Article
Biology
Wenbo Chen, Xin Chen, Zhenyu Zhao, Menglu Li, Shuang Dong, Sheng Hu, Xiaoyu Li, Mingqian Feng, Ke Chen, Shan Zhong, Chunjiang He
Summary: This study systematically analyzed the relationship between metabolic pathways and prognosis in multiple cancers, and found significant associations between the expression of metabolic checkpoint genes, activity of metabolic pathways, and survival of cancer patients. This provides important clues for further research on cancer diagnosis and therapy.
Article
Genetics & Heredity
Sree Karani Kondapuram, Mohane Selvaraj Coumar
Summary: This study identifies important autophagy genes and potential drug targets by analyzing the expression levels of genes in 21 cancers. The findings shed light on the role of autophagy in cancer and provide potential targets for cancer treatment.
Article
Biochemistry & Molecular Biology
Zixi Wang, Shijia Zhu, Yuemeng Jia, Yunguan Wang, Naoto Kubota, Naoto Fujiwara, Ruth Gordillo, Cheryl Lewis, Min Zhu, Tripti Sharma, Lin Li, Qiyu Zeng, Yu-Hsuan Lin, Meng-Hsiung Hsieh, Purva Gopal, Tao Wang, Matt Hoare, Peter Campbell, Yujin Hoshida, Hao Zhu
Summary: Somatic mutations in nonmalignant tissues accumulate with age and injury, and this study investigates whether these mutations are beneficial for cellular or organismal levels. Using lineage tracing in mice with somatic mosaicism subjected to nonalcoholic steatohepatitis (NASH), the researchers identified genetic mutations that ameliorate lipotoxicity and protect against hepatic steatosis. The study provides insights into the pathways that regulate metabolic disease.
Article
Biology
Mohd Afzal, Abdullah Alarifi, Naaser. A. Y. Abduh, Arusha Ayub, Mohd. Muddassir
Summary: Apoptosis is regulated by the BCL-2 family, and inhibition of the pro-apoptotic and anti-apoptotic protein-protein interactions has been studied for developing anticancer drugs. In this study, the hydrophobic nature of 74 organometallic compounds was analyzed, and their effectiveness against the BCL-2 protein was determined using molecular docking. The results identified several important compounds that could bind to the less solvent-accessible site of BCL-2.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Multidisciplinary Sciences
Pathum Kossinna, Weijia Cai, Xuewen Lu, Carrie S. Shemanko, Qingrun Zhang
Summary: This article introduces a tool called SCOPE, which integrates bootstrapped least absolute shrinkage and selection operator and coexpression analysis to obtain stable results that are insensitive to variations in the data. By applying SCOPE to cancer expression datasets, core genes capturing interaction effects in crucial pan-cancer pathways related to genome instability and DNA damage response were identified, highlighting the pivotal role of CD63 as an oncogenic driver and potential therapeutic target in kidney cancer.
Article
Biochemical Research Methods
Shudong Wang, Yuanyuan Zhang, Hongting Mu, Shanchen Pang
Summary: This study identified 44 genes related to cancer traits in five types of cancer using a structural equation model, confirming their combined effects and discovering key gene pathways and significant gene functional modules.
CURRENT BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Yiqun Zhang, Fengju Chen, Darshan S. Chandrashekar, Sooryanarayana Varambally, Chad J. Creighton
Summary: Pan-cancer proteomics analysis reveals 11 distinct subtypes across multiple cancer types, linking pathway activity levels with somatic alteration of specific genes. The interplay between the genome and proteome is observed, and MYC pathway activity is found in cancers without MYC copy gain but with mutations in genes with noncanonical roles in MYC.
NATURE COMMUNICATIONS
(2022)
Article
Medicine, General & Internal
Xin Ke, Hao Wu, Yi-Xiao Chen, Yan Guo, Shi Yao, Ming-Rui Guo, Yuan-Yuan Duan, Nai-Ning Wang, Wei Shi, Chen Wang, Shan-Shan Dong, Huafeng Kang, Zhijun Dai, Tie-Lin Yang
Summary: This study introduces a novel method called individualized pathway activity measurement (IPAM) for analyzing the dysregulation of biological pathways in cancer. IPAM accurately quantifies pathway activity and shows better performance in cancer classification and prognosis prediction compared to other tools. The study identifies characteristic dysregulated pathways in different cancer types and confirms the dominant role of metabolic pathways in cancer development. The findings provide new insights into the pathological mechanisms of cancer and have the potential to contribute to personalized medicine.
Article
Biochemical Research Methods
Xiangtao Li, Shaochuan Li, Yunhe Wang, Shixiong Zhang, Ka-Chun Wong
Summary: In the field of precision oncology, the identification of hidden responders is a crucial challenge. A nature-inspired deep Ras activation pan-cancer (NatDRAP) deep neural network model is proposed to overcome limitations like high dimensionality, data sparsity, and model performance for identifying hidden responders in cancer treatment.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Helene Lasolle, Andrea Schiavo, Adrien Tourneur, Pierre Gillotay, Barbara de Faria da Fonseca, Lucieli Ceolin, Olivier Monestier, Benilda Aganahi, Laura Chomette, Marina Malta Letro Kizys, Lieven Haenebalcke, Tim Pieters, Steven Goossens, Jody Haigh, Vincent Detours, Ana Luiza Silva Maia, Sabine Costagliola, Mirian Romitti
Summary: In this study, mESC-derived thyroid organoids were used to establish a model that can replicate the features of papillary thyroid cancer in vitro. The results demonstrate that these organoids can mimic tumor development and features, and provide an effective tool for testing novel targeted therapies.
Article
Multidisciplinary Sciences
Kaibin Wang, Jinhuan Meng, Xudong Wang, Mo Yan, Shuaibing Liu, Shaobo Yang, Shengxian Xu, Dongze Liu, Changying Li, Kuo Yang
Summary: In this study, PAQR4 was found to be up-regulated in multiple cancers and associated with poor prognosis. High expression of PAQR4 was closely related to tumor stage, immune cell infiltration, tumor mutation burden, and microsatellite instability in different cancer types. Moreover, PAQR4 was highly expressed in bladder cancer and renal clear cell carcinoma, and knocking down PAQR4 significantly inhibited cell proliferation, migration, and invasion. The study revealed the role of PAQR4 in carcinogenesis and tumor immunity.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Yize Li, Yongchao Dou, Felipe Da Veiga Leprevost, Yifat Geffen, Anna P. Calinawan, Yo Akiyama, Shankara Anand, Chet Birger, Song Cao, Rekha Chaudhary, Padmini Chilappagari, Marcin Cieslik, Antonio Colaprico, Daniel Cui Zhou, Corbin Day, Marcin J. Domagalski, Francois Aguet, David Fenyo, Myvizhi Esai Selvan, Steven M. Foltz, Alicia Francis, Tania Gonzalez-Robles, Zeynep H. Euromueuros, David Heiman, Michael Holck, Runyu Hong, Yingwei Hu, Eric J. Jaehnig, Jiayi Ji, Wen Jiang, Lizabeth Katsnelson, Karen A. Ketchum, Robert J. Klein, Jonathan T. Lei, Wen-Wei Liang, Yuxing Liao, Caleb M. Lindgren, Weiping Ma, Lei Ma, Michael J. Maccoss, Fernanda Martins Rodrigues, Wilson Mckerrow, Ngoc Nguyen, Robert Oldroyd, Alexander Pilozzi, Pietro Pugliese, Boris Reva, Paul Rudnick, Kelly V. Ruggles, Dmitry Rykunov, Sara R. Savage, Michael Schnaubelt, Tobias Schraink, Zhiao Shi, Deepak Singhal, Xiaoyu Song, Erik Storrs, Nadezhda V. Terekhanova, Ratna R. Thangudu, Mathangi Thiagarajan, Liang-Bo Wang, Joshua M. Wang, Ying Wang, Bo Wen, Yige Wu, Matthew A. Wyczalkowski, Yi Xin, Lijun Yao, Xinpei Yi, Hui Zhang, Qing Zhang, Maya Zuhl, Gad Getz, Li Ding, Alexey I. Nesvizhskii, Pei Wang, Ana I. Robles, Bing Zhang, Samuel H. Payne, Clin Proteomic Tumor Anal Consortium
Summary: The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. We have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to facilitate pan-cancer investigations and aid scientific discovery. Challenges of integrating nucleotide sequencing and mass spectrometry proteomics data are also discussed.
Article
Multidisciplinary Sciences
Rasif Ajwad, Michael Domaratzki, Qian Liu, Nikta Feizi, Pingzhao Hu
Summary: Recent studies have shown that significantly mutated subnetworks in the breast cancer genome can serve as biomarkers for predicting patient survival, with the retinol metabolism pathway being significantly enriched. By examining copy number alterations, it is possible to predict alterations in the retinol pathway and potentially utilize retinoids as a personalized therapy for breast cancer patients. Application of multiple bioinformatics algorithms simultaneously has the potential to identify new network-based biomarkers for guiding optimal treatments for cancer patients.
SCIENTIFIC REPORTS
(2021)
Article
Oncology
Jakob Landau, Linoy Tsaban, Adar Yaacov, Gil Ben Cohen, Shai Rosenberg
Summary: Driver mutations provide tumors with selective advantages and cause various pathogenic effects. Understanding the function of somatic variants is crucial in cancer biology and treatment selection. In this study, a shared dataset from multiple cancer genomic databases was compiled, and two measures were used to analyze 535 cancer genes. The tumor variant amplitude (TVA) outperformed other computational tools in predicting functional scores of cancer mutations, drug response, overall survival, and clinical implications in relevant cancer genes. This study highlights the importance of a large cancer dataset in understanding the impact of driver variants and their clinical implications.
Article
Computer Science, Information Systems
Guoqing Bao, Ran Xu, Xiuying Wang, Jianxiong Ji, Linlin Wang, Wenjie Li, Qing Zhang, Bin Huang, Anjing Chen, Di Zhang, Beihua Kong, Qifeng Yang, Cunzhong Yuan, Xinyu Wang, Jian Wang, Xingang Li
Summary: This study proposed a 5-lncRNA signature for pan-cancer prognosis prediction, which showed better performance in long-term prognostic estimation and was validated in external cohorts. The identified lncRNAs associated with overall survival of pan-cancer patients and may serve as viable molecular targets common among diverse cancers.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2021)