molecular landscape of colorectal polyps, considering their genomic, microbial and immunological features, and discuss the potential clinical utility of these data. Abstract Colorectal cancer (CRC) develops from pre-cancerous cellular lesions in the gut epithelium, known as polyps. Polyps themselves arise through the accumulation of mutations that disrupt the function of key tumour suppressor genes, activate proto-oncogenes and allow proliferation in an environment where immune control has been compromised. Consequently, colonoscopic surveillance and polypectomy are central pillars of cancer control strategies. Recent advances in genomic sequencing technologies have enhanced our knowledge of key driver mutations in polyp lesions that likely contribute to CRC. In accordance with the prognostic significance of Immunoscores for CRC survival, there is also a likely role for early immunological changes in polyps, including an increase in regulatory T cells and a decrease in mature dendritic cell numbers. Gut microbiotas are under increasing research interest for their potential contribution to CRC evolution, and changes in the gut microbiome have been reported from analyses of adenomas. Given that early changes to molecular components of bowel polyps may have a direct impact on cancer development and/or act as indicators of early disease, we review the molecular landscape of colorectal polyps, with an emphasis on immunological and microbial alterations occurring in the gut and propose the potential clinical utility of these data.
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25
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Exploration of the Key Proteins in the Normal-Adenoma-Carcinoma Sequence of Colorectal Cancer Evolution Using In-Depth Quantitative Proteomics. JOURNAL OF ONCOLOGY 2021; 2021:5570058. [PMID: 34194496 PMCID: PMC8214504 DOI: 10.1155/2021/5570058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 12/30/2022]
Abstract
Purpose In most cases, the carcinogenesis of colorectal cancer (CRC) follows the normal-adenoma-carcinoma (N-A-C) sequence. In this study, we aimed to identify the key proteins in the N-A-C sequence. Methods Differentially expressed proteins (DEPs) in normal, adenoma, and carcinoma tissues were identified using the Tandem Mass Tag- (TMT-) based quantitative proteomics approach. The landscape of proteomic variation in the N-A-C sequence was explored using gene set enrichment analysis (GSEA) and Proteomaps. Key proteins in the N-A-C sequence were identified, verified, and validated based on our proteomic data, external proteomic data, and external transcriptomic data in the ProteomeXchange, CPTAC, GEO, and TCGA databases. The prognostic value of the key proteins in our database was evaluated by univariate and multivariate Cox regression analysis. The effects of the key proteins on adenoma organoids and colorectal cancer cells were explored in functional studies. Results Based on our proteomic profiles, we identified 1,294 DEPs between the carcinoma (CG) and normal (NG) groups, 919 DEPs between the adenoma group (AG) and NG, and 1,030 DEPs between the CG and AG. Ribosome- and spliceosome-related pathways were mainly enriched in the N-A process. Extracellular matrix- and epithelial-mesenchymal transition- (EMT-) related pathways were mainly enriched in the A-C process. RRP12 and SERPINH1 were identified, verified, and validated as candidate key proteins in the N-A and A-C processes, respectively. Furthermore, RRP12 and SERPINH1 knockdown impeded the viability and proliferation of adenoma organoids. SERPINH1 was validated as a risk factor for disease-free survival (DFS) based on the TCGA and our database, whereas RRP12 did not show prognostic value. SERPINH1 knockdown was accompanied by EMT-related protein variation, increased apoptosis, and reduced proliferation, invasion, and migration of CRC cells in vitro. Conclusions RRP12 and SERPINH1 may play an important role in the N-A and A-C processes, respectively. Furthermore, SERPINH1 showed favorable prognostic value for DFS in CRC patients. We speculate that SERPINH1 might promote not only the A-C process but also the development of CRC.
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26
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Discovering the Mutational Profile of Early Colorectal Lesions: A Translational Impact. Cancers (Basel) 2021; 13:cancers13092081. [PMID: 33923068 PMCID: PMC8123354 DOI: 10.3390/cancers13092081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is one of the most common malignancies worldwide. Next-generation sequencing technologies have identified new candidate genes and deepened the knowledge of the molecular mechanisms underlying the progression of colonic adenomas towards CRC. The main genetic, epigenetic, and molecular alterations driving the onset and progression of CRC in both hereditary and sporadic settings have also been investigated. The evaluation of the CRC risk based on the molecular characterization of early pre-cancerous lesions may contribute to the development of targeted preventive strategies development, help define specific risk profiles, and identify patients who will benefit from targeted endoscopic surveillance. Abstract Colorectal cancer (CRC) develops through a multi-step process characterized by the acquisition of multiple somatic mutations in oncogenes and tumor-suppressor genes, epigenetic alterations and genomic instability. These events lead to the progression from precancerous lesions to advanced carcinomas. This process requires several years in a sporadic setting, while occurring at an early age and or faster in patients affected by hereditary CRC-predisposing syndromes. Since advanced CRC is largely untreatable or unresponsive to standard or targeted therapies, the endoscopic treatment of colonic lesions remains the most efficient CRC-preventive strategy. In this review, we discuss recent studies that have assessed the genetic alterations in early colorectal lesions in both hereditary and sporadic settings. Establishing the genetic profile of early colorectal lesions is a critical goal in the development of risk-based preventive strategies.
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Hull MA, Rees CJ, Sharp L, Koo S. A risk-stratified approach to colorectal cancer prevention and diagnosis. Nat Rev Gastroenterol Hepatol 2020; 17:773-780. [PMID: 33067592 PMCID: PMC7562765 DOI: 10.1038/s41575-020-00368-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 02/06/2023]
Abstract
Population screening and endoscopic surveillance are used widely to prevent the development of and death from colorectal cancer (CRC). However, CRC remains a major cause of cancer mortality and the increasing burden of endoscopic investigations threatens to overwhelm some health services. This Perspective describes the rationale for and approach to improved risk stratification and decision-making for CRC prevention and diagnosis. Limitations of current approaches will be discussed using the UK as an example of the challenges faced by a particular health-care system, followed by discussion of novel risk biomarker utilization. We explore how risk stratification will be advantageous to current health-care providers and users, enabling more efficient use of limited colonoscopy resources. We discuss risk stratification in the setting of population screening as well as the surveillance of high-risk groups and investigation of symptomatic patients. We also address challenges in the development and validation of risk stratification tools and identify key research priorities.
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Affiliation(s)
- Mark A Hull
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.
| | - Colin J Rees
- Population Health Sciences Institute, Newcastle University, Newcastle, UK
| | - Linda Sharp
- Population Health Sciences Institute, Newcastle University, Newcastle, UK
| | - Sara Koo
- Population Health Sciences Institute, Newcastle University, Newcastle, UK
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Arnold A, Tronser M, Sers C, Ahadova A, Endris V, Mamlouk S, Horst D, Möbs M, Bischoff P, Kloor M, Bläker H. The majority of β-catenin mutations in colorectal cancer is homozygous. BMC Cancer 2020; 20:1038. [PMID: 33115416 PMCID: PMC7594410 DOI: 10.1186/s12885-020-07537-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/16/2020] [Indexed: 12/30/2022] Open
Abstract
Background β-catenin activation plays a crucial role for tumourigenesis in the large intestine but except for Lynch syndrome (LS) associated cancers stabilizing mutations of β-catenin gene (CTNNB1) are rare in colorectal cancer (CRC). Previous animal studies provide an explanation for this observation. They showed that CTNNB1 mutations induced transformation in the colon only when CTNNB1 was homozygously mutated or when membranous β-catenin binding was hampered by E-cadherin haploinsufficiency. We were interested, if these mechanisms are also found in human CTNNB1 mutated CRCs. Results Among 869 CRCs stabilizing CTNNB1 mutations were found in 27 cases. Homo- or hemizygous CTNNB1 mutations were detected in 74% of CTNNB1 mutated CRCs (13 microsatellite instabile (MSI-H), 7 microsatellite stabile (MSS)) but only in 3% (1/33) of extracolonic CTNNB1 mutated cancers. In contrast to MSS CRC, CTNNB1 mutations at codon 41 or 45 were highly selected in MSI-H CRC. Of the examined three CRC cell lines, β-catenin and E-cadherin expression was similar in cell lines without or with hetereozygous CTNNB1 mutations (DLD1 and HCT116), while a reduced E-cadherin expression combined with cytoplasmic accumulation of β-catenin was found in a cell line with homozygous CTNNB1 mutation (LS180). Reduced expression of E-cadherin in human MSI-H CRC tissue was identified in 60% of investigated cancers, but no association with the CTNNB1 mutational status was found. Conclusions In conclusion, this study shows that in contrast to extracolonic cancers stabilizing CTNNB1 mutations in CRC are commonly homo- or hemizygous indicating a higher threshold of β-catenin stabilization to be required for transformation in the colon as compared to extracolonic sites. Moreover, we found different mutational hotspots in CTNNB1 for MSI-H and MSS CRCs suggesting a selection of different effects on β-catenin stabilization according to the molecular pathway of tumourigenesis. Reduced E-cadherin expression in CRC may further contribute to higher levels of transcriptionally active β-catenin, but it is not directly linked to the CTNNB1 mutational status. Supplementary information Supplementary information accompanies this paper at 10.1186/s12885-020-07537-2.
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Affiliation(s)
- Alexander Arnold
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Virchoweg 15 / Charitéplatz 1, 10117, Berlin, Germany.
| | - Moritz Tronser
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Virchoweg 15 / Charitéplatz 1, 10117, Berlin, Germany
| | - Christine Sers
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Virchoweg 15 / Charitéplatz 1, 10117, Berlin, Germany
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ); Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, Heidelberg, Germany
| | - Volker Endris
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Soulafa Mamlouk
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Virchoweg 15 / Charitéplatz 1, 10117, Berlin, Germany
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Virchoweg 15 / Charitéplatz 1, 10117, Berlin, Germany
| | - Markus Möbs
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Virchoweg 15 / Charitéplatz 1, 10117, Berlin, Germany
| | - Philip Bischoff
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Virchoweg 15 / Charitéplatz 1, 10117, Berlin, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ); Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, Heidelberg, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Virchoweg 15 / Charitéplatz 1, 10117, Berlin, Germany.,Present address: Institute of Pathology, Universitätsklinikum Leipzig, Leipzig, Germany
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Genetic Alterations of Metastatic Colorectal Cancer. Biomedicines 2020; 8:biomedicines8100414. [PMID: 33066148 PMCID: PMC7601984 DOI: 10.3390/biomedicines8100414] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Genome sequencing studies have characterized the genetic alterations of different tumor types, highlighting the diversity of the molecular processes driving tumor development. Comprehensive sequencing studies have defined molecular subtypes of colorectal cancers (CRCs) through the identification of genetic events associated with microsatellite stability (MSS), microsatellite-instability-high (MSI-H), and hypermutation. Most of these studies characterized primary tumors. Only recent studies have addressed the characterization of the genetic and clinical heterogeneity of metastatic CRC. Metastatic CRC genomes were found to be not fundamentally different from primary CRCs in terms of the mutational landscape or of genes that drive tumorigenesis, and a genomic heterogeneity associated with tumor location of primary tumors helps to define different clinical behaviors of metastatic CRCs. Although CRC metastatic spreading was traditionally seen as a late-occurring event, growing evidence suggests that this process can begin early during tumor development and the clonal architecture of these tumors is consistently influenced by cancer treatment. Although the survival rate of patients with metastatic CRC patients improved in the last years, the response to current treatments and prognosis of many of these patients remain still poor, indicating the need to discover new improvements for therapeutic vulnerabilities and to formulate a rational prospective of personalized therapies.
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Liao Q, Chen L, Zhang N, Xi Y, Hu S, Ng DM, Ahmed FYH, Zhao G, Fan X, Xie Y, Dai X, Jin Y, Ge J, Dong C, Zhang X, Guo J. Network analysis of KLF5 targets showing the potential oncogenic role of SNHG12 in colorectal cancer. Cancer Cell Int 2020; 20:439. [PMID: 32943987 PMCID: PMC7487661 DOI: 10.1186/s12935-020-01527-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/29/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND KLF5 is a member of the Kruppel-like factor, subfamily of zinc finger proteins that are involved in cancers. KLF5 functions as a transcription factor and regulates the diverse protein-coding genes (PCGs) in colorectal cancer (CRC). However, the long non-coding RNAs (lncRNAs) regulated by KLF5 in CRC are currently unknown. METHODS In this study, we first designed a computational pipeline to determine the PCG and lncRNA targets of KLF5 in CRC. Then we analyzed the motif pattern of the binding regions for the lncRNA targets. The regulatory co-factors of KLF5 were then searched for through bioinformatics analysis. We also constructed a regulatory network for KLF5 and annotated its functions. Finally, one of the KLF5 lncRNA targets, SNHG12, was selected to further explore its expression pattern and functions in CRC. RESULTS We were able to identify 19 lncRNA targets of KLF5 and found that the motifs of the lncRNA binding sites were GC-enriched. Next, we pinpointed the transcription factors AR and HSF1 as the regulatory co-factors of KLF5 through bioinformatics analysis. Then, through the analysis of the regulatory network, we found that KLF5 may be involved in DNA replication, DNA repair, and the cell cycle. Furthermore, in the cell cycle module, the SNHG12 up-regulating expression pattern was verified in the CRC cell lines and tissues, associating it to CRC invasion and distal metastasis. This indicates that SNHG12 may play a critical part in CRC tumorigenesis and progression. Additionally, expression of SNHG12 was found to be down-regulated in CRC cell lines when KLF5 expression was knocked-down by siRNA; and a strong correlation was observed between the expression levels of SNHG12 and KLF5, further alluding to their regulatory relationship. CONCLUSIONS In conclusion, the network analysis of KLF5 targets indicates that SNHG12 may be a significant lncRNA in CRC.
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Affiliation(s)
- Qi Liao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Linbo Chen
- Department of Gastroenterology, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040 Zhejiang China
| | - Ning Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080 China
| | - Yang Xi
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Shiyun Hu
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Derry Minyao Ng
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Fatma Yislam Hadi Ahmed
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Guofang Zhao
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, 315000 China
| | - Xiaoxiang Fan
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, 315000 China
| | - Yangyang Xie
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, 315000 China
| | - Xiaoyu Dai
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, 315000 China
| | - Yanping Jin
- The Affiliated Hospital of School of Medicine, Ningbo University, Ningbo, 315020 China
| | - Jiaxin Ge
- The Affiliated Hospital of School of Medicine, Ningbo University, Ningbo, 315020 China
| | - Changzheng Dong
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Xinjun Zhang
- The Affiliated Hospital of School of Medicine, Ningbo University, Ningbo, 315020 China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
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New LncRNAs in Chronic Hepatitis C progression: from fibrosis to hepatocellular carcinoma. Sci Rep 2020; 10:9886. [PMID: 32555359 PMCID: PMC7303194 DOI: 10.1038/s41598-020-66881-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death in the world, and about 80% of the cases are associated with hepatitis B or C. Genetic and epigenetic alterations are accumulated over decades of chronic injury and may affect the functioning of tumor suppressor genes and protooncogenes. Studies have evidenced the role of Long non-coding RNAs (LncRNA) with oncogenic or tumor suppressor activities, suggesting a great potential in the treatment, diagnosis or indicator of prognosis in cancer. In this context, the aim of this study was to evaluate the global expression profile lncRNA in hepatic tissue samples with different stages of fibrosis associated with chronic hepatitis C, HCC and normal liver, in order to identify new lncRNAs that could contribute to study the progression of hepatic fibrosis to HCC associated with chronic hepatitis C. RNA-Seq was performed on Illumina NextSeq platform to identify lncRNAs expressed differently in 15 patients with chronic hepatitis C, three patients with HCC and three normal liver specimens. When the pathological tissues (fibrosis and carcinoma) were compared to normal hepatic tissue, were identified 2, 6 e 34 differentially expressed lncRNAs in moderate fibrosis, advanced fibrosis and HCC, respectively. The carcinoma group had the highest proportion of differentially expressed lncRNA (34) and of these, 29 were exclusive in this type of tissue. A heat map of the deregulated lncRNA revealed different expression patterns along the progression of fibrosis to HCC. The results showed the deregulation of some lncRNA already classified as tumor suppressors in HCC and other cancers, as well as some unpublished lncRNA whose function is unknown. Some of these lncRNAs are dysregulated since the early stages of liver injury in patients with hepatitis C, others overexpressed only in tumor tissue, indicating themselves as candidates of markers of fibrosis progression or tumor, with potential clinical applications in prognosis as well as a therapeutic target. Although there are already studies on lncRNA in hepatocellular carcinoma, this is the first study conducted in samples exclusively of HCV-related liver and HCV HCC.
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Lee SH, Yoo J, Song YS, Lim CH, Kim TM. Mutation Analysis of Colorectal and Gastric Carcinomas Originating from Adenomas: Insights into Genomic Evolution Associated with Malignant Progression. Cancers (Basel) 2020; 12:cancers12020325. [PMID: 32023847 PMCID: PMC7072232 DOI: 10.3390/cancers12020325] [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: 12/23/2019] [Revised: 01/26/2020] [Accepted: 01/27/2020] [Indexed: 12/30/2022] Open
Abstract
Small malignant tumor foci arising from benign lesions are rare but offer a unique opportunity to investigate the genomic evolution that occurs during malignant transformation. In this study, we analyzed 11 colorectal and 10 gastric adenoma–carcinoma pairs, each of which represented malignant tumors (carcinomas) embedded in benign lesions (adenomas) found in the same patient. Whole-exome sequencing revealed that mutation abundance was variable across different cases, but comparable between adenoma–carcinoma pairs. When mutations were classified as adenoma-specific, carcinoma-specific, or common, adenoma-specific mutations were more enriched with subclonal mutations than were carcinoma-specific mutations, indicative of a perturbation in mutational subclonal architecture (such as selective sweep) during malignant transformation. Among the recurrent mutations in colorectal cancers, APC and KRAS mutations were common between adenomas and carcinomas, indicative of their early occurrence during genomic evolution. TP53 mutations were often observed as adenoma-specific and therefore likely not associated with the emergence of malignant clones. Clonality-based enrichment analysis revealed that subclonal mutations of extracellular matrix genes in adenomas are more likely to be clonal in carcinomas, indicating potential roles for these genes in malignant transformation. Compared with colorectal cancers, gastric cancers showed more lesion-specific mutations than common mutations and higher levels of discordance in copy number profiles between matched adenomas and carcinomas, which may explain the elevated evolutionary dynamics and heterogeneity of gastric cancers compared to colorectal cancers. Taken together, this study demonstrates that co-existing benign and malignant lesions enable the evolution-based categorization of genomic alterations that may reveal clinically important biomarkers in colorectal and gastric cancers.
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Affiliation(s)
- Sung Hak Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222 Banpodae-ro, Seocho-gu, Seoul 06591, Korea;
| | - Jinseon Yoo
- Department of Medical Informatics, The Catholic University of Korea, 222 Banpodae-ro, Seocho-gu, Seoul 06591, Korea;
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpodae-ro, Seocho-gu, Seoul 06591, Korea
| | - Young Soo Song
- Department of Pathology, College of Medicine, Konyang University, 158 Gwanjeodong-ro, Seo-gu, Daejeon 35365, Korea;
| | - Chul-Hyun Lim
- Division of Gastroenterology, Department of Internal Medicine, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 1021, Tongil-ro, Eunpyeong-gu, Seoul 03312, Korea
- Correspondence: (C.-H.L.); (T.-M.K.); Tel.: +82-2-2030-4316 (C.-H.L.); +82-2-2258-7483 (T.-M.K.)
| | - Tae-Min Kim
- Department of Medical Informatics, The Catholic University of Korea, 222 Banpodae-ro, Seocho-gu, Seoul 06591, Korea;
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpodae-ro, Seocho-gu, Seoul 06591, Korea
- Correspondence: (C.-H.L.); (T.-M.K.); Tel.: +82-2-2030-4316 (C.-H.L.); +82-2-2258-7483 (T.-M.K.)
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Mutation Profiling of Premalignant Colorectal Neoplasia. Gastroenterol Res Pract 2019; 2019:2542640. [PMID: 31781186 PMCID: PMC6875414 DOI: 10.1155/2019/2542640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
Accumulation of allelic variants in genes that regulate cellular proliferation, differentiation, and apoptosis may result in expansion of the aberrant intestinal epithelium, generating adenomas. Herein, we compared the mutation profiles of conventional colorectal adenomas (CNADs) across stages of progression towards early carcinoma. DNA was isolated from 17 invasive adenocarcinomas (ACs) and 58 large CNADs, including 19 with low-grade dysplasia (LGD), 21 with LGD adjacent to areas of high-grade dysplasia and/or carcinoma (LGD-H), and 28 with high-grade dysplasia (HGD). Ion AmpliSeq Comprehensive Cancer Panel libraries were prepared and sequenced on the Ion Proton. We identified 956 unique allelic variants; of these, 499 were considered nonsynonymous variants. Eleven genes (APC, KRAS, SYNE1, NOTCH4, BLNK, FBXW7, GNAS, KMT2D, TAF1L, TCF7L2, and TP53) were mutated in at least 15% of all samples. Out of frequently mutated genes, TP53 and BCL2 had a consistent trend in mutation prevalence towards malignancy, while two other genes (HNF1A and FBXW7) exhibited the opposite trend. HGD adenomas had significantly higher mutation rates than LGD adenomas, while LGD-H adenomas exhibited mutation frequencies similar to those of LGD adenomas. A significant increase in copy number variant frequency was observed from LGD through HGD to malignant samples. The profiling of advanced CNADs demonstrated variations in mutation patterns among colorectal premalignancies. Only limited numbers of genes were repeatedly mutated while the majority were altered in single cases. Most genetic alterations in adenomas can be considered early contributors to colorectal carcinogenesis.
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Dabir PD, Bruggeling CE, van der Post RS, Dutilh BE, Hoogerbrugge N, Ligtenberg MJL, Boleij A, Nagtegaal ID. Microsatellite instability screening in colorectal adenomas to detect Lynch syndrome patients? A systematic review and meta-analysis. Eur J Hum Genet 2019; 28:277-286. [PMID: 31695176 DOI: 10.1038/s41431-019-0538-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 11/09/2022] Open
Abstract
The colorectal cancer spectrum has changed due to population screening programs, with a shift toward adenomas and early cancers. Whether it would be a feasible option to test these adenomas for detection of Lynch syndrome (LS) patients is unclear. Through meta-analysis and systematic review, risk factors for DNA mismatch repair deficiency (dMMR) and microsatellite instability (MSI) in adenomas were identified in LS and unselected patient cohorts. Data were extracted for patient age and MMR variant together with adenoma type, grade, size, and location. A total of 41 studies were included, and contained more than 519 LS patients and 1698 unselected patients with 1142 and 2213 adenomas respectively. dMMR/MSI was present in 69.5% of conventional adenomas in LS patients, compared with 2.8% in unselected patients. In the LS cohort, dMMR/MSI was more frequently present in patients older than 60 years (82% versus 54%). dMMR/MSI was also more common in villous adenomas (84%), adenomas over 1 cm (81%), and adenomas with high grade dysplasia (88%). No significant differences were observed for dMMR/MSI in relation to MMR variants and location of adenomas. In the context of screening, we conclude that detection of dMMR/MSI in conventional adenomas of unselected patients is uncommon and might be considered as indication for LS testing. Within the LS cohort, 69.5% of LS patients could have been detected through dMMR/MSI screening of their conventional adenomas.
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Affiliation(s)
- Parag D Dabir
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Pathology, Randers Regional Hospital, Randers, Denmark
| | - Carlijn E Bruggeling
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Annemarie Boleij
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.
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Recurrent Mutations in APC and CTNNB1 and Activated Wnt/β-catenin Signaling in Intraductal Papillary Neoplasms of the Bile Duct: A Whole Exome Sequencing Study. Am J Surg Pathol 2019; 42:1674-1685. [PMID: 30212390 DOI: 10.1097/pas.0000000000001155] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study aimed to elucidate the genetic landscape of biliary papillary neoplasms. Of 28 cases examined, 7 underwent whole exome sequencing, while the remaining 21 were used for validation studies with targeted sequencing. In the whole exome sequencing study, 4/7 cases had mutations in either APC or CTNNB1, both of which belong to the Wnt/β-catenin pathway. Somatic mutations were also identified in genes involved in RAS signaling (KRAS, BRAF), a cell cycle regulator (CDC27), histone methyltransferase (KMT2C, KMT2D), and DNA mismatch repair (MSH3, MSH6, PMS1). Combined with discovery and validation cohorts, mutations in APC or CTNNB1 were observed in 6/28 subjects (21%) and were mutually exclusive. When the cases were classified into intraductal papillary neoplasms of the bile duct (IPNBs, n=14) and papillary cholangiocarcinomas (n=14) based on the recently proposed classification criteria, mutations in APC and CTNNB1 appeared to be entirely restricted to IPNBs with 6/14 cases (43%) harboring mutations in either gene. These genetic alterations were detected across the 3 nonintestinal histologic types. In immunohistochemistry, the aberrant cytoplasmic and/or nuclear expression of β-catenin was found in not only 5/6 IPNBs with APC or CTNNB1 mutations, but also 6/8 cases with wild-type APC and CTNNB1 (total 79%). In addition, APC and CTNNB1 alterations were exceptional in nonpapillary cholangiocarcinomas (n=29) with a single case harboring CTNNB1 mutation (3%). This study demonstrated recurrent mutations in APC and CTNNB1 in nonintestinal-type IPNBs, suggesting that activation of the Wnt/β-catenin signaling pathway is relevant to the development and progression of IPNBs.
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Willis JA, Reyes-Uribe L, Chang K, Lipkin SM, Vilar E. Immune Activation in Mismatch Repair-Deficient Carcinogenesis: More Than Just Mutational Rate. Clin Cancer Res 2019; 26:11-17. [PMID: 31383734 DOI: 10.1158/1078-0432.ccr-18-0856] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/26/2019] [Accepted: 07/31/2019] [Indexed: 01/08/2023]
Abstract
Mismatch repair (MMR)-deficient colorectal cancers (dMMR colorectal cancer) are characterized by the expression of highly immunogenic neoantigen peptides, which stimulate lymphocytic infiltration as well as upregulation of inflammatory cytokines. These features are key to understanding why immunotherapy (specifically PD-1 and/or CTLA-4 checkpoint blockade) has proved to be highly effective for the treatment of patients with advanced dMMR colorectal cancer. Importantly, preclinical studies also suggest that this correlation between potent tumor neoantigens and the immune microenvironment is present in early (premalignant) stages of dMMR colorectal tumorigenesis as well, even in the absence of a high somatic mutation burden. Here, we discuss recent efforts to characterize how neoantigens and the tumor immune microenvironment coevolve throughout the dMMR adenoma-to-carcinoma pathway. We further highlight how this preclinical evidence forms the rational basis for developing novel immunotherapy-based colorectal cancer prevention strategies for patients with Lynch syndrome.
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Affiliation(s)
- Jason A Willis
- Hematology and Oncology Fellowship Program, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Laura Reyes-Uribe
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle Chang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas.,MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas
| | - Steven M Lipkin
- Department of Medicine, Weill-Cornell Medical College, Cornell University, New York, New York
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas
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Intarajak T, Udomchaiprasertkul W, Bunyoo C, Yimnoon J, Soonklang K, Wiriyaukaradecha K, Lamlertthon W, Sricharunrat T, Chaiwiriyawong W, Siriphongpreeda B, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Jenjaroenpun P, Wongsurawat T, Nookaew I, Auewarakul C, Cheevadhanarak S. Genetic Aberration Analysis in Thai Colorectal Adenoma and Early-Stage Adenocarcinoma Patients by Whole-Exome Sequencing. Cancers (Basel) 2019; 11:E977. [PMID: 31336886 PMCID: PMC6679221 DOI: 10.3390/cancers11070977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal adenomas are precursor lesions of colorectal adenocarcinoma. The transition from adenoma to carcinoma in patients with colorectal cancer (CRC) has been associated with an accumulation of genetic aberrations. However, criteria that can screen adenoma progression to adenocarcinoma are still lacking. This present study is the first attempt to identify genetic aberrations, such as the somatic mutations, copy number variations (CNVs), and high-frequency mutated genes, found in Thai patients. In this study, we identified the genomic abnormality of two sample groups. In the first group, five cases matched normal-colorectal adenoma-colorectal adenocarcinoma. In the second group, six cases matched normal-colorectal adenomas. For both groups, whole-exome sequencing was performed. We compared the genetic aberration of the two sample groups. In both normal tissues compared with colorectal adenoma and colorectal adenocarcinoma analyses, somatic mutations were observed in the tumor suppressor gene APC (Adenomatous polyposis coli) in eight out of ten patients. In the group of normal tissue comparison with colorectal adenoma tissue, somatic mutations were also detected in Catenin Beta 1 (CTNNB1), Family With Sequence Similarity 123B (FAM123B), F-Box And WD Repeat Domain Containing 7 (FBXW7), Sex-Determining Region Y-Box 9 (SOX9), Low-Density Lipoprotein Receptor-Related Protein 5 (LRP5), Frizzled Class Receptor 10 (FZD10), and AT-Rich Interaction Domain 1A (ARID1A) genes, which are involved in the Wingless-related integration site (Wnt) signaling pathway. In the normal tissue comparison with colorectal adenocarcinoma tissue, Kirsten retrovirus-associated DNA sequences (KRAS), Tumor Protein 53 (TP53), and Ataxia-Telangiectasia Mutated (ATM) genes are found in the receptor tyrosine kinase-RAS (RTK-RAS) signaling pathway and p53 signaling pathway, respectively. These results suggest that APC and TP53 may act as a potential screening marker for colorectal adenoma and early-stage CRC. This preliminary study may help identify patients with adenoma and early-stage CRC and may aid in establishing prevention and surveillance strategies to reduce the incidence of CRC.
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Affiliation(s)
- Thoranin Intarajak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Bioinformatics Unit for Genomic Analysis, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Wandee Udomchaiprasertkul
- Molecular Biology and Genomic Laboratory, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Chakrit Bunyoo
- Bioinformatics Unit for Genomic Analysis, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Jutamas Yimnoon
- Cytogenetics Unit, Central Research Laboratory, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Kamonwan Soonklang
- Data Management Unit, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Kriangpol Wiriyaukaradecha
- Molecular Biology and Genomic Laboratory, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Wisut Lamlertthon
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Thaniya Sricharunrat
- Pathology Laboratory Unit, Chulabhorn Hospital, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Worawit Chaiwiriyawong
- Department of Medical Oncology, Chulabhorn Hospital, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Bunchorn Siriphongpreeda
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Sawannee Sutheeworapong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Kanthida Kusonmano
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Weerayuth Kittichotirat
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Chinae Thammarongtham
- Biochemical Engineering and Systems Biology research group, National Center for Genetic Engineering and Biotechnology (BIOTEC) at King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Chirayu Auewarakul
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand.
| | - Supapon Cheevadhanarak
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand.
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand.
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A new era for understanding genetic evolution of multistep carcinogenesis. J Gastroenterol 2019; 54:667-668. [PMID: 30923915 DOI: 10.1007/s00535-019-01576-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 02/04/2023]
Abstract
Cancer development is a multistep process involving genetic and cellular alterations, and recent advances in next-generation sequencing have elucidated mutation landscapes of premalignant lesions as well as early- and late-stage tumors. In this issue of Journal of Gastroenterology, Kim and colleagues contributed to the better understanding of genetic events in putative precursors of hepatocellular carcinoma (HCC). Precancerous tissues are divided into canonical and non-canonical types, which share common driver mutations with cancerous lesions or not, and potential gatekeeper gene(s) for clonal selection play a critical role in driving precursors to cancers not only in HCC, but also in esophageal, gastric, colorectal, and pancreatic cancers.
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Functional characterization of CNOT3 variants identified in familial adenomatous polyposis adenomas. Oncotarget 2019; 10:3939-3951. [PMID: 31231471 PMCID: PMC6570471 DOI: 10.18632/oncotarget.27003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/20/2019] [Indexed: 01/28/2023] Open
Abstract
Germline mutations in the tumor suppressor Adenomatous Polyposis Coli (APC) define Familial Adenomatous Polyposis (FAP), the genetic predisposition to developing adenomatous polyps. Recent sequencing of FAP adenomas have challenged established dogma that APC mutations alone represent the adenoma mutational landscape because recurrent somatic mutations in non-WNT pathway genes were also discovered. In particular, one of these novel genes, CNOT3, presented E20K and E70K mutations that are predicted to be deleterious in silico. We utilized zebrafish embryos to determine if these mutations affect CNOT3 function and perform novel biology in an APC-dependent pathway in vivo. Human CNOT3 (hCNOT3) and E20K mRNA injection rescued zebrafish cnot3a knockdown lordosis phenotype while E70K did not. In the FAP apcmcr zebrafish model, we show that ctbp1, but not retinoic acid, regulates cnot3a expression. Injection of hCNOT3 and E20K, but not E70K, to homozygous apcmcr zebrafish initiated gut differentiation while cnot3a knockdown in wildtype embryos led to decreased intestinal development and differentiation. Finally, targeted sequencing of 37 additional FAP adenomas revealed CNOT3 mutations in 20% of these samples. Overall, our work supports a mechanism where CTBP1 regulates CNOT3 and that overall CNOT3 perturbation could work in concert with germline APC mutations in advancing adenomas to a more transformed state prior to progression to adenocarcinoma.
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Travaglino A, D'Armiento FP, Cassese G, Campanino MR, Borrelli G, Pignatiello S, Luglio G, Maione F, De Palma GD, D'Armiento M. Clinicopathological factors associated with BRAF-V600E mutation in colorectal serrated adenomas. Histopathology 2019; 75:160-173. [PMID: 30815911 DOI: 10.1111/his.13846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Serrated adenomas are genetically heterogeneous, and the histological classification into sessile serrated (SSA) adenoma and traditional serrated adenoma (TSA) does not reflect the molecular landscape. The objective of this study was to assess clinical or pathological factors associated with BRAF-V600E mutation in serrated adenomas. Systematic review and meta-analysis was performed by searching electronic databases from January 2011 to January 2019 for studies assessing the association of BRAF-V600E mutation with clinical or pathological features of serrated adenomas. Odds ratio (OR) was calculated for each factor; a P-value <0.05 was considered significant. Forty studies assessing 3511 serrated adenomas (2375 SSAs and 1136 TSAs) were included. BRAF-V600E mutation was significantly associated with proximal localisation (OR = 2.71; P < 0.00001) and CIMP-H status (OR = 4.81; P < 0.0001) in both SSA and TSA, with polyp size <10 mm (OR = 0.41; P = 0.02) in TSA, and with endoscopic pit pattern II-O (OR = 13.11; P < 0.00001) and expression of MUC5A5 (OR = 4.43; P = 0.003) and MUC6 (OR = 2.28; P < 0.05) in SSA. Conversely, BRAF mutation was not associated with age <70 years (OR = 1.63; P = 0.34), age <60 years (OR = 0.86; P = 0.79), female sex (OR = 0.77; P = 0.12), flat morphology (OR = 1.52; P = 0.16), presence of any dysplasia (OR = 1.01; P = 0.59), serrated dysplasia (OR = 1.23; P = 0.72) and invasive cancer (OR = 0.67; P = 0.32), nuclear β-catenin expression (OR = 0.73; P = 0.21) and p53 overexpression (OR = 1.24; P = 0.82). In conclusion, BRAF-V600E mutation is associated with proximal localisation and CIMP-H status in both SSA and TSA, with size <10 mm only in TSA, and with expression of MUC5A5 and MUC6 and endoscopic pit pattern II-O at least in SSA. In serrated adenomas, BRAF-V600E mutation does not seem to be associated with age and sex, with the prevalence of dysplasia and cancer and with the morphology of the dysplastic component.
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Affiliation(s)
- Antonio Travaglino
- Department of Advanced Biomedical Sciences, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Francesco P D'Armiento
- Department of Advanced Biomedical Sciences, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Gianluca Cassese
- Department of Clinical Medicine and Surgery, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Maria R Campanino
- Department of Advanced Biomedical Sciences, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Giorgio Borrelli
- Department of Advanced Biomedical Sciences, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Sara Pignatiello
- Department of Advanced Biomedical Sciences, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Gaetano Luglio
- Department of Clinical Medicine and Surgery, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Francesco Maione
- Department of Clinical Medicine and Surgery, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Giovanni D De Palma
- Department of Clinical Medicine and Surgery, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Maria D'Armiento
- Department of Public Health, School of Medicine, University of Naples Federico II, Naples, Italy
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Abstract
Cancer is caused by the effects of somatic mutations known as drivers. Although a number of major cancer drivers have been identified, it is suspected that many more comparatively rare and conditional drivers exist, and the interactions between different cancer-associated mutations that might be relevant for tumor progression are not well understood. We applied an advanced neural network approach to learn the sequence of mutations and the mutational burden in colon and lung cancers and to identify mutations that are associated with individual drivers. A significant ordering of driver mutations is demonstrated, and numerous, previously undetected conditional drivers are identified. These findings broaden the existing understanding of the mechanisms of tumor progression and have implications for therapeutic strategies. Cancer arises through the accumulation of somatic mutations over time. Understanding the sequence of mutation occurrence during cancer progression can assist early and accurate diagnosis and improve clinical decision-making. Here we employ long short-term memory (LSTM) networks, a class of recurrent neural network, to learn the evolution of a tumor through an ordered sequence of mutations. We demonstrate the capacity of LSTMs to learn complex dynamics of the mutational time series governing tumor progression, allowing accurate prediction of the mutational burden and the occurrence of mutations in the sequence. Using the probabilities learned by the LSTM, we simulate mutational data and show that the simulation results are statistically indistinguishable from the empirical data. We identify passenger mutations that are significantly associated with established cancer drivers in the sequence and demonstrate that the genes carrying these mutations are substantially enriched in interactions with the corresponding driver genes. Breaking the network into modules consisting of driver genes and their interactors, we show that these interactions are associated with poor patient prognosis, thus likely conferring growth advantage for tumor progression. Thus, application of LSTM provides for prediction of numerous additional conditional drivers and reveals hitherto unknown aspects of cancer evolution.
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Parker HR, Orjuela S, Martinho Oliveira A, Cereatti F, Sauter M, Heinrich H, Tanzi G, Weber A, Komminoth P, Vavricka S, Albanese L, Buffoli F, Robinson MD, Marra G. The proto CpG island methylator phenotype of sessile serrated adenomas/polyps. Epigenetics 2018; 13:1088-1105. [PMID: 30398409 PMCID: PMC6342079 DOI: 10.1080/15592294.2018.1543504] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sessile serrated adenomas/polyps (SSA/Ps) are the putative precursors of the ~20% of colon cancers with the CpG island methylator phenotype (CIMP). To investigate the epigenetic phenotype of these precancers, we prospectively collected fresh-tissue samples of 17 SSA/Ps and 15 conventional adenomas (cADNs), each with a matched sample of normal mucosa. Their DNA was subjected to bisulfite next-generation sequencing to assess methylation levels at ~2.7 million CpGs located predominantly in gene regulatory regions and spanning 80.5Mb; RNA was sequenced to define the samples' transcriptomes. Compared with normal mucosa, SSA/Ps and cADNs exhibited markedly remodeled methylomes. In cADNs, hypomethylated regions were far more numerous (18,417 vs 4288 in SSA/Ps) and rarely affected CpG islands/shores. SSA/Ps seemed to have escaped this wave of demethylation. Cytosine hypermethylation in SSA/Ps was more pervasive (hypermethylated regions: 22,147 vs 15,965 in cADNs; hypermethylated genes: 4938 vs 3443 in cADNs) and more extensive (region for region), and it occurred mainly within CpG islands and shores. Given its resemblance to the CIMP typical of SSA/Ps' putative descendant colon cancers, we refer to the SSA/P methylation phenotype as proto-CIMP. Verification studies of six hypermethylated regions in an independent series of precancers demonstrated DNA methylation markers' high potential for predicting the diagnosis of SSA/Ps and cADNs. Surprisingly, proto-CIMP in SSA/Ps was associated with upregulated gene expression; downregulation was more common in cADNs. In conclusion, the epigenetic landscape of SSA/Ps differs markedly from that of cADNs. These differences are a potentially rich source of novel tissue-based and noninvasive biomarkers.
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Affiliation(s)
- Hannah R Parker
- a Institute of Molecular Cancer Research , University of Zurich , Zurich , Switzerland
| | - Stephany Orjuela
- a Institute of Molecular Cancer Research , University of Zurich , Zurich , Switzerland.,b Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics , University of Zurich , Zurich , Switzerland
| | | | - Fabrizio Cereatti
- c Gastroenterology and Endoscopy Unit , Hospital of Cremona , Cremona , Italy
| | - Matthias Sauter
- d Division of Gastroenterology , Triemli Hospital , Zurich , Switzerland
| | - Henriette Heinrich
- d Division of Gastroenterology , Triemli Hospital , Zurich , Switzerland
| | - Giulia Tanzi
- e Division of Pathology , Hospital of Cremona , Cremona , Italy
| | - Achim Weber
- f Institute of Surgical Pathology , University of Zurich , Zurich , Switzerland
| | - Paul Komminoth
- g Division of Pathology , Triemli Hospital , Zurich , Switzerland
| | - Stephan Vavricka
- d Division of Gastroenterology , Triemli Hospital , Zurich , Switzerland
| | - Luca Albanese
- a Institute of Molecular Cancer Research , University of Zurich , Zurich , Switzerland
| | - Federico Buffoli
- c Gastroenterology and Endoscopy Unit , Hospital of Cremona , Cremona , Italy
| | - Mark D Robinson
- b Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics , University of Zurich , Zurich , Switzerland
| | - Giancarlo Marra
- a Institute of Molecular Cancer Research , University of Zurich , Zurich , Switzerland
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Al Bakir I, Curtius K, Graham TA. From Colitis to Cancer: An Evolutionary Trajectory That Merges Maths and Biology. Front Immunol 2018; 9:2368. [PMID: 30386335 PMCID: PMC6198656 DOI: 10.3389/fimmu.2018.02368] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/24/2018] [Indexed: 12/25/2022] Open
Abstract
Patients with inflammatory bowel disease have an increased risk of developing colorectal cancer, and this risk is related to disease duration, extent, and cumulative inflammation burden. Carcinogenesis follows the principles of Darwinian evolution, whereby somatic cells acquire genomic alterations that provide them with a survival and/or growth advantage. Colitis represents a unique situation whereby routine surveillance endoscopy provides a serendipitous opportunity to observe somatic evolution over space and time in vivo in a human organ. Moreover, somatic evolution in colitis is evolution in the ‘fast lane': the repeated rounds of inflammation and mucosal healing that are characteristic of the disease accelerate the evolutionary process and likely provide a strong selective pressure for inflammation-adapted phenotypic traits. In this review, we discuss the evolutionary dynamics of pre-neoplastic clones in colitis with a focus on how measuring their evolutionary trajectories could deliver a powerful way to predict future cancer occurrence. Measurements of somatic evolution require an interdisciplinary approach that combines quantitative measurement of the genotype, phenotype and the microenvironment of somatic cells–paying particular attention to spatial heterogeneity across the colon–together with mathematical modeling to interpret these data within an evolutionary framework. Here we take a practical approach in discussing how and why the different “evolutionary ingredients” can and should be measured, together with our viewpoint on subsequent translation into clinical practice. We highlight the open questions in the evolution of colitis-associated cancer as a stimulus for future work.
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Affiliation(s)
- Ibrahim Al Bakir
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom.,Inflammatory Bowel Disease Unit, St Mark's Hospital, Harrow, United Kingdom
| | - Kit Curtius
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom
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Falzone L, Scola L, Zanghì A, Biondi A, Di Cataldo A, Libra M, Candido S. Integrated analysis of colorectal cancer microRNA datasets: identification of microRNAs associated with tumor development. Aging (Albany NY) 2018; 10:1000-1014. [PMID: 29779016 PMCID: PMC5990389 DOI: 10.18632/aging.101444] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/07/2018] [Indexed: 12/15/2022]
Abstract
Colorectal cancer (CRC) is one of the leading cause of cancer death worldwide. Currently, no effective early diagnostic biomarkers are available for colorectal carcinoma. Therefore, there is a need to discover new molecules able to identify pre-cancerous lesions. Recently, microRNAs (miRNAs) have been associated with the onset of specific pathologies, thus the identification of miRNAs associated to colorectal cancer may be used to detect this pathology at early stages. On these bases, the expression levels of miRNAs were analyzed to compare the miRNAs expression levels of colorectal cancer samples and normal tissues in several miRNA datasets. This analysis revealed a group of 19 differentially expressed miRNAs. To establish the interaction between miRNAs and the most altered genes in CRC, the mirDIP gene target analysis was performed in such group of 19 differentially expressed miRNAs. To recognize miRNAs able to activate or inhibit genes and pathways involved in colorectal cancer development DIANA-mirPath prediction analysis was applied. Overall, these analyses showed that the up-regulated hsa-miR-183-5p and hsa-miR-21-5p, and the down-regulated hsa-miR-195-5p and hsa-miR-497-5p were directly related to colorectal cancer through the interaction with the Mismatch Repair pathway and Wnt, RAS, MAPK, PI3K, TGF-β and p53 signaling pathways involved in cancer development.
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Affiliation(s)
- Luca Falzone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania 95123, Italy
| | - Letizia Scola
- Department of Pathobiology and Medical Biotechnologies, University of Palermo, Palermo 90127, Italy
| | - Antonino Zanghì
- Department of Medical and Surgical Sciences and Advanced Technology "G.F. Ingrassia", University of Catania, Catania 95125, Italy
| | - Antonio Biondi
- Department of General Surgery, Vittorio Emanuele Hospital, University of Catania, Catania 95124, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer (PreDiCT), University of Catania, Catania 95123, Italy
| | - Antonio Di Cataldo
- Department of Medical and Surgical Sciences and Advanced Technology "G.F. Ingrassia", University of Catania, Catania 95125, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer (PreDiCT), University of Catania, Catania 95123, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania 95123, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer (PreDiCT), University of Catania, Catania 95123, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania 95123, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer (PreDiCT), University of Catania, Catania 95123, Italy
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45
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Testa U, Pelosi E, Castelli G. Colorectal cancer: genetic abnormalities, tumor progression, tumor heterogeneity, clonal evolution and tumor-initiating cells. Med Sci (Basel) 2018; 6:E31. [PMID: 29652830 PMCID: PMC6024750 DOI: 10.3390/medsci6020031] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/24/2018] [Accepted: 04/03/2018] [Indexed: 02/08/2023] Open
Abstract
Colon cancer is the third most common cancer worldwide. Most colorectal cancer occurrences are sporadic, not related to genetic predisposition or family history; however, 20-30% of patients with colorectal cancer have a family history of colorectal cancer and 5% of these tumors arise in the setting of a Mendelian inheritance syndrome. In many patients, the development of a colorectal cancer is preceded by a benign neoplastic lesion: either an adenomatous polyp or a serrated polyp. Studies carried out in the last years have characterized the main molecular alterations occurring in colorectal cancers, showing that the tumor of each patient displays from two to eight driver mutations. The ensemble of molecular studies, including gene expression studies, has led to two proposed classifications of colorectal cancers, with the identification of four/five non-overlapping groups. The homeostasis of the rapidly renewing intestinal epithelium is ensured by few stem cells present at the level of the base of intestinal crypts. Various experimental evidence suggests that colorectal cancers may derive from the malignant transformation of intestinal stem cells or of intestinal cells that acquire stem cell properties following malignant transformation. Colon cancer stem cells seem to be involved in tumor chemoresistance, radioresistance and relapse.
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Affiliation(s)
- Ugo Testa
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
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