Article
Computer Science, Artificial Intelligence
Jingli Wu, Cong Wu, Gaoshi Li
Summary: This paper proposes an algorithm to solve the problem of identifying common driver modules in pan-cancer data. The algorithm combines a K-nearest neighbors based imputation algorithm and a random walk algorithm based on the harmonic mean. Experimental results show that the algorithm performs competitively in revealing known cancer genes and producing modules with satisfactory coverage and mutual exclusivity for each cancer. It also recognizes cancer-associated genes overlooked by other methods.
Article
Cell Biology
Jaime Iranzo, George Gruenhagen, Jorge Calle-Espinosa, Eugene V. Koonin
Summary: A method called Coselens has been developed to quantify conditional selection on the excess of nonsynonymous substitutions in cancer genes, identifying 296 conditionally selected gene pairs. This study reveals a more complex scenario in cancer subtypes where gene-specific across-pathway epistasis shapes differentiated cancer subtypes.
Article
Biochemistry & Molecular Biology
Paulina Galka-Marciniak, Martyna Olga Urbanek-Trzeciak, Paulina Maria Nawrocka, Piotr Kozlowski
Summary: The levels of many miRNAs are differentiated in cancer, and the study identified some miRNA biogenesis genes that are over-mutated in specific cancers and associated with patient survival. Hotspot mutations in DICER1 were found to affect the levels of miRNAs, ultimately creating an atlas of miRNA biogenesis alterations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Rafsan Ahmed, Cesim Erten, Aissa Houdjedj, Hilal Kazan, Cansu Yalcin
Summary: A network-centric framework is proposed to evaluate mutual exclusivity tests in cancer driver gene identification. The framework consists of three main components including metrics for network-centric evaluations, mechanisms to avoid confounders, and tissue-specific networks to resolve interference issues.
FRONTIERS IN GENETICS
(2021)
Editorial Material
Genetics & Heredity
Kirsty Minton
Summary: A study published in Nature combines single-cell RNA-sequencing data from over 1,000 tumor samples to present a pan-cancer atlas that reveals the transcriptional heterogeneity within tumors.
NATURE REVIEWS GENETICS
(2023)
Article
Oncology
Md Faqrul Hasan, Kavya Ganapathy, Jiao Sun, Ayman Khatib, Thomas Andl, Julia N. Soulakova, Domenico Coppola, Wei Zhang, Ratna Chakrabarti
Summary: The long noncoding RNA PAINT plays a promotive role in prostate cancer progression, with its inhibition reducing cell proliferation and migration while improving drug sensitivity. This study establishes a novel oncogenic function of PAINT in prostate cancer, providing new insights for potential therapeutic strategies.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Cell Biology
Neha Rohatgi, Umesh Ghoshdastider, Probhonjon Baruah, Tanmay Kulshrestha, Anders Jacobsen Skanderup
Summary: Through a tumor transcriptome deconvolution approach, we identified fundamental differences in metabolic states of cancer and stromal cells inside tumors, including the upregulation of deoxythymidine triphosphate (dTTP) and overexpression of tryptophan catabolism rate-limiting enzymes in stroma. Furthermore, we found that oxidative phosphorylation is more upregulated in cancer cells in vivo compared to stromal cells and a large atlas of cancer cell lines, suggesting a less pronounced Warburg effect in cancer cells.
Article
Biochemical Research Methods
Ziyu Tao, Shixiang Wang, Chenxu Wu, Tao Wu, Xiangyu Zhao, Wei Ning, Guangshuai Wang, Jinyu Wang, Jing Chen, Kaixuan Diao, Fuxiang Chen, Xue-Song Liu
Summary: This study developed a mechanism-agnostic method to categorize CNAs based on various fragment properties and revealed novel patterns of CNA. The activities of some CNA signatures consistently predicted cancer patients' prognosis. This study provides important insights into the role of CNA in cancer and its potential implications for cancer prognosis, evolution, and etiology.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Oncology
Yujia Lan, Wei Liu, Wanmei Zhang, Jing Hu, Xiaojing Zhu, Linyun Wan, A. Suru, Yanyan Ping, Yun Xiao
Summary: This study analyzed 506 LUAD tumors and identified mutually exclusive relationships among driver gene mutations in different subtypes, playing crucial roles in cancer progression. Functional analysis revealed enrichment of these mutually exclusive pairs in nuclear division and immune response. Some of the mutually exclusive triples were associated with overall survival and disease-specific survival of LUAD patients.
Article
Multidisciplinary Sciences
Bo Gao, Yue Zhao, Yonghang Gao, Guojun Li, Ling-Yun Wu
Summary: High-throughput biological data has provided an opportunity to illuminate the mechanisms of tumor emergence and evolution, with the tool ComCovEx being developed to explore common cancer driver gene modules between two cancers and reveal their associations. The research results offer new insights into the pathological basis of different cancer types and provide new clues for the diagnosis and treatment of associated cancers.
Article
Oncology
Jing Yang, Shilin Zhao, Jing Wang, Quanhu Sheng, Qi Liu, Yu Shyr
Summary: Cancer-Immu is a comprehensive platform that integrates various omics data and clinical phenotypes to explore immunogenomic connections. It provides easy access to data and helps researchers translate omics datasets into biological insights and clinical applications.
Article
Biochemical Research Methods
Cesim Erten, Aissa Houdjedj, Hilal Kazan, Ahmed Amine Taleb Bahmed
Summary: This article introduces a novel method for personalized identification of driver genes in cancer, which outperforms existing methods in TCGA and cell line data, and contributes to the development of personalized treatments and therapies.
Article
Genetics & Heredity
Chiara Vischioni, Fabio Bove, Matteo De Chiara, Federica Mandreoli, Riccardo Martoglia, Valentino Pisi, Gianni Liti, Cristian Taccioli
Summary: This study identified novel gene targets linked to tumor predisposition and found that miRNA copy number patterns are associated with cancer progression and susceptibility.
Article
Health Care Sciences & Services
Medi Kori, Gullu Elif Ozdemir, Kazim Yalcin Arga, Raghu Sinha
Summary: Cancer hallmark genes and proteins play important roles in regulating and driving carcinogenesis. This study analyzed transcriptome data from 12 common cancers and identified differentially interacting hallmarks of cancer proteins (DIHCP) and DIHCP-centric modules. These modules showed significant changes in interaction patterns between tumor and control phenotypes, and some of them had diagnostic and prognostic capabilities. The study also investigated the druggability of the identified DIHCPs. Overall, the study presents candidate system biomarkers that could enhance understanding of tumorigenesis and improve personalized treatment strategies for various cancers, focusing on their ten hallmark characteristics.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Sijin Cheng, Ziyi Li, Ranran Gao, Baocai Xing, Yunong Gao, Yu Yang, Shishang Qin, Lei Zhang, Hanqiang Ouyang, Peng Du, Liang Jiang, Bin Zhang, Yue Yang, Xiliang Wang, Xianwen Ren, Jin-Xin Bei, Xueda Hu, Zhaode Bu, Jiafu Ji, Zemin Zhang
Summary: This study conducted a pan-cancer analysis of single myeloid cells from 210 patients across 15 human cancer types, revealing distinct features of TIMs in different cancer types. For example, mast cells in nasopharyngeal cancer were associated with better prognosis, and pro-angiogenic TAMs showed diverse markers across different cancer types. The composition of TIMs appeared to be linked with certain features of somatic mutations and gene expressions.
Article
Medicine, Research & Experimental
Yanjun Xu, Qun Dong, Feng Li, Yingqi Xu, Congxue Hu, Jingwen Wang, Desi Shang, Xuan Zheng, Haixiu Yang, Chunlong Zhang, Mengting Shao, Mohan Meng, Zhiying Xiong, Xia Li, Yunpeng Zhang
JOURNAL OF TRANSLATIONAL MEDICINE
(2019)
Article
Biochemistry & Molecular Biology
Yongsheng Li, Jun Xiao, Jing Bai, Yi Tian, Yinwei Qu, Xiang Chen, Qi Wang, Xinhui Li, Yunpeng Zhang, Juan Xu
Article
Biochemistry & Molecular Biology
Li Wang, Hongying Zhao, Jing Li, Yingqi Xu, Yujia Lan, Wenkang Yin, Xiaoqin Liu, Lei Yu, Shihua Lin, Michael Yifei Du, Xia Li, Yun Xiao, Yunpeng Zhang
Article
Medicine, Research & Experimental
Yong Zhang, Gaoming Liao, Jing Bai, Xinxin Zhang, Liwen Xu, Chunyu Deng, Min Yan, Aimin Xie, Tao Luo, Zhilin Long, Yun Xiao, Xia Li
MOLECULAR THERAPY-NUCLEIC ACIDS
(2019)
Article
Biochemistry & Molecular Biology
Guanxiong Zhang, Yujia Lan, Aimin Xie, Jian Shi, Hongying Zhao, Liwen Xu, Shiwei Zhu, Tao Luo, Tingting Zhao, Yun Xiao, Xia Li
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Peng Wang, Xin Li, Yue Gao, Qiuyan Guo, Shangwei Ning, Yunpeng Zhang, Shipeng Shang, Junwei Wang, Yanxia Wang, Hui Zhi, Ying Fang, Weitao Shen, Guangmei Zhang, Steven Xi Chen, Xia Li
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemical Research Methods
Yanjun Xu, Tan Wu, Feng Li, Qun Dong, Jingwen Wang, Desi Shang, Yingqi Xu, Chunlong Zhang, Yiying Dou, Congxue Hu, Haixiu Yang, Xuan Zheng, Yunpeng Zhang, Lihua Wang, Xia Li
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Qun Dong, Feng Li, Yanjun Xu, Jing Xiao, Yingqi Xu, Desi Shang, Chunlong Zhang, Haixiu Yang, Zihan Tian, Kai Mi, Xia Li, Yunpeng Zhang
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemistry & Molecular Biology
Zishan Wang, Jiaqi Yin, Weiwei Zhou, Jing Bai, Yunjin Xie, Kang Xu, Xiangyi Zheng, Jun Xiao, Li Zhou, Xiaolin Qi, Yongsheng Li, Xia Li, Juan Xu
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Yongsheng Li, Tiantongfei Jiang, Weiwei Zhou, Junyi Li, Xinhui Li, Qi Wang, Xiaoyan Jin, Jiaqi Yin, Liuxin Chen, Yunpeng Zhang, Juan Xu, Xia Li
NATURE COMMUNICATIONS
(2020)
Article
Oncology
Dezhong Lv, Kang Xu, Xiyun Jin, Junyi Li, Yuchen Shi, Mengying Zhang, Xiaoyan Jin, Yongsheng Li, Juan Xu, Xia Li
Article
Biochemical Research Methods
Yulan Deng, Hao Luo, Zhenyu Yang, Lunxu Liu
Summary: The LncAS2Cancer database focuses on cancer-related alternative splicing of lncRNAs, with a comprehensive collection of RNA sequencing samples and six splicing algorithms. It not only confirms known cancer-associated lncRNA isoforms, but also indicates new ones. Through data comparison and analysis within the database, important insights into the functional roles of lncRNAs in human cancers can be gained for further research.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Liang Xia, Jiandong Mei, Ran Kang, Senyi Deng, Yaohui Chen, Ying Yang, Gang Feng, Yulan Deng, Fanyi Gan, Yidan Lin, Qiang Pu, Lin Ma, Feng Lin, Yong Yuan, Yang Hu, Chenglin Guo, Hu Liao, Chengwu Liu, Yunke Zhu, Wenping Wang, Zheng Liu, Yuyang Xu, Kaidi Li, Chuan Li, Qingyun Li, Ji He, Weizhi Chen, Xiaolong Zhang, Yingli Kou, Yun Wang, Zhu Wu, Guowei Che, Longqi Chen, Lunxu Liu
Summary: This study assessed the use of perioperative circulating tumor DNA (ctDNA) analysis in early detection of molecular residual disease (MRD) and prediction of postoperative relapse in non-small cell lung cancer (NSCLC). The results showed that preoperative ctDNA positivity was associated with lower recurrence-free survival (RFS) and the presence of MRD after surgery was a strong predictor for disease relapse. Furthermore, MRD-positive patients who received adjuvant therapies had improved RFS, while MRD-negative patients receiving adjuvant therapies had lower RFS compared to those without adjuvant therapy.
CLINICAL CANCER RESEARCH
(2022)
Article
Oncology
Zhenyu Yang, Shiyou Wei, Yulan Deng, Zihuai Wang, Lunxu Liu
JAPANESE JOURNAL OF CLINICAL ONCOLOGY
(2020)
Review
Biochemical Research Methods
Feng Li, Tan Wu, Yanjun Xu, Qun Dong, Jing Xiao, Yingqi Xu, Qian Li, Chunlong Zhang, Jianxia Gao, Liqiu Liu, Xiaoxu Hu, Jian Huang, Xia Li, Yunpeng Zhang
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Oncology
Andra S. Martinikova, Miroslav Stoyanov, Anna Oravetzova, Yannick P. Kok, Shibo Yu, Jana Dobrovolna, Pavel Janscak, Marcel van Vugt, Libor Macurek
Summary: Oncogene-induced replication stress is a major cause of genome instability in cancer cells. This study reveals that increased activity of PPM1D exacerbates replication stress caused by cyclin E1 overexpression, leading to abnormal cell cycle progression and accumulation of DNA copy number alterations. Pharmacological inhibition of PPM1D can alleviate replication stress-induced genome instability.
MOLECULAR ONCOLOGY
(2024)
Article
Oncology
Alamelu G. Bharadwaj, Meghan E. McLean, Margaret L. Dahn, Hannah F. Cahill, Marie-Claire D. Wasson, Raj Pranap Arun, Olivia L. Walker, Brianne M. Cruickshank, Wasundara Fernando, Jaganathan Venkatesh, Penelope J. Barnes, Gillian Bethune, Gregory Knapp, Lucy K. Helyer, Carman A. Giacomantonio, David M. Waisman, Paola Marcato
Summary: ALDH1A3 regulates the plasminogen activation pathway to promote breast cancer metastasis. Co-expression of ALDH1A3 and tPA is associated with TNBC subtype, high tumor grade, and recurrent metastatic disease.
MOLECULAR ONCOLOGY
(2024)
Article
Oncology
Nayela N. Chowdhury, Yi Yang, Ananya Dutta, Michelle Luo, Zimu Wei, Sara R. Abrahams, Alexey S. Revenko, Fenil Shah, Lindsey A. Miles, Robert J. Parmer, Bas de Laat, Alisa S. Wolberg, James P. Luyendyk, Melissa L. Fishel, Matthew J. Flick
Summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal metastatic disease associated with robust activation of the coagulation and fibrinolytic systems. Primary fibrinolytic protease plasminogen promotes PDAC tumor growth and metastatic potential through engaging plasminogen receptors on tumor cells.
MOLECULAR ONCOLOGY
(2024)
Article
Oncology
Nuria Gendrau-Sanclemente, Agnes Figueras, Kristina Gracova, Alvaro Lahiguera, Elisenda Alsina-Sanchis, Juan A. Marin-Jimenez, August Vidal, Xavier Matias-Guiu, Sergi Fernandez-Gonzalez, Marc Barahona, Lola Marti, Jordi Ponce, Francesc Vinals
Summary: High-grade serous ovarian cancer (HGSOC), the deadliest gynecological malignancy, spreads through transcoelomic dissemination. This study reveals that platelet-derived growth factor receptor beta (PDGFRβ) is essential for the formation of tumorspheres in HGSOC. Inhibition of PDGFRβ blocks the clustering of ovarian cancer cells and prevents peritoneal dissemination.
MOLECULAR ONCOLOGY
(2024)