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Data Mining, Network Pharmacology, and Molecular Docking Explore the Effects of Core Traditional Chinese Medicine Prescriptions in Patients with Rectal Cancer and Qi and Blood Deficiency Syndrome

Shiyu Ma, Lin Zheng, Lan Zheng, Xiaolan Bian, Swee Keong Yeap
2021 Evidence-Based Complementary and Alternative Medicine  
In this study, we elucidated the core prescriptions for patients with rectal cancer and Qi and blood deficiency syndrome, and we explored the potential mechanisms of the prescriptions using an integrated  ...  Network pharmacology identified 15 high-degree active ingredients among the 3 core prescriptions and 16 high-degree hub genes linked with both rectal cancer and the 3 core prescriptions.  ...  in FuZhengXiaoJi therapy for the intervention of Qi deficiency and blood stasis in patients with type III gastric cancer (2020LZ007). e authors thank Dr.  ... 
doi:10.1155/2021/1353674 pmid:34394377 pmcid:PMC8360715 fatcat:n4egzhj7dbbwtkgcayodozigqe

Integrated genomic profiling identifies microRNA-92a regulation of IQGAP2 in locally advanced rectal cancer

Raphael Pelossof, Oliver S. Chow, Lauren Fairchild, J. Joshua Smith, Manu Setty, Chin-Tung Chen, Zhenbin Chen, Fumiko Egawa, Karin Avila, Christina S. Leslie, Julio Garcia-Aguilar
2016 Genes, Chromosomes and Cancer  
We show that endogenous miR-92a expression is inversely associated with endogenous KLF4 expression in multiple cell lines, and that this relationship is also present in rectal cancers of TCGA.  ...  Our integrative model predicted regulators of gene expression change in LARC using pre-treatment FFPE tissues.  ...  We acknowledge with appreciation the specimen donors and research groups, and their contributions to that work.  ... 
doi:10.1002/gcc.22329 pmid:26865277 pmcid:PMC4755360 fatcat:ochx4glbzfeupmhbcmy4fgtbtu

Screening candidate microRNA-mRNA regulatory pairs for predicting the response to chemoradiotherapy in rectal cancer by a bioinformatics approach

Qiliang Peng, Junjia Zhu, Peipei Shen, Wenyan Yao, Yu Lei, Li Zou, Yingying Xu, Yuntian Shen, Yaqun Zhu
2017 Scientific Reports  
Extensive efforts have been undertaken in search of biomarkers for predicting the chemoradiotherapy response in rectal cancer.  ...  Pathway analysis and literature validation revealed that the mRNA lists were highly related to the ionizing radiation.  ...  Based on the above comprehensive functional analysis and validation in PubMed, the identified miRNAs and the two lists of mRNAs provide potential miRNA-mRNA regulatory pairs as network biomarkers for predicting  ... 
doi:10.1038/s41598-017-11840-7 pmid:28900297 pmcid:PMC5595906 fatcat:zybp6hiumrco5ave6emgbpe3hi

Natural killer-like signature observed post therapy in locally advanced rectal cancer is a determinant of pathological response and improved survival

Matthew Alderdice, Philip D Dunne, Aidan J Cole, Paul G O'Reilly, Darragh G McArt, Vicky Bingham, Marc-Aurel Fuchs, Stephen McQuaid, Maurice B Loughrey, Graeme I Murray, Leslie M Samuel, Mark Lawler (+3 others)
2017 Modern Pathology  
To this end, we performed high-throughput gene expression profiling in 40 pairs of formalin-fixed paraffin-embedded rectal cancer biopsies and matched resections following long-course preoperative chemoradiotherapy  ...  Enumeration of the tumor microenvironment cell population was undertaken using in silico analysis of the transcriptional data, and real-time PCR validation of NCR1 undertaken.  ...  These are supported by the Research and Development Division of the N. Ireland Public Health Agency and Cancer Research UK.  ... 
doi:10.1038/modpathol.2017.47 pmid:28621318 fatcat:osjkrf7dubc3jaz4osjs6kxmze

Circadian Clock Genes Are Correlated with Prognosis and Immune Cell Infiltration in Colon Adenocarcinoma

Aoxiao He, Zhihao Huang, Rongguiyi Zhang, Hongcheng Lu, Jiakun Wang, Jiaqing Cao, Qian Feng, Peng Li
2022 Computational and Mathematical Methods in Medicine  
Genomic data obtained from The Cancer Genome Atlas (TCGA) database was analyzed for expression level, mutation status, potential biological functions, and prognostic performance of core circadian clock  ...  Dysfunction of circadian clock genes and disruption of normal rhythms are associated with the occurrence and progression of many cancer types.  ...  GJJ180083), the Science and Technology Project of Health Commission of Jiangxi Province (No. 20204266), and the Traditional Chinese Medicine Science and Technology Project of Jiangxi Province (No. 2019A015  ... 
doi:10.1155/2022/1709918 pmid:35116071 pmcid:PMC8807038 fatcat:w2c322mt6rgyrdaecjamj2dzmu

Genetic predisposition to colon and rectal adenocarcinoma is mediated by a super-enhancer polymorphism co-activating CD9 and PLEKHG6

Juntao Ke, Jianbo Tian, Shufang Mei, Pingting Ying, Nan Yang, Xiaoyang Wang, Danyi Zou, Xiating Peng, Yang Yang, Ying Zhu, Yajie Gong, Zhihua Wang (+4 others)
2020 Cancer Epidemiology, Biomarkers and Prevention  
Through a comprehensive bioinformatics analysis on multi-omics data, we screen potential single nucleotide polymorphisms (SNPs) in cancer-specific SEs, and then subject them to a two-stage case-control  ...  of CD9 and PLEKHG6 which are both putative tumor suppressor genes for colon and rectal adenocarcinoma.  ...  In this study, we screened potential SNPs via a comprehensive bioinformatics analysis on multi-omics data, evaluated their associations with risk of colon and rectal adenocarcinoma in a two-stage case-control  ... 
doi:10.1158/1055-9965.epi-19-1116 pmid:31988071 fatcat:imtq6qpvdff7nethp3lmbh4yse

An Immune-Related Gene Signature for Predicting Neoadjuvant Chemoradiotherapy Efficacy in Rectal Carcinoma

Liwen Qian, Xiaojing Lai, Benxing Gu, Xiaonan Sun
2022 Frontiers in Immunology  
BackgroundLocally advanced rectal cancers (LARC) show a highly variable response to neoadjuvant chemoradiotherapy (nCRT), and the impact of the tumor immune response in this process is poorly understood  ...  and clinical data of Rectal carcinoma from the Gene Expression Omnibus database and Immune-related genes (IRGs) from ImmPort were downloaded to identify the differentially expressed immune-related genes  ...  Three independent datasets were enrolled in our study (Table 1 ). Initially, we focused on gene expression profiles (GEP) of rectal carcinoma to reveal the underlying mechanism of rectal cancer.  ... 
doi:10.3389/fimmu.2022.784479 fatcat:rl7mbbcwlbfi3h3mhvdrsxlf7q

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

Katarzyna Tomczak, Patrycja Czerwińska, Maciej Wiznerowicz
2015 Contemporary Oncology  
The Cancer Genome Atlas (TCGA) is a public funded project that aims to catalogue and discover major cancer-causing genomic alterations to create a comprehensive "atlas" of cancer genomic profiles.  ...  Studies of individual cancer types, as well as comprehensive pan-cancer analyses have extended current knowledge of tumorigenesis.  ...  Colon and rectal cancer Initially, colon and rectal cancers were considered as distinct groups and examined separately.  ... 
doi:10.5114/wo.2014.47136 pmid:25691825 pmcid:PMC4322527 fatcat:voqiajllnjc7xl7cmbmdy2k2fu

Comparative study of joint bioinformatics analysis of underlying potential of 'neurimmiR', miR-212-3P/miR-132-3P, being involved in epilepsy and its emerging role in human cancer

Lu Xia, Daojiang Li, Changwei Lin, Shuchun Ou, Xiaorong Li, Songqing Pan
2017 OncoTarget  
Meanwhile, the emerging role of miR-132-3p/212-3p being involved in human cancer also been analyzed by several webtools for TCGA data integrative analysis, most remarkably and well worth exploring in our  ...  GEO database are comprehensive employed, miR-132-3p/212-3p and its target gene were found have highly expressed in brain and lots of molecular function and metabolic pathways associated with epilepsy  ...  genes of miR-212-3p/miR-132-3p have highly expression in brain Before comprehensive target gene analysis, it's experimentally validated miRNA:gene interactions.  ... 
doi:10.18632/oncotarget.16541 pmid:28380454 pmcid:PMC5522300 fatcat:dxbhcac74zhlxec64uakhbxdpm

Rectal cancer sub-clones respond differentially to neoadjuvant therapy

Lynn M Frydrych, Peter Ulintz, Armand Bankhead, Christopher Sifuentes, Joel Greenson, Lillias Maguire, Regina Irwin, Eric R. Fearon, Karin M Hardiman
2019 Neoplasia: An International Journal for Oncology Research  
Analysis of the influence of nCRT on the extent and nature of intra-tumoral genetic heterogeneity in rectal cancer may provide insights into mechanisms of resistance.  ...  Intra-tumoral heterogeneity is evident in pre-treatment rectal cancer.  ...  This is the first study using comprehensive genomic analysis of intra-tumor heterogeneity in treatment response in rectal cancer patients.  ... 
doi:10.1016/j.neo.2019.08.004 pmid:31521947 pmcid:PMC6745489 fatcat:k5lvn2xibfc6jmtvwvzrsei6ym

Potential therapeutic targets and molecular details of anthocyan-treated inflammatory bowel disease: a systematic bioinformatics analysis of network pharmacology

Yuqi Lin, Lianxiang Luo, Haowen Lin, Xiaoling Li, Riming Huang
2021 RSC Advances  
Anthocyans, containing anthocyanins and anthocyanidins, play a crucial role in preventing and treating inflammatory bowel disease (IBD).  ...  The core targets in the key pathway were highlighted and their anti-inammatory effects were analyzed to accomplish a comprehensive understanding of the potential mechanisms of the anthocyanidins in treating  ...  According to the KEGG pathway analysis, the most potential pharmacological mechanisms of anthocyanidins in treatment of IBD includes the EGFR tyrosine kinase inhibitor resistance pathway involving 4 core  ... 
doi:10.1039/d0ra09117k pmid:35423341 pmcid:PMC8695082 fatcat:eg2pnvscynae5gynqkhcap32qy

Demethylation and Overexpression of CSF2 are Involved in Immune Response, Chemotherapy Resistance, and Poor Prognosis in Colorectal Cancer

Zongbin Xu, Yiyi Zhang, Meifang Xu, Xin Zheng, Mengxin Lin, Jie Pan, Chengwei Ye, Yu Deng, Caiyun Jiang, Yu Lin, Xingrong Lu, Pan Chi
2019 OncoTargets and Therapy  
Protein-protein interaction (PPI), molecular complex detection (MOCDE), and qRT-PCR analysis verified CSF2 as the hub gene in chemotherapy resistance.  ...  Moreover, CSF2 expression was lower in the normal tissue than in the cancerous tissue (P<0.05). Higher expression of CSF2 was associated with poor OS and DFS in colon cancer patients (P<0.05).  ...  tissues. 16 Gene Set Enrichment Analysis (GSEA) and Co-Expression Gene Analysis To figure out the potential function of CSF2 in CRC, GSEA was conducted in CRC parental and FOLFOX resistant cells  ... 
doi:10.2147/ott.s216829 pmid:31908491 pmcid:PMC6927609 fatcat:osibna4dbngrnghx7lhrgtbl2m

Chemoprevention of Colorectal Neoplasia by Estrogen: Potential Role of Vitamin D Activity

P. Protiva, H. S. Cross, M. E. Hopkins, E. Kallay, G. Bises, E. Dreyhaupt, L. Augenlicht, M. Lipkin, M. Lesser, E. Livote, P. R. Holt
2009 Cancer Prevention Research  
Gene array group analysis showed activation of the VDR pathway and down-regulation of inflammatory and immune signaling pathways.  ...  The aims of our study were to determine whether estrogen intervention affects global gene expression in rectal mucosal biopsies and whether vitamin D-related genes are affected.  ...  Experimental evidence from animal studies has pointed to several potential mechanisms of action of estradiol, including changes in ER signaling (10, 11, 18) or in bile salt composition (28, 29) .  ... 
doi:10.1158/1940-6207.capr-08-0103 pmid:19139017 fatcat:5k3aq2azy5bijimz7euw3y7aoe

By inhibiting snail signaling, osthole suppresses the EMT-mediated metastatic ability in prostate cancer

Yu-Ching Wen, Liang-Ming Lee, Ming-Hsien Chien
2015 Urological Science  
Further study is necessary to identify the molecular mechanisms of miR-145 involved in the cancerous processes of UTUC.  ...  Purpose: To evaluate the anti-metastatic potential of osthole in prostate cancer cells and xenograft animal model.  ...  Further study is necessary to identify the molecular mechanisms of miR-145 involved in the cancerous processes of UTUC.  ... 
doi:10.1016/j.urols.2015.11.100 fatcat:b3o3eqkherbhplkop4agea6hfy

Characterization of Expression Quantitative Trait Loci in the Human Colon

Tarjinder Singh, Adam P. Levine, Philip J. Smith, Andrew M. Smith, Anthony W. Segal, Jeffrey C. Barrett
2015 Inflammatory Bowel Diseases  
Twenty-six percent of genes with rectal eQTLs were novel and unique compared with 7 published eQTL datasets. Rectal eQTLs were significantly enriched for genes expressed in the colon.  ...  A colorectal cancer locus at 11q23 contained a rectal eQTL for COLCA2, a protein implicated in colon cancer pathogenesis. Conclusions: This study defines a catalog of ileal and colonic eQTLs.  ...  Singh and A. P. Levine; Jointly supervised the work: A. W. Segal and J. C. Barrett; Study conception and design: T. Singh, A. P. Levine, P. J. Smith, A. M. Smith, A. W. Segal, and J. C.  ... 
doi:10.1097/mib.0000000000000265 pmid:25569741 pmcid:PMC4345969 fatcat:mnizcvcvnze53p5hds54i5msqm
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