Article
Multidisciplinary Sciences
Sujath Abbas, Oriol A. Pich, Ginny Devonshire, Shahriar Zamani, Annalise Katz-Summercorn, Sarah Killcoyne, Calvin Cheah, Barbara Nutzinger, Nicola Grehan, Nuria Lopez-Bigas, Paul A. W. Edwards, Elwira M. Fidziukiewicz, Aisling Redmond, Adam C. Freeman, Elizabeth Smyth, Maria O'Donovan, Ahmad Miremadi, Shalini Malhotra, Monika Tripathi, Hannah Coles, Conor Flint, Matthew Eldridge, Sriganesh Jammula, Jim Davies, Charles Crichton, Nick H. Carroll, Richard Hardwick, Peter Safranek, Andrew Hindmarsh, Vijayendran J. Sujendran, Stephen Hayes, Yeng Ang, Andrew R. Sharrocks, Shaun Preston, Izhar Bagwan, Vicki Save, Richard J. E. R. Skipworth, Ted Hupp, J. Robert O'Neill, Olga Tucker, Andrew Beggs, Philippe Taniere, Sonia Puig, Gianmarco J. Contino, Timothy C. Underwood, Robert L. Walker, Ben Grace, Jesper Lagergren, James Gossage, Andrew Davies, Fuju Chang, Ula Mahadeva, Vicky D. Goh, Francesca Ciccarelli, Grant Sanders, Richard Berrisford, David Chan, Ed Cheong, Bhaskar Kumar, L. L. Sreedharan, Simon Parsons, Irshad Soomro, Philip Kaye, John Saunders, Laurence Lovat, Rehan Haidry, Michael Scott, Sharmila Sothi, Suzy B. Lishman, George J. Hanna, Christopher Peters, Krishna Moorthy, Anna Grabowska, Richard Turkington, Damian McManus, Helen D. Coleman, Russell Petty, Freddie C. Bartlett, Rebecca Fitzgerald, Maria Secrier
Summary: The mutational processes of oesophageal adenocarcinoma (OAC) progression from Barrett's Oesophagus have been characterized, with C[T > C/G]T substitution enriched signatures SBS17a/b being dominant. TP53 mutations, increased proliferation, genomic instability, and disease progression are associated with these mutations. Alterations in DNA damage repair pathways, including base excision repair deficiencies, are also linked to poor prognosis.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Qinghua Wang, Wenjing Zhang, Yuxian Guo, Fuyan Shi, Yuting Li, Yujia Kong, Juncheng Lyu, Suzhen Wang
Summary: In this study, we identified new molecular biomarkers predictive of immunotherapy efficacy across multiple cancers. Mutational signatures, molecular subtypes, and significantly mutated genes (SMGs) were determined and their connections with ICI response and outcome were evaluated. We discovered that a mutational signature featuring T > C substitutions was associated with ICI resistance, and a molecular subtype based on mutational activities correlated with improved ICI response rate and outcome. Additionally, patients with COL11A1 or COL4A6 mutations exhibited superior ICI treatment efficacy.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Multidisciplinary Sciences
Musalula Sinkala
Summary: This study analyzes the genomic sequences of 20,331 primary tumors, identifying driver mutations in 727 known cancer genes and revealing significant variations in mutation frequency and co-occurrence in different cancer types. The study also finds that patients with tumors displaying different combinations of gene mutation patterns have variable survival outcomes, providing new insights into the genetic landscape and mechanisms of cancer development.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Haozhe Zou, Tao Pan, Yueying Gao, Renwei Chen, Si Li, Jing Guo, Zhanyu Tian, Gang Xu, Juan Xu, Yanlin Ma, Yongsheng Li
Summary: This study comprehensively characterized the mutational landscapes of intrinsically disordered protein regions (IDRs) in cancer and developed a computational method to identify putative driver genes in these regions. The results showed that IDRs have higher mutation frequencies across diverse cancers and mutations in these regions disrupt phase separation in key cellular pathways. Additionally, clinically relevant genes enriched in IDR mutational hotspots were identified and associated with cancer patient survival. The combination of mutational effects on IDRs can significantly improve the sensitivity of driver detection and offer new therapeutic avenues for cancer treatment.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Jiri Jungwirth, Marketa Urbanova, Arnoud Boot, Petr Hosek, Petra Bendova, Anna Siskova, Jiri Svec, Milan Kment, Daniela Tumova, Sandra Summerova, Zdenek Benes, Tomas Buchler, Pavel Kohout, Tomas Hucl, Radoslav Matej, Ludmila Vodickova, Tom van Wezel, Pavel Vodicka, Veronika Vymetalkova
Summary: A large proportion of colorectal carcinomas evolve from colorectal adenomas, which have a high frequency of pathogenic variants in genes such as APC, KRAS, and TP53. The mutation frequencies of APC, KRAS, and TP53 are slightly lower in adenoma samples compared to in situ carcinoma samples. KRAS mutation is associated with villous histology, and methylation of the APC promoter is significantly associated with the presence of POLE genetic variations.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Yun-Yun Tang, Pi-Jing Wei, Jian-Ping Zhao, Junfeng Xia, Rui-Fen Cao, Chun-Hou Zheng
Summary: The study proposed a method called mutations effect and network centrality to effectively identify driver genes in cancer. Experimental data showed that this method was superior to existing network-centric methods, as it could quickly and easily identify driver genes and rare driver factors in The Cancer Genome Atlas dataset.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
David Chen, Gurjit S. Randhawa, Maximillian P. M. Soltysiak, Camila P. E. de Souza, Lila Kari, Shiva M. Singh, Kathleen A. Hill
Summary: SomaticSiMu is a mutational signature simulator that allows for the simulation of single and double base substitutions, as well as base insertions and deletions in a genomic sequence. It provides a graphical user interface, control of mutation rates, and built-in visualization tools for the simulated mutations. This tool can be used to generate simulated datasets for testing the accuracy and sensitivity of DNA sequence classification tools and mutational signature extraction tools.
Review
Biochemistry & Molecular Biology
Aik Seng Ng, Dedrick Kok Hong Chan
Summary: Advances in sequencing have revealed a highly diverse landscape of mutational signatures and somatic driver mutations in normal tissues. Different normal tissues have varying mutation rates, with the liver having 11 mutations per cell per year and the bladder having 1879 mutations per cell per year. Understanding the relationship between normal tissue somatic mutations and tumor initiation remains limited. This study describes the mutational signatures and somatic driver mutations in different organs, highlighting unique characteristics and seeking commonalities to develop a unified theory on the role of these mutations in tumor initiation.
Article
Biochemistry & Molecular Biology
Judy Bai, Katherine Ma, Shangyang Xia, Richard Geng, Claire Shen, Limin Jiang, Xi Gong, Hui Yu, Shuguang Leng, Yan Guo
Summary: This study explores the differences in mutational signatures between different races and their association with environmental pollutant exposures. It shows that increased pollution levels are associated with worse cancer prognosis and that Asians may have a genetic or genomic disadvantage concerning aflatoxin exposure.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
John K. L. Wong, Christian Aichmueller, Markus Schulze, Mario Hlevnjak, Shaymaa Elgaafary, Peter Lichter, Marc Zapatka
Summary: Cancer driving mutations, especially in the non-coding part of the genome, are difficult to identify. In this study, researchers developed an algorithm called sigDriver to call driver mutations. They used a large dataset of tumor genome sequences and discovered multiple mutational processes associated with known and putative tumor drivers and hotspots, particularly in the non-coding regions of the genome, including APOBEC activity and somatic hypermutation signatures.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Xiangxin Zhang, Liu Yang, Ming Kong, Jian Ma, Yutao Wei
Summary: The study constructed a prediction signature with 12 IRGs related to EAC, showing that the high-risk group had significantly shorter survival rates compared to the low-risk group. Multivariate Cox analysis and Nomogram demonstrated that the combined analysis of risk score, Sex, M stage, and Stage accurately predicted the 1- and 3-year survival rates of patients.
BMC BIOINFORMATICS
(2021)
Article
Medicine, Research & Experimental
Liying Sun, Yingzhao Huang, Sen Zhao, Junhui Zhao, Zihui Yan, Yang Guo, Mao Lin, Wenyao Zhong, Yuehan Yin, Zefu Chen, Nan Zhang, Yuanqiang Zhang, Zongxuan Zhao, Qingyang Li, Lianlei Wang, Xiying Dong, Yaqi Li, Xiaoxin Li, Guixing Qiu, Terry Jianguo Zhang, Zhihong Wu, Wen Tian, Nan Wu
Summary: This study aimed to decipher the mutational signature of congenital limb malformations (CLM) using exome sequencing, identifying novel pathogenic variants and candidate genes. By expanding the phenotypic spectrum of CLM, the researchers discovered RPL9 and UBA2 as potential new genes for CLM. The study significantly increased diagnosis rates among patients with a family history of CLM or multiple affected limbs, providing valuable insights into the genetic basis of these syndromes.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Biochemical Research Methods
Caitlin Timmons, Quaid Morris, Caitlin F. Harrigan
Summary: This study presents regional profiles of mutational signature activities in cancer genomes, showcasing changes in these activities during tumor development. The research reveals shared changepoints across multiple tumor types and activity tradeoffs between signatures active in early and late cancer development.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Palash Pandey, Sanjeevani Arora, Gail L. Rosen
Summary: This article introduces a user-friendly software that can aggregate and visually present results from different refitting packages for effective comparison of mutational signatures.
Article
Multidisciplinary Sciences
Yang Wu, Ellora Hui Zhen Chua, Alvin Wei Tian Ng, Arnoud Boot, Steven G. Rozen
Summary: Mutational signatures are important for various fields such as DNA damage and repair, aging, cancer biology, etc. Unsupervised learning can infer mutational signatures, but separating correlated signatures is a challenge. While evaluating different methods, some outperform others, highlighting the complexity of mutational signature extraction.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Baifeng Zhang, Peilin Jia, Jiayin Wang, Guangsheng Pei, Changxi Wang, Shimei Pei, Xiangchun Li, Zhongming Zhao, Xin Yi, Xin-yuan Guan, Yi Huang
Summary: The genomic architectures of 505 bladder cancer patients from Asian/Black/White populations were analyzed, revealing an unknown association between AHNAK mutations and APOBEC-a mutational signature activity. The prevalence of TP53 and ATM clonal mutations as well as the burden of SCNAs is significantly higher in Whites/Blacks than in Asians. A trans-ancestry prognostic subtype of bladder cancer was identified, characterized by enrichment of non-muscle-invasive patients and muscle-invasive patients with good prognosis, specific mutations, decreased intra-tumor heterogeneity and genome instability, and an activated tumor microenvironment.
MOLECULAR ONCOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Yongxu Jia, Baifeng Zhang, Chunyang Zhang, Dora Lai-Wan Kwong, Zhiwei Chang, Shanshan Li, Zehua Wang, Huiqiong Han, Jing Li, Yali Zhong, Xin Sui, Li Fu, Xinyuan Guan, Yanru Qin
Summary: In this study, the authors analyzed the transcriptomes of 85,263 single cells from four ESCC patients with lymph node metastasis. They identified various cells and genes that play a role in the metastatic microenvironment, including IFIT3(+) T and B cells, APOC1(+)APOE(+) macrophages, myofibroblasts, and immunoglobulin genes. They also discovered an epithelial-immune dual expression program that regulates immune processes in metastatic cells. Additionally, they found differential intercellular communications in the metastatic ESCC microenvironment, mainly involving the interaction of APOC1(+)APOE(+) macrophages with tumor and stromal cells. These findings provide insights into the molecular mechanisms underlying lymph-node metastasis and offer potential targets for inhibiting tumor growth and improving clinical outcomes.
Article
Biochemical Research Methods
Wei Zhang, Jia Ju, Yong Zhou, Teng Xiong, Mengyao Wang, Chaohui Li, Shixin Lu, Zefeng Lu, Liya Lin, Xiao Liu, Shuai Cheng Li
Summary: The Adaptive Immune Receptor Repertoire (AIRR) is crucial in cancer immunotherapy and MRD detection. A software package called IMperm was developed to efficiently merge PE reads, successfully handling low-quality and non-overlapping reads. Compared to existing tools, IMperm showed better performance in both simulated and sequencing data, and also demonstrated its effectiveness in handling PE reads from other sources.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Oncology
Jin Zhou, Wenqian Yu, Jing Xia, Shiyi Li, Linshen Xie, Xin Wang
Summary: This study aims to determine if all rectal cancer patients benefit from surgery in terms of overall survival. The results showed that surgery has a protective effect on the prognosis of rectal cancer patients, especially those with advanced age and distant metastasis. These findings can guide clinicians in tailoring treatment regimens and making surgical decisions.
Article
Multidisciplinary Sciences
Hongru Shen, Jilei Liu, Jiani Hu, Xilin Shen, Chao Zhang, Dan Wu, Mengyao Feng, Meng Yang, Yang Li, Yichen Yang, Wei Wang, Qiang Zhang, Jilong Yang, Kexin Chen, Xiangchun Li
Summary: tGPT is a method for learning feature representation of transcriptomes, which efficiently handles the exponential growth of single-cell transcriptome data. It shows good performance on tasks such as single-cell analysis and tumor tissue analysis.
Letter
Oncology
Li Zhang, Lingxi Chen, Shuai Cheng Li, Mengyao Wang, Chaohui Li, Tingting Song, Yinyun Ni, Ying Yang, Zhiqiang Liu, Menglin Yao, Bairong Shen, Weimin Li
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Letter
Oncology
Hao Zou, Yinan Wang, Lianfang Lu, Ke Yao, Chang Wang, Kai Ma, Chengzhan Zhu, Zhongyi Guo, Yujie Feng, Zehua Wu, Mengqi Song, Bin Zhou, Xiao Hu, Bing Han, Weidong Guo, Fabo Qiu, Bingyuan Zhang, Xingsi Qi, Xiaowei Wang, Mengyao Wang, Guangze Pan, Qixuan Sun, Jingyu Cao, Song Gong, Zicheng Zhao, Chuandong Sun, Shichun Lu, Lantian Tian
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Biochemical Research Methods
Shuai Wang, Mengyao Wang, Lingxi Chen, Guangze Pan, Yanfei Wang, Shuai Cheng Li
Summary: This study presents a new method, SpecHLA, for accurate full-resolution HLA typing, achieving satisfactory results in different types of sequencing data and pedigree data. In experiments, SpecHLA demonstrated high accuracy in typing and detection in human samples and simulated cancer cell line samples.
CELL REPORTS METHODS
(2023)
Meeting Abstract
Oncology
Yuma Yang, Lanqi Gong, Jie Luo, Xiaona Fang, Jiao Huang, Lu Bai, Qin Liu, Beilei Liu, Shan Liu, Jinlin Huang, Ching Ngar Wong, Baifeng Zhang, Danyang Zheng, Yu Zhang, Wei Dai, Xinyuan Guan
Meeting Abstract
Oncology
Baifeng Zhang, Dora Lai-Wan Kwong, Xin-Yuan Guan
Meeting Abstract
Oncology
Beilei Liu, Baifeng Zhang, Hongyu Zhou, Licheng Tan, Xiaona Fang, Lanqi Gong, Jie Luo, Jinlin Huang, Jiao Huang, Yuma Yang, Xinyuan Guan
Meeting Abstract
Oncology
Shan Liu, Xiaona Fang, Jie Luo, Jiao Huang, Yuma Yang, Beilei Liu, Jinlin Huang, Ching Ngar Wong, Baifeng Zhang, Lanqi Gong, Liuxian Ban, Qian Yan, Xinyuan Guan
Meeting Abstract
Oncology
Xiaona Fang, Shan Liu, Liuxian Ban, Jiao Huang, Jie Luo, Lanqi Gong, Baifeng Zhang, Beilei Liu, Jinlin Huang, Yuma Yang, Ching Ngar Wong, Qian Yan, Xin-Yuan Guan
Meeting Abstract
Oncology
Jiao Huang, Wai Ying Tsang, Xiaona Fang, Yu Zhang, Jie Luo, Lanqi Gong, Baifeng Zhang, Ching Ngar Wong, Beilei Liu, Jinlin Huang, Yuma Yang, Shan Liu, Zhihong Li, Xinyuan Guan
Article
Health Care Sciences & Services
Xinwei Peng, Jibin Li, Yuwan Wu, Hongji Dai, Henry S. Lynn, Xi Zhang
Summary: This study aimed to evaluate the individual and joint associations of stool frequency and consistency with all-cause and cause-specific mortality. The results showed that less than 7 times/week of stool frequency is a significant risk factor for mortality. Additionally, irregular soft stools are associated with increased risks of all-cause, cancer, and cardiovascular disease mortality, emphasizing the importance of bowel health.
