Review
Oncology
Xihan Guo, Xueqin Dai, Xue Wu, Neng Cao, Xu Wang
Summary: Micronuclei, small structures resembling nuclei, are common in cancer cells and have distinct genetic activities contributing to intratumoral genetic heterogeneity. Recent studies have shown that most micronuclei display a mutational signature of chromothripsis, indicating their role as mutation factories with short- and long-term effects on cancer genomes.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Editorial Material
Biochemistry & Molecular Biology
Sara Bernardo, Mathilde Meyenberg, Joanna I. Loizou
Summary: Mutational signatures are the outcomes of mutagenic processes before and during tumorigenesis due to DNA damage, repair, and replication. Wojtowicz et al. introduce a new computational model in this issue of Cell Systems aimed at deconstructing the mutational processes shaping cancer genomes.
Article
Genetics & Heredity
Jonas Demeulemeester, Stefan C. Dentro, Moritz Gerstung, Peter Van Loo
Summary: The infinite sites model is an important theoretical framework in tumor biology that analyzes the mutation patterns in the genome to understand tumor evolution. This study identified biallelic mutations that play a crucial role in tumor development and gene function. The findings have significant implications for accurately predicting mutation rates and understanding tumor evolution.
Editorial Material
Oncology
Axel Rosendahl Huber, Cayetano Pleguezuelos-Manzano, Jens Puschhof
Summary: Changes in the microbiome are linked to colorectal cancer development, with certain bacteria inducing mutational patterns present in colorectal cancer genomes. More research is needed to understand the microbial role in oncogenic mutation induction, cancer development, and preventive strategies.
BRITISH JOURNAL OF CANCER
(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
Multidisciplinary Sciences
Heather E. Machado, Emily Mitchell, Nina F. Obro, Kirsten Kubler, Megan Davies, Daniel Leongamornlert, Alyssa Cull, Francesco Maura, Mathijs A. Sanders, Alex T. J. Cagan, Craig McDonald, Miriam Belmonte, Mairi S. Shepherd, Felipe A. Vieira Braga, Robert J. Osborne, Krishnaa Mahbubani, Inigo Martincorena, Elisa Laurenti, Anthony R. Green, Gad Getz, Paz Polak, Kourosh Saeb-Parsy, Daniel J. Hodson, David G. Kent, Peter J. Campbell
Summary: The lymphocyte genome is prone to many threats, including programmed mutation during differentiation, antigen-driven proliferation, and residency in diverse microenvironments. This study found that lymphocyte subsets carry more mutations than hematopoietic stem cells, with memory cells having higher burdens than naive cells. T cells accumulate mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for half of the additional mutations in lymphocytes. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering and the consequences of differentiation, proliferation, and residency in diverse microenvironments.
Article
Genetics & Heredity
Abdullah, Claudia L. Henriquez, Thomas B. Croat, Peter Poczai, Ibrar Ahmed
Summary: The study investigated correlations among mutational events at different classification levels within the Araceae family, revealing strong relationships between SNPs, InDels, and repeats, which support the hypothesis of oligonucleotide repeats distribution as mutational hotspots.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Rohan Singh, Sunil Nagpal, Nishal K. Pinna, Sharmila S. Mande
Summary: This article describes how natural language processing algorithms can be used to analyze the genomes and mutations of SARS-CoV-2, revealing its characteristics and evolution. The research found that NLP algorithms can not only study the temporal mutation features through dynamic topic modeling, but also track the semantic drift to understand the correlation of genomic mutations. In addition, this method is promising in uncovering the mutation relevance to patient health status.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Keun Pyo Lee, Mengping Li, Mengshuang Li, Kaiwei Liu, Laura Medina-Puche, Shan Qi, Chaojun Cui, Rosa Lozano-Duran, Chanhong Kim
Summary: The GENOMES UNCOUPLED1 (GUN1)-mediated chloroplast-to-nucleus retrograde signaling pathway modulates salicylic acid (SA) signaling in Arabidopsis. GUN1 represses the transcription of GLK1/2, which positively regulate chloroplast biogenesis. Knockout of GLK1/2 leads to enhanced stress responses through the upregulation of SA-responsive genes.
Article
Genetics & Heredity
Scout R. L. Thompson, Dong Kyung Lee, Marc-Andre Lachance, David Roy Smith
Summary: Studying homologous recombination with self-splicing introns in Metschnikowia yeasts' mitochondrial genomes sheds light on the mutational effects of these introns, revealing a higher density of polymorphisms near the insertion sites. This suggests that carrying self-splicing introns may come with fitness costs.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Lucile Vigue, Giancarlo Croce, Marie Petitjean, Etienne Ruppe, Olivier Tenaillon, Martin Weigt
Summary: Characterizing the effect of mutations is crucial for understanding protein sequence evolution and distinguishing between harmful and neutral changes. Epistatic interactions between residues can lead to a context dependence of mutation effects, constraining the range of amino acid changes.
NATURE COMMUNICATIONS
(2022)
Article
Health Care Sciences & Services
Cecilia Pop-Bica, Cristina Alexandra Ciocan, Cornelia Braicu, Antonia Harangus, Marioara Simon, Andreea Nutu, Laura Ancuta Pop, Ondrej Slaby, Atanas G. Atanasov, Radu Pirlog, Nadim Al Hajjar, Ioana Berindan-Neagoe
Summary: This study investigated the genetic profile of lung cancer using TCGA datasets and NGS experiments, revealing differences in mutational landscape among histotypes. The findings suggest that certain genetic alterations may be correlated with patient survival rates.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Oncology
Peng Li, Qingyu Meng, Yonggan Xue, Zhipeng Teng, Hanlin Chen, Junli Zhang, Yang Xu, Sha Wang, Ruoying Yu, Qiuxiang Ou, Xue Wu, Baoqing Jia
Summary: By performing genomic analysis, we identified differences and potential molecular mechanisms underlying different subgroups of colorectal cancer, providing new targets for precision treatment development.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemical Research Methods
Avantika Lal, Keli Liu, Robert Tibshirani, Arend Sidow, Daniele Ramazzotti
Summary: The study introduces a novel framework, SparseSignatures, for extracting signatures from somatic point mutation data. Experimental results on simulated data demonstrate that SparseSignatures outperforms current state-of-the-art methods in terms of accuracy. When applied to whole genome sequences of pancreatic and breast tumors, well-differentiated signatures linked to known mutagenic mechanisms and strongly associated with patient clinical features were discovered.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Elena Rensen, Florian Mueller, Viviana Scoca, Jyotsana J. Parmar, Philippe Souque, Christophe Zimmer, Francesca Di Nunzio
Summary: Infected macrophages exhibit large nuclear foci of viral DNA and RNA, with clusters forming that do not require chromosomal integration and consist predominantly of incoming genomic RNA. This indicates a different understanding of the early HIV-1 replication cycle and potential implications for addressing viral persistence.
Article
Genetics & Heredity
Michalina Janiszewska, Lin Liu, Vanessa Almendro, Yanan Kuang, Cloud Paweletz, Rita A. Sakr, Britta Weigelt, Ariella B. Hanker, Sarat Chandarlapaty, Tari A. King, Jorge S. Reis-Filho, Carlos L. Arteaga, So Yeon Park, Franziska Michor, Kornelia Polyak
Article
Biochemical Research Methods
Jasmine Foo, Lin L. Liu, Kevin Leder, Markus Riester, Yoh Iwasa, Christoph Lengauer, Franziska Michor
PLOS COMPUTATIONAL BIOLOGY
(2015)
Article
Cell Biology
Lin L. Liu, Justin Brumbaugh, Ori Bar-Nur, Zachary Smith, Matthias Stadtfeld, Alexander Meissner, Konrad Hochedlinger, Franziska Michor
Article
Biochemistry & Molecular Biology
Kyle S. Smith, Lin L. Liu, Shridar Ganesan, Franziska Michor, Subhajyoti De
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2017)
Article
Multidisciplinary Sciences
Lin Liu, Subhajyoti De, Franziska Michor
NATURE COMMUNICATIONS
(2013)
Article
Statistics & Probability
Lin Liu, Rajarshi Mukherjee, James M. Robins
STATISTICAL SCIENCE
(2020)
Editorial Material
Statistics & Probability
Lin Liu, Rajarshi Mukherjee, James M. Robins
STATISTICAL SCIENCE
(2020)
Review
Oncology
Philipp M. Altrock, Lin L. Liu, Franziska Michor
NATURE REVIEWS CANCER
(2015)