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Hoseini SH, Enayati P, Nazari M, Babakhanzadeh E, Rastgoo M, Sohrabi NB. Biomarker Profile of Colorectal Cancer: Current Findings and Future Perspective. J Gastrointest Cancer 2024; 55:497-510. [PMID: 38168859 DOI: 10.1007/s12029-023-00990-9] [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] [Accepted: 11/19/2023] [Indexed: 01/05/2024]
Abstract
OBJECTIVE Breakthroughs in omics technology have led to a deeper understanding of the fundamental molecular changes that play a critical role in the development and progression of cancer. This review delves into the hidden molecular drivers of colorectal cancer (CRC), offering potential for clinical translation through novel biomarkers and personalized therapies. METHODS We summarizes recent studies utilizing various omics approaches, including genomics, transcriptomics, proteomics, epigenomics, metabolomics and data integration with computational algorithms, to investigate CRC. RESULTS Integrating multi-omics data in colorectal cancer research unlocks hidden biological insights, revealing new pathways and mechanisms. This powerful approach not only identifies potential biomarkers for personalized prognosis, diagnosis, and treatment, but also predicts patient response to specific therapies, while computational tools illuminate the landscape by deciphering complex datasets. CONCLUSIONS Future research should prioritize validating promising biomarkers and seamlessly translating them into clinical practice, ultimately propelling personalized CRC management to new heights.
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Affiliation(s)
| | - Parisa Enayati
- Biological Sciences Department, Northern Illinois University, DeKalb, IL, USA
| | - Majid Nazari
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
- , P.O. Box, Tehran, 64155-65117, Iran.
| | - Emad Babakhanzadeh
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rastgoo
- Department of Microbiology, Shiraz Islamic Azad University, Shiraz, Iran
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Ra H, Jeong S, Lee H, Chung JW, Kim KO, Lee WS, Kim J, Kwon KA, Kim JH. Clinicopathological Differences between Right and Left Colorectal Cancer by Sex. J Clin Med 2024; 13:2810. [PMID: 38792352 PMCID: PMC11122515 DOI: 10.3390/jcm13102810] [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: 03/27/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Background: Until now, studies on colorectal cancer (CRC) have focused on clinicopathological characteristics based on location without considering sex differences. However, as men and women have fundamentally different physiological characteristics, research results in the clinical field are limited. We aimed to elucidate the differences in the clinicopathological characteristics between right-sided CRC (RCC) and left-sided CRC (LCC) according to sex. Methods: We classified 1492 South Korean patients with no history of colon surgery between July 2005 and June 2015 based on tumor location and sex. For these patients, differences in the clinical characteristics according to sex were compared using univariate and multivariate analyses. Results: Of the 1269 patients, 951 (74.9%) had LCC, and 318 (25.1%) had RCC, making LCC approximately three times more common than RCC. When sex was not taken into account, patients with RCC had significantly higher rates of anemia and undifferentiated cancers than the rates in those with LCC. Even considering sex, anemia and undifferentiated cancer were more prevalent in RCC than in LCC in both men and women. In contrast, age over 65 years and abnormal white blood cell count differed between RCC and LCC only in women. Conclusions: The clinicopathologic characteristics of CRC vary according to the location and sex. Therefore, sex must be considered as a fundamental characteristic of personalized treatment.
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Affiliation(s)
- Hannah Ra
- Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea; (H.R.); (H.L.); (J.-W.C.); (K.O.K.); (K.A.K.)
| | - Soyeon Jeong
- Gachon Biomedical Convergence Institute, Gachon University Gil Medical Center, College of Medicine, Incheon 21565, Republic of Korea;
- Gachon Medical Research Institute, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea
| | - Hannah Lee
- Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea; (H.R.); (H.L.); (J.-W.C.); (K.O.K.); (K.A.K.)
| | - Jun-Won Chung
- Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea; (H.R.); (H.L.); (J.-W.C.); (K.O.K.); (K.A.K.)
| | - Kyoung Oh Kim
- Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea; (H.R.); (H.L.); (J.-W.C.); (K.O.K.); (K.A.K.)
| | - Won-Suk Lee
- Department of Surgery, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea;
| | - Jisup Kim
- Department of Pathology, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea;
| | - Kwang An Kwon
- Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea; (H.R.); (H.L.); (J.-W.C.); (K.O.K.); (K.A.K.)
| | - Jung Ho Kim
- Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea; (H.R.); (H.L.); (J.-W.C.); (K.O.K.); (K.A.K.)
- Gachon Biomedical Convergence Institute, Gachon University Gil Medical Center, College of Medicine, Incheon 21565, Republic of Korea;
- Gachon Medical Research Institute, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea
- Department of Translational-Clinical Medicine, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea
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Kolisnik T, Sulit AK, Schmeier S, Frizelle F, Purcell R, Smith A, Silander O. Identifying important microbial and genomic biomarkers for differentiating right- versus left-sided colorectal cancer using random forest models. BMC Cancer 2023; 23:647. [PMID: 37434131 PMCID: PMC10337110 DOI: 10.1186/s12885-023-10848-9] [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: 10/30/2022] [Accepted: 04/13/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a heterogeneous disease, with subtypes that have different clinical behaviours and subsequent prognoses. There is a growing body of evidence suggesting that right-sided colorectal cancer (RCC) and left-sided colorectal cancer (LCC) also differ in treatment success and patient outcomes. Biomarkers that differentiate between RCC and LCC are not well-established. Here, we apply random forest (RF) machine learning methods to identify genomic or microbial biomarkers that differentiate RCC and LCC. METHODS RNA-seq expression data for 58,677 coding and non-coding human genes and count data for 28,557 human unmapped reads were obtained from 308 patient CRC tumour samples. We created three RF models for datasets of human genes-only, microbes-only, and genes-and-microbes combined. We used a permutation test to identify features of significant importance. Finally, we used differential expression (DE) and paired Wilcoxon-rank sum tests to associate features with a particular side. RESULTS RF model accuracy scores were 90%, 70%, and 87% with area under curve (AUC) of 0.9, 0.76, and 0.89 for the human genomic, microbial, and combined feature sets, respectively. 15 features were identified as significant in the model of genes-only, 54 microbes in the model of microbes-only, and 28 genes and 18 microbes in the model with genes-and-microbes combined. PRAC1 expression was the most important feature for differentiating RCC and LCC in the genes-only model, with HOXB13, SPAG16, HOXC4, and RNLS also playing a role. Ruminococcus gnavus and Clostridium acetireducens were the most important in the microbial-only model. MYOM3, HOXC4, Coprococcus eutactus, PRAC1, lncRNA AC012531.25, Ruminococcus gnavus, RNLS, HOXC6, SPAG16 and Fusobacterium nucleatum were most important in the combined model. CONCLUSIONS Many of the identified genes and microbes among all models have previously established associations with CRC. However, the ability of RF models to account for inter-feature relationships within the underlying decision trees may yield a more sensitive and biologically interconnected set of genomic and microbial biomarkers.
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Affiliation(s)
- Tyler Kolisnik
- School of Natural Sciences, Massey University, Auckland, New Zealand.
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
| | - Arielle Kae Sulit
- School of Natural Sciences, Massey University, Auckland, New Zealand
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | | | - Frank Frizelle
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Rachel Purcell
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Adam Smith
- School of Mathematical and Computational Sciences, Massey University, Auckland, New Zealand
| | - Olin Silander
- School of Natural Sciences, Massey University, Auckland, New Zealand
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Rao X, Xue J, Du Y, Zhou Z, Lu Y. Prognosis Prediction of Lung Adenocarcinoma Patients Based on Molecular Subgroups of DNA Methylation. Appl Immunohistochem Mol Morphol 2023; 31:255-265. [PMID: 36877181 DOI: 10.1097/pai.0000000000001114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 11/13/2022] [Indexed: 03/07/2023]
Abstract
Lung adenocarcinoma (LUAD) is a malignant tumor with high mortality. At present, the clinicopathologic feature is the main breakthrough to assess the prognosis of LUAD patients. However, in most cases, the results are less than satisfactory. Cox regression analysis was conducted in this study to obtain methylation sites with significant prognostic relevance based on mRNA expression, DNA methylation data, and clinical data of LUAD from The Cancer Genome Atlas Program database. LUAD patients were grouped into 4 subtypes according to different methylation levels using K-means consensus cluster analysis. By survival analysis, patients were grouped into high-methylation and low-methylation groups. Later, 895 differentially expressed genes (DEGs) were obtained. Eight optimal methylation signature genes associated with prognosis were screened by Cox regression analysis, and a risk assessment model was constructed based on these genes. Samples were then classified into high-risk and low-risk groups depending on the risk assessment model, and prognostic, predictive ability was assessed using survival and receiver operating characteristic (ROC) curves. The results showed that this risk model had a great efficacy in predicting the prognosis of patients, and it was, therefore, able to be an independent prognostic factor. At last, the enrichment analysis demonstrated that the signaling pathways, including cell cycle, homologous recombination, P53 signaling pathway, DNA replication, pentose phosphate pathway, and glycolysis gluconeogenesis were remarkably activated in the high-risk group. In general, we construct an 8-gene model based on DNA methylation molecular subtypes by a series of bioinformatics methods, which can provide new insights for predicting the prognosis of patients with LUAD.
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Affiliation(s)
- Xiao Rao
- Department of Cardio-Thoracic Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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Puccini A, Seeber A, Berger MD. Biomarkers in Metastatic Colorectal Cancer: Status Quo and Future Perspective. Cancers (Basel) 2022; 14:4828. [PMID: 36230751 PMCID: PMC9564318 DOI: 10.3390/cancers14194828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer (CRC) is the third most frequent cancer worldwide, and its incidence is steadily increasing. During the last two decades, a tremendous improvement in outcome has been achieved, mainly due to the introduction of novel drugs, targeted treatment, immune checkpoint inhibitors (CPIs) and biomarker-driven patient selection. Moreover, progress in molecular diagnostics but also improvement in surgical techniques and local ablative treatments significantly contributed to this success. However, novel therapeutic approaches are needed to further improve outcome in patients diagnosed with metastatic CRC. Besides the established biomarkers for mCRC, such as microsatellite instability (MSI) or mismatch repair deficiency (dMMR), RAS/BRAF, sidedness and HER2 amplification, new biomarkers have to be identified to better select patients who derive the most benefit from a specific treatment. In this review, we provide an overview about therapeutic relevant and established biomarkers but also shed light on potential promising markers that may help us to better tailor therapy to the individual mCRC patient in the near future.
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Affiliation(s)
- Alberto Puccini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), School of Medicine, University of Genoa, 16132 Genoa, Italy
| | - Andreas Seeber
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Martin D. Berger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
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Xu Y, Wei Z, Feng M, Zhu D, Mei S, Wu Z, Feng Q, Chang W, Ji M, Liu C, Zhu Y, Shen L, Yang F, Chen Y, Feng Y, Xu J, Zhu D. Tumor-infiltrated activated B cells suppress liver metastasis of colorectal cancers. Cell Rep 2022; 40:111295. [PMID: 36044847 DOI: 10.1016/j.celrep.2022.111295] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/13/2022] [Accepted: 08/10/2022] [Indexed: 12/23/2022] Open
Abstract
More than 40% of patients with late-stage colorectal cancer (CRC) develop liver metastasis (LM). Which immune cells play important roles in CRC-LM and contribute to the difference between left-sided CRC (LCC) and right-sided CRC (RCC) remain unclear. By single-cell RNA sequencing (scRNA-seq), we not only find that activated B cells are significantly depleted in CRC with LM, but also find a subtype of B cells developed from activated B cells, namely immature plasma cell population alpha (iMPA), highly correlated with metastasis. Mechanistically, inhibition of the Wnt and transforming growth factor β (TGF-β) pathways in cancer cell promotes activated B cell migration via the SDF-1-CXCR4 axis. This study reveals that B cell subpopulations in the tumor immune microenvironment (TIME) play a key role in CRC-LM as well as in LCC and RCC. The preventive effects of modulating B cell subpopulations in CRC may provide a rationale for subsequent drug development and CRC-LM management.
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Affiliation(s)
- Yuqiu Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhuang Wei
- Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Mei Feng
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dexiang Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shenglin Mei
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai 200433, China
| | - Zhongen Wu
- School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 201203, China
| | - Qingyang Feng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wenju Chang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Meiling Ji
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chenglong Liu
- School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 201203, China
| | - Yuanyuan Zhu
- School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 201203, China
| | - Lian Shen
- School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 201203, China
| | - Fan Yang
- School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 201203, China
| | - Yijiao Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yuxiong Feng
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Di Zhu
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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Effects of Anesthetics on Proliferation and Apoptosis of Drug-Resistant Human Colon Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4080585. [PMID: 35968236 PMCID: PMC9371867 DOI: 10.1155/2022/4080585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/06/2022] [Accepted: 07/12/2022] [Indexed: 11/20/2022]
Abstract
In recent years, people's living standards are getting higher and higher, and life pressure is also increasing, and there are also many problems in eating habits. This is also the direct cause of colon cancer. The aim of this paper was to investigate whether anesthetic drugs could positively affect the proliferation and apoptosis of colon cancer cells. In this paper, the significance of anesthetic drugs is proposed, and an artificial neural network algorithm based on artificial intelligence is proposed. It is well known that artificial neural networks play an important role in medicine. The experimental results of this paper show that the incidence of colon cancer in 2020 will be in the range of 5%-35%, and the incidence of colon cancer in 2021 will be in the range of 7%-30%. While colon cancer rates in 2021 do not appear to be as high as colon cancer rates in 2020, they are generally much higher than colon cancer rates in 2020. It can be seen that as the population ages, the number of colon cancer patients is increasing due to the lack of emphasis on health. This also means that the incidence of colon cancer is getting higher and higher, and traditional drug chemotherapy has been unable to play a good role in inhibiting the proliferation of colon cancer cells. Therefore, this paper investigated the effects of anesthetic drugs on the proliferation and apoptosis of human colon cancer cells.
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Wang K, Yang Y, Zheng S, Hu W. Association Mining Identifies MAL2 as a Novel Tumor Suppressor in Colorectal Cancer. Onco Targets Ther 2022; 15:761-769. [PMID: 35847380 PMCID: PMC9278979 DOI: 10.2147/ott.s369670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/04/2022] [Indexed: 12/09/2022] Open
Abstract
Introduction Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. However, the driver genes that promote CRC metastasis remain poorly understood. Association mining mines and extracts the repeated correlations and relevance in a dataset to predict the appearance of other data items according to the appearance of one item. Methods Here, the Apriori algorithm was used to find the frequent mutational gene sets (FMGSs) and hidden association rules (ARs) within these FMGSs from 383 CRCs with whole exome sequencing datasets. The weighted correlation network analysis (WGCNA) was used to identify the hub genes in CRC. CCK8, colony formation, cell migration and invasion assays were adopted to detect the roles of hub genes in CRC. Results Intriguingly, we found that MAL2 (myelin and lymphocyte protein 2) was associated with TP53 and APC in stage IV of CRC, and further subnetwork exploration based on WGCNA identified MAL2 as a potent hub gene. To validate the metastasis-related role of MAL2 in CRC, a lentivirus-based overexpression system was utilized to construct MAL2-overexpressing human CRC LOVO cells. Overexpression of MAL2 remarkably inhibited CRC cell proliferation and invasion. Conclusion Our results highlighted that MAL2 acts as a tumor suppressor in CRC and could serve as a potential therapeutic target.
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Affiliation(s)
- Kailai Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, People's Republic of China
| | - Yanmei Yang
- Key Laboratory of Reproductive and Genetics, Ministry of Education, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, People's Republic of China
| | - Wangxiong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, People's Republic of China
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Identification of multi-omics biomarkers and construction of the novel prognostic model for hepatocellular carcinoma. Sci Rep 2022; 12:12084. [PMID: 35840618 PMCID: PMC9287549 DOI: 10.1038/s41598-022-16341-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/08/2022] [Indexed: 12/05/2022] Open
Abstract
Genome changes play a crucial role in carcinogenesis, and many biomarkers can be used as effective prognostic indicators in various tumors. Although previous studies have constructed many predictive models for hepatocellular carcinoma (HCC) based on molecular signatures, the performance is unsatisfactory. Because multi-omics data can more comprehensively reflect the biological phenomenon of disease, we hope to build a more accurate predictive model by multi-omics analysis. We use the TCGA to identify crucial biomarkers and construct prognostic models through difference analysis, univariate Cox, and LASSO/stepwise Cox analysis. The performances of predictive models were evaluated and validated through survival analysis, Harrell’s concordance index (C-index), receiver operating characteristic (ROC) curve, and decision curve analysis (DCA). Multiple mRNAs, lncRNAs, miRNAs, CNV genes, and SNPs were significantly associated with the prognosis of HCC. We constructed five single-omic models, and the mRNA and lncRNA models showed good performance with c-indexes over 0.70. The multi-omics model presented a robust predictive ability with a c-index over 0.77. This study identified many biomarkers that may help study underlying carcinogenesis mechanisms in HCC. In addition, we constructed multiple single-omic models and an integrated multi-omics model that may provide practical and reliable guides for prognosis assessment.
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Dynamic Co-Evolution of Cancer Cells and Cancer-Associated Fibroblasts: Role in Right- and Left-Sided Colon Cancer Progression and Its Clinical Relevance. BIOLOGY 2022; 11:biology11071014. [PMID: 36101394 PMCID: PMC9312176 DOI: 10.3390/biology11071014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/22/2022]
Abstract
Simple Summary The versatile crosstalk between cancer cells and cancer-associated fibroblasts (CAFs) of the tumour microenvironment (TME) drives colorectal carcinogenesis and heterogeneity. Colorectal cancer (CRC) can be classified by the anatomical sites from which the cancer arises, either from the right or left colon. Although the cancer cell–CAF interaction is being widely studied, its role in the progression of cancer in the right and left colon and cancer heterogeneity are still yet to be elucidated. Further insight into the complex interaction between different cellular components in the cancer niche, their evolutionary process and their influence on cancer progression would propel the discovery of effective targeted CRC therapy. Abstract Cancer is a result of a dynamic evolutionary process. It is composed of cancer cells and the tumour microenvironment (TME). One of the major cellular constituents of TME, cancer-associated fibroblasts (CAFs) are known to interact with cancer cells and promote colorectal carcinogenesis. The accumulation of these activated fibroblasts is linked to poor diagnosis in colorectal cancer (CRC) patients and recurrence of the disease. However, the interplay between cancer cells and CAFs is yet to be described, especially in relation to the sidedness of colorectal carcinogenesis. CRC, which is the third most commonly diagnosed cancer globally, can be classified according to the anatomical region from which they originate: left-sided (LCRC) and right-sided CRC (RCR). Both cancers differ in many aspects, including in histology, evolution, and molecular signatures. Despite occurring at lower frequency, RCRC is often associated with worse diagnosis compared to LCRC. The differences in molecular profiles between RCRC and LCRC also influence the mode of treatment that can be used to specifically target these cancer entities. A better understanding of the cancer cell–CAF interplay and its association with RCRC and LRCR progression will provide better insight into potential translational aspects of targeted treatment for CRC.
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Myer PA, Lee JK, Madison RW, Pradhan K, Newberg JY, Isasi CR, Klempner SJ, Frampton GM, Ross JS, Venstrom JM, Schrock AB, Das S, Augenlicht L, Verma A, Greally JM, Raj SM, Goel S, Ali SM. The Genomics of Colorectal Cancer in Populations with African and European Ancestry. Cancer Discov 2022; 12:1282-1293. [PMID: 35176763 PMCID: PMC9169495 DOI: 10.1158/2159-8290.cd-21-0813] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/28/2021] [Accepted: 02/11/2022] [Indexed: 11/16/2022]
Abstract
Black people have a higher incidence of colorectal cancer and worse survival rates when compared with white people. Comprehensive genomic profiling was performed in 46,140 colorectal adenocarcinoma cases. Ancestry-informative markers identified 5,301 patients of African descent (AFR) and 33,770 patients of European descent (EUR). AFR were younger, had fewer microsatellite instability-high (MSI-H) tumors, and had significantly more frequent alterations in KRAS, APC, and PIK3CA. AFR had increased frequency of KRAS mutations, specifically KRASG12D and KRASG13. There were no differences in rates of actionable kinase driver alterations (HER2, MET, NTRK, ALK, ROS1, and RET). In patients with young-onset colorectal cancer (<50 years), AFR and EUR had a similar frequency of MSI-H and tumor mutational burden-high (TMB-H) tumors, and strikingly different trends in APC mutations by age, as well as differences in MAPK pathway alterations. These findings inform treatment decisions, impact prognosis, and underscore the need for model systems representative of the diverse U.S. population. SIGNIFICANCE KRAS (particularly KRASG12D/G13), APC, and PIK3CA were more frequently altered in AFR who had a lower frequency of MSI-H tumors. There were no differences in actionable kinase driver alterations. In young-onset colorectal cancer, both ancestries had a similar frequency of MSI-H/TMB-H tumors, but strikingly different trends in APC. See related commentary by Eng and Holowatyj, p. 1187. This article is highlighted in the In This Issue feature, p. 1171.
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Affiliation(s)
- Parvathi A. Myer
- Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
- Albert Einstein College of Medicine, Bronx, New York
| | | | | | - Kith Pradhan
- Albert Einstein College of Medicine, Bronx, New York
| | | | | | | | | | - Jeffery S. Ross
- Foundation Medicine, Cambridge, Massachusetts
- Upstate Medical University, Syracuse, New York
| | | | | | - Sudipto Das
- Royal College of Surgeons, School of Pharmacy and Biomolecular Sciences, Dublin, Ireland
| | | | - Amit Verma
- Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
- Albert Einstein College of Medicine, Bronx, New York
| | | | | | - Sanjay Goel
- Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
- Albert Einstein College of Medicine, Bronx, New York
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12
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Seely KD, Morgan AD, Hagenstein LD, Florey GM, Small JM. Bacterial Involvement in Progression and Metastasis of Colorectal Neoplasia. Cancers (Basel) 2022; 14:1019. [PMID: 35205767 PMCID: PMC8870662 DOI: 10.3390/cancers14041019] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 02/06/2023] Open
Abstract
While the gut microbiome is composed of numerous bacteria, specific bacteria within the gut may play a significant role in carcinogenesis, progression, and metastasis of colorectal carcinoma (CRC). Certain microbial species are known to be associated with specific cancers; however, the interrelationship between bacteria and metastasis is still enigmatic. Mounting evidence suggests that bacteria participate in cancer organotropism during solid tumor metastasis. A critical review of the literature was conducted to better characterize what is known about bacteria populating a distant site and whether a tumor depends upon the same microenvironment during or after metastasis. The processes of carcinogenesis, tumor growth and metastatic spread in the setting of bacterial infection were examined in detail. The literature was scrutinized to discover the role of the lymphatic and venous systems in tumor metastasis and how microbes affect these processes. Some bacteria have a potent ability to enhance epithelial-mesenchymal transition, a critical step in the metastatic cascade. Bacteria also can modify the microenvironment and the local immune profile at a metastatic site. Early targeted antibiotic therapy should be further investigated as a measure to prevent metastatic spread in the setting of bacterial infection.
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Affiliation(s)
- Kevin D. Seely
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA; (A.D.M.); (L.D.H.)
| | - Amanda D. Morgan
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA; (A.D.M.); (L.D.H.)
| | - Lauren D. Hagenstein
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA; (A.D.M.); (L.D.H.)
| | - Garrett M. Florey
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80134, USA;
| | - James M. Small
- Department of Biomedical Sciences, Rocky Vista University, Parker, CO 80134, USA;
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13
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Alorda-Clara M, Torrens-Mas M, Morla-Barcelo PM, Martinez-Bernabe T, Sastre-Serra J, Roca P, Pons DG, Oliver J, Reyes J. Use of Omics Technologies for the Detection of Colorectal Cancer Biomarkers. Cancers (Basel) 2022; 14:817. [PMID: 35159084 PMCID: PMC8834235 DOI: 10.3390/cancers14030817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most frequently diagnosed cancers with high mortality rates, especially when detected at later stages. Early detection of CRC can substantially raise the 5-year survival rate of patients, and different efforts are being put into developing enhanced CRC screening programs. Currently, the faecal immunochemical test with a follow-up colonoscopy is being implemented for CRC screening. However, there is still a medical need to describe biomarkers that help with CRC detection and monitor CRC patients. The use of omics techniques holds promise to detect new biomarkers for CRC. In this review, we discuss the use of omics in different types of samples, including breath, urine, stool, blood, bowel lavage fluid, or tumour tissue, and highlight some of the biomarkers that have been recently described with omics data. Finally, we also review the use of extracellular vesicles as an improved and promising instrument for biomarker detection.
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Affiliation(s)
- Marina Alorda-Clara
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (T.M.-B.); (J.S.-S.); (P.R.); (D.G.P.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
| | - Margalida Torrens-Mas
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (T.M.-B.); (J.S.-S.); (P.R.); (D.G.P.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Translational Research in Aging and Longevity (TRIAL) Group, Instituto de Investigación Sanitaria Illes Balears (IdISBa), E-07120 Palma de Mallorca, Illes Balears, Spain
| | - Pere Miquel Morla-Barcelo
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (T.M.-B.); (J.S.-S.); (P.R.); (D.G.P.)
| | - Toni Martinez-Bernabe
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (T.M.-B.); (J.S.-S.); (P.R.); (D.G.P.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
| | - Jorge Sastre-Serra
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (T.M.-B.); (J.S.-S.); (P.R.); (D.G.P.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Ciber Fisiopatología Obesidad y Nutrición (CB06/03) Instituto Salud Carlos III, E-28029 Madrid, Madrid, Spain
| | - Pilar Roca
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (T.M.-B.); (J.S.-S.); (P.R.); (D.G.P.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Ciber Fisiopatología Obesidad y Nutrición (CB06/03) Instituto Salud Carlos III, E-28029 Madrid, Madrid, Spain
| | - Daniel Gabriel Pons
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (T.M.-B.); (J.S.-S.); (P.R.); (D.G.P.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
| | - Jordi Oliver
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (T.M.-B.); (J.S.-S.); (P.R.); (D.G.P.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Ciber Fisiopatología Obesidad y Nutrición (CB06/03) Instituto Salud Carlos III, E-28029 Madrid, Madrid, Spain
| | - Jose Reyes
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (T.M.-B.); (J.S.-S.); (P.R.); (D.G.P.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Servicio Aparato Digestivo, Hospital Comarcal de Inca, E-07300 Inca, Illes Balears, Spain
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14
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Su MW, Chang CK, Lin CW, Chu HW, Tsai TN, Su WC, Chen YC, Chang TK, Huang CW, Tsai HL, Wu CC, Chou HC, Shiu BH, Wang JY. Genomic and Metabolomic Landscape of Right-Sided and Left-Sided Colorectal Cancer: Potential Preventive Biomarkers. Cells 2022; 11:cells11030527. [PMID: 35159336 PMCID: PMC8834628 DOI: 10.3390/cells11030527] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 12/27/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. The incidence and mortality rates of CRC are significantly higher in Taiwan than in other developed countries. Genes involved in CRC tumorigenesis differ depending on whether the tumor occurs on the left or right side of the colon, and genomic analysis is a keystone in the study and treatment of CRC subtypes. However, few studies have focused on the genetic landscape of Taiwanese patients with CRC. This study comprehensively analyzed the genomes of 141 Taiwanese patients with CRC through whole-exome sequencing. Significant genomic differences related to the site of CRC development were observed. Blood metabolomic profiling and polygenic risk score analysis were performed to identify potential biomarkers for the early identification and prevention of CRC in the Taiwanese population. Our findings provide vital clues for establishing population-specific treatments and health policies for CRC prevention in Taiwan.
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Affiliation(s)
- Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Chien-Wei Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Tsen-Ni Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
| | - Wei-Chih Su
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yen-Cheng Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Tsung-Kun Chang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
| | - Ching-Wen Huang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hsiang-Lin Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chang-Chieh Wu
- Department of Surgery, Tri-Service General Hospital Keelung Branch, National Defense Medical Center, Keelung 20042, Taiwan;
| | - Huang-Chi Chou
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan; (H.-C.C.); (B.-H.S.)
- Division of Colon and Rectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung 402306, Taiwan
| | - Bei-Hao Shiu
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan; (H.-C.C.); (B.-H.S.)
- Division of Colon and Rectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung 402306, Taiwan
| | - Jaw-Yuan Wang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Pingtung Hospital, Ministry of Health and Welfare, Pingtung 900, Taiwan
- Correspondence: & ; Tel.: +886-7-312-2805
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15
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Beheshti-Maal A, Tamimi A, Iravani S, Memarnejadian A, Sorouri M, Aghdaei HA, Zali MR, Hossein Khannazer N, Vosough M. PSC associated inflammatory bowel disease: a distinct entity. Expert Rev Gastroenterol Hepatol 2022; 16:129-139. [PMID: 35078376 DOI: 10.1080/17474124.2022.2031979] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Primary sclerosing cholangitis (PSC) is a rare, chronic, and progressive cholestatic disease involving intra- and/or extrahepatic bile ducts. PSC in many patients results in end-stage liver diseases. Nearly 60% of the PSC patients suffer from concomitant inflammatory bowel diseases (IBDs). Classically, IBDs are divided into two principle types: Crohn's disease (CD) and ulcerative colitis (UC). However, with growing knowledge, PSC-associated IBD (PSC-IBD) seems to be a rather distinct entity with specific genetics, clinical, and microbiota characteristics. AREAS COVERED In this article, we aim to review the unique characteristics of PSC-IBD from clinical, genetic, and microbiota point of view. EXPERT OPINION PSC-IBD's unique characteristics contribute to the notion that it could be a distinct entity. Acknowledgment of PSC-IBD as a novel entity necessitates designing new clinical guidelines for diagnosis and developing novel therapies.
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Affiliation(s)
- Alireza Beheshti-Maal
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Acecr, Tehran, Iran
| | - Atena Tamimi
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Acecr, Tehran, Iran
| | - Shahrokh Iravani
- Gastroenterology and Hepatobiliary Research Center, Imam Reza Hospital, Tehran, Iran
| | | | - Majid Sorouri
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nikoo Hossein Khannazer
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Acecr, Tehran, Iran
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16
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Myer PA, Kim H, Blümel AM, Finnegan E, Kel A, Thompson TV, Greally JM, Prehn JHM, O’Connor DP, Friedman RA, Floratos A, Das S. Master Transcription Regulators and Transcription Factors Regulate Immune-Associated Differences Between Patients of African and European Ancestry With Colorectal Cancer. GASTRO HEP ADVANCES 2022; 1:328-341. [PMID: 35711675 PMCID: PMC9151447 DOI: 10.1016/j.gastha.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/20/2022] [Indexed: 11/21/2022]
Abstract
Background and Aims Individuals of African (AFR) ancestry have a higher incidence of colorectal cancer (CRC) than those of European (EUR) ancestry and exhibit significant health disparities. Previous studies have noted differences in the tumor microenvironment between AFR and EUR patients with CRC. However, the molecular regulatory processes that underpin these immune differences remain largely unknown. Methods Multiomics analysis was carried out for 55 AFR and 456 EUR patients with microsatellite-stable CRC using The Cancer Genome Atlas. We evaluated the tumor microenvironment by using gene expression and methylation data, transcription factor, and master transcriptional regulator analysis to identify the cell signaling pathways mediating the observed phenotypic differences. Results We demonstrate that downregulated genes in AFR patients with CRC showed enrichment for canonical pathways, including chemokine signaling. Moreover, evaluation of the tumor microenvironment showed that cytotoxic lymphocytes and neutrophil cell populations are significantly decreased in AFR compared with EUR patients, suggesting AFR patients have an attenuated immune response. We further demonstrate that molecules called "master transcriptional regulators" (MTRs) play a critical role in regulating the expression of genes impacting key immune processes through an intricate signal transduction network mediated by disease-associated transcription factors (TFs). Furthermore, a core set of these MTRs and TFs showed a positive correlation with levels of cytotoxic lymphocytes and neutrophils across both AFR and EUR patients with CRC, thus suggesting their role in driving the immune infiltrate differences between the two ancestral groups. Conclusion Our study provides an insight into the intricate regulatory landscape of MTRs and TFs that orchestrate the differences in the tumor microenvironment between patients with CRC of AFR and EUR ancestry.
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Key Words
- AFR, African
- African Americans.
- CMA, Composite Module Analyst
- CRC, colorectal cancer
- ChAMP, Chip Analysis Methylation Pipeline
- Colorectal Cancer
- DEGs, differentially expressed genes
- DMPs, differentially methylated CpG positions
- EUR, European
- FDR, false discovery rate
- Genomic Profiling
- Health Disparities
- MCP, microenvironment cell population
- MSI-H, microsatellite high
- MSI-L, microsatellite low
- MSS, microsatellite stable
- MTRs, master transcriptional regulators
- TCGA, The Cancer Genome Atlas
- TFBS, TF binding site
- TFs, transcription factors
- TMB, tumor mutation burden
- TSS, transcription start site
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Affiliation(s)
- Parvathi A. Myer
- Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, NY
| | - Hyunjin Kim
- St. Jude’s Children’s Research Hospital, Memphis, Tennessee TN
| | - Anna M. Blümel
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ellen Finnegan
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
| | - Alexander Kel
- GeneXplain GmbH, Wolfenbuettel, Germany
- BIOSOFT.RU, LLC, Novobirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine SBRAS, Novobirsk, Russia
| | | | | | - Jochen HM. Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Darran P. O’Connor
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
| | - Richard A. Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, and Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY
| | - Aris Floratos
- Department of Systems Biology, Columbia University, New York, NY
- Department of Biomedical Informatics, Columbia University, New York, NY
| | - Sudipto Das
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
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17
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Xin J, Wu Y, Ben S, Li S, Chu H, Wang M, Wang M, Song M, Du M, Zhang Z. CoSMeD: a user-friendly web server to estimate 5-year survival probability of left-sided and right-sided colorectal cancer patients using molecular data. Bioinformatics 2021; 38:278-281. [PMID: 34260718 DOI: 10.1093/bioinformatics/btab523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 02/05/2023] Open
Abstract
SUMMARY Colorectal cancer is a heterogeneous disease with diverse prognoses between left-sided and right-sided patients; therefore, it is necessary to precisely evaluate the survival probability of side-specific colorectal cancer patients. Here, we collected multi-omics data from The Cancer Genome Atlas program, including gene expression, DNA methylation and microRNA expression. Specificity measure and robust likelihood-based survival analysis were used to identify 6 left-sided and 28 right-sided prognostic biomarkers. Compared to the performance of clinical prognostic models, the addition of these biomarkers could significantly improve the discriminatory ability and calibration in predicting side-specific 5-year survival for colorectal cancer. Additional dataset derived from Gene Expression Omnibus was used to validate the prognostic value of side-specific genes. Finally, we constructed colorectal cancer side-specific molecular database (CoSMeD), a user-friendly interface for estimating side-specific colorectal cancer 5-year survival probability, which can lay the basis for personalized management of left-sided and right-sided colorectal cancer patients. AVAILABILITY AND IMPLEMENTATION CoSMeD is freely available at https://mulongdu.shinyapps.io/cosmed. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 211166 Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 211166 Nanjing, China.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yanling Wu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 211166 Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 211166 Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 211166 Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 211166 Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 211166 Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 211166 Nanjing, China
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 211166 Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 211166 Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 211166 Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 211166 Nanjing, China
| | - Molin Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mingyang Song
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Mulong Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, 211166 Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 211166 Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 211166 Nanjing, China
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18
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Yi T, Zhang Y, Ng DM, Xi Y, Ye M, Cen L, Li J, Fan X, Li Y, Hu S, Rong H, Xie Y, Zhao G, Chen L, Chen C, Ni S, Mi J, Dai X, Liao Q. Regulatory Network Analysis of Mutated Genes Based on Multi-Omics Data Reveals the Exclusive Features in Tumor Immune Microenvironment Between Left-Sided and Right-Sided Colon Cancer. Front Oncol 2021; 11:685515. [PMID: 34211853 PMCID: PMC8239301 DOI: 10.3389/fonc.2021.685515] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/29/2021] [Indexed: 01/11/2023] Open
Abstract
Left-sided colon cancer (LCC) and right-sided colon cancer (RCC) have distinct characteristics in tumor immune microenvironment (TIME). Although existing studies have shown a strong association between gene mutations and TIME, whether the regulatory mechanisms between gene mutations and TIME are different between RCC and LCC is still unclear. In this study, we showed the fractions of CD8+ T cells were higher while those of regulatory T cells were lower in RCC. Besides, a stronger association between gene mutations and TIME was observed in RCC. Specifically, using multi-omics data, we demonstrated the mutations of most top mutated genes (TMGs) including BRAF, PCLO, MUC16, LRP2, ANK3, KMT2D, RYR2 made great contributions to elevated fraction of immune cells by up-regulating immune-related genes directly or indirectly through miRNA and DNA methylation, whereas the effects of APC, TP53 and KRAS mutations on TIME were reversed in RCC. Remarkably, we found the expression levels of several immune checkpoint molecules such as PD-1 and LAG3 were correlated with corresponding DNA methylation levels, which were associated with the mutations of TMGs in RCC. In contrast, the associations between gene mutations and TIME were less significant in LCC. Besides, survival analyses showed APC mutation had adverse impact on immunotherapy while patients with BRAF mutation were more suitable for immunotherapy in colon cancer. We hope that our results will provide a deeper insight into the sophisticated mechanism underlying the regulation between mutations and TIME, and thus boost the discovery of differential immunotherapeutic strategies for RCC and LCC.
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Affiliation(s)
- Tianfei Yi
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China.,Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Yuwei Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Derry Minyao Ng
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Yang Xi
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Meng Ye
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Lvjun Cen
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Jianjiong Li
- Hua Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Xiaoxiang Fan
- Hua Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Yanguo Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
| | - Shiyun Hu
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China.,Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Hao Rong
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China.,Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Yangyang Xie
- Hua Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Guofang Zhao
- Hua Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Leyi Chen
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Chen Chen
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Shujing Ni
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Jiaying Mi
- Hua Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Xiaoyu Dai
- Hua Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Qi Liao
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China.,Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
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19
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Banerjee S, Zhang X, Kuang S, Wang J, Li L, Fan G, Luo Y, Sun S, Han P, Wu Q, Yang S, Ji X, Li Y, Deng L, Tian X, Wang Z, Zhang Y, Wu K, Zhu S, Bolund L, Yang H, Xu X, Liu J, Lu Y, Liu X. Comparative analysis of clonal evolution among patients with right- and left-sided colon and rectal cancer. iScience 2021; 24:102718. [PMID: 34258553 PMCID: PMC8254024 DOI: 10.1016/j.isci.2021.102718] [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: 10/16/2020] [Revised: 12/21/2020] [Accepted: 06/09/2021] [Indexed: 12/15/2022] Open
Abstract
Tumor multiregion sequencing reveals intratumor heterogeneity (ITH) and clonal evolution playing a key role in tumor progression and metastases. Large-scale high-depth multiregional sequencing of colorectal cancer, comparative analysis among patients with right-sided colon cancer (RCC), left-sided colon cancer (LCC), and rectal cancer (RC), as well as the study of lymph node metastasis (LN) with extranodal tumor deposits (ENTDs) from evolutionary perspective remain weakly explored. Here, we recruited 68 patients with RCC (18), LCC (20), and RC (30). We performed high-depth whole-exome sequencing of 206 tumor regions including 176 primary tumors, 19 LN, and 11 ENTD samples. Our results showed ITH with a Darwinian pattern of evolution and the evolution pattern of LCC and RC was more complex and divergent than RCC. Genetic and evolutionary evidences found that both LN and ENTD originated from different clones. Moreover, ENTD was a distinct entity from LN and evolved later.
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Affiliation(s)
- Santasree Banerjee
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xianxiang Zhang
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shan Kuang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jigang Wang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Lei Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yonglun Luo
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Peng Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Qingyao Wu
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shujian Yang
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Xiaobin Ji
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Yong Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Li Deng
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaofen Tian
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhiwei Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yue Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Lars Bolund
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, Zhejiang, China
| | - Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Junnian Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yun Lu
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China.,Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao University, Qingdao, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
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20
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Almuzzaini B, Alghamdi J, Alomani A, AlGhamdi S, Alsharm AA, Alshieban S, Sayed A, Alhejaily AG, Aljaser FS, Abudawood M, Almajed F, Samman A, Balwi MAA, Aziz MA. Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel. J Pers Med 2021; 11:jpm11060535. [PMID: 34207827 PMCID: PMC8230213 DOI: 10.3390/jpm11060535] [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: 04/14/2021] [Revised: 05/25/2021] [Accepted: 05/30/2021] [Indexed: 02/07/2023] Open
Abstract
Biomarker discovery would be an important tool in advancing and utilizing the concept of precision and personalized medicine in the clinic. Discovery of novel variants in local population provides confident targets for developing biomarkers for personalized medicine. We identified the need to generate high-quality sequencing data from local colorectal cancer patients and understand the pattern of occurrence of variants. In this report, we used archived samples from Saudi Arabia and used the AmpliSeq comprehensive cancer panel to identify novel somatic variants. We report a comprehensive analysis of next-generation sequencing results with a coverage of >300X. We identified 466 novel variants which were previously unreported in COSMIC and ICGC databases. We analyzed the genes associated with these variants in terms of their frequency of occurrence, probable pathogenicity, and clinicopathological features. Among pathogenic somatic variants, 174 were identified for the first time in the large intestine. APC, RET, and EGFR genes were most frequently mutated. A higher number of variants were identified in the left colon. Occurrence of variants in ERBB2 was significantly correlated with those of EGFR and ATR genes. Network analyses of the identified genes provide functional perspective of the identified genes and suggest affected pathways and probable biomarker candidates. This report lays the ground work for biomarker discovery and identification of driver gene mutations in local population.
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Affiliation(s)
- Bader Almuzzaini
- King Abdullah International Medical Research Center, Medical Genomics Research Department, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia;
- Correspondence: (B.A.); (M.A.A.); Tel.: +966-11-429-4533 (B.A.); +966-11-429-4582 (M.A.A.)
| | - Jahad Alghamdi
- King Abdullah International Medical Research Center, Saudi Biobank, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11481, Saudi Arabia; (J.A.); (A.S.)
| | - Alhanouf Alomani
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13318, Saudi Arabia;
| | - Saleh AlGhamdi
- Clinical Research Department, Research Center, King Fahad Medical City, Riyadh 11564, Saudi Arabia;
| | - Abdullah A. Alsharm
- Comprehensive Cancer Center, King Fahad Medical City, Riyadh 11564, Saudi Arabia;
| | - Saeed Alshieban
- King Abdul Aziz Medical City-National Guard Health Affairs (NGHA), King Abdullah International Medical Research Center, King Saud Bin Abdul Aziz University for Health Sciences (KSAU-HS), Riyadh 14611, Saudi Arabia;
| | - Ahood Sayed
- King Abdullah International Medical Research Center, Saudi Biobank, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11481, Saudi Arabia; (J.A.); (A.S.)
| | | | - Feda S. Aljaser
- Department of Clinical Laboratory Sciences, Chair of Medical and Molecular Genetics Research, College of Applied Medical Sciences, King Saud University Riyadh, Riyadh 11564, Saudi Arabia; (F.S.A.); (M.A.)
| | - Manal Abudawood
- Department of Clinical Laboratory Sciences, Chair of Medical and Molecular Genetics Research, College of Applied Medical Sciences, King Saud University Riyadh, Riyadh 11564, Saudi Arabia; (F.S.A.); (M.A.)
| | - Faisal Almajed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11481, Saudi Arabia;
| | - Abdulhadi Samman
- Department of Pathology, Faculty of Medicine, University of Jeddah, Jeddah 23218, Saudi Arabia;
| | - Mohammed A. Al Balwi
- King Abdullah International Medical Research Center, Medical Genomics Research Department, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia;
| | - Mohammad Azhar Aziz
- King Abdullah International Medical Research Center, Colorectal Cancer Research Program, Department of Cellular Therapy and Cancer Research, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
- Correspondence: (B.A.); (M.A.A.); Tel.: +966-11-429-4533 (B.A.); +966-11-429-4582 (M.A.A.)
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21
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HomeoboxC6 promotes metastasis by orchestrating the DKK1/Wnt/β-catenin axis in right-sided colon cancer. Cell Death Dis 2021; 12:337. [PMID: 33795652 PMCID: PMC8016886 DOI: 10.1038/s41419-021-03630-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/30/2022]
Abstract
Patients with right-sided colon cancer (RCC) generally have a poorer prognosis than those with left-sided colon cancer (LCC). We previously found that homeobox C6 (HOXC6) was the most significantly upregulated gene in RCC compared to LCC. However, it remains unclear whether HOXC6 plays a role in tumor proliferation and metastasis. Our study aimed to explore the potential oncogenic role and the detailed molecular mechanism of HOXC6 in RCC. In this study, HOXC6 was validated to be overexpressed in RCC and associated with poor prognosis. Furthermore, overexpression of HOXC6 promoted the migration and invasion of colon cancer cells through inducing EMT by activating the Wnt/β-catenin signaling pathway and inhibition of DKK1 secretion. Lastly, we preliminary explored the translational effect of HOXC6 and found that silencing of HOXC6 made HCT116 and HT29 cells more sensitive to irinotecan.
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22
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AlMusawi S, Ahmed M, Nateri AS. Understanding cell-cell communication and signaling in the colorectal cancer microenvironment. Clin Transl Med 2021; 11:e308. [PMID: 33635003 PMCID: PMC7868082 DOI: 10.1002/ctm2.308] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/31/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
Carcinomas are complex heterocellular systems containing epithelial cancer cells, stromal fibroblasts, and multiple immune cell-types. Cell-cell communication between these tumor microenvironments (TME) and cells drives cancer progression and influences response to existing therapies. In order to provide better treatments for patients, we must understand how various cell-types collaborate within the TME to drive cancer and consider the multiple signals present between and within different cancer types. To investigate how tissues function, we need a model to measure both how signals are transferred between cells and how that information is processed within cells. The interplay of collaboration between different cell-types requires cell-cell communication. This article aims to review the current in vitro and in vivo mono-cellular and multi-cellular cultures models of colorectal cancer (CRC), and to explore how they can be used for single-cell multi-omics approaches for isolating multiple types of molecules from a single-cell required for cell-cell communication to distinguish cancer cells from normal cells. Integrating the existing single-cell signaling measurements and models, and through understanding the cell identity and how different cell types communicate, will help predict drug sensitivities in tumor cells and between- and within-patients responses.
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Affiliation(s)
- Shaikha AlMusawi
- Cancer Genetics & Stem Cell Group, BioDiscovery Institute, Division of Cancer & Stem Cells, School of MedicineUniversity of NottinghamNottinghamUK
| | - Mehreen Ahmed
- Cancer Genetics & Stem Cell Group, BioDiscovery Institute, Division of Cancer & Stem Cells, School of MedicineUniversity of NottinghamNottinghamUK
- Department of Laboratory Medicine, Division of Translational Cancer ResearchLund UniversityLundSweden
| | - Abdolrahman S. Nateri
- Cancer Genetics & Stem Cell Group, BioDiscovery Institute, Division of Cancer & Stem Cells, School of MedicineUniversity of NottinghamNottinghamUK
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23
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Roy S, Singh AP, Gupta D. Unsupervised subtyping and methylation landscape of pancreatic ductal adenocarcinoma. Heliyon 2021; 7:e06000. [PMID: 33521362 PMCID: PMC7820567 DOI: 10.1016/j.heliyon.2021.e06000] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/14/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is an aggressive form of pancreatic cancer that typically manifests itself at an advanced stage and does not respond to most treatment modalities. The survival rate of a PDAC patient is less than 5%, with a median survival of just a couple of months. A better understanding of the molecular pathology of PDAC is needed to guide research for the development of better clinical treatment modalities for PDAC patients. Gene expression studies performed to date have identified different subtypes of PDAC with prognostic and clinical relevance. Subtypes identified to date are highly heterogeneous since pancreatic cancer is heterogeneous cancer. Tumor microenvironment and stroma constitute a major chunk of PDAC and contribute to the heterogeneity. Better subtyping methods are need of the hour for better prognosis and classification of PDAC for future personalized treatment. In this work, we have performed an integrated analysis of DNA methylation and gene expression datasets to provide better mechanistic and molecular insights into Pancreatic cancers, especially PDAC. The use of varied and diverse datasets has provided valuable insights into different cancer types and can play an integral role in revealing the complex nature of underlying biological mechanisms. We performed subtyping of TCGA-PAAD gene expression and methylation datasets into different subtypes using state-of-the-art normalization methods and unsupervised clustering methods that reveal latent hidden factors, leading to additional insights for subtyping. Differential expression and differential methylation were performed for each of the subtypes obtained from clustering. Our analysis gave a consensus of five cluster solution with relevant pathways like MAPK, MET. The five subtypes corresponded to the tumor and stromal subtypes. This analysis helps in distinguishing and identifying different subtypes based on enriched putative genes. These results help propose novel experimentally-verifiable PDAC subtyping and demonstrate that using varied data sets and integrated methods can contribute to disease prognostication and precision medicine in PDAC treatment.
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Affiliation(s)
- Shikha Roy
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Amar Pratap Singh
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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24
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Huang W, Li H, Shi X, Lin M, Liao C, Zhang S, Shi W, Zhang L, Zhang X, Gan J. Characterization of genomic alterations in Chinese colorectal cancer patients. Jpn J Clin Oncol 2021; 51:120-129. [PMID: 33106877 DOI: 10.1093/jjco/hyaa182] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Colorectal cancer is one of the most prevalent types of cancer worldwide. Right-sided and left-sided colorectal cancer (RCC and LCC) patients respond differently to treatment. We aimed to identify the different mutational profile between RCC and LCC and provided evidence for future precision therapy. METHODS A total of 630 Chinese colorectal cancer patients, including 467 (74.1%) LCC and 163 (25.9%) RCC, were enrolled in this cohort. Both formalin-fixed paraffin-embedded tumor tissues and matching blood samples were collected and deep sequenced targeting 450 cancer genes for genomic alteration analysis. Tumor mutational burden was measured by an algorithm developed in-house. Correlation analysis was performed by Fisher's exact test. RESULTS The most common mutated genes were TP53 (77.0%), APC (71.7%), KRAS (50.0%), SMAD4 (19.8%), PIK3CA (18.3%), FBXW7 (17.5%), TCF7L2 (12.5%), SOX9 (11.3%), LRP1B (10.8%), ARID1A (10.3%) and FAT4 (10.3%). The mutation frequencies of TP53 and APC in LCC were significantly higher than that of RCC, while the mutation frequency of PIK3CA was lower than that of RCC. Six gene fusions were specifically detected in RCC patients. Colorectal cancer sites were associated with gender (P = 4.15 × 10-5) and tumor differentiation (P = 0.059). In LCC, the gender-associated genes were FAT4, EP300, FAT1, LRP1, ARID1B, AR, FYN and TAF1, while in RCC, they were ARID1A, SMARCA4, LRP1 and GRIN2A. The mutations of 18 genes were associated with tumor differentiation (8 for LCC and 10 for RCC). High tumor mutational burden was more common in RCC. Our results implied more potential targeted drug therapy opportunities for RCC. CONCLUSION We describe the different molecular characteristics of LCC and RCC. Our result supported a better prognosis of RCC than LCC in Chinese colorectal cancer patients.
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Affiliation(s)
- Wei Huang
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Hui Li
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | | | - Minglin Lin
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Cun Liao
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | | | | | - Lin Zhang
- Origimed Co. Ltd, Shanghai, P. R. China
| | - Xiaolong Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Jialiang Gan
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
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25
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Adam RS, van Neerven SM, Pleguezuelos-Manzano C, Simmini S, Léveillé N, de Groot NE, Holding AN, Markowetz F, Vermeulen L. Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development. Cancer Cell Int 2020; 20:578. [PMID: 33292279 PMCID: PMC7713000 DOI: 10.1186/s12935-020-01661-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 11/16/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Cancer results from the accumulation of mutations leading to the acquisition of cancer promoting characteristics such as increased proliferation and resistance to cell death. In colorectal cancer, an early mutation leading to such features usually occurs in the APC or CTNNB1 genes, thereby activating Wnt signalling. However, substantial phenotypic differences between cancers originating within the same organ, such as molecular subtypes, are not fully reflected by differences in mutations. Indeed, the phenotype seems to result from a complex interplay between the cell-intrinsic features and the acquired mutations, which is difficult to disentangle when established tumours are studied. METHODS We use a 3D in vitro organoid model to study the early phase of colorectal cancer development. From three different murine intestinal locations we grow organoids. These are transformed to resemble adenomas after Wnt activation through lentiviral transduction with a stable form of β-Catenin. The gene expression before and after Wnt activation is compared within each intestinal origin and across the three locations using RNA sequencing. To validate and generalize our findings, we use gene expression data from patients. RESULTS In reaction to Wnt activation we observe downregulation of location specific genes and differentiation markers. A similar effect is seen in patient data, where genes with significant differential expression between the normal left and right colon are downregulated in the cancer samples. Furthermore, the signature of Wnt target genes differs between the three intestinal locations in the organoids. The location specific Wnt signatures are dominated by genes which have been lowly expressed in the tissue of origin, and are the targets of transcription factors that are activated following enhanced Wnt signalling. CONCLUSION We observed that the region-specific cell identity has a substantial effect on the reaction to Wnt activation in a simple intestinal adenoma model. These findings provide a way forward in resolving the distinct biology between left- and right-sided human colon cancers with potential clinical relevance.
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Affiliation(s)
- Ronja S Adam
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sanne M van Neerven
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Salvatore Simmini
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Research & Development Department at STEMCELL Technologies UK, 7100 Cambridge Research Park, Beach Drive Waterbeach, Cambridge, CB25 9TL, UK
| | - Nicolas Léveillé
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Nina E de Groot
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Andrew N Holding
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- The Alan Turing Institute, 96 Euston Road, Kings Cross, London, NW1 2DB, UK
- University of York, Wentworth Way, York, YO10 5DD, UK
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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Jiang Y, Yan X, Liu K, Shi Y, Wang C, Hu J, Li Y, Wu Q, Xiang M, Zhao R. Discovering the molecular differences between right- and left-sided colon cancer using machine learning methods. BMC Cancer 2020; 20:1012. [PMID: 33076847 PMCID: PMC7574488 DOI: 10.1186/s12885-020-07507-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/07/2020] [Indexed: 12/24/2022] Open
Abstract
Background In recent years, the differences between left-sided colon cancer (LCC) and right-sided colon cancer (RCC) have received increasing attention due to the clinicopathological variation between them. However, some of these differences have remained unclear and conflicting results have been reported. Methods From The Cancer Genome Atlas (TCGA), we obtained RNA sequencing data and gene mutation data on 323 and 283 colon cancer patients, respectively. Differential analysis was firstly done on gene expression data and mutation data between LCC and RCC, separately. Machine learning (ML) methods were then used to select key genes or mutations as features to construct models to classify LCC and RCC patients. Finally, we conducted correlation analysis to identify the correlations between differentially expressed genes (DEGs) and mutations using logistic regression (LR) models. Results We found distinct gene mutation and expression patterns between LCC and RCC patients and further selected the 30 most important mutations and 17 most important gene expression features using ML methods. The classification models created using these features classified LCC and RCC patients with high accuracy (areas under the curve (AUC) of 0.8 and 0.96 for mutation and gene expression data, respectively). The expression of PRAC1 and BRAF V600E mutation (rs113488022) were the most important feature for each model. Correlations of mutations and gene expression data were also identified using LR models. Among them, rs113488022 was found to have significance relevance to the expression of four genes, and thus should be focused on in further study. Conclusions On the basis of ML methods, we found some key molecular differences between LCC and RCC, which could differentiate these two groups of patients with high accuracy. These differences might be key factors behind the variation in clinical features between LCC and RCC and thus help to improve treatment, such as determining the appropriate therapy for patients.
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Affiliation(s)
- Yimei Jiang
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Xiaowei Yan
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Kun Liu
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Yiqing Shi
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Changgang Wang
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Jiele Hu
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - You Li
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Qinghua Wu
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Ming Xiang
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China.
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China.
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Song J, Yang J, Lin R, Cai X, Zheng L, Chen Y. Molecular heterogeneity of guanine nucleotide binding-protein γ subunit 4 in left- and right-sided colon cancer. Oncol Lett 2020; 20:334. [PMID: 33123245 PMCID: PMC7584031 DOI: 10.3892/ol.2020.12197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022] Open
Abstract
Molecular heterogeneity determines the differences in the pathological features, prognosis and survival after relapse when comparing left-sided colon cancer (LCC) and right-sided colon cancer (RCC). At present, the discrepancy in the underlying molecular events between the two types of colon cancer has not been thoroughly investigated. The present study aimed to explore novel targets to predict the disease stage and prognosis of LCC and RCC. Expression analysis of guanine nucleotide binding-protein γ subunit 4 (GNG4) was performed using the Gene Expression Profiling Interactive Analysis (GEPIA) and Oncomine databases. Survival and association analyses were performed using GEPIA and the colon adenocarcinoma dataset from The Cancer Genome Atlas database. GNG4-positive cells in a tissue microarray were examined using immunohistochemistry. According to the GNG4 expression data from Caucasian patients included in the TCGA dataset, GNG4 was highly expressed and positively associated with pathological stage and overall survival (OS) rates in colon cancer. GNG4 expression was higher in LCC than in RCC. Patients with LCC with high GNG4 expression exhibited higher pathological stage and lower survival rates, whereas this was not observed in patients with RCC. In addition, the clinical tissues used in the microarray showed that GNG4 expression was increased in Chinese patients with LCC compared with that in patients with RCC. Consistently, GNG4 expression was negatively associated with OS in patients with LCC, but not in patients with RCC. However, no association was observed between GNG4 expression and the disease stage of colon cancer in both patients with LCC and RCC. Overall, the molecular heterogeneity of GNG4 in LCC and RCC suggests that GNG4 may be used as a diagnostic and prognostic biomarker in patients with LCC.
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Affiliation(s)
- Jintian Song
- Department of Abdominal Oncology, The Affiliated Cancer Hospital of Fujian Medical University, Fuzhou, Fujian 350014, P.R. China
| | - Jianwei Yang
- Department of Abdominal Oncology, The Affiliated Cancer Hospital of Fujian Medical University, Fuzhou, Fujian 350014, P.R. China
| | - Rongbo Lin
- Department of Abdominal Oncology, The Affiliated Cancer Hospital of Fujian Medical University, Fuzhou, Fujian 350014, P.R. China
| | - Xiongchao Cai
- Department of Abdominal Oncology, The Affiliated Cancer Hospital of Fujian Medical University, Fuzhou, Fujian 350014, P.R. China
| | - Liang Zheng
- Department of Abdominal Oncology, The Affiliated Cancer Hospital of Fujian Medical University, Fuzhou, Fujian 350014, P.R. China
| | - Yigui Chen
- Department of Abdominal Oncology, The Affiliated Cancer Hospital of Fujian Medical University, Fuzhou, Fujian 350014, P.R. China
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Quraishi MN, Acharjee A, Beggs AD, Horniblow R, Tselepis C, Gkoutos G, Ghosh S, Rossiter AE, Loman N, van Schaik W, Withers D, Walters JRF, Hirschfield GM, Iqbal TH. A Pilot Integrative Analysis of Colonic Gene Expression, Gut Microbiota, and Immune Infiltration in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Association of Disease With Bile Acid Pathways. J Crohns Colitis 2020; 14:935-947. [PMID: 32016358 PMCID: PMC7392170 DOI: 10.1093/ecco-jcc/jjaa021] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Although a majority of patients with PSC have colitis [PSC-IBD; primary sclerosing cholangitis-inflammatory bowel disease], this is phenotypically different from ulcerative colitis [UC]. We sought to define further the pathophysiological differences between PSC-IBD and UC, by applying a comparative and integrative approach to colonic gene expression, gut microbiota and immune infiltration data. METHODS Colonic biopsies were collected from patients with PSC-IBD [n = 10], UC [n = 10], and healthy controls [HC; n = 10]. Shotgun RNA-sequencing for differentially expressed colonic mucosal genes [DEGs], 16S rRNA analysis for microbial profiling, and immunophenotyping were performed followed by multi-omic integration. RESULTS The colonic transcriptome differed significantly between groups [p = 0.01]. Colonic transcriptomes from HC were different from both UC [1343 DEGs] and PSC-IBD [4312 DEGs]. Of these genes, only 939 had shared differential gene expression in both UC and PSC-IBD compared with HC. Imputed pathways were predominantly associated with upregulation of immune response and microbial defense in both disease cohorts compared with HC. There were 1692 DEGs between PSC-IBD and UC. Bile acid signalling pathways were upregulated in PSC-IBD compared with UC [p = 0.02]. Microbiota profiles were different between the three groups [p = 0.01]; with inferred function in PSC-IBD also being consistent with dysregulation of bile acid metabolism. Th17 cells and IL17-producing CD4 cells were increased in both PSC-IBD and UC when compared with HC [p < 0.05]. Multi-omic integration revealed networks involved in bile acid homeostasis and cancer regulation in PSC-IBD. CONCLUSIONS Colonic transcriptomic and microbiota analysis in PSC-IBD point toward dysregulation of colonic bile acid homeostasis compared with UC. This highlights important mechanisms and suggests the possibility of novel approaches in treating PSC-IBD.
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Affiliation(s)
- Mohammed Nabil Quraishi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Department of Gastroenterology, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, UK
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
| | - Animesh Acharjee
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University Hospitals Birmingham, Birmingham, UK
| | - Andrew D Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Richard Horniblow
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Chris Tselepis
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Georgios Gkoutos
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University Hospitals Birmingham, Birmingham, UK
- MRC Health Data Research UK [HDR UK], Wellcome Trust, London, UK
- NIHR Experimental Cancer Medicine Centre, NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham, UK
| | - Subrata Ghosh
- Department of Gastroenterology, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, UK
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University Hospitals Birmingham, Birmingham, UK
| | - A E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Nicholas Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - David Withers
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | | | - Gideon M Hirschfield
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
- Toronto Centre for Liver Disease, University of Toronto, Toronto General Hospital, Toronto, ON, Canada
| | - Tariq H Iqbal
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Department of Gastroenterology, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, UK
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Centre for Liver and Gastroenterology Research, NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
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Yang H, Jin W, Liu H, Wang X, Wu J, Gan D, Cui C, Han Y, Han C, Wang Z. A novel prognostic model based on multi-omics features predicts the prognosis of colon cancer patients. Mol Genet Genomic Med 2020; 8:e1255. [PMID: 32396280 PMCID: PMC7336766 DOI: 10.1002/mgg3.1255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background As a common malignant tumor in the colon, colon cancer (CC) has high incidence and recurrence rates. This study is designed to build a prognostic model for CC. Methods The gene expression dataset, microRNA‐seq dataset, copy number variation (CNV) dataset, DNA methylation dataset, and transcription factor (TF) dataset of CC were downloaded from UCSC Xena database. Using limma package, the differentially methylated genes (DMGs), and differentially expressed genes (DEGs) and miRNAs (DEMs) were identified. Based on random forest method, prognostic model for each omics dataset were constructed. After the omics features related to prognosis were selected using logrank test, the prognostic model based on multi‐omics features was built. Finally, the clinical phenotypes correlated with prognosis were screened using Kaplan–Meier survival analysis, and the nomogram model was established. Results There were 1625 DEGs, 268 DEMs, and 386 DMGs between the tumor and normal samples. A total of 105, 29, 159, five, and six genes/sites significantly correlated with prognosis were identified in the gene expression dataset (GABRD), miRNA‐seq dataset (miR‐1271), CNV dataset (RN7SKP247), DNA methylation dataset (cg09170112 methylation site [located in SFSWAP]), and TF dataset (SIX5), respectively. The prognostic model based on multi‐omics features was more effective than those based on single omics dataset. The number of lymph nodes, pathologic_M stage, and pathologic_T stage were the clinical phenotypes correlated with prognosis, based on which the nomogram model was constructed. Conclusion The prognostic model based on multi‐omics features and the nomogram model might be valuable for the prognostic prediction of CC.
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Affiliation(s)
- Haojie Yang
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Jin
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hua Liu
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoxue Wang
- Department of Coloproctology, The Sixth Affiliated Hospital of Sun Yat-sen University (Gastrointestinal & Anal Hospital of Sun Yat-sen University), Guangzhou, China
| | - Jiong Wu
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dan Gan
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Can Cui
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yilin Han
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Changpeng Han
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhenyi Wang
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Salem ME, Battaglin F, Goldberg RM, Puccini A, Shields AF, Arguello D, Korn WM, Marshall JL, Grothey A, Lenz H. Molecular Analyses of Left- and Right-Sided Tumors in Adolescents and Young Adults with Colorectal Cancer. Oncologist 2020; 25:404-413. [PMID: 31848314 PMCID: PMC7216442 DOI: 10.1634/theoncologist.2019-0552] [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: 07/22/2019] [Accepted: 09/13/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The incidence of colorectal cancer (CRC), particularly left-sided tumors (LT), in adolescents and young adults (AYA) is rising. Epigenetic events appear to play an important role in tumorigenesis and cancer progression, especially in younger patients. We compared molecular features of LT to right-sided tumors (RT) in AYA. MATERIALS AND METHODS A total of 246 LT and 56 RT were identified in a cohort of 612 AYA with primary CRC. Tumors were examined by next-generation sequencing (NGS), protein expression, and gene amplification. Tumor mutational burden (TMB) and microsatellite instability (MSI) were determined based on NGS data. RESULTS RT showed higher mutation rates compared with LT in several genes including BRAF (10.3% vs. 2.8%), KRAS (64.1% vs. 45.5%), PIK3CA (27% vs. 11.2%), and RNF43 (24.2% vs. 2.9%). Notably, additional mutations in distinct genes involved in histone modification and chromatin remodeling, as well as genes associated with DNA repair and cancer-predisposing syndromes, were characteristic of RT; most frequently KMT2D (27.8% vs. 3.4%), ARID1A (53.3% vs. 21.4%), MSH6 (11.1% vs. 2.3%), MLH1 (10.5% vs. 2.3%), MSH2 (10.5% vs. 1.2%), POLE (5.9% vs. 0.6%), PTEN (10.8% vs. 2.3%), and BRCA1 (5.4% vs. 0.6%). MSI was seen in 20.8% of RT versus 4.8% of LT. RT had a higher frequency of TMB-high regardless of MSI status. CONCLUSION Molecular profiling of AYA CRC revealed different molecular characteristics in RT versus LT. Epigenetic mechanisms and alteration in DNA repair genes warrant further investigation and may be a promising treatment target for CRC in AYA. IMPLICATIONS FOR PRACTICE Colorectal cancer (CRC) in adolescents and young adults (AYA) comprises a distinct entity with different clinicopathologic features and prognosis compared with older patients. Molecular profiling of right- and left-sided tumors in AYA is needed to gain novel insight into CRC biology and to tailor targeted treatment in this age group. This study found that right- and left-sided CRC show distinct molecular features in AYA, overall and in subgroups based on microsatellite instability status. Alterations in DNA double-strand break repair and homologous recombination repair, as well as epigenetic mechanisms, appear to play a critical role. The present molecular profiling data may support the development of personalized treatment strategies in the AYA population.
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Affiliation(s)
- Mohamed E. Salem
- Department of Medical Oncology, Levine Cancer Institute, Atrium HealthCharlotteNorth CarolinaUSA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | | | - Alberto Puccini
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, University of GenoaItaly
| | - Anthony F. Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State UniversityDetroitMichiganUSA
| | | | - W. Michael Korn
- Caris Life SciencesPhoenixArizonaUSA
- University of California at San FranciscoSan FranciscoCaliforniaUSA
| | - John L. Marshall
- The Ruesch Center and Georgetown Lombardi Comprehensive Cancer CenterWashingtonDCUSA
| | | | - Heinz‐Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
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Mukund K, Syulyukina N, Ramamoorthy S, Subramaniam S. Right and left-sided colon cancers - specificity of molecular mechanisms in tumorigenesis and progression. BMC Cancer 2020; 20:317. [PMID: 32293332 PMCID: PMC7161305 DOI: 10.1186/s12885-020-06784-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
Background Given the differences in embryonic origin, vascular and nervous supplies, microbiotic burden, and main physiological functions of left and right colons, tumor location is increasingly suggested to dictate tumor behavior affecting pathology, progression and prognosis. Right-sided colon cancers arise in the cecum, ascending colon, hepatic flexure and/or transverse colon, while left-sided colon cancers arise in the splenic flexure, descending, and/or sigmoid colon. In contrast to prior reports, we attempt to delineate programs of tumorigenesis independently for each side. Methods Four hundred and eleven samples were extracted from The Cancer Genome Atlas-COAD cohort, based on a conservative sample inclusion criterion. Each side was independently analyzed with respect to their respective normal tissue, at the level of transcription, post-transcription, miRNA control and methylation in both a stage specific and stage-agnostic manner. Results Our results indicate a suppression of enzymes involved in various stages of carcinogen breakdown including CYP2C8, CYP4F12, GSTA1, and UGT1A within right colon tumors. This implies its reduced capacity to detoxify carcinogens, contributing to a genotoxic tumor environment, and subsequently a more aggressive phenotype. Additionally, we highlight a crucial nexus between calcium homeostasis (sensing, mobilization and absorption) and immune/GPCR signaling within left-sided tumors, possibly contributing to its reduced proliferative and metastatic potential. Interestingly, two genes SLC6A4 and HOXB13 show opposing regulatory trends within right and left tumors. Post-transcriptional regulation mediated by both RNA-binding proteins (e.g. NKRF (in left) and MSI2 (in right)) and miRNAs (e.g. miR-29a (in left); miR-155, miR181-d, miR-576 and miR23a (in right)) appear to exhibit side-specificity in control of their target transcripts and is pronounced in right colon tumors. Additionally, methylation results depict location-specific differences, with increased hypomethylation in open seas within left tumors, and increased hypermethylation of CpG islands within right tumors. Conclusions Differences in molecular mechanisms captured here highlight distinctions in tumorigenesis and progression between left and right colon tumors, which will serve as the basis for future studies, influencing the efficacies of existing and future diagnostic, prognostic and therapeutic interventions.
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Affiliation(s)
- Kavitha Mukund
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Natalia Syulyukina
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Sonia Ramamoorthy
- Division of Colon and Rectal Surgery, Moores Cancer Center, University of California San Diego Health System, La Jolla, CA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. .,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
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Sinicrope FA, Shi Q, Hermitte F, Zemla TJ, Mlecnik B, Benson AB, Gill S, Goldberg RM, Kahlenberg MS, Nair SG, Shields AF, Smyrk TC, Galon J, Alberts SR. Contribution of Immunoscore and Molecular Features to Survival Prediction in Stage III Colon Cancer. JNCI Cancer Spectr 2020; 4:pkaa023. [PMID: 32455336 PMCID: PMC7236783 DOI: 10.1093/jncics/pkaa023] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/17/2020] [Accepted: 03/24/2020] [Indexed: 12/23/2022] Open
Abstract
Background The American Joint Committee on Cancer staging and other prognostic tools fail to account for stage-independent variability in outcome. We developed a prognostic classifier adding Immunoscore to clinicopathological and molecular features in patients with stage III colon cancer. Methods Patient (n = 559) data from the FOLFOX arm of adjuvant trial NCCTG N0147 were used to construct Cox models for predicting disease-free survival (DFS). Variables included age, sex, T stage, positive lymph nodes (+LNs), N stage, performance status, histologic grade, sidedness, KRAS/BRAF, mismatch repair, and Immunoscore (CD3+, CD8+ T-cell densities). After determining optimal functional form (continuous or categorical) and within Cox models, backward selection was performed to analyze all variables as candidate predictors. All statistical tests were two-sided. Results Poorer DFS was found for tumors that were T4 vs T3 (hazard ratio [HR] = 1.76, 95% confidence interval [CI] = 1.19 to 2.60; P = .004), right- vs left-sided (HR = 1.52, 95% CI = 1.14 to 2.04; P = .005), BRAF V600E (HR = 1.74, 95% CI = 1.26 to 2.40; P < .001), mutant KRAS (HR = 1.66, 95% CI = 1.08 to 2.55; P = .02), and low vs high Immunoscore (HR = 1.69, 95% CI = 1.22 to 2.33; P = .001) (all P < .02). Increasing numbers of +LNs and lower continuous Immunoscore were associated with poorer DFS that achieved significance (both Ps< .0001). After number of +LNs, T stage, and BRAF/KRAS, Immunoscore was the most informative predictor of DFS shown multivariately. Among T1–3 N1 tumors, Immunoscore was the only variable associated with DFS that achieved statistical significance. A nomogram was generated to determine the likelihood of being recurrence-free at 3 years. Conclusions The Immunoscore can enhance the accuracy of survival prediction among patients with stage III colon cancer.
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Affiliation(s)
- Frank A Sinicrope
- Division of Oncology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Qian Shi
- Alliance Statistics and Data Center, Rochester, MN, USA
| | | | - Tyler J Zemla
- Alliance Statistics and Data Center, Rochester, MN, USA
| | - Bernhard Mlecnik
- INSERM, UMRS 1138, Laboratory of Integrative Cancer Immunology, Université Paris Descartes, Paris, France.,Inovarion, Paris, France
| | | | - Sharlene Gill
- British Columbia Cancer Agency- Vancouver Cancer Centre, Vancouver, BC, Canada
| | | | | | | | | | - Thomas C Smyrk
- Division of Oncology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jerome Galon
- INSERM, UMRS 1138, Laboratory of Integrative Cancer Immunology, Université Paris Descartes, Paris, France
| | - Steven R Alberts
- Division of Oncology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
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Lee JD, Kim HY, Kang K, Jeong HG, Song MK, Tae IH, Lee SH, Kim HR, Lee K, Chae S, Hwang D, Kim S, Kim HS, Kim KB, Lee BM. Integration of transcriptomics, proteomics and metabolomics identifies biomarkers for pulmonary injury by polyhexamethylene guanidine phosphate (PHMG-p), a humidifier disinfectant, in rats. Arch Toxicol 2020; 94:887-909. [PMID: 32080758 DOI: 10.1007/s00204-020-02657-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 02/03/2020] [Indexed: 12/16/2022]
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34
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Xie B, Bai B, Xu Y, Liu Y, Lv Y, Gao X, Wu F, Fang Z, Lou Y, Pan H, Han W. Tumor-suppressive function and mechanism of HOXB13 in right-sided colon cancer. Signal Transduct Target Ther 2019; 4:51. [PMID: 31815008 PMCID: PMC6882800 DOI: 10.1038/s41392-019-0086-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/07/2019] [Accepted: 10/10/2019] [Indexed: 01/05/2023] Open
Abstract
Right-sided colon cancer (RCC) and left-sided colon cancer (LCC) differ in their clinical and molecular features. An investigation of differentially expressed genes (DEGs) between RCC and LCC could contribute to targeted therapy for colon cancer, especially RCC, which has a poor prognosis. Here, we identified HOXB13, which was significantly less expressed in RCC than in LCC and associated with prognosis in RCC, by using 5 datasets from the Gene Expression Omnibus (GEO). Tissue sample analysis showed that HOXB13 was differentially expressed between normal and only RCC tumor tissues. HOXB13 inhibited colon cancer cell proliferation and induced apoptosis both in vitro and in vivo. Furthermore, we found that HOXB13 might be regulated by DNMT3B and suppress C-myc expression to exert antitumor effects via β-catenin/TCF4 signals in RCC. In conclusion, the current study is the first to demonstrate that HOXB13 has a tumor-suppressive effect in RCC. High expression levels of HOXB13 are associated with prolonged overall survival in patients with RCC. The DNMT3B-HOXB13-C-myc signaling axis might be a molecular target for the treatment of RCC.
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Affiliation(s)
- Binbin Xie
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Bingjun Bai
- Department of Colorectal Surgery; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Yuzi Xu
- Department of Stomatology; Stomatology Hospital; School of Medicine, Zhejiang University, Hangzhou, 310000 PR China
| | - Yunlong Liu
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Yiming Lv
- Department of Colorectal Surgery; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Xing Gao
- Department of Medical Oncology; The Second Affiliated Hospital of Suzhou University; School of Medicine, Suzhou University, Suzhou, 215000 PR China
| | - Fei Wu
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001 PR China
| | - Zhipeng Fang
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Ying Lou
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Hongming Pan
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Weidong Han
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
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35
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Sun Y, Mironova V, Chen Y, Lundh EPF, Zhang Q, Cai Y, Vasiliou V, Zhang Y, Garcia-Milian R, Khan SA, Johnson CH. Molecular Pathway Analysis Indicates a Distinct Metabolic Phenotype in Women With Right-Sided Colon Cancer. Transl Oncol 2019; 13:42-56. [PMID: 31760268 PMCID: PMC6883319 DOI: 10.1016/j.tranon.2019.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/17/2022] Open
Abstract
Colon cancer is the third most commonly diagnosed cancer in the United States. Recent reports have shown that the location of the primary tumor is of clinical importance. Patients with right-sided colon cancers (RCCs) (tumors arising between the cecum and proximal transverse colon) have poorer clinical outcomes than those with left-sided colon cancers (LCCs) (tumors arising between the distal transverse colon and sigmoid colon, excluding the rectum). Interestingly, women have a lower incidence of colon cancer than men, but have a higher propensity for RCC. The reason for this difference is not known; however, identification of sex-specific differences in gene expression by tumor anatomical location in the colon could provide further insight. Moreover, it could reveal important predictive markers for response to various treatments. This study provides a comprehensive bioinformatic analysis of various genes and molecular pathways that correlated with sex and anatomical location of colon cancers using four publicly available annotated data sets housed in the National Center for Biotechnology Information's Gene Expression Omnibus. We identified differentially expressed genes in tumor tissues from women with RCC, which showed attenuated energy and nutrient metabolism when compared with women with LCC. Specifically, we showed the downregulation of 5′ AMP-activated protein kinase alpha subunit (AMPKα) and anti-tumor immune responses in women with RCC. This difference was not seen when comparing tumor tissues from men with RCC to men with LCC. Therefore, women with RCC may have a specific metabolic and immune phenotype which accounts for differences in prognosis and treatment response.
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Affiliation(s)
- Yazhi Sun
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Varvara Mironova
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA; Department of Surgery, Section of Surgical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Ying Chen
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Elliott P F Lundh
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Qian Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA; Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuping Cai
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA; Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Rolando Garcia-Milian
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA; Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale School of Medicine, New Haven, CT, USA
| | - Sajid A Khan
- Department of Surgery, Section of Surgical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Caroline H Johnson
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT USA.
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36
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Hu W, Yang Y, Qi L, Chen J, Ge W, Zheng S. Subtyping of microsatellite instability-high colorectal cancer. Cell Commun Signal 2019; 17:79. [PMID: 31331345 PMCID: PMC6647262 DOI: 10.1186/s12964-019-0397-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/15/2019] [Indexed: 12/12/2022] Open
Abstract
Background Patients with microsatellite instability-high (MSI-H) colorectal cancer (CRC) generally have a better prognosis than patients with microsatellite stable (MSS) CRC. However, some MSI-H CRC patients do not gain overall survival benefits from immune checkpoint-blockade treatment. In other words, heterogeneity within the subgroup of MSI-H tumors remains poorly understood. Thus, an in-depth molecular characterization of MSI-H tumors is urgently required. Methods Here, we use nonnegative matrix factorization (NMF)-based consensus clustering to define CRC MSI-H subtypes in The Cancer Genome Atlas and a French multicenter cohort GSE39582. CIBERSORT was used to calculate the proportions of 22 lymphocytes in tumor tissue in MSI-H subtypes. Results MSI-H CRC samples basically clustered into two subgroups (MSI-H1 and MSI-H2). MSI-H1 was characterized by a lower BRAF mutational status, higher frequency of chromosomal instability, global hypomethylation, and worse survival than MSI-H2. Further examination of the immune landscape showed that macrophages of the M2 phenotype were enriched in MSI-H1, which may be associated with poor prognosis in this subgroup. Conclusions Our results illustrate the genetic heterogeneity in MSI-H CRCs and macrophages may serve as good targets for anticancer therapy in MSI-H1. Graphical abstract ![]()
Electronic supplementary material The online version of this article (10.1186/s12964-019-0397-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wangxiong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310009, Hangzhou, China.
| | - Yanmei Yang
- Key Laboratory of Reproductive and Genetics, Ministry of Education, Women's Hospital, Zhejiang University School of Medicine, Zhejiang, 310006, Hangzhou, China
| | - Lina Qi
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310009, Hangzhou, China
| | - Jiani Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310009, Hangzhou, China
| | - Weiting Ge
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310009, Hangzhou, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310009, Hangzhou, China.
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37
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Imperial R, Ahmed Z, Toor OM, Erdoğan C, Khaliq A, Case P, Case J, Kennedy K, Cummings LS, Melton N, Raza S, Diri B, Mohammad R, El-Rayes B, Pluard T, Hussain A, Subramanian J, Masood A. Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profiles. Mol Cancer 2018; 17:177. [PMID: 30577807 PMCID: PMC6303985 DOI: 10.1186/s12943-018-0923-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/30/2018] [Indexed: 12/27/2022] Open
Abstract
Right-sided colon cancer (RCC) has worse prognosis compared to left-sided colon cancer (LCC) and rectal cancer. The reason for this difference in outcomes is not well understood. We performed comparative somatic and proteomic analyses of RCC, LCC and rectal cancers to understand the unique molecular features of each tumor sub-types. Utilizing a novel in silico clonal evolution algorithm, we identified common tumor-initiating events involving APC, KRAS and TP53 genes in RCC, LCC and rectal cancers. However, the individual role-played by each event, their order in tumor development and selection of downstream somatic alterations were distinct in all three anatomical locations. Some similarities were noted between LCC and rectal cancer. Hotspot mutation analysis identified a nonsense mutation, APC R1450* specific to RCC. In addition, we discovered new significantly mutated genes at each tumor location, Further in silico proteomic analysis, developed by our group, found distinct central or hub proteins with unique interactomes among each location. Our study revealed significant differences between RCC, LCC and rectal cancers not only at somatic but also at proteomic level that may have therapeutic relevance in these highly complex and heterogeneous tumors.
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Affiliation(s)
- Robin Imperial
- Department of Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
| | - Zaheer Ahmed
- Department of Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
| | - Omer M Toor
- Department of Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA.,Division of Oncology, Saint Luke's Cancer Institute, University of Missouri School of Medicine, 4321 Washington St, Kansas City, MO, 64111, USA
| | - Cihat Erdoğan
- Department of Computer Engineering, Namik Kemal University, Tekirdag, Turkey
| | - Ateeq Khaliq
- Division of Oncology, Saint Luke's Cancer Institute, University of Missouri School of Medicine, 4321 Washington St, Kansas City, MO, 64111, USA
| | - Paul Case
- Division of Oncology, Saint Luke's Cancer Institute, University of Missouri School of Medicine, 4321 Washington St, Kansas City, MO, 64111, USA
| | - James Case
- ASPIRE Foundation, Saint Luke's Health System of Kansas City, Kansas City, MO, 64111, USA
| | - Kevin Kennedy
- Division of Cardiovascular Research, Saint Luke's Hospital, Kansas City, MO, 64111, USA
| | - Lee S Cummings
- Department of Surgery, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Niklas Melton
- Department of Computer Sciences, Missouri University of Science and Technology, Rolla, MO, 65409, USA
| | - Shahzad Raza
- Department of Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA.,Division of Oncology, Saint Luke's Cancer Institute, University of Missouri School of Medicine, 4321 Washington St, Kansas City, MO, 64111, USA
| | - Banu Diri
- Department of Computer Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Ramzi Mohammad
- Wayne State University, Karmanos Cancer Institute, Detroit, MI, 48201, USA
| | - Bassel El-Rayes
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Timothy Pluard
- Department of Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA.,Division of Oncology, Saint Luke's Cancer Institute, University of Missouri School of Medicine, 4321 Washington St, Kansas City, MO, 64111, USA
| | - Arif Hussain
- Division of Oncology, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD, 20201, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, MD, 21201, USA
| | - Janakiraman Subramanian
- Department of Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA. .,Division of Oncology, Saint Luke's Cancer Institute, University of Missouri School of Medicine, 4321 Washington St, Kansas City, MO, 64111, USA.
| | - Ashiq Masood
- Division of Hematology/Oncology and Cell Therapy, Rush University Medical Center, Chicago, IL, 60612, USA.
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38
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Hu W, Yang Y, Ge W, Zheng S. Deciphering molecular properties of hypermutated gastrointestinal cancer. J Cell Mol Med 2018; 23:370-379. [PMID: 30381870 PMCID: PMC6307802 DOI: 10.1111/jcmm.13941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/17/2022] Open
Abstract
Great mutational heterogeneity is observed both across cancer types (>1000-fold) and within a given cancer type, with a fraction harboring >10 mutations per million bases, thus termed hypermutation. We determined the genome-wide effects of high mutation load on the transcriptome and methylome of two cancer types; namely, colorectal cancer (CRC) and stomach adenocarcinoma (STAD). Briefly, hierarchical clustering of the expression and methylation profiles showed that the majority of CRC and STAD hypermutated samples were mixed and separated from their respective non-hypermutated samples, exceeding the boundary of tissue specificity. Further in-detailed exploration uncovered that the underlying molecular mechanism may be related to the perturbation of chromatin remodeling genes.
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Affiliation(s)
- Wangxiong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Yanmei Yang
- Key Laboratory of Reproductive and Genetics, Ministry of Education, Women's Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Weiting Ge
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
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39
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Deng K, Han P, Song W, Wang Z, Zhang F, Xie H, Zhao W, Xu H, Cai Y, Rong Z, Yu X, Cui BB, Li K. Plasma metabolomic profiling distinguishes right-sided from left-sided colon cancer. Clin Chim Acta 2018; 487:357-362. [PMID: 30296444 DOI: 10.1016/j.cca.2018.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 09/24/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Many studies have demonstrated that right-sided colon cancer (RCC) has a higher mortality rate and worse prognosis than left-sided colon cancer (LCC). However, the underlying biological mechanism that can account for these differences is unclear. METHODS In this study, plasma metabolic profiles in 147 LCC patients and 105 RCC patients were systematically analyzed by the ultra high performance liquid chromatography quadruple time-of-flight mass spectrometry (UHPLC-QTOF/MS) platform in conjunction with univariate and multivariate statistical analysis. RESULTS Metabolic signatures revealed considerable differences between patients with RCC and LCC, and clear separations were observed between the two groups in partial least-squares discriminant analysis score plots. In total, six metabolites were identified as potential metabolite markers for tumor location in RCC compared with LCC, including upregulated trimethylamine N-oxide and indoxyl sulfate, and downregulated anserine, L-targinine, gamma-glutamyl-gamma-aminobutyraldehyde and pyridoxal 5'-phosphate. These differences highlight that significant alternations occur in the pathways of methane metabolism, arginine and proline metabolism, histidine metabolism, beta-alanine metabolism and vitamin B6 metabolism in RCC compared with LCC. CONCLUSIONS Identified biomarkers and metabolic pathways may facilate our understanding of the different mortality rates and prognoses between RCC and LCC.
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Affiliation(s)
- Kui Deng
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Peng Han
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin 150086, China
| | - Wei Song
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Zhuozhong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Fan Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Hongyu Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Weiwei Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Huan Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Yuqing Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Zhiwei Rong
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Xiwen Yu
- Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin 150086, China
| | - Bin-Bin Cui
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin 150086, China.
| | - Kang Li
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China.
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