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Rahmatallah Y, Glazko G. Improving data interpretability with new differential sample variance gene set tests. RESEARCH SQUARE 2024:rs.3.rs-4888767. [PMID: 39315246 PMCID: PMC11419169 DOI: 10.21203/rs.3.rs-4888767/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Background Gene set analysis methods have played a major role in generating biological interpretations from omics data such as gene expression datasets. However, most methods focus on detecting homogenous pattern changes in mean expression and methods detecting pattern changes in variance remain poorly explored. While a few studies attempted to use gene-level variance analysis, such approach remains under-utilized. When comparing two phenotypes, gene sets with distinct changes in subgroups under one phenotype are overlooked by available methods although they reflect meaningful biological differences between two phenotypes. Multivariate sample-level variance analysis methods are needed to detect such pattern changes. Results We use ranking schemes based on minimum spanning tree to generalize the Cramer-Von Mises and Anderson-Darling univariate statistics into multivariate gene set analysis methods to detect differential sample variance or mean. We characterize these methods in addition to two methods developed earlier using simulation results with different parameters. We apply the developed methods to microarray gene expression dataset of prednisolone-resistant and prednisolone-sensitive children diagnosed with B-lineage acute lymphoblastic leukemia and bulk RNA-sequencing gene expression dataset of benign hyperplastic polyps and potentially malignant sessile serrated adenoma/polyps. One or both of the two compared phenotypes in each of these datasets have distinct molecular subtypes that contribute to heterogeneous differences. Our results show that methods designed to detect differential sample variance are able to detect specific hallmark signaling pathways associated with the two compared phenotypes as documented in available literature. Conclusions The results in this study demonstrate the usefulness of methods designed to detect differential sample variance in providing biological interpretations when biologically relevant but heterogeneous changes between two phenotypes are prevalent in specific signaling pathways. Software implementation of the developed methods is available with detailed documentation from Bioconductor package GSAR. The available methods are applicable to gene expression datasets in a normalized matrix form and could be used with other omics datasets in a normalized matrix form with available collection of feature sets.
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Affiliation(s)
- Yasir Rahmatallah
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Galina Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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Sayed IM, Vo DT, Alcantara J, Inouye KM, Pranadinata RF, Luo L, Boland CR, Goyal NP, Kuo DJ, Huang SC, Sahoo D, Ghosh P, Das S. Molecular Signatures for Microbe-Associated Colorectal Cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595902. [PMID: 38853996 PMCID: PMC11160670 DOI: 10.1101/2024.05.26.595902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Genetic factors and microbial imbalances play crucial roles in colorectal cancers (CRCs), yet the impact of infections on cancer initiation remains poorly understood. While bioinformatic approaches offer valuable insights, the rising incidence of CRCs creates a pressing need to precisely identify early CRC events. We constructed a network model to identify continuum states during CRC initiation spanning normal colonic tissue to pre-cancer lesions (adenomatous polyps) and examined the influence of microbes and host genetics. Methods A Boolean network was built using a publicly available transcriptomic dataset from healthy and adenoma affected patients to identify an invariant Microbe-Associated Colorectal Cancer Signature (MACS). We focused on Fusobacterium nucleatum ( Fn ), a CRC-associated microbe, as a model bacterium. MACS-associated genes and proteins were validated by RT-qPCR, RNA seq, ELISA, IF and IHCs in tissues and colon-derived organoids from genetically predisposed mice ( CPC-APC Min+/- ) and patients (FAP, Lynch Syndrome, PJS, and JPS). Results The MACS that is upregulated in adenomas consists of four core genes/proteins: CLDN2/Claudin-2 (leakiness), LGR5/leucine-rich repeat-containing receptor (stemness), CEMIP/cell migration-inducing and hyaluronan-binding protein (epithelial-mesenchymal transition) and IL8/Interleukin-8 (inflammation). MACS was induced upon Fn infection, but not in response to infection with other enteric bacteria or probiotics. MACS induction upon Fn infection was higher in CPC-APC Min+/- organoids compared to WT controls. The degree of MACS expression in the patient-derived organoids (PDOs) generally corresponded with the known lifetime risk of CRCs. Conclusions Computational prediction followed by validation in the organoid-based disease model identified the early events in CRC initiation. MACS reveals that the CRC-associated microbes induce a greater risk in the genetically predisposed hosts, suggesting its potential use for risk prediction and targeted cancer prevention.
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Hijazi A, Galon J. Principles of risk assessment in colon cancer: immunity is key. Oncoimmunology 2024; 13:2347441. [PMID: 38694625 PMCID: PMC11062361 DOI: 10.1080/2162402x.2024.2347441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/16/2024] [Indexed: 05/04/2024] Open
Abstract
In clinical practice, the administration of adjuvant chemotherapy (ACT) following tumor surgical resection raises a critical dilemma for stage II colon cancer (CC) patients. The prognostic features used to identify high-risk CC patients rely on the pathological assessment of tumor cells. Currently, these factors are considered for stratifying patients who may benefit from ACT at early CC stages. However, the extent to which these factors predict clinical outcomes (i.e. recurrence, survival) remains highly controversial, also uncertainty persists regarding patients' response to treatment, necessitating further investigation. Therefore, an imperious need is to explore novel biomarkers that can reliably stratify patients at risk, to optimize adjuvant treatment decisions. Recently, we evaluated the prognostic and predictive value of Immunoscore (IS), an immune digital-pathology assay, in stage II CC patients. IS emerged as the sole significant parameter for predicting disease-free survival (DFS) in high-risk patients. Moreover, IS effectively stratified patients who would benefit most from ACT based on their risk of recurrence, thus predicting their outcomes. Notably, our findings revealed that digital IS outperformed the visual quantitative assessment of the immune response conducted by expert pathologists. The latest edition of the WHO classification for digestive tumor has introduced the evaluation of the immune response, as assessed by IS, as desirable and essential diagnostic criterion. This supports the revision of current cancer guidelines and strongly recommends the implementation of IS into clinical practice as a patient stratification tool, to guide CC treatment decisions. This approach may provide appropriate personalized therapeutic decisions that could critically impact early-stage CC patient care.
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Affiliation(s)
- Assia Hijazi
- INSERM, Laboratory of Integrative Cancer Immunology, Paris, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Paris, France
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Paris, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Paris, France
- Veracyte, Marseille, France
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McDonald HG, Kerekes DM, Kim J, Khan SA. Precision Oncology in Gastrointestinal and Colorectal Cancer Surgery. Surg Oncol Clin N Am 2024; 33:321-341. [PMID: 38401913 DOI: 10.1016/j.soc.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
Precision medicine is used to treat gastrointestinal malignancies including esophageal, gastric, small bowel, colorectal, and pancreatic cancers. Cutting-edge assays to detect and treat these cancers are active areas of research and will soon become standard of care. Colorectal cancer is a prime example of precision oncology as disease site is no longer the final determinate of treatment. Here, the authors describe how leveraging an understanding of tumor biology translates to individualized patient care using evidence-based practices.
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Affiliation(s)
- Hannah G McDonald
- Department of General Surgery, Division of Surgical Oncology, The University of Kentucky, 800 Rose Street, Lexington, KY 40508, USA
| | - Daniel M Kerekes
- Department of General Surgery, Division of Surgical Oncology, Yale University, 15 York Street, New Haven, CT 06510, USA
| | - Joseph Kim
- Department of General Surgery, Division of Surgical Oncology, The University of Kentucky, 800 Rose Street, Lexington, KY 40508, USA
| | - Sajid A Khan
- Department of Surgery, Yale University, 15 York Street, New Haven, CT 06510, USA.
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5
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Gao Z, Wan Z, Yu P, Shang Y, Zhu G, Jiang H, Chen Y, Wang S, Lei F, Huang W, Zeng Q, Wang Y, Rong W, Hong Y, Gao Q, Niu P, Zhai Z, An K, Ding C, Wang Y, Gu G, Wang X, Meng Q, Ye S, Liu H, Gu J. A recurrence-predictive model based on eight genes and tumor mutational burden/microsatellite instability status in Stage II/III colorectal cancer. Cancer Med 2024; 13:e6720. [PMID: 38111983 PMCID: PMC10807589 DOI: 10.1002/cam4.6720] [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: 03/16/2023] [Revised: 06/18/2023] [Accepted: 10/27/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Although adjuvant chemotherapy (ACT) is widely used to treat patients with Stage II/III colorectal cancer (CRC), administering ACT to specific patients remains a challenge. The decision to ACT requires an accurate assessment of recurrence risk and absolute treatment benefit. However, the traditional TNM staging system does not accurately assess a patient's individual risk of recurrence. METHODS To identify recurrence risk-related genetic factors for Stage II/III CRC patients after radical surgery, we conducted an analysis of whole-exome sequencing of 47 patients with Stage II/III CRC who underwent radical surgery at five institutions. Patients were grouped into non-recurrence group (NR, n = 24, recurrence-free survival [RFS] > 5 years) and recurrence group (R, n = 23, RFS <2 years). The TCGA-COAD/READ cohort was employed as the validation dataset. RESULTS A recurrence-predictive model (G8plus score) based on eight gene (CUL9, PCDHA12, HECTD3, DCX, SMARCA2, FAM193A, AATK, and SORCS2) mutations and tumor mutation burden/microsatellite instability (TMB/MSI) status was constructed, with 97.87% accuracy in our data and 100% negative predictive value in the TCGA-COAD/READ cohort. For the TCGA-COAD/READ cohort, the G8plus-high group had better RFS (HR = 0.22, p = 0.024); the G8plus-high tumors had significantly more infiltrated immune cell types, higher tertiary lymphoid structure signature scores, and higher immunological signature scores. The G8plus score was also a predict biomarker for immunotherapeutic in advanced CRC in the PUCH cohort. CONCLUSIONS In conclusion, the G8plus score is a powerful biomarker for predicting the risk of recurrence in patients with stage II/III CRC. It can be used to stratify patients who benefit from ACT and immunotherapy.
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Affiliation(s)
- Zhaoya Gao
- Department of General SurgeryPeking University First HospitalBeijingChina
| | - Zhiyi Wan
- Genecast Biotechnology Co., Ltd.Wuxi CityJiangsu ProvinceChina
| | - Pengfei Yu
- Department of General SurgeryAir Force Medical Center, Chinese People's Liberation ArmyBeijingChina
| | - Yan Shang
- Department of Colorectal SurgeryCancer Hospital of China Medical University, Liaoning Cancer Hospital and InstituteShenyangLiaoning ProvinceChina
| | - Guangsheng Zhu
- Department of Gastrointestinal SurgeryHubei Cancer HospitalWuhanHubei ProvinceChina
| | - Huiyuan Jiang
- Department of Colorectal and Anal SurgeryShanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanShanxi ProvinceChina
| | - Yawei Chen
- Genecast Biotechnology Co., Ltd.Wuxi CityJiangsu ProvinceChina
| | - Shengzhou Wang
- Genecast Biotechnology Co., Ltd.Wuxi CityJiangsu ProvinceChina
| | - Fuming Lei
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Wensheng Huang
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Qingmin Zeng
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Yanzhao Wang
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Wanshui Rong
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Yuming Hong
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Qingkun Gao
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Pengfei Niu
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Zhichao Zhai
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Ke An
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Changmin Ding
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Yunfan Wang
- Department of PathologyPeking University Shougang HospitalBeijingChina
| | - Guoli Gu
- Department of General SurgeryAir Force Medical Center, Chinese People's Liberation ArmyBeijingChina
| | - Xin Wang
- Department of General SurgeryPeking University First HospitalBeijingChina
| | - Qingkai Meng
- Department of Colorectal SurgeryCancer Hospital of China Medical University, Liaoning Cancer Hospital and InstituteShenyangLiaoning ProvinceChina
| | - Shengwei Ye
- Department of Gastrointestinal SurgeryHubei Cancer HospitalWuhanHubei ProvinceChina
| | - Haiyi Liu
- Department of Colorectal and Anal SurgeryShanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanShanxi ProvinceChina
| | - Jin Gu
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal SurgeryPeking University Cancer Hospital & InstituteBeijingChina
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
- Peking University International Cancer InstituteBeijingChina
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Rejali L, Seifollahi Asl R, Sanjabi F, Fatemi N, Asadzadeh Aghdaei H, Saeedi Niasar M, Ketabi Moghadam P, Nazemalhosseini Mojarad E, Mini E, Nobili S. Principles of Molecular Utility for CMS Classification in Colorectal Cancer Management. Cancers (Basel) 2023; 15:2746. [PMID: 37345083 PMCID: PMC10216373 DOI: 10.3390/cancers15102746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Colorectal cancer (CRC) is the second cause of cancer-related deaths in both sexes globally and presents different clinical outcomes that are described by a range of genomic and epigenomic alterations. Despite the advancements in CRC screening plans and treatment strategies, the prognosis of CRC is dismal. In the last two decades, molecular biomarkers predictive of prognosis have been identified in CRC, although biomarkers predictive of treatment response are only available for specific biological drugs used in stage IV CRC. Translational clinical trials mainly based on "omic" strategies allowed a better understanding of the biological heterogeneity of CRCs. These studies were able to classify CRCs into subtypes mainly related to prognosis, recurrence risk, and, to some extent, also to treatment response. Accordingly, the comprehensive molecular characterizations of CRCs, including The Cancer Genome Atlas (TCGA) and consensus molecular subtype (CMS) classifications, were presented to improve the comprehension of the genomic and epigenomic landscapes of CRCs for a better patient management. The CMS classification obtained by the CRC subtyping consortium categorizes CRC into four consensus molecular subtypes (CMS1-4) characterized by different prognoses. In this review, we discussed the CMS classification in different settings with a focus on its relationships with precursor lesions, tumor immunophenotype, and gut microbiota, as well as on its role in predicting prognosis and/or response to pharmacological treatments, as a crucial step towards precision medicine.
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Affiliation(s)
- Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Romina Seifollahi Asl
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Fatemeh Sanjabi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran P.O. Box 14496-14535, Iran;
| | - Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Mahsa Saeedi Niasar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Pardis Ketabi Moghadam
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yaman Street, Chamran Expressway, Tehran P.O. Box 19857-17411, Iran;
| | - Enrico Mini
- Department of Health Sciences, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy;
| | - Stefania Nobili
- Department of Neuroscience, Psychology, Drug Research and Child Health—NEUROFARBA—Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy
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7
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Yao Z, An W, Tuerdi M, Zhao J. Identification of novel prognostic indicators for oral squamous cell carcinoma based on proteomics and metabolomics. Transl Oncol 2023; 33:101672. [PMID: 37084685 PMCID: PMC10172993 DOI: 10.1016/j.tranon.2023.101672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/27/2023] [Accepted: 04/09/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND The low 5-year survival rate of oral squamous cell carcinoma (OSCC) suggests that new prognostic indicators need to be identified to aid the clinical management of patients. METHODS Saliva samples from OSCC patients and healthy controls were collected for proteomic and metabolomic sequencing. Gene expressed profiling was downloaded from TCGA and GEO databases. After the differential analysis, proteins with a significant impact on the prognosis of OSCC patients were screened. Correlation analysis was performed with metabolites and core proteins were identified. Cox regression analysis was utilized to stratify OSCC samples based on core proteins. The prognostic predictive ability of the core protein was then evaluated. Differences in infiltration of immune cells between the different strata were identified. RESULTS There were 678 differentially expressed proteins (DEPs), 94 intersected DEPs among them by intersecting with differentially expressed genes in TCGA and GSE30784 dataset. Seven core proteins were identified that significantly affected OSCC patient survival and strongly correlated with differential metabolites (R2 > 0.8). The samples were divided into high- and low-risk groups according to median risk score. The risk score and core proteins were well prognostic factor in OSCC patients. Genes in high-risk group were enriched in Notch signaling pathway, epithelial mesenchymal transition (EMT), and angiogenesis. Core proteins were strongly associated with the immune status of OSCC patients. CONCLUSIONS The results established a 7-protein signatures with the hope of early detection and the capacity for risk assessment of OSCC patient prognosis. Further providing more potential targets for the treatment of OSCC.
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Affiliation(s)
- Zhitao Yao
- Department of Trauma and Orthopedics, the First Affiliated Hospital of Xinjiang Medical University, No. 137 South Liyushan Road, Urumqi 830054, China; Oral Disease Institute of Xinjiang Uyghur Autonomous Region, No.137 South Liyushan Road, Urumqi 830054, China
| | - Wei An
- Department of Trauma and Orthopedics, the First Affiliated Hospital of Xinjiang Medical University, No. 137 South Liyushan Road, Urumqi 830054, China; Oral Disease Institute of Xinjiang Uyghur Autonomous Region, No.137 South Liyushan Road, Urumqi 830054, China
| | - Maimaitituxun Tuerdi
- Department of Trauma and Orthopedics, the First Affiliated Hospital of Xinjiang Medical University, No. 137 South Liyushan Road, Urumqi 830054, China; Oral Disease Institute of Xinjiang Uyghur Autonomous Region, No.137 South Liyushan Road, Urumqi 830054, China
| | - Jin Zhao
- Department of Trauma and Orthopedics, the First Affiliated Hospital of Xinjiang Medical University, No. 137 South Liyushan Road, Urumqi 830054, China; Oral Disease Institute of Xinjiang Uyghur Autonomous Region, No.137 South Liyushan Road, Urumqi 830054, China.
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de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A. Genomic Signature in Evolutionary Biology: A Review. BIOLOGY 2023; 12:biology12020322. [PMID: 36829597 PMCID: PMC9953303 DOI: 10.3390/biology12020322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
Organisms are unique physical entities in which information is stored and continuously processed. The digital nature of DNA sequences enables the construction of a dynamic information reservoir. However, the distinction between the hardware and software components in the information flow is crucial to identify the mechanisms generating specific genomic signatures. In this work, we perform a bibliometric analysis to identify the different purposes of looking for particular patterns in DNA sequences associated with a given phenotype. This study has enabled us to make a conceptual breakdown of the genomic signature and differentiate the leading applications. On the one hand, it refers to gene expression profiling associated with a biological function, which may be shared across taxa. This signature is the focus of study in precision medicine. On the other hand, it also refers to characteristic patterns in species-specific DNA sequences. This interpretation plays a key role in comparative genomics, identifying evolutionary relationships. Looking at the relevant studies in our bibliographic database, we highlight the main factors causing heterogeneities in genome composition and how they can be quantified. All these findings lead us to reformulate some questions relevant to evolutionary biology.
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Affiliation(s)
- Rebeca de la Fuente
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Correspondence:
| | - Wladimiro Díaz-Villanueva
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Vicente Arnau
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
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9
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Yuan L, Lu Z, Sun G, Cao D. Identification and verification of a 4-gene signature predicting the overall survival of cervical cancer. Medicine (Baltimore) 2022; 101:e31299. [PMID: 36281082 PMCID: PMC9592452 DOI: 10.1097/md.0000000000031299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cervical cancer (CC) is one of the most common gynecological malignancies, ranking fourth in both incidence and mortality in women worldwide. Early screening and treatment are of great significance in reducing the incidence and mortality of CC. Due to the complex molecular mechanisms of tumor progression, the predictive power of traditional clinical information is limited. In this study, an effective molecular model is established to assess prognosis of patients with CC and guide clinical treatment so as to improve their survival rate. Three high quality datasets (GSE138080, GSE52904, GSE67522) of expression profiling were obtained from gene expression omnibus (GEO) database. Another mRNA expression and clinicopathological data of CC were obtained from The Cancer Genome Atlas (TCGA) dataset. The bioinformatic analyses such as univariate analysis, multivariate Cox proportional-hazards model (Cox) analysis and lasso regression analysis were conducted to select survival-related differentially expressed genes (DEGs) and further establish a prognostic gene signature. Moreover, the performance of prognostic gene signature was evaluated based on Kaplan-Meier curve and receiver operating characteristic (ROC) curve. Gene set enrichment analysis (GSEA) and tumor immunity analysis were carried out to elucidate the molecular mechanisms and immune relevance. A 4-gene signature comprising procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2), spondin1 (SPON1), secreted phosphoprotein 1 (SPP1), ribonuclease H2 subunit A (RNASEH2A) was established to predict overall survival (OS) of CC. The ROC curve indicated good performance of the 4-gene signature in predicting OS of CC based on the TCGA dataset. The 4-gene signature classified the patients into high-risk and low-risk groups with distinct OS rates of CC. Univariate analysis and multivariate Cox regression analysis revealed that the 4-gene signature was an independent factor affecting the prognosis of patients with CC. Our study developed a 4-gene signature capable of predicting the OS of CC. The findings may be beneficial to individualized clinical treatment and timely follow-up for patients with CC.
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Affiliation(s)
- Lu Yuan
- From the Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, No. 745, Wuhan, China
| | - Zijun Lu
- From the Department of Gynecology and Obstetrics, Wuhan University of Science and Technology, No. 2, Wuhan, China
| | - Guoqiang Sun
- From the Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, No. 745, Wuhan, China
- * Correspondence: Dongmei Cao, Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, No. 745, Wuluo Road, Hongshan District, Wuhan 430070, China (e-mail: ), and Guoqiang Sun, Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, No. 745, Wuluo Road, Hongshan District, Wuhan 430070, China (e-mail: )
| | - Dongmei Cao
- From the Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, No. 745, Wuhan, China
- * Correspondence: Dongmei Cao, Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, No. 745, Wuluo Road, Hongshan District, Wuhan 430070, China (e-mail: ), and Guoqiang Sun, Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, No. 745, Wuluo Road, Hongshan District, Wuhan 430070, China (e-mail: )
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Crafa F, Vanella S, Catalano OA, Pomykala KL, Baiamonte M. Role of one-step nucleic acid amplification in colorectal cancer lymph node metastases detection. World J Gastroenterol 2022; 28:4019-4043. [PMID: 36157105 PMCID: PMC9403438 DOI: 10.3748/wjg.v28.i30.4019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/03/2022] [Accepted: 07/22/2022] [Indexed: 02/06/2023] Open
Abstract
Current histopathological staging procedures in colorectal cancer (CRC) depend on midline division of the lymph nodes (LNs) with one section of hematoxylin and eosin staining. Cancer cells outside this transection line may be missed, which could lead to understaging of Union for International Cancer Control Stage II high-risk patients. The one-step nucleic acid amplification (OSNA) assay has emerged as a rapid molecular diagnostic tool for LN metastases detection. It is a molecular technique that can analyze the entire LN tissue using a reverse-transcriptase loop-mediated isothermal amplification reaction to detect tumor-specific cytokeratin 19 mRNA. Our findings suggest that the OSNA assay has a high diagnostic accuracy in detecting metastatic LNs in CRC and a high negative predictive value. OSNA is a standardized, observer-independent technique, which may lead to more accurate staging. It has been suggested that in stage II CRC, the upstaging can reach 25% and these patients can access postoperative adjuvant chemotherapy. Moreover, intraoperative OSNA sentinel node evaluation may allow early CRC to be treated with organ-preserving surgery, while in more advanced-stage disease, a tailored lymphadenectomy can be performed considering the presence of aberrant lymphatic drainage and skip metastases.
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Affiliation(s)
- Francesco Crafa
- Division of General and Surgical Oncology, St. Giuseppe Moscati Hospital, Center of National Excellence and High Specialty, Avellino 83100, Italy
| | - Serafino Vanella
- Division of General and Surgical Oncology, St. Giuseppe Moscati Hospital, Center of National Excellence and High Specialty, Avellino 83100, Italy
| | - Onofrio A Catalano
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States
| | - Kelsey L Pomykala
- Department of Nuclear Medicine, Department of Radiological Sciences, David Geffen School of Medicine at University of California, Los Angeles, University Hospital Essen, University of Duisburg-Essen, Essen 45141, Germany
| | - Mario Baiamonte
- Division of General and Surgical Oncology, St. Giuseppe Moscati Hospital, Center of National Excellence and High Specialty, Avellino 83100, Italy
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11
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Zhang S, Zeng X, Lin S, Liang M, Huang H. Identification of seven-gene marker to predict the survival of patients with lung adenocarcinoma using integrated multi-omics data analysis. J Clin Lab Anal 2021; 36:e24190. [PMID: 34951053 PMCID: PMC8841135 DOI: 10.1002/jcla.24190] [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: 11/01/2021] [Revised: 12/04/2021] [Accepted: 12/10/2021] [Indexed: 12/28/2022] Open
Abstract
Background The mechanism of cancer occurrence and development could be understood with multi‐omics data analysis. Discovering genetic markers is highly necessary for predicting clinical outcome of lung adenocarcinoma (LUAD). Methods Clinical follow‐up information, copy number variation (CNV) data, single nucleotide polymorphism (SNP), and RNA‐Seq were acquired from The Cancer Genome Atlas (TCGA). To obtain robust biomarkers, prognostic‐related genes, genes with SNP variation, and copy number differential genes in the training set were selected and further subjected to feature selection using random forests. Finally, a gene‐based prediction model for LUAD was validated in validation datasets. Results The study filtered 2071 prognostic‐related genes and 230 genomic variants, 1878 copy deletions, and 438 significant mutations. 218 candidate genes were screened through integrating genomic variation genes and prognosis‐related genes. 7 characteristic genes (RHOV, CSMD3, FBN2, MAGEL2, SMIM4, BCKDHB, and GANC) were identified by random forest feature selection, and many genes were found to be tumor progression‐related. A 7‐gene signature constructed by Cox regression analysis was an independent prognostic factor for LUAD patients, and at the same time a risk factor in the test set, external validation set, and training set. Noticeably, the 5‐year AUC of survival in the validation set and training set was all ˃ 0.67. Similar results were obtained from multi‐omics validation datasets. Conclusions The study builds a novel 7‐gene signature as a prognostic marker for the survival prediction of patients with LUAD. The current findings provided a set of new prognostic and diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Surong Zhang
- Department of Infectious Diseases, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou City, China
| | - Xueni Zeng
- Department of Infectious Diseases, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou City, China.,Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou City, China
| | - Shaona Lin
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou City, China
| | - Minchao Liang
- Department of Medicine, Shenzhen Haplox Biotechnology Co., Ltd, Shenzhen City, China
| | - Huaxing Huang
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou City, China
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12
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Glaab E, Rauschenberger A, Banzi R, Gerardi C, Garcia P, Demotes J. Biomarker discovery studies for patient stratification using machine learning analysis of omics data: a scoping review. BMJ Open 2021; 11:e053674. [PMID: 34873011 PMCID: PMC8650485 DOI: 10.1136/bmjopen-2021-053674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To review biomarker discovery studies using omics data for patient stratification which led to clinically validated FDA-cleared tests or laboratory developed tests, in order to identify common characteristics and derive recommendations for future biomarker projects. DESIGN Scoping review. METHODS We searched PubMed, EMBASE and Web of Science to obtain a comprehensive list of articles from the biomedical literature published between January 2000 and July 2021, describing clinically validated biomarker signatures for patient stratification, derived using statistical learning approaches. All documents were screened to retain only peer-reviewed research articles, review articles or opinion articles, covering supervised and unsupervised machine learning applications for omics-based patient stratification. Two reviewers independently confirmed the eligibility. Disagreements were solved by consensus. We focused the final analysis on omics-based biomarkers which achieved the highest level of validation, that is, clinical approval of the developed molecular signature as a laboratory developed test or FDA approved tests. RESULTS Overall, 352 articles fulfilled the eligibility criteria. The analysis of validated biomarker signatures identified multiple common methodological and practical features that may explain the successful test development and guide future biomarker projects. These include study design choices to ensure sufficient statistical power for model building and external testing, suitable combinations of non-targeted and targeted measurement technologies, the integration of prior biological knowledge, strict filtering and inclusion/exclusion criteria, and the adequacy of statistical and machine learning methods for discovery and validation. CONCLUSIONS While most clinically validated biomarker models derived from omics data have been developed for personalised oncology, first applications for non-cancer diseases show the potential of multivariate omics biomarker design for other complex disorders. Distinctive characteristics of prior success stories, such as early filtering and robust discovery approaches, continuous improvements in assay design and experimental measurement technology, and rigorous multicohort validation approaches, enable the derivation of specific recommendations for future studies.
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Affiliation(s)
- Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Armin Rauschenberger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rita Banzi
- Center for Health Regulatory Policies, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Chiara Gerardi
- Center for Health Regulatory Policies, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Paula Garcia
- European Clinical Research Infrastructure Network, ECRIN, Paris, France
| | - Jacques Demotes
- European Clinical Research Infrastructure Network, ECRIN, Paris, France
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13
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Fu Y, Wei X, Han Q, Le J, Ma Y, Lin X, Xu Y, Liu N, Wang X, Kong X, Gu J, Tong Y, Wu H. Identification and characterization of a 25-lncRNA prognostic signature for early recurrence in hepatocellular carcinoma. BMC Cancer 2021; 21:1165. [PMID: 34717566 PMCID: PMC8556945 DOI: 10.1186/s12885-021-08827-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/30/2021] [Indexed: 02/06/2023] Open
Abstract
Background Early recurrence is the major cause of poor prognosis in hepatocellular carcinoma (HCC). Long non-coding RNAs (lncRNAs) are deeply involved in HCC prognosis. In this study, we aimed to establish a prognostic lncRNA signature for HCC early recurrence. Methods The lncRNA expression profile and corresponding clinical data were retrieved from total 299 HCC patients in TCGA database. LncRNA candidates correlated to early recurrence were selected by differentially expressed gene (DEG), univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. A 25-lncRNA prognostic signature was constructed according to receiver operating characteristic curve (ROC). Kaplan-Meier and multivariate Cox regression analyses were used to evaluate the performance of this signature. ROC and nomogram were used to evaluate the integrated models based on this signature with other independent clinical risk factors. Gene set enrichment analysis (GSEA) was used to reveal enriched gene sets in the high-risk group. Tumor infiltrating lymphocytes (TILs) levels were analyzed with single sample Gene Set Enrichment Analysis (ssGSEA). Immune therapy response prediction was performed with TIDE and SubMap. Chemotherapeutic response prediction was conducted by using Genomics of Drug Sensitivity in Cancer (GDSC) pharmacogenomics database. Results Compared to low-risk group, patients in high-risk group showed reduced disease-free survival (DFS) in the training (p < 0.0001) and validation cohort (p = 0.0132). The 25-lncRNA signature, AFP, TNM and vascular invasion could serve as independent risk factors for HCC early recurrence. Among them, the 25-lncRNA signature had the best predictive performance, and combination of those four risk factors further improves the prognostic potential. Moreover, GSEA showed significant enrichment of “E2F TARGETS”, “G2M CHECKPOINT”, “MYC TARGETS V1” and “DNA REPAIR” pathways in the high-risk group. In addition, increased TILs were observed in the low-risk group compared to the high-risk group. The 25-lncRNA signature negatively associates with the levels of some types of antitumor immune cells. Immunotherapies and chemotherapies prediction revealed differential responses to PD-1 inhibitor and several chemotherapeutic drugs in the low- and high-risk group. Conclusions Our study proposed a 25-lncRNA prognostic signature for predicting HCC early recurrence, which may guide postoperative treatment and recurrence surveillance in HCC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08827-z.
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Affiliation(s)
- Yi Fu
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.,Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.,School of Medical Instruments, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Xindong Wei
- Nanjing University of Traditional Chinese Medicine, Nanjing, 210000, China
| | - Qiuqin Han
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.,Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Jiamei Le
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.,Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Yujie Ma
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Xinjie Lin
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Yuhui Xu
- Graduate School of Art and Sciences, Columbia University, New York, NY, 10027, USA
| | - Ning Liu
- Department of Clinical Oncology, Taian City Central Hospital, Taian, 271000, Shandong, China
| | - Xuan Wang
- Department of General Surgery, Nanjing General Hospital of Nanjing Military Command, Nanjing, 210000, China
| | - Xiaoni Kong
- Institute of Clinical Immunology, Department of Liver Diseases, Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200021, China
| | - Jinyang Gu
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Ying Tong
- Department of Liver Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Hailong Wu
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China. .,Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
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14
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Cui H, Weng Y, Ding N, Cheng C, Wang L, Zhou Y, Zhang L, Cui Y, Zhang W. Autophagy-Related Three-Gene Prognostic Signature for Predicting Survival in Esophageal Squamous Cell Carcinoma. Front Oncol 2021; 11:650891. [PMID: 34336650 PMCID: PMC8321089 DOI: 10.3389/fonc.2021.650891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 12/24/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive malignant tumors in China, and its prognosis remains poor. Autophagy is an evolutionarily conserved catabolic process involved in the occurrence and development of ESCC. In this study, we described the expression profile of autophagy-related genes (ARGs) in ESCC and developed a prognostic prediction model for ESCC patients based on the expression pattern of ARGs. We used four ESCC cohorts, GSE53624 (119 samples) set as the discovery cohort, The Cancer Genome Atlas (TCGA) ESCC set (95 samples) as the validation cohort, 155 ESCC cohort, and Oncomine cohort were used to screen and verify differentially expressed ARGs. We identified 34 differentially expressed genes out of 222 ARGs. In the discovery cohort, we divided ESCC patients into three groups that showed significant differences in prognosis. Then, we analyzed the prognosis of 34 differentially expressed ARGs. Three genes [poly (ADP-ribose) polymerase 1 (PARP1), integrin alpha-6 (ITGA6), and Fas-associated death domain (FADD)] were ultimately obtained through random forest feature selection and were constructed as an ARG-related prognostic model. This model was further validated in TCGA ESCC set. Cox regression analysis confirmed that the three-gene signature was an independent prognostic factor for ESCC patients. This signature effectively stratified patients in both discovery and validation cohorts by overall survival (P = 5.162E-8 and P = 0.052, respectively). We also constructed a clinical nomogram with a concordance index of 0.713 to predict the survival possibility of ESCC patients by integrating clinical characteristics and the ARG signature. The calibration curves substantiated fine concordance between nomogram prediction and actual observation. In conclusion, we constructed a new ARG-related prognostic model, which shows the potential to improve the ability of individualized prognosis prediction in ESCC.
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Affiliation(s)
- Heyang Cui
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Yongjia Weng
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Ning Ding
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Chen Cheng
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Longlong Wang
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Yong Zhou
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Ling Zhang
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Yongping Cui
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Weimin Zhang
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
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15
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Pei JP, Zhang CD, Fu X, Ba Y, Yue S, Zhao ZM, Dai DQ. A Novel TNM Classification for Colorectal Cancers based on the Metro-ticket Paradigm. J Cancer 2021; 12:3299-3306. [PMID: 33976739 PMCID: PMC8100802 DOI: 10.7150/jca.55097] [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: 10/27/2020] [Accepted: 03/09/2021] [Indexed: 01/24/2023] Open
Abstract
Background: Several revisions of the TNM classifications for colorectal cancer (CRC) have acknowledged that the oncological outcomes of stage IIB/IIC CRC are worse than those of stage IIIA. We aimed to develop a novel TNM (nTNM) classification based on the metro-ticket paradigm. Methods: We identified eligible CRC patients from the Surveillance, Epidemiology, and End Results database. The nTNM was developed using distance from the origin on a Cartesian plane incorporating the pN (x-axis) and pT (y-axis) stages, and was compared with the AJCC TNM classification. The areas under the curves (AUCs), calibration curves, and Akaike's information criterion (AIC) were used to evaluate the predictive performances of the two classifications. Clinical benefits were further estimated by decision curve analyses. The validation cohort was applied to validate these findings. Results: A total of 58,192 CRC patients (40,736 training cohort, 17,456 validation cohort) were finally included. In the training cohort, 18,476 patients (45.4%) experienced upstaging and 15,907 patients (39.0%) experienced downstaging in the nTNM classification compared with the TNM classification. Taking the prognosis of stage I as the reference, survival decreased with increasing nTNM stage. The nTNM classification showed better discrimination (AUC, 0.678 vs. 0.667, P<0.001), model-fitting (AIC, 236,525 vs. 237,741), and clinical benefits than the TNM classification. Similar results were found in the validation cohort. Conclusions: The nTNM classification for CRC has better predictive performances and superior accuracy for predicting prognosis compared with the TNM classification. The nTNM classification should therefore be considered in future revisions of the TNM classification.
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Affiliation(s)
- Jun-Peng Pei
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Chun-Dong Zhang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.,Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Xiang Fu
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Yong Ba
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Shuai Yue
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Zhe-Ming Zhao
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Dong-Qiu Dai
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.,Cancer Center, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
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16
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Prognostic Cancer Gene Expression Signatures: Current Status and Challenges. Cells 2021; 10:cells10030648. [PMID: 33804045 PMCID: PMC8000474 DOI: 10.3390/cells10030648] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/27/2022] Open
Abstract
Current staging systems of cancer are mainly based on the anatomical extent of disease. They need refinement by biological parameters to improve stratification of patients for tumor therapy or surveillance strategies. Thanks to developments in genomic, transcriptomic, and big-data technologies, we are now able to explore molecular characteristics of tumors in detail and determine their clinical relevance. This has led to numerous prognostic and predictive gene expression signatures that have the potential to establish a classification of tumor subgroups by biological determinants. However, only a few gene signatures have reached the stage of clinical implementation so far. In this review article, we summarize the current status, and present and future challenges of prognostic gene signatures in three relevant cancer entities: breast cancer, colorectal cancer, and hepatocellular carcinoma.
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17
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Li R, Wang G, Wu Z, Lu H, Li G, Sun Q, Cai M. Identification of 6 gene markers for survival prediction in osteosarcoma cases based on multi-omics analysis. Exp Biol Med (Maywood) 2021; 246:1512-1523. [PMID: 33563042 DOI: 10.1177/1535370221992015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Multiple-omics sequencing information with high-throughput has laid a solid foundation to identify genes associated with cancer prognostic process. Multiomics information study is capable of revealing the cancer occurring and developing system according to several aspects. Currently, the prognosis of osteosarcoma is still poor, so a genetic marker is needed for predicting the clinically related overall survival result. First, Office of Cancer Genomics (OCG Target) provided RNASeq, copy amount variations information, and clinically related follow-up data. Genes associated with prognostic process and genes exhibiting copy amount difference were screened in the training group, and the mentioned genes were integrated for feature selection with least absolute shrinkage and selection operator (Lasso). Eventually, effective biomarkers received the screening process. Lastly, this study built and demonstrated one gene-associated prognosis mode according to the set of the test and gene expression omnibus validation set; 512 prognosis-related genes (P < 0.01), 336 copies of amplified genes (P < 0.05), and 36 copies of deleted genes (P < 0.05) were obtained, and those genes of the mentioned genomic variants display close associations with tumor occurring and developing mechanisms. This study generated 10 genes for candidates through the integration of genomic variant genes as well as prognosis-related genes. Six typical genes (i.e. MYC, CHIC2, CCDC152, LYL1, GPR142, and MMP27) were obtained by Lasso feature selection and stepwise multivariate regression study, many of which are reported to show a relationship to tumor progressing process. The authors conducted Cox regression study for building 6-gene sign, i.e. one single prognosis-related element, in terms of cases carrying osteosarcoma. In addition, the samples were able to be risk stratified in the training group, test set, and externally validating set. The AUC of five-year survival according to the training group and validation set reached over 0.85, with superior predictive performance as opposed to the existing researches. Here, 6-gene sign was built to be new prognosis-related marking elements for assessing osteosarcoma cases' surviving state.
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Affiliation(s)
- Runmin Li
- Department of Orthopaedics, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, China
| | - Guosheng Wang
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310029, China
| | - ZhouJie Wu
- Department of Orthopaedics, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, China
| | - HuaGuang Lu
- Department of Orthopaedics, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, China
| | - Gen Li
- Department of Orthopaedics, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, China
| | - Qi Sun
- Department of Orthopaedics, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, China
| | - Ming Cai
- Department of Orthopaedics, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, China
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18
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Miyamoto Y, Hiyoshi Y, Sawayama H, Tokunaga R, Baba H. Precision medicine for adjuvant chemotherapy of resected colorectal cancer. Ann Gastroenterol Surg 2020; 4:635-645. [PMID: 33319153 PMCID: PMC7726679 DOI: 10.1002/ags3.12397] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/16/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) is the most common cancer and the second leading cause of cancer death in Japan. Surgical resection is the only curative option for localized disease. However, undetectable micrometastases remaining after curative surgery may cause disease recurrence. Adjuvant chemotherapy aims to eradicate these micrometastases to improve the cure rate. Unfortunately, few reliable prognostic and predictive markers are available that identify patients at high risk for CRC during early-stage disease. However, promising biomarkers may become available in the near future. Such biomarkers provide information for stratifying a patient's risk and for selecting the optimal treatment. Here, we provide an overview of current relevant prognostic and predictive biomarkers applicable to adjuvant treatment of early-stage CRC and focus on the future of this field.
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Affiliation(s)
- Yuji Miyamoto
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Yukiharu Hiyoshi
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Hiroshi Sawayama
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Ryuma Tokunaga
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Hideo Baba
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityKumamotoJapan
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19
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Lu Y, Wu S, Cui C, Yu M, Wang S, Yue Y, Liu M, Sun Z. Gene Expression Along with Genomic Copy Number Variation and Mutational Analysis Were Used to Develop a 9-Gene Signature for Estimating Prognosis of COAD. Onco Targets Ther 2020; 13:10393-10408. [PMID: 33116619 PMCID: PMC7569059 DOI: 10.2147/ott.s255590] [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: 04/02/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
PURPOSE This study aims to systematically analyze multi-omics data to explore new prognosis biomarkers in colon adenocarcinoma (COAD). MATERIALS AND METHODS Multi-omics data of COAD and clinical information were obtained from The Cancer Genome Atlas (TCGA). Univariate Cox analysis was used to select genes which significantly related to the overall survival. GISTIC 2.0 software was used to identify significant amplification or deletion. Mutsig 2.0 software was used to identify significant mutation genes. The 9-gene signature was screened by random forest algorithm and Cox regression analysis. GSE17538 dataset was used as an external dataset to verify the predictive ability of 9-gene signature. qPCR was used to detect the expression of 9 genes in clinical specimens. RESULTS A total of 71 candidate genes are obtained by integrating genomic variation, mutation and prognostic data. Then, 9-gene signature was established, which includes HOXD12, RNF25, CBLN3, DOCK3, DNAJB13, PYGO2, CTNNA1, PTPRK, and NAT1. The 9-gene signature is an independent prognostic risk factor for COAD patients. In addition, the signature shows good predicting performance and clinical practicality in training set, testing set and external verification set. The results of qPCR based on clinical samples showed that the expression of HOXD12, RNF25, CBLN3, DOCK3, DNAJB13, and PYGO2 was increased in colon cancer tissues and the expression of CTNNA1, PTPRK, NAT1 was decreased in colon cancer tissues. CONCLUSION In this study, 9-gene signature is constructed as a new prognostic marker to predict the survival of COAD patients.
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Affiliation(s)
- Yiping Lu
- BioBank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, People's Republic of China
| | - Si Wu
- BioBank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, People's Republic of China
| | - Changwan Cui
- BioBank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, People's Republic of China
| | - Miao Yu
- BioBank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, People's Republic of China
| | - Shuang Wang
- BioBank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, People's Republic of China
| | - Yuanyi Yue
- BioBank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, People's Republic of China
| | - Miao Liu
- BioBank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, People's Republic of China
| | - Zhengrong Sun
- BioBank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, People's Republic of China
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20
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Tsimberidou AM, Fountzilas E, Bleris L, Kurzrock R. Transcriptomics and solid tumors: The next frontier in precision cancer medicine. Semin Cancer Biol 2020; 84:50-59. [PMID: 32950605 DOI: 10.1016/j.semcancer.2020.09.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 08/16/2020] [Accepted: 09/09/2020] [Indexed: 01/08/2023]
Abstract
Transcriptomics, which encompasses assessments of alternative splicing and alternative polyadenylation, identification of fusion transcripts, explorations of noncoding RNAs, transcript annotation, and discovery of novel transcripts, is a valuable tool for understanding cancer mechanisms and identifying biomarkers. Recent advances in high-throughput technologies have enabled large-scale gene expression profiling. Importantly, RNA expression profiling of tumor tissue has been successfully used to determine clinically actionable molecular alterations. The WINTHER precision medicine clinical trial was the first prospective trial in diverse solid malignancies that assessed both genomics and transcriptomics to match treatments to specific molecular alterations. The use of transcriptome analysis in WINTHER and other trials increased the number of targetable -omic changes compared to genomic profiling alone. Other applications of transcriptomics involve the evaluation of tumor and circulating noncoding RNAs as predictive and prognostic biomarkers, the improvement of risk stratification by the use of prognostic and predictive multigene assays, the identification of fusion transcripts that drive tumors, and an improved understanding of the impact of DNA changes as some genomic alterations are silenced at the RNA level. Finally, RNA sequencing and gene expression analysis have been incorporated into clinical trials to identify markers predicting response to immunotherapy. Many issues regarding the complexity of the analysis, its reproducibility and variability, and the interpretation of the results still need to be addressed. The integration of transcriptomics with genomics, proteomics, epigenetics, and tumor immune profiling will improve biomarker discovery and our understanding of disease mechanisms and, thereby, accelerate the implementation of precision oncology.
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Affiliation(s)
- Apostolia M Tsimberidou
- The University of Texas MD Anderson Cancer Center, Department of Investigational Cancer Therapeutics, Houston, TX, USA.
| | - Elena Fountzilas
- Department of Medical Oncology, Euromedica General Clinic, Thessaloniki, Greece
| | - Leonidas Bleris
- Bioengineering Department, The University of Texas at Dallas, Richardson, TX, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UC San Diego Moores Cancer Center, San Diego, CA, USA
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21
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Shinto E, Yoshida Y, Kajiwara Y, Okamoto K, Mochizuki S, Yamadera M, Shiraishi T, Nagata K, Tsuda H, Hase K, Kishi Y, Ueno H. Clinical Significance of a Gene Signature Generated from Tumor Budding Grade in Colon Cancer. Ann Surg Oncol 2020; 27:4044-4054. [PMID: 32328985 DOI: 10.1245/s10434-020-08498-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Tumor budding, a microscopic finding of dedifferentiation at the invasive margin, has been reported as a definite prognostic marker in colon cancer (CC). Herein, we aimed to generate a molecular budding signature (MBS) based on DNA microarray data and to examine its prognostic significance. METHODS Frozen tissue samples from 85 patients with stage II/III CC were used for DNA microarray analyses. First, we selected candidate genes that were differentially expressed (twofold change) between the invasive frontal regions and corresponding tumor centers of three extremely high-grade budding tumors. Subsequently, using microarray data from whole-tissue sections of the 85 patients, we selected MBS-constituent genes from the candidates based on correlation to the pathological budding grade. The MBS score was calculated using the sum of the logarithm of the expression of each gene. RESULTS We selected seven MBS-constituent genes: MSLN, SLC4A11, WNT11, SCEL, RUNX2, MGAT3, FOXC1. A comparison of relapse-free survival (RFS) rates revealed a significant impact of the MBS score [5-year RFS, 77.4% (score-high) vs. 95.1% (score-low); P = 0.044]. Analyses of public databases revealed that low MBS score patients exhibited better prognosis than those with high-score cancers (GSE14333: 5-year RFS, 83.1% vs. 66.6%, P = 0.028; GSE39582: 5-year disease-free survival, 72.2% vs. 58.1%, P = 0.0005). Multivariate analysis revealed that the MBS score is an independent prognostic indicator in GSE39582 (hazard ratio, 1.611; P = 0.013). CONCLUSIONS We developed a new gene classification method, i.e., MBS, and demonstrated its clinical relevance as an indicator of high recurrence risk of CC.
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Affiliation(s)
- Eiji Shinto
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan.
| | | | - Yoshiki Kajiwara
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Koichi Okamoto
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Satsuki Mochizuki
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Masato Yamadera
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Takehiro Shiraishi
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Ken Nagata
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hitoshi Tsuda
- Department of Pathology, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Kazuo Hase
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yoji Kishi
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hideki Ueno
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
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22
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Ji MY, Yuan L, Lu SM, Gao MT, Zeng Z, Zhan N, Ding YJ, Liu ZR, Huang PX, Lu C, Dong WG. Glandular orientation and shape determined by computational pathology could identify aggressive tumor for early colon carcinoma: a triple-center study. J Transl Med 2020; 18:129. [PMID: 32178690 PMCID: PMC7077008 DOI: 10.1186/s12967-020-02297-w] [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: 11/19/2019] [Accepted: 03/11/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Identifying the early-stage colon adenocarcinoma (ECA) patients who have lower risk cancer vs. the higher risk cancer could improve disease prognosis. Our study aimed to explore whether the glandular morphological features determined by computational pathology could identify high risk cancer in ECA via H&E images digitally. METHODS 532 ECA patients retrospectively from 2 independent data centers, as well as 113 from The Cancer Genome Atlas (TCGA), were enrolled in this study. Four tissue microarrays (TMAs) were constructed across ECA hematoxylin and eosin (H&E) stained slides. 797 quantitative glandular morphometric features were extracted and 5 most prognostic features were identified using minimum redundancy maximum relevance to construct an image classifier. The image classifier was evaluated on D2/D3 = 223, D4 = 46, D5 = 113. The expression of Ki67 and serum CEA levels were scored on D3, aiming to explore the correlations between image classifier and immunohistochemistry data and serum CEA levels. The roles of clinicopathological data and ECAHBC were evaluated by univariate and multivariate analyses for prognostic value. RESULTS The image classifier could predict ECA recurrence (accuracy of 88.1%). ECA histomorphometric-based image classifier (ECAHBC) was an independent prognostic factor for poorer disease-specific survival [DSS, (HR = 9.65, 95% CI 2.15-43.12, P = 0.003)]. Significant correlations were observed between ECAHBC-positive patients and positivity of Ki67 labeling index (Ki67Li) and serum CEA. CONCLUSION Glandular orientation and shape could predict the high risk cancer in ECA and contribute to precision oncology. Computational pathology is emerging as a viable and objective means of identifying predictive biomarkers for cancer patients.
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Affiliation(s)
- Meng-Yao Ji
- Department of Gastroenterology, Wuhan University Renmin Hospital, Wuhan, Hubei, China.,Key Laboratory of Hubei Province for Digestive System Disease, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Lei Yuan
- Department of Information Center, Wuhan University Renmin Hospital, Wuhan, Hubei, China. .,Key Laboratory of Hubei Province for Digestive System Disease, Wuhan University Renmin Hospital, Wuhan, Hubei, China.
| | - Shi-Min Lu
- Department of Gastroenterology, Wuhan University Renmin Hospital, Wuhan, Hubei, China.,Key Laboratory of Hubei Province for Digestive System Disease, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Meng-Ting Gao
- Department of Information Center, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Zhi Zeng
- Department of Pathology, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Na Zhan
- Department of Pathology, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Yi-Juan Ding
- Department of Gastroenterology, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Zheng-Ru Liu
- Department of Gastroenterology, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Ping-Xiao Huang
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Lu
- College of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, China.
| | - Wei-Guo Dong
- Department of Gastroenterology, Wuhan University Renmin Hospital, Wuhan, Hubei, China.
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23
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Prognostic and Predictive Molecular Biomarkers for Colorectal Cancer: Updates and Challenges. Cancers (Basel) 2020; 12:cancers12020319. [PMID: 32019056 PMCID: PMC7072488 DOI: 10.3390/cancers12020319] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is a leading cause of death among cancer patients. This heterogeneous disease is characterized by alterations in multiple molecular pathways throughout its development. Mutations in RAS, along with the mismatch repair gene deficiency, are currently routinely tested in clinics. Such biomarkers provide information for patient risk stratification and for the choice of the best treatment options. Nevertheless, reliable and powerful prognostic markers that can identify “high-risk” CRC patients, who might benefit from adjuvant chemotherapy, in early stages, are currently missing. To bridge this gap, genomic information has increasingly gained interest as a potential method for determining the risk of recurrence. However, due to several limitations of gene-based signatures, these have not yet been clinically implemented. In this review, we describe the different molecular markers in clinical use for CRC, highlight new markers that might become indispensable over the next years, discuss recently developed gene expression-based tests and highlight the challenges in biomarker research.
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24
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Wang J, Chen X, Tian Y, Zhu G, Qin Y, Chen X, Pi L, Wei M, Liu G, Li Z, Chen C, Lv Y, Cai G. Six-gene signature for predicting survival in patients with head and neck squamous cell carcinoma. Aging (Albany NY) 2020; 12:767-783. [PMID: 31927533 PMCID: PMC6977678 DOI: 10.18632/aging.102655] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/24/2019] [Indexed: 12/21/2022]
Abstract
The prognosis of head and neck squamous cell carcinoma (HNSCC) patients remains poor. High-throughput sequencing data have laid a solid foundation for identifying genes related to cancer prognosis, but a gene marker is needed to predict clinical outcomes in HNSCC. In our study, we downloaded RNA Seq, single nucleotide polymorphism, copy number variation, and clinical follow-up data from TCGA. The samples were randomly divided into training and test. In the training set, we screened genes and used random forests for feature selection. Gene-related prognostic models were established and validated in a test set and GEO verification set. Six genes (PEX11A, NLRP2, SERPINE1, UPK, CTTN, D2HGDH) were ultimately obtained through random forest feature selection. Cox regression analysis confirmed the 6-gene signature is an independent prognostic factor in HNSCC patients. This signature effectively stratified samples in the training, test, and external verification sets (P < 0.01). The 5-year survival AUC in the training and verification sets was greater than 0.74. Thus, we have constructed a 6-gene signature as a new prognostic marker for predicting survival of HNSCC patients.
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Affiliation(s)
- Juncheng Wang
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Xun Chen
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou 362000, People's Republic of China
| | - Yuxi Tian
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008 People's Republic of China
| | - Gangcai Zhu
- Department of Otolaryngology, Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Yuexiang Qin
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Xuan Chen
- Department of Stomatology, Changzheng Hospital, Second Military Medcial University, Shanghai 200003, People's Republic of China
| | - Leiming Pi
- Department of Otolaryngology, Head and Neck Surgery, HeYuan People's Hospital, Jinan University, He Yuan,517000, People's Republic of China
| | - Ming Wei
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Guancheng Liu
- Department of Otolaryngology, Head and Neck Surgery, Affiliated Hospital of Guilin University, Guilin 541000, People's Republic of China
| | - Zhexuan Li
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Changhan Chen
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Yunxia Lv
- Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, People's Republic of China
| | - Gengming Cai
- Department of Otolaryngology, Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou 362000, People's Republic of China
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25
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Gawel DR, Lee EJ, Li X, Lilja S, Matussek A, Schäfer S, Olsen RS, Stenmarker M, Zhang H, Benson M. An algorithm-based meta-analysis of genome- and proteome-wide data identifies a combination of potential plasma biomarkers for colorectal cancer. Sci Rep 2019; 9:15575. [PMID: 31666584 PMCID: PMC6821706 DOI: 10.1038/s41598-019-51999-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/10/2019] [Indexed: 12/16/2022] Open
Abstract
Screening programs for colorectal cancer (CRC) often rely on detection of blood in stools, which is unspecific and leads to a large number of colonoscopies of healthy subjects. Painstaking research has led to the identification of a large number of different types of biomarkers, few of which are in general clinical use. Here, we searched for highly accurate combinations of biomarkers by meta-analyses of genome- and proteome-wide data from CRC tumors. We focused on secreted proteins identified by the Human Protein Atlas and used our recently described algorithms to find optimal combinations of proteins. We identified nine proteins, three of which had been previously identified as potential biomarkers for CRC, namely CEACAM5, LCN2 and TRIM28. The remaining proteins were PLOD1, MAD1L1, P4HA1, GNS, C12orf10 and P3H1. We analyzed these proteins in plasma from 80 patients with newly diagnosed CRC and 80 healthy controls. A combination of four of these proteins, TRIM28, PLOD1, CEACAM5 and P4HA1, separated a training set consisting of 90% patients and 90% of the controls with high accuracy, which was verified in a test set consisting of the remaining 10%. Further studies are warranted to test our algorithms and proteins for early CRC diagnosis.
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Affiliation(s)
- Danuta R Gawel
- Centre for Personalized Medicine, Linköping University, Linköping, Sweden.
| | - Eun Jung Lee
- Centre for Personalized Medicine, Linköping University, Linköping, Sweden.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Xinxiu Li
- Centre for Personalized Medicine, Linköping University, Linköping, Sweden
| | - Sandra Lilja
- Centre for Personalized Medicine, Linköping University, Linköping, Sweden
| | - Andreas Matussek
- Laboratory Medicine, Division of Psychiatrics & Rehabilitation & Diagnostics, Region Jönköping County, Jönköping, Sweden.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| | - Samuel Schäfer
- Centre for Personalized Medicine, Linköping University, Linköping, Sweden
| | - Renate Slind Olsen
- Pathology Laboratory, Division of Psychiatrics & Rehabilitation & Diagnostics, Region Jönköping County, Jönköping, Sweden.,Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Margaretha Stenmarker
- Department of Paediatrics, Jönköping, Region Jönköping County, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Huan Zhang
- Centre for Personalized Medicine, Linköping University, Linköping, Sweden.
| | - Mikael Benson
- Centre for Personalized Medicine, Linköping University, Linköping, Sweden
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26
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Qiao GJ, Chen L, Wu JC, Li ZR. Identification of an eight-gene signature for survival prediction for patients with hepatocellular carcinoma based on integrated bioinformatics analysis. PeerJ 2019; 7:e6548. [PMID: 30918751 PMCID: PMC6431139 DOI: 10.7717/peerj.6548] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/25/2019] [Indexed: 11/25/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) remains one of the leading causes of cancer-related death worldwide. Despite recent advances in imaging techniques and therapeutic intervention for HCC, the low overall 5-year survival rate of HCC patients remains unsatisfactory. This study aims to find a gene signature to predict clinical outcomes in HCC. Methods Bioinformatics analysis including Cox’s regression analysis, Kaplan-Meier (KM) and receiver operating characteristic curve (ROC) analysis and the random survival forest algorithm were performed to mine the expression profiles of 553 hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public database. Results We selected a signature comprising eight protein-coding genes (DCAF13, FAM163A, GPR18, LRP10, PVRIG, S100A9, SGCB, and TNNI3K) in the training dataset (AUC = 0.77 at five years, n = 332). The signature stratified patients into high- and low-risk groups with significantly different survival in the training dataset (median 2.20 vs. 8.93 years, log-rank test P < 0.001) and in the test dataset (median 2.68 vs. 4.24 years, log-rank test P = 0.004, n = 221, GSE14520). Further multivariate Cox regression analysis showed that the signature was an independent prognostic factor for patients with HCC. Compared with TNM stage and another reported three-gene model, the signature displayed improved survival prediction power in entire dataset (AUC signature = 0.66 vs. AUC TNM = 0.64 vs. AUC gene model = 0.60, n = 553). Stratification analysis shows that it can be used as an auxiliary marker for many traditional staging models. Conclusions We constructed an eight-gene signature that can be a novel prognostic marker to predict the survival of HCC patients.
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Affiliation(s)
- Guo-Jie Qiao
- Institute of Tropical Agriculture and Forestry, Hainan University, Hainkou, China.,Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, Hainan Medical College, Hainkou, China
| | - Liang Chen
- Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, Hainan Medical College, Hainkou, China
| | - Jin-Cai Wu
- Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, Hainan Medical College, Hainkou, China
| | - Zhou-Ri Li
- Institute of Tropical Agriculture and Forestry, Hainan University, Hainkou, China.,Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, Hainan Medical College, Hainkou, China
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27
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Allen WL, Dunne PD, McDade S, Scanlon E, Loughrey M, Coleman H, McCann C, McLaughlin K, Nemeth Z, Syed N, Jithesh P, Arthur K, Wilson R, Coyle V, McArt D, Murray GI, Samuel L, Nuciforo P, Jimenez J, Argiles G, Dienstmann R, Tabernero J, Messerini L, Nobili S, Mini E, Sheahan K, Ryan E, Johnston PG, Van Schaeybroeck S, Lawler M, Longley DB. Transcriptional subtyping and CD8 immunohistochemistry identifies poor prognosis stage II/III colorectal cancer patients who benefit from adjuvant chemotherapy. JCO Precis Oncol 2018; 2018. [PMID: 30088816 PMCID: PMC6040635 DOI: 10.1200/po.17.00241] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Purpose Transcriptomic profiling of colorectal cancer (CRC) has led to the identification of four consensus molecular subtypes (CMS1 to 4) that have prognostic value in stage II and III disease. More recently, the Colorectal Cancer Intrinsic Subtypes (CRIS) classification system has helped to define the biology specific to the epithelial component of colorectal tumors; however, the clinical value of these classification systems in the prediction of response to standard-of-care adjuvant chemotherapy remains unknown. Patients and Methods Using samples from four European sites, we assembled a novel cohort of patients with stage II and III CRC (n = 156 samples) and performed transcriptomic profiling and targeted sequencing and generated a tissue microarray to enable integrated multiomics analyses. We also accessed data from two published cohorts of patients with stage II and III CRC: GSE39582 and GSE14333 (n = 479 and n = 185 samples, respectively). Results The epithelial-rich CMS2 subtype of CRC benefitted significantly from treatment with adjuvant chemotherapy in both stage II and III disease (P = .02 and P < .001, respectively), whereas the CMS3 subtype significantly benefitted in stage III only (P = .001). After CRIS substratification of CMS2, we observed that only the CRIS-C subtype significantly benefitted from treatment with adjuvant chemotherapy in stage II and III disease (P = .0081 and P < .001, respectively), whereas the CRIS-D subtype significantly benefitted in stage III only (P = .0034). We also observed that CRIS-C patients with low levels of CD8+ tumor-infiltrating lymphocytes were most at risk for relapse in both stage II and III disease (log-rank P = .0031; hazard ratio, 12.18 [95% CI, 1.51 to 98.58]). Conclusion Patient stratification using a combination of transcriptional subtyping and CD8 immunohistochemistry analyses is capable of identifying patients with poor prognostic stage II and III disease who benefit from adjuvant standard-of-care chemotherapy. These findings are particularly relevant for patients with stage II disease, where the overall benefit of adjuvant chemotherapy is marginal.
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Affiliation(s)
- W L Allen
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - P D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - S McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - E Scanlon
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - M Loughrey
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - H Coleman
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - C McCann
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - K McLaughlin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Z Nemeth
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - N Syed
- Sidra Medical and Research Center, Qatar
| | - P Jithesh
- Sidra Medical and Research Center, Qatar
| | - K Arthur
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - R Wilson
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - V Coyle
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - D McArt
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | | | | | - P Nuciforo
- University Hospital Vall d'Hebron, Barcelona, Spain
| | - J Jimenez
- University Hospital Vall d'Hebron, Barcelona, Spain
| | - G Argiles
- University Hospital Vall d'Hebron, Barcelona, Spain
| | - R Dienstmann
- University Hospital Vall d'Hebron, Barcelona, Spain
| | - J Tabernero
- University Hospital Vall d'Hebron, Barcelona, Spain
| | | | | | - E Mini
- University of Florence, Italy
| | - K Sheahan
- School of Medicine and Medical Science, University College Dublin
| | - E Ryan
- School of Medicine and Medical Science, University College Dublin
| | - P G Johnston
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - S Van Schaeybroeck
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - M Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - D B Longley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
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28
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Sperlich A, Balmert A, Doll D, Bauer S, Franke F, Keller G, Wilhelm D, Mur A, Respondek M, Friess H, Nitsche U, Janssen KP. Genetic and immunological biomarkers predict metastatic disease recurrence in stage III colon cancer. BMC Cancer 2018; 18:998. [PMID: 30340556 PMCID: PMC6194664 DOI: 10.1186/s12885-018-4940-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023] Open
Abstract
Background Even though the post-operative outcome varies greatly among patients with nodal positive colon cancer (UICC stage III), personalized prediction of systemic disease recurrence is currently insufficient. We investigated in a retrospective setting whether genetic and immunological biomarkers can be applied for stratification of distant metastasis occurrence risk. Methods Eighty four patients with complete resection (R0) of stage III colon cancer from two clinical centres were analysed for genetic biomarkers: microsatellite instability, oncogenic mutations in KRAS exon2 and BRAF exon15, expression of osteopontin and the metastasis-associated genes SASH1 and MACC1. Tumor-infiltrating CD3 and CD8 positive T-cells were quantified by immunocytochemistry. Results were correlated with outcome and response to 5-FU based adjuvant chemotherapy, using Cox’s proportional hazard models and integrative two-step cluster analysis. Results Distant metastasis risk was significantly correlated with oncogenic KRAS mutations (p = 0.015), expression of SASH1 (p = 0.016), and the density of CD8-positive T-cells (p = 0.007) in Kaplan-Meier analysis. Upon multivariate Cox-regression analysis, KRAS mutation (p = 0.008) and density of CD8-positive TILs (p = 0.009) were retained as prognostic parameters for metachronous distant metastasis. Integrative two-step cluster analysis was used to combine all genetic markers, allowing stratification of patient subgroups. Post-operative distant metastasis risk ranged from 31% (low-risk) to 41% (intermediate), and 57% (high-risk) (p = 0.032). Increased expression of osteopontin (p = 0.019) and low density of CD8-positive T-cells (p = 0.043) were significantly associated with unfavourable response to 5-FU. Conclusions Integrative biomarker analysis allows stratification of stage III colon cancer patients for the risk of metastatic disease recurrence and may indicate response to 5-FU. Thus, biomarker analysis might facilitate the use of adjuvant therapy for high risk patients. Electronic supplementary material The online version of this article (10.1186/s12885-018-4940-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Sperlich
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Alexander Balmert
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Dietrich Doll
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany.,Darmzentrum Vechta, St. Marienhospital, Marienstraße 6-8, 49377, Vechta, Germany
| | - Sabine Bauer
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Fabian Franke
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Gisela Keller
- Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675, Munich, Germany
| | - Dirk Wilhelm
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Anna Mur
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Michael Respondek
- St. Marienhospital, Praxis für Pathologie Vechta, Marienstr. 11, 49377, Vechta, Germany
| | - Helmut Friess
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Ulrich Nitsche
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany.
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Eskandari E, Mahjoubi F, Motalebzadeh J. An integrated study on TFs and miRNAs in colorectal cancer metastasis and evaluation of three co-regulated candidate genes as prognostic markers. Gene 2018; 679:150-159. [PMID: 30193961 DOI: 10.1016/j.gene.2018.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/06/2018] [Accepted: 09/03/2018] [Indexed: 01/20/2023]
Abstract
Molecular alterations that occur in cancer have the potential to be considered as either cancer biomarkers or targeted therapies or even both. In the presented study, we aimed to elucidate the gene regulatory network of metastatic colorectal cancer using data acquired from microarrays to reach the most common DEGs in colorectal cancer metastasis and find their possible regulatory mechanism by DETFs and DEmiRs. In this regards, seven microarray datasets were employed to assess the most important DEGs, DETFs and DEmiRs in colorectal cancer metastasis. Afterward, GRN based on DETFs and DEmiRs were constructed. Also ARACNE algorithm was used to construct an accurate GRN. GRN was analyzed structurally and then, two DETFs (LEF1 and ETV4) and a less-well known DEG (FABP6) by real time qRT-PCR in 50 patients with colorectal cancer were quantified. The constructed GRN highlighted the importance of some DETFs and DEmiRs in colorectal cancer metastasis. Interestingly the gene expression analysis by qRT-PCR on three candidate genes (LEF1, ETV4 and FABP6) indicated that the three genes were co-expressed in tumor samples, and were significantly associated with metastasis in colorectal cancer. Therefore, our experimental results proved a part of our comprehensive data analysis and system biology results. In summary, according to our empirical study we found the importance of three candidate genes as the potent prognostic factors in colorectal cancer metastasis. Also our study in a holistic insight on gene regulatory mechanism revealed the importance of some gene regulatory factors (DETFs and DEmiRs) and their potential as prognostic factors and/or targets in molecular targeted therapies in colorectal cancer.
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Affiliation(s)
- Elaheh Eskandari
- Department of Clinical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Frouzandeh Mahjoubi
- Department of Clinical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Jamshid Motalebzadeh
- Department of Clinical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Peyravian N, Larki P, Gharib E, Nazemalhosseini-Mojarad E, Anaraki F, Young C, McClellan J, Ashrafian Bonab M, Asadzadeh-Aghdaei H, Zali MR. The Application of Gene Expression Profiling in Predictions of Occult Lymph Node Metastasis in Colorectal Cancer Patients. Biomedicines 2018; 6:E27. [PMID: 29498671 PMCID: PMC5874684 DOI: 10.3390/biomedicines6010027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/24/2018] [Accepted: 03/01/2018] [Indexed: 01/06/2023] Open
Abstract
A key factor in determining the likely outcome for a patient with colorectal cancer is whether or not the tumour has metastasised to the lymph nodes-information which is also important in assessing any possibilities of lymph node resection so as to improve survival. In this review we perform a wide-range assessment of literature relating to recent developments in gene expression profiling (GEP) of the primary tumour, to determine their utility in assessing node status. A set of characteristic genes seems to be involved in the prediction of lymph node metastasis (LNM) in colorectal patients. Hence, GEP is applicable in personalised/individualised/tailored therapies and provides insights into developing novel therapeutic targets. Not only is GEP useful in prediction of LNM, but it also allows classification based on differences such as sample size, target gene expression, and examination method.
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Affiliation(s)
- Noshad Peyravian
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Live Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran.
| | - Pegah Larki
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Live Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran.
| | - Ehsan Gharib
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Live Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran.
| | - Fakhrosadate Anaraki
- Colorectal Division of Department of Surgery, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113b, Iran.
| | - Chris Young
- School of Allied Health Sciences, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK.
| | - James McClellan
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2UP, UK.
| | | | - Hamid Asadzadeh-Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Live Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran.
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran.
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Colorectal Cancer Surveillance: What Is the Optimal Frequency of Follow-up and Which Tools Best Predict Recurrence? CURRENT COLORECTAL CANCER REPORTS 2017. [DOI: 10.1007/s11888-017-0382-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Meunier K, Ferron M, Calmel C, Fléjou JF, Pocard M, Praz F. Impact of MLH1 expression on tumor evolution after curative surgical tumor resection in a murine orthotopic xenograft model for human MSI colon cancer. Genes Chromosomes Cancer 2017; 56:681-690. [PMID: 28512763 DOI: 10.1002/gcc.22472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 04/27/2017] [Accepted: 04/27/2017] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancers (CRCs) displaying microsatellite instability (MSI) most often result from MLH1 deficiency. The aim of this study was to assess the impact of MLH1 expression per se on tumor evolution after curative surgical resection using a xenograft tumor model. Transplantable tumors established with the human MLH1-deficient HCT116 cell line and its MLH1-complemented isogenic clone, mlh1-3, were implanted onto the caecum of NOD/SCID mice. Curative surgical resection was performed at day 10 in half of the animals. The HCT116-derived tumors were more voluminous compared to the mlh1-3 ones (P = .001). Lymph node metastases and peritoneal carcinomatosis occurred significantly more often in the group of mice grafted with HCT116 (P = .007 and P = .035, respectively). Mlh1-3-grafted mice did not develop peritoneal carcinomatosis or liver metastasis. After surgical resection, lymph node metastases only arose in the group of mice implanted with HCT116 and the rate of cure was significantly lower than in the mlh1-3 group (P = .047). The murine orthotopic xenograft model based on isogenic human CRC cell lines allowed us to reveal the impact of MLH1 expression on tumor evolution in mice who underwent curative surgical resection and in mice whose tumor was left in situ. Our data indicate that the behavior of MLH1-deficient CRC is not only governed by mutations arising in genes harboring microsatellite repeated sequences but also from their defect in MLH1 as such.
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Affiliation(s)
- Katy Meunier
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Marianne Ferron
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Claire Calmel
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Jean-François Fléjou
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Service d'Anatomie Pathologique, Paris, France
| | - Marc Pocard
- Digestive and Oncology Surgery Department, Assistance Publique - Hôpitaux de Paris, Hôpital Lariboisière, Paris, France.,Paris Diderot University, USPC, Sorbonne Paris Cité, Paris, France.,INSERM UMR 965, Angiogenesis and Translational Research Department, Hôpital Lariboisière, Paris, France
| | - Françoise Praz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
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33
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Trifiletti DM, Sturz VN, Showalter TN, Lobo JM. Towards decision-making using individualized risk estimates for personalized medicine: A systematic review of genomic classifiers of solid tumors. PLoS One 2017; 12:e0176388. [PMID: 28486497 PMCID: PMC5423583 DOI: 10.1371/journal.pone.0176388] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/10/2017] [Indexed: 12/16/2022] Open
Abstract
Recent advances in the understanding of the genetic underpinnings of cancer offer the promise to customize cancer treatments to the individual through the use of genomic classifiers (GCs). At present, routine clinical utilization of GCs is uncommon and their current scope and status, in a broad sense, are unknown. As part of a registered review (PROSPERO 2014:CRD42014013371), we systematically reviewed the literature evaluating the utility of commercially available GCs by searching Ovid Medline (PubMed), EMBASE, the Cochrane Database of Systematic Reviews, and CINAHL on September 2, 2014. We excluded articles involving pediatric malignancies, non-solid or non-invasive cancers, hereditary risk of cancer, non-validated GCs, and GCs involving fewer than 3 biomarkers. A total of 3,625 studies were screened, but only 37 met the pre-specified inclusion criteria. Of these, 15 studies evaluated outcomes and clinical utility of GCs through clinical trials, and the remainder through the use of mathematical models. Most studies (29 of 37) were specific to hormone-receptor positive breast cancer, whereas only 4 studies evaluated GCs in non-breast cancer (prostate, colon, and lung cancers). GCs have spurred excitement across disciplines in recent decades. While there are several GCs that have been validated, the general quality of the data are weak. Further research, including prospective validation is needed, particularly in the non-breast cancer GCs.
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Affiliation(s)
- Daniel M. Trifiletti
- Department of Radiation Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Vanessa N. Sturz
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Timothy N. Showalter
- Department of Radiation Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Jennifer M. Lobo
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, United States of America
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Cienfuegos JA, Martínez P, Baixauli J, Beorlegui C, Rosenstone S, Sola JJ, Rodríguez J, Hernández-Lizoáin JL. Perineural Invasion is a Major Prognostic and Predictive Factor of Response to Adjuvant Chemotherapy in Stage I–II Colon Cancer. Ann Surg Oncol 2017; 24:1077-1084. [DOI: 10.1245/s10434-016-5561-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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35
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Miles A, Chronakis I, Fox J, Mayer A. Use of a computerised decision aid (DA) to inform the decision process on adjuvant chemotherapy in patients with stage II colorectal cancer: development and preliminary evaluation. BMJ Open 2017; 7:e012935. [PMID: 28341685 PMCID: PMC5372112 DOI: 10.1136/bmjopen-2016-012935] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVES To develop a computerised decision aid (DA) to inform the decision process on adjuvant chemotherapy in patients with stage II colorectal cancer, and examine perceived usefulness, acceptability and areas for improvement of the DA. DESIGN Mixed methods. SETTING Single outpatient oncology department in central London. PARTICIPANTS Consecutive recruitment of 13 patients with stage II colorectal cancer, 12 of whom completed the study. Inclusion criteria were: age >18 years; complete resection for stage II adenocarcinoma of the colon or rectum; patients within 14-56 days after surgery; no contraindication to adjuvant chemotherapy; able to give written informed consent. Exclusion criterion: previous chemotherapy. PRIMARY OUTCOMES Patient perceived usefulness (assessed by the PrepDM questionnaire) and acceptability of the DA. RESULTS PrepDM scores, measuring the perceived usefulness of the DA in preparing the patient to communicate with their doctor and make a health decision, were above those reported in other patient groups. Patient acceptability scores were also high; however, interviews showed that there was evidence of a lack of understanding of key information among some patients, in particular their baseline risk of recurrence, the net benefit of combination chemotherapy and the rationale for having chemotherapy when cancer had apparently gone. CONCLUSIONS Patients found the DA acceptable and useful in supporting their decision about whether or not to have adjuvant chemotherapy. Suggested improvements for the DA include: sequential presentation of treatment options (eg, no treatment vs 1 drug, 1 drug vs 2 drugs) to enhance patient understanding of the difference between combination and single therapy, diagrams to help patients understand the rationale for chemotherapy to prevent a recurrence and inbuilt checks on patient understanding of baseline risk of recurrence and net benefit of chemotherapy.
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Affiliation(s)
- A Miles
- Birkbeck, University of London, London, UK
| | | | - J Fox
- University College London, London, UK
- Oxford University, Oxford, UK
| | - A Mayer
- Royal Free London NHS Trust, London, UK
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36
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Ubink I, Elias SG, Moelans CB, Laclé MM, van Grevenstein WMU, van Diest PJ, Borel Rinkes IHM, Kranenburg O. A Novel Diagnostic Tool for Selecting Patients With Mesenchymal-Type Colon Cancer Reveals Intratumor Subtype Heterogeneity. J Natl Cancer Inst 2017; 109:3064533. [DOI: 10.1093/jnci/djw303] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
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37
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Colorectal Carcinoma: A General Overview and Future Perspectives in Colorectal Cancer. Int J Mol Sci 2017; 18:ijms18010197. [PMID: 28106826 PMCID: PMC5297828 DOI: 10.3390/ijms18010197] [Citation(s) in RCA: 767] [Impact Index Per Article: 109.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/06/2017] [Accepted: 01/11/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the fourth most common cause of cancer-related death. Most cases of CRC are detected in Western countries, with its incidence increasing year by year. The probability of suffering from colorectal cancer is about 4%–5% and the risk for developing CRC is associated with personal features or habits such as age, chronic disease history and lifestyle. In this context, the gut microbiota has a relevant role, and dysbiosis situations can induce colonic carcinogenesis through a chronic inflammation mechanism. Some of the bacteria responsible for this multiphase process include Fusobacterium spp, Bacteroides fragilis and enteropathogenic Escherichia coli. CRC is caused by mutations that target oncogenes, tumour suppressor genes and genes related to DNA repair mechanisms. Depending on the origin of the mutation, colorectal carcinomas can be classified as sporadic (70%); inherited (5%) and familial (25%). The pathogenic mechanisms leading to this situation can be included in three types, namely chromosomal instability (CIN), microsatellite instability (MSI) and CpG island methylator phenotype (CIMP). Within these types of CRC, common mutations, chromosomal changes and translocations have been reported to affect important pathways (WNT, MAPK/PI3K, TGF-β, TP53), and mutations; in particular, genes such as c-MYC, KRAS, BRAF, PIK3CA, PTEN, SMAD2 and SMAD4 can be used as predictive markers for patient outcome. In addition to gene mutations, alterations in ncRNAs, such as lncRNA or miRNA, can also contribute to different steps of the carcinogenesis process and have a predictive value when used as biomarkers. In consequence, different panels of genes and mRNA are being developed to improve prognosis and treatment selection. The choice of first-line treatment in CRC follows a multimodal approach based on tumour-related characteristics and usually comprises surgical resection followed by chemotherapy combined with monoclonal antibodies or proteins against vascular endothelial growth factor (VEGF) and epidermal growth receptor (EGFR). Besides traditional chemotherapy, alternative therapies (such as agarose tumour macrobeads, anti-inflammatory drugs, probiotics, and gold-based drugs) are currently being studied to increase treatment effectiveness and reduce side effects.
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Punt CJA, Koopman M, Vermeulen L. From tumour heterogeneity to advances in precision treatment of colorectal cancer. Nat Rev Clin Oncol 2016; 14:235-246. [PMID: 27922044 DOI: 10.1038/nrclinonc.2016.171] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In recent years, the high heterogeneity of colorectal cancer (CRC) has become evident. Hence, biomarkers need to be developed that enable the stratification of patients with CRC into different prognostic subgroups and in relation to response to therapies, according to the distinctive tumour biology. Currently, only RAS-mutation status is used routinely as a negative predictive marker to avoid treatment with anti-EGFR agents in patients with metastatic CRC, and mismatch-repair status can guide the use of adjuvant chemotherapy in patients with early stage colon cancer. Advances in molecular biology over the past decade have enabled a better understanding of the development of CRC, as well as the more-precise use of innovative targeted therapies for this disease, and include three fundamental achievements. First, the availability of large databases to capture and store the genomic landscape of patients with CRC, providing information on the genes that are frequently deregulated in CRC. Second, the possibility of using gene-expression profiling to differentiate the subtypes of CRC into prognostic groups. Third, results from highly sensitive next-generation sequencing analyses have led to an appreciation of the extensive intratumoural heterogeneity of CRC. Herein, we discuss these advances and place them into the clinical context, and present the novel targets and therapeutic opportunities that are on the horizon.
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Affiliation(s)
- Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, Netherlands
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Centre Utrecht, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, Netherlands.,Centre for Experimental Molecular Medicine (CEMM), Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, Netherlands
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39
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Caritg O, Navarro A, Moreno I, Martínez-Rodenas F, Cordeiro A, Muñoz C, Ruiz-Martinez M, Santasusagna S, Castellano JJ, Monzó M. Identifying High-Risk Stage II Colon Cancer Patients: A Three-MicroRNA-Based Score as a Prognostic Biomarker. Clin Colorectal Cancer 2016; 15:e175-e182. [DOI: 10.1016/j.clcc.2016.04.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 04/01/2016] [Accepted: 04/27/2016] [Indexed: 12/19/2022]
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Hoshino N, Hasegawa S, Hida K, Kawada K, Ganeko R, Sugihara K, Sakai Y. Nomogram for predicting recurrence in stage II colorectal cancer. Acta Oncol 2016; 55:1414-1417. [PMID: 27581839 DOI: 10.1080/0284186x.2016.1223881] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND There have been no established criteria to distinguish patients at high and low risk of recurrence in stage II colorectal cancer. Several risk factors have been identified but recurrence could not be fully predicted by each factor alone. This retrospective study sought to develop a nomogram for accurate prediction of recurrence in stage II colorectal cancer. MATERIAL AND METHODS We reviewed the data for 4167 patients with stage II colorectal cancer who underwent surgery between January 1997 and December 2006. The risk factors for recurrence were identified, and a nomogram for recurrence was created using the factors. The performance of the nomogram was assessed with a bootstrapped-concordance index and calibration plots. RESULTS Sex, carcinoembryonic antigen, tumor location, tumor depth, lymphatic invasion, venous invasion and number of lymph nodes studied were significantly associated with recurrence. A nomogram for five-year freedom from recurrence was created with these factors. The bootstrapped-concordance index of the nomogram was 0.64, and it was well calibrated. CONCLUSIONS Our nomogram can be a useful tool for accurate prediction of recurrence in stage II colorectal cancer.
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Affiliation(s)
- Nobuaki Hoshino
- Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Suguru Hasegawa
- Department of Surgery, Fukuoka University Hospital, Fukuoka, Japan
| | - Koya Hida
- Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Kawada
- Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Riki Ganeko
- Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenichi Sugihara
- Department of Surgical Oncology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiharu Sakai
- Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
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41
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den Uil SH, Coupé VMH, Linnekamp JF, van den Broek E, Goos JACM, Delis-van Diemen PM, Belt EJT, van Grieken NCT, Scott PM, Vermeulen L, Medema JP, Bril H, Stockmann HBAC, Cormier RT, Meijer GA, Fijneman RJA. Loss of KCNQ1 expression in stage II and stage III colon cancer is a strong prognostic factor for disease recurrence. Br J Cancer 2016; 115:1565-1574. [PMID: 27855440 PMCID: PMC5155368 DOI: 10.1038/bjc.2016.376] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/29/2016] [Accepted: 10/17/2016] [Indexed: 01/04/2023] Open
Abstract
Background: Colorectal cancer (CRC) is the third most common cancer worldwide. Accurately identifying stage II CRC patients at risk for recurrence is an unmet clinical need. KCNQ1 was previously identified as a tumour suppressor gene and loss of expression was associated with poor survival in patients with CRC liver metastases. In this study the prognostic value of KCNQ1 in stage II and stage III colon cancer patients was examined. Methods: KCNQ1 mRNA expression was assessed in 90 stage II colon cancer patients (AMC-AJCCII-90) using microarray gene expression data. Subsequently, KCNQ1 protein expression was evaluated in an independent cohort of 386 stage II and stage III colon cancer patients by immunohistochemistry of tissue microarrays. Results: Low KCNQ1 mRNA expression in stage II microsatellite stable (MSS) colon cancers was associated with poor disease-free survival (DFS) (P=0.025). Loss of KCNQ1 protein expression from epithelial cells was strongly associated with poor DFS in stage II MSS (P<0.0001), stage III MSS (P=0.0001) and stage III microsatellite instable colon cancers (P=0.041). KCNQ1 seemed an independent prognostic value in addition to other high-risk parameters like angio-invasion, nodal stage and microsatellite instability-status. Conclusions: We conclude that KCNQ1 is a promising biomarker for prediction of disease recurrence and may aid stratification of patients with stage II MSS colon cancer for adjuvant chemotherapy.
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Affiliation(s)
- Sjoerd H den Uil
- Department of Pathology, VU University Medical Center, Amsterdam 1081HV, The Netherlands.,Department of Surgery, Spaarne Gasthuis, Haarlem 2035RC, The Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam 1081HV, The Netherlands
| | - Janneke F Linnekamp
- Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam 1100DD, The Netherlands
| | - Evert van den Broek
- Department of Pathology, VU University Medical Center, Amsterdam 1081HV, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Jeroen A C M Goos
- Department of Pathology, VU University Medical Center, Amsterdam 1081HV, The Netherlands
| | - Pien M Delis-van Diemen
- Department of Pathology, VU University Medical Center, Amsterdam 1081HV, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Eric J Th Belt
- Department of Surgery, Albert Schweitzer Hospital, Dordrecht 3300AK, The Netherlands
| | - Nicole C T van Grieken
- Department of Pathology, VU University Medical Center, Amsterdam 1081HV, The Netherlands
| | - Patricia M Scott
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota, MN 55812, USA
| | - Louis Vermeulen
- Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam 1100DD, The Netherlands
| | - Jan Paul Medema
- Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam 1100DD, The Netherlands
| | - Herman Bril
- Department of Pathology, Spaarne Gasthuis, Haarlem 2035RC, The Netherlands
| | | | - Robert T Cormier
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota, MN 55812, USA
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam 1081HV, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, VU University Medical Center, Amsterdam 1081HV, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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Han Y, Lu S, Yu F, Liu X, Sun H, Wang J, Zhu X, Lu H, Yue H, Wang J, Lin J, Zhou C, Tang H, Peng Z. A comparative analysis and guidance for individualized chemotherapy of stage II and III colorectal cancer patients based on pathological markers. Sci Rep 2016; 6:37240. [PMID: 27845412 PMCID: PMC5109035 DOI: 10.1038/srep37240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 10/27/2016] [Indexed: 12/17/2022] Open
Abstract
Adjuvant chemotherapy is considered the standard of care for patients with colorectal cancer after curative resection. Although current guidelines provide clear instructions for chemotherapy for stage II high-risk and stage III colorectal cancer, it is insufficient to individualize therapy. We analyzed the outcomes of 902 patients with colorectal cancer treated with or without chemotherapy in our hospital. We found Chinese survival benefit for chemotherapy was consistent with current guidelines. Moreover, our data added to the evidence that chemotherapy might be used for elderly patients with stage II high-risk colorectal cancer. Pathological markers could predict response to individualize therapy in a convenient, fast and inexpensive way. We compared survivals of patients with stage II high-risk and stage III colorectal cancer with chemotherapy in different pathological markers expression, and furthermore used 458 colon adenocarcinoma samples from The Cancer Genome Atlas to verify our preliminary results. We confirmed TOPIIα, EGFR and P170 may be sufficiently predictive markers to individualize chemotherapy. FOLFOX was the optimal adjuvant chemotherapy for patients with stage II high-risk and stage III colorectal cancer when TOPIIα was positive or EGFR or P170 was negative.
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Affiliation(s)
- Yang Han
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Su Lu
- Department of Pathology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Fudong Yu
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Xisheng Liu
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Huimin Sun
- Department of Pathology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Jingtao Wang
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Xingwu Zhu
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Huijun Lu
- Department of Pathology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Hao Yue
- Department of Pathology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Jing Wang
- Department of Pathology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Jun Lin
- Department of Pathology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Chongzhi Zhou
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Huamei Tang
- Department of Pathology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
| | - Zhihai Peng
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 20080, China
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Manne U, Jadhav T, Putcha BDK, Samuel T, Soni S, Shanmugam C, Suswam EA. Molecular Biomarkers of Colorectal Cancer and Cancer Disparities: Current Status and Perspective. CURRENT COLORECTAL CANCER REPORTS 2016. [PMID: 28626361 DOI: 10.1007/s11888-016-0338-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This review provides updates on the efforts for the development of prognostic and predictive markers in colorectal cancer based on the race/ethnicity of patients. Since the clinical consequences of genetic and molecular alterations differ with patient race and ethnicity, the usefulness of these molecular alterations as biomarkers needs to be evaluated in different racial/ethnic groups. To accomplish personalized patient care, a combined analysis of multiple molecular alterations in DNA, RNA, microRNAs (miRNAs), metabolites, and proteins in a single test is required to assess disease status in a precise way. Therefore, a special emphasis is placed on issues related to utility of recently identified genetic and molecular alterations in genes, miRNAs, and various "-omes" (e.g., proteomes, kinomes, metabolomes, exomes, methylomes) as candidate molecular markers to determine cancer progression (disease recurrence/relapse and metastasis) and to assess the efficacy of therapy in colorectal cancer in relation to patient race and ethnicity. This review will be useful for oncologists, pathologists, and basic and translational researchers.
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Affiliation(s)
- Upender Manne
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Comprehensive Cancer Center, Wallace Tumor Institute, University of Alabama at Birmingham, Room # 420A, 1530 3rd Avenue South, Birmingham, AL 35294, USA
| | - Trafina Jadhav
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,Wallace Tumor Institute, University of Alabama at Birmingham, Room # 430A, 1530 3rd Avenue South, Birmingham, AL 35294, USA.,Present address: Division of Cardiovascular Medicine, Vanderbilt University, 1215 21st Avenue South, Medical Center East, Suite 5050, Nashville, TN 37232-8802, USA
| | - Balananda-Dhurjati Kumar Putcha
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,Wallace Tumor Institute, University of Alabama at Birmingham, Room # 430A, 1530 3rd Avenue South, Birmingham, AL 35294, USA.,Present address: 2502 East Woodlands, Saint Joseph, MO 64506, USA
| | - Temesgen Samuel
- Department of Pathobiology, College of Veterinary Medicine, Nursing and Allied Health, Tuskegee University, Tuskegee, AL 36088, USA
| | - Shivani Soni
- Department of Biological Sciences, Alabama State University, Room # 325, Life Science Building, 1627, Hall Street, Montgomery, AL 36104, USA
| | - Chandrakumar Shanmugam
- Wallace Tumor Institute, University of Alabama at Birmingham, Room # 430A, 1530 3rd Avenue South, Birmingham, AL 35294, USA.,Present address: Department of Pathology, ESIC Medical College and Hospital, Sanathnagar, Hyderabad, Telangana 500 038, India
| | - Esther A Suswam
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Pathology, Wallace Tumor Institute, University of Alabama at Birmingham, 1720 2nd Avenue South, # 410C, Birmingham, AL 35294-3300, USA
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Lopez NE, Weiss AC, Robles J, Fanta P, Ramamoorthy SL. A systematic review of clinically available gene expression profiling assays for stage II colorectal cancer: initial steps toward genetic staging. Am J Surg 2016; 212:700-714. [PMID: 27637150 DOI: 10.1016/j.amjsurg.2016.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/27/2016] [Accepted: 06/27/2016] [Indexed: 01/09/2023]
Abstract
BACKGROUND In recent years, increasingly accessible and novel genetic technologies have spurred keen interest in the application of cancer genetics in predicting prognosis and response to treatment. In particular, investigators have eagerly sought to establish and validate genetic signatures that might improve the identification of patients with stage II colorectal cancer (CRC) who are at highest risk of recurrence. To better understand the evidence for incorporation of genetic assays into clinical practice, we have systematically reviewed those assays that have been validated and are available for clinical use in stage II CRC. METHODS A systematic review was performed using PubMed, Web of Science and Scopus databases. The GRADE system was used to evaluate level of evidence and strength of recommendations. RESULTS After duplicates were removed and exclusion criteria were applied, there were 13 articles for review. CONCLUSION Identifying high-risk patients with stage II CRC using molecular profiling has been the primary aim of many investigators, and the approach is translating into clinical utility.
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Affiliation(s)
- Nicole E Lopez
- Division of Surgical Oncology, University of North Carolina Medical Center, Chapel Hill, NC, USA
| | - Anna C Weiss
- Division of Colorectal, Department of Surgery, UC San Diego Health System, Moores Cancer Center, 3855 Health Sciences Drive #0987, La Jolla, CA 92093-0987, USA
| | - Julie Robles
- Division of Colorectal, Department of Surgery, UC San Diego Health System, Moores Cancer Center, 3855 Health Sciences Drive #0987, La Jolla, CA 92093-0987, USA
| | - Paul Fanta
- Division of Hematology and Oncology, Department of Medicine, UC San Diego Health System, Moores Cancer Center, La Jolla, CA, USA
| | - Sonia L Ramamoorthy
- Division of Colorectal, Department of Surgery, UC San Diego Health System, Moores Cancer Center, 3855 Health Sciences Drive #0987, La Jolla, CA 92093-0987, USA.
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45
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Morley-Bunker A, Walker LC, Currie MJ, Pearson J, Eglinton T. Translating colorectal cancer genetics into clinically useful biomarkers. Colorectal Dis 2016; 18:749-62. [PMID: 26990814 DOI: 10.1111/codi.13334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 01/22/2016] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) is a major health problem worldwide accounting for over a million deaths annually. While many patients with Stage II and III CRC can be cured with combinations of surgery, radiotherapy and chemotherapy, this is morbid costly treatment and a significant proportion will suffer recurrence and eventually die of CRC. Increased understanding of the molecular pathogenesis of CRC has the potential to identify high risk patients and target therapy more appropriately. Despite increased understanding of the molecular events underlying CRC development, established molecular techniques have only produced a limited number of biomarkers suitable for use in routine clinical practice to predict risk, prognosis and response to treatment. Recent rapid technological developments, however, have made genomic sequencing of CRC more economical and efficient, creating potential for the discovery of genetic biomarkers that have greater diagnostic, prognostic and therapeutic capabilities for the management of CRC. This paper reviews the current understanding of the molecular pathogenesis of CRC, and summarizes molecular biomarkers that surgeons will encounter in current clinical use as well as those under development in clinical and preclinical trials. New molecular technologies are reviewed together with their potential impact on the understanding of the molecular pathogenesis of CRC and their potential clinical utility in classification, diagnosis, prognosis and targeting of therapy.
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Affiliation(s)
- A Morley-Bunker
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - L C Walker
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - M J Currie
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - J Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - T Eglinton
- Department of Surgery, University of Otago, Christchurch, New Zealand.
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Märkl B, Märkl M, Schaller T, Mayr P, Schenkirsch G, Kriening B, Anthuber M. A new simple morphology-based risk score is prognostic in stage I/II colon cancers. Cancer Med 2016; 5:1492-501. [PMID: 27167601 PMCID: PMC4867555 DOI: 10.1002/cam4.737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/27/2022] Open
Abstract
A portion of stage I/II colon cancers (10-20%) exhibit an adverse clinical course. The administration of adjuvant chemotherapy is recommended only in certain high-risk situations. However, these risk factors recently failed to predict benefit from adjuvant therapy. We composed a new morphology-based risk score that includes pT1/2 versus 3/4 stage, vascular or lymphovascular invasion, invasion type according to Jass, tumor budding and paucity (less than two) of lymph nodes larger than 5 mm. The occurrence of each of these factors accounts for one point in the score (Range 0-5). This score was evaluated in a retrospective study that included 301 cases. The overall survival differed significantly between the three groups with median survival times of 103, 90, and 48 months, respectively. Multivariable analysis revealed morphology-based risk-high risk and low risk-as the sole independent factors for the prediction of death. Morphology-based risk scoring was superior to microsatellite status and NCCN risk stratification. This method identifies a group of patients that comprises 18% of the stage II cases with an adverse clinical course. Further studies are necessary to confirm its prognostic value and the possible therapeutic consequences.
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Affiliation(s)
- Bruno Märkl
- Institute of Pathology, Klinikum Augsburg, Augsburg, Germany
| | | | - Tina Schaller
- Institute of Pathology, Klinikum Augsburg, Augsburg, Germany
| | - Patrick Mayr
- Institute of Pathology, Klinikum Augsburg, Augsburg, Germany
| | - Gerhard Schenkirsch
- Clinical and Population-Based Cancer Registry Augsburg, Klinikum Augsburg, Augsburg, Germany
| | - Bernadette Kriening
- Department of Visceral- and Transplantation Surgery, Klinikum Augsburg, Augsburg, Germany
| | - Matthias Anthuber
- Department of Visceral- and Transplantation Surgery, Klinikum Augsburg, Augsburg, Germany
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Abstract
OBJECTIVES To evaluate the influence of IGFBP-3 methylation on recurrence in patients with stage II colorectal cancer (CRC) from 2 independent cohorts. BACKGROUND The relationship between IGFBP-3 methylation in primary tumors (PTs) or lymph nodes (LNs) and risk of recurrence in patients with stage II CRC treated with surgery alone is unknown. METHODS IGFBP-3 methylation of DNA from 115 PTs and 1641 LNs in patients with stage II CRC from 2 independent cohorts was analyzed. Forty patients developed recurrence, whereas 75 matched patients remained recurrence free for more than 2 years after surgery. Cox proportional hazard models were used to calculate hazard ratios (HRs) of recurrence, adjusted for patient and tumor characteristics. RESULTS Methylation of IGFBP-3 in PTs was identified to be significantly associated with risk of recurrence in the training set. The signature was tested in a validation set and classified 40.7% of patients as high risk. Five-year recurrence-free survival rates were 76.4% and 58.3% for low- and high-risk patients, respectively, with an HR of 2.21 (95% confidence interval, 1.04-4.68; P = 0.039). In multivariate analysis, the signature remained the most significant prognostic factor, with an HR of 2.40 (95% confidence interval, 1.10-5.25; P = 0.029). A combined analysis of 1641 LNs from the 2 sets identified IGFBP-3 methylation in LNs was not associated with risk of recurrence. CONCLUSIONS Detection of IGFBP-3 methylation in PTs, but not in LNs, provides a powerful tool for the identification of patients with stage II CRC at high risk of recurrence.
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48
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Ma H, Chen G, Guo M. Mass spectrometry based translational proteomics for biomarker discovery and application in colorectal cancer. Proteomics Clin Appl 2016; 10:503-15. [PMID: 26616366 DOI: 10.1002/prca.201500082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/17/2015] [Accepted: 11/25/2015] [Indexed: 12/29/2022]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related death in the world. Clinically, early detection of the disease is the most effective approach to tackle this tough challenge. Discovery and development of reliable and effective diagnostic tools for the assessment of prognosis and prediction of response to drug therapy are urgently needed for personalized therapies and better treatment outcomes. Among many ongoing efforts in search for potential CRC biomarkers, MS-based translational proteomics provides a unique opportunity for the discovery and application of protein biomarkers toward better CRC early detection and treatment. This review updates most recent studies that use preclinical models and clinical materials for the identification of CRC-related protein markers. Some new advances in the development of CRC protein markers such as CRC stem cell related protein markers, SRM/MRM-MS and MS cytometry approaches are also discussed in order to address future directions and challenges from bench translational research to bedside clinical application of CRC biomarkers.
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Affiliation(s)
- Hong Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China.,Haematology and Oncology Division, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
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49
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Duffy MJ. Personalized treatment for patients with colorectal cancer: role of biomarkers. Biomark Med 2016; 9:337-47. [PMID: 25808438 DOI: 10.2217/bmm.15.3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The systemic treatment of patients with colorectal cancer (CRC) has traditionally been based on clinical and tumor histological criteria. Recently however, several prognostic and predictive biomarkers have been proposed for patients with newly diagnosed CRC, including the subgroup with stage II disease. Among the best validated prognostic biomarkers for CRC are CEA levels, MS instability status and certain gene signatures. Although no biomarker currently exists for identifying patients likely to benefit from chemotherapy, the mutational status of KRAS and NRAS is used to predict response to cetuximab and panitumumab. For upfront identification of patients at high risk of suffering from severe therapy-related toxicity, specific variants of dihydropyrimidine dehydrogenase may be measured for predicting toxicity from fluoropyrimidines and uridine diphosphate glucuronosyltransferase*28 (UGT1A1*28) for predicting toxicity from irinotecan.
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50
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Becerra AZ, Probst CP, Tejani MA, Aquina CT, González MG, Hensley BJ, Noyes K, Monson JR, Fleming FJ. Evaluating the Prognostic Role of Elevated Preoperative Carcinoembryonic Antigen Levels in Colon Cancer Patients: Results from the National Cancer Database. Ann Surg Oncol 2016; 23:1554-61. [PMID: 26759308 DOI: 10.1245/s10434-015-5014-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Indexed: 12/22/2022]
Abstract
OBJECTIVES Carcinoembryonic antigen (CEA) is a reliable tumor marker for the management and surveillance of colon cancer. However, limitations in previous studies have made it difficult to elucidate whether CEA should be established as a prognostic indicator. This study examines the association between elevated preoperative CEA levels and overall survival in colon cancer patients using a national population-based registry. METHODS Stage I-III colon cancer patients were identified from the 2004-2006 National Cancer Database. A multivariable Cox proportional hazards model was used to estimate the association between elevated CEA levels and overall survival after controlling for important patient, hospital, and tumor characteristics. A Monte Carlo Markov Chain was used to impute the large degree of missing CEA data. All models controlled for the propensity score in order to account for selection bias. RESULTS A total of 137,381 patients met the inclusion criteria. Overall, 34 % of patients had an elevated CEA level and 66 % had a normal CEA level, with a median survival of 70 and 100 months, respectively. Patients with an elevated CEA level had a 62 % increase in the hazard of death (HR 1.62, 95 % CI 1.53-1.74) compared with patients with a normal CEA level. CONCLUSIONS Preoperative CEA was an independent predictor of overall survival across all stages. The results support recommendations to include CEA levels as another high-risk feature that clinicians can use to counsel patients on adjuvant chemotherapy, especially for stage II patients.
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Affiliation(s)
- Adan Z Becerra
- Department of Surgery, Surgical Health Outcomes and Research Enterprise, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
| | - Christian P Probst
- Department of Surgery, Surgical Health Outcomes and Research Enterprise, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Mohamedtaki A Tejani
- Department of Medicine, Hematology/Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Christopher T Aquina
- Department of Surgery, Surgical Health Outcomes and Research Enterprise, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Maynor G González
- Department of Surgery, Surgical Health Outcomes and Research Enterprise, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Bradley J Hensley
- Department of Surgery, Surgical Health Outcomes and Research Enterprise, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Katia Noyes
- Department of Surgery, Surgical Health Outcomes and Research Enterprise, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - John R Monson
- Department of Surgery, Surgical Health Outcomes and Research Enterprise, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Fergal J Fleming
- Department of Surgery, Surgical Health Outcomes and Research Enterprise, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
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