MKRN1 promotes colorectal cancer metastasis by activating the TGF-β signalling pathway through SNIP1 protein degradation by Yi Zhang, Qin-shan Li, Hong-lin Liu, Hong-ting Tang, Han-lin Yang, Dao-qiu Wu, Yu-ying Huang, Li-cheng Li, Li-hong Liu, Meng-xing Li

“…Methods MKRN1 expression in CRC was analysed using the Cancer Cell Line Encyclopaedia and the Cancer Genome Atlas (TCGA) databases. Rectal tumour tissues were frozen to explore the MKRN1 expression in CRC and its clinical significance. …”
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A prognostic signature of Glutathione metabolism-associated long non-coding RNAs for lung adenocarcinoma with immune microenvironment insights by Junxi Hu, Junxi Hu, Shuyu Tian, Shuyu Tian, Qingwen Liu, Qingwen Liu, Jiaqi Hou, Jiaqi Hou, Jun wu, Jun wu, Xiaolin Wang, Xiaolin Wang, Yusheng Shu, Yusheng Shu

“…This study developed a prognostic model using GSH-related lncRNAs to predict LUAD outcomes and assess tumor immunity.MethodsThis study analyzed survival data from The Cancer Genome Atlas (TCGA) and identified GSH metabolism-related lncRNAs using Pearson correlation. …”
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Loss of Lkb1 cooperates with BrafV600E and ultraviolet radiation, increasing melanoma multiplicity and neural‐like dedifferentiation by Kimberley McGrail, Elena González‐Sánchez, Paula Granado‐Martínez, Roberto Orsenigo, Yuxin Ding, Berta Ferrer, Javier Hernández‐Losa, Iván Ortega, Juan Martín‐Caballero, Eva Muñoz‐Couselo, Vicente García‐Patos, Juan A. Recio

“…Analysis of human melanoma tumors [data from The Cancer Genome Atlas (TCGA)] revealed that 50% or more of the samples expressed no or low amounts of serine/threonine protein kinase STK11 (also known as LKB1) protein. …”
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Promotive effect of cancer-testis antigen CT57 on proliferation, invasion, migration and epithelial-mesenchymal transition of liver cancer cells by LUO Lange, ZHENG Chao, LEI Ming

“…Results·Bioinformatics analysis of multiple tumors and corresponding normal tissues in The Cancer Genome Atlas Program (TCGA) database showed that CT57 was highly expressed in most tumor tissues, including liver cancer, and the expression level of CT57 was significantly correlated with the prognosis of liver cancer patients. …”
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“Subtype-precise” therapy leads diagnostic and therapeutic innovations: a new pattern for precision treatment of breast cancer by ZHANG Siwei, MA Ding, JIANG Yizhou, SHAO Zhimin

“…Over the past decade, the multidisciplinary team at Fudan University Shanghai Cancer Center has established a comprehensive molecular portrait of Chinese Breast Cancer Genome Atlas (CBCGA). They deeply analyzed the molecular characteristics of TNBC, leading to the development of a “Fudan subtype” closely related to clinical outcomes: luminal androgen receptor subtype (LAR), which can be targeted with anti-HER2 and CDK4/6 inhibitors; the immunomodulatory subtype (IM), suitable for immunotherapy; basal-like immune-suppressed subtype (BLIS), which can be treated with platinum-based drugs or poly (ADP-ribose) polymerase (PARP) inhibitors; and mesenchymal-like subtype (MES), which can be treated with anti-cancer stem cell and anti-angiogenic therapies. …”
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Immune regulatory genes impact the hot/cold tumor microenvironment, affecting cancer treatment and patient outcomes by Mengmeng Sang, Jia Ge, Juan Ge, Juan Ge, Gu Tang, Qiwen Wang, Jiarun Wu, Liming Mao, Liming Mao, Xiaoling Ding, Xiaorong Zhou

“…Nevertheless, as yet there is no consensus regarding the clinically relevant definition of hot/cold tumors, and the influence of immune genes on the formation of hot/cold tumors remains poorly understood.MethodsData for 33 different types of cancer were obtained from The Cancer Genome Atlas database, and their immune composition was assessed using the CIBERSORT algorithm. …”
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Macrophage heterogeneity and oncogenic mechanisms in lung adenocarcinoma: insights from scRNA-seq analysis and predictive modeling by Han Zhang, Jiaxing Dai, Qiuqiao Mu, Xiaojiang Zhao, Ziao Lin, Ziao Lin, Kai Wang, Meng Wang, Meng Wang, Daqiang Sun

“…Specifically, we used scRNA-seq data processing, intercellular communication analysis, pseudotime trajectory analysis, and transcription factor regulatory analysis to reveal the complexity of macrophage subpopulations. Data from The Cancer Genome Atlas (TCGA) was used to assess the impact of various macrophage subtypes on LUAD prognosis. …”
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Association of tumour mutation burden with prognosis and its clinical significance in stage III gastric cancer by Ya-Lin Han, Li Chen, Xu-Ning Wang, Mao-Lin Xu, Rui Qin, Fang-Ming Gong, Peng Sun, Hong-Yi Liu, Zhi-Peng Teng, Zhao-Xia Li, Guang-Hai Dai

“…Methods: Patients with stage III GC were divided into a high TMB and low TMB group in both a study cohort of 38 patients and the Cancer Genome Atlas (TCGA) cohort of 173 patients. In the study cohort, next-generation sequencing was used to detect mutated GC genes and obtain TMB data. …”
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MTMR6 downregulation contributes to cisplatin resistance in oral squamous cell carcinoma by Kah Young Lee, Su Young Oh, Heon-Jin Lee, Tae-Geon Kwon, Jin-Wook Kim, Chang-Geol Shin, Su-Hyung Hong, So-Young Choi

“…A survival analysis based on The Cancer Genome Atlas (TCGA) head and neck squamous cell carcinoma (HNSCC) dataset was performed to evaluate the correlation between MTMR6 expression and patient outcomes following cisplatin treatment. …”
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Mutation in CDC42 Gene Set as a Response Biomarker for Immune Checkpoint Inhibitor Therapy by Kun Wang, Yingying Zhang, Zhaoming Su, Bei Wang, Yuanyang Zhou, Xiaochu Tong, Chengying Xie, Xiaomin Luo, Sulin Zhang, Mingyue Zheng

“…We explored the mechanism based on The Cancer Genome Atlas database. We also examined whether combining a CDC42 inhibitor with ICI could enhance ICI's efficacy. …”
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Oncolytic peptide LTX-315 induces anti-pancreatic cancer immunity by targeting the ATP11B-PD-L1 axis by Meng Wang, Xing Huang, Tingbo Liang, Tianyu Tang, Gang Zhang, Minghao Lu, Zhengtao Hong, Junming Huang, Xiao Zhi

“…Both in-house tissue microarray and open accessed The Cancer Genome Atlas data sets were used to evaluate the clinical relevance in pancreatic cancer prognosis.Results LTX-315 treatment inhibited PD-L1 expression and enhanced lymphocyte infiltration in pancreatic tumors. …”
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Characterizing immune biomarkers and effector CD8+ T-cell exhaustion in pancreatic adenocarcinoma via single-cell RNA sequencing profiling by Rawaa AlChalabi, Raghda Makia, Semaa A. Shaban, Ahmed AbdulJabbar Suleiman

“…We analyzed mutations in the shortlisted biomarkers from The Cancer Genome Atlas (TCGA) and performed in silico mutational analysis using Maestro to evaluate the impact of an IL7R mutation (K110N) on protein function. …”
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FBXO31-mediated ubiquitination of OGT maintains O-GlcNAcylation homeostasis to restrain endometrial malignancy by Na Zhang, Yang Meng, Song Mao, Huiling Ni, Canhua Huang, Licong Shen, Kun Fu, Lu Lv, Chunhong Yu, Piyanat Meekrathok, Chunmei Kuang, Fang Chen, Yu Zhang, Kai Yuan

“…Here we report that O-GlcNAcylation level is positively correlated with EC histologic grade in a Chinese cohort containing 219 tumors, validated in The Cancer Genome Atlas dataset. Increasing O-GlcNAcylation in patient-derived endometrial epithelial organoids promotes proliferation and stem-like cell properties, whereas decreasing O-GlcNAcylation limits the growth of endometrial cancer organoids. …”
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Exploring the prognostic significance of lactate-mitochondria-related genes in prostate cancer by Yuan Wang, Ronghui Chen, Feng-Le Jiang, Feng-Le Jiang, Xin Jiang, Xin Jiang, Yuehong Zhou, Yingying Zhou, Xinyi Hong, Chaoying Lin, Wei-Jia Wang, Wei-Jia Wang, Sufang Qiu

“…To identify novel prognostic markers of PCa based on lactate-mitochondria-related genes (LMRGs), RNA sequencing data and clinical information of PCa from The Cancer Genome Atlas (TCGA) and the cBioPortal database were used to construct a lactate-mitochondria-related risk signature. …”
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Novel pyroptosis-immune-related lncRNA signature exhibits a distinct immune cell infiltration landscape in breast cancer by Dedi Kong, Dedi Kong, Hongju Cheng, Meihong Wang

“…IntroductionThis study investigated pyroptosis- and immunity-related long non-coding RNAs (lncRNAs) to identify promising therapeutic targets for breast cancer (BC), and constructed lncRNA signatures to determine the prognosis and immunotherapy responses of BC patients.MethodsPearson’s correlation coefficient was used to identify pyroptosis- and immune-related differentially expressed lncRNAs (DE-pyrolncRNAs and DE-ImmlncRNAs, respectively). The Cancer Genome Atlas dataset was allocated to training and testing subsets. …”
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Analysis of mRNA Pentatricopeptide Repeat Domain 1 as a prospective oncogene in clear cell renal cell carcinoma that accelerates tumor cells proliferation and invasion via the Akt/... by Zhongbao Zhou, Yulong Li, Yumeng Chai, Yong Zhang, Pu Yan

“…Abstract Background Although pentatricopeptide repeat domain 1 (PTCD1) has been found to modulate mitochondrial metabolic and oxidative phosphorylation, its contribution in the growth of clear cell renal cell carcinoma (ccRCC) remains unknown. Methods The Cancer Genome Atlas (TCGA) dataset was utilized to examine the transcriptional alterations, patient characteristics, clinical outcomes, as well as pathway activation of PTCD1. …”
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Viral Transcript and Tumor Immune Microenvironment-Based Transcriptomic Profiling of HPV-Associated Head and Neck Squamous Cell Carcinoma Identifies Subtypes Associated with Progno... by Anastasiia Nikitina, Daria Kiriy, Andrey Tyshevich, Dmitry Tychinin, Zoya Antysheva, Anastasya Sobol, Vladimir Kushnarev, Nara Shin, Jessica H. Brown, James Lewis, Krystle A. Lang Kuhs, Robert Ferris, Lori Wirth, Nikita Kotlov, Daniel L. Faden

“…In order to understand specific factors associated with prognosis, we used the unsupervised clustering of an HPV-positive HNSCC cohort from The Cancer Genome Atlas (TCGA) (n = 53) based on HPV transcript expression, and identified four HPV-related subtypes (E2/E5, E6/E7, E1/E4 and L1/L2). …”
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Construction of a radiogenomic signature based on endoplasmic reticulum stress for predicting prognosis and systemic combination therapy response in hepatocellular carcinoma by Huai-Yu Wu, Shu-Ya Cao, Zheng-Gang Xu, Tian- Wang, Gu-Wei Ji, Ke Wang

“…Methods Using data from The Cancer Genome Atlas Program (TCGA) as a training cohort and data from International cancer genome consortium (ICGC) as a testing cohort. …”
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Cuproptosis-Related Signature Predicts the Prognosis, Tumor Microenvironment, and Drug Sensitivity of Hepatocellular Carcinoma by Xiangjun Qi, Jiayun Guo, Guoming Chen, Caishan Fang, Leihao Hu, Jing Li, Chi Zhang

“…The mRNA transcriptome profiling data, somatic mutation data, and copy number gene level data of The Cancer Genome Atlas-Liver Hepatocellular Carcinoma project (TCGA-LIHC) were downloaded for subsequent analysis. …”
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Expression and prognostic significance of the m6A RNA methylation regulator HNRNPC in HNSCC by Yulin Zhang, Yixu Wang, Jilin Peng, Kun Zhao, Ling Li, Yuan Zhang, Ziyu Zhai, Sijie Yuan, Shichao Li, Shichao Li, Shichao Li, Fanglei Ye, Le Wang

“…BackgroundN6-methyladenosine (m6A) RNA modification is crucial for tumor development and progression; however, which m6A regulators play a pivotal role in head and neck squamous cell carcinoma (HNSCC) remains ambiguous.MethodsUtilizing the Cancer Genome Atlas (TCGA) database, the expression levels of m6A regulators in HNSCC were examined, which led to the identification of heterogeneous nuclear ribonucleoprotein C (HNRNPC) as a key gene. …”
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