Prognosis conferred by molecular features of appendix-derived Pseudomyxoma Peritonei by Ruiqing Ma, Guojun Li, Yingjiang Ye, Lei Liang, Chong Wang, Haipeng Zhou, Pu Zhang, Lubiao An, Guanjun Shi, Qian Chen, Hongbin Xu, Zhidong Gao

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Mutational signature analysis predicts bacterial hypermutation and multidrug resistance by Kalen M. Hall, Leonard G. Williams, Richard D. Smith, Erin A. Kuang, Robert K. Ernst, Christine M. Bojanowski, William C. Wimley, Lisa A. Morici, Zachary F. Pursell

“…Mutational signature analysis of patient samples is a promising diagnostic tool that may predict MDR and guide precision-based medical care.…”
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Tumor Mutation Signature Reveals the Risk Factors of Lung Adenocarcinoma with or Mutation by Jialiang Wang MM, Chang Guo BMed, Jiexiao Wang MM, Xiaopeng Zhang BS, Jian Qi PhD, Xiang Huang MM, Zongtao Hu MM, Hongzhi Wang MM, Bo Hong PhD

“…Introduction EGFR and KRAS mutations are frequently detected in lung adenocarcinoma (LUAD). Tumor mutational signature (TMS) determination is an approach to identify somatic mutational patterns associated with pathogenic factors. …”
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Decoding mutational signatures in breast cancer: Insights from a multi-cohort study by Margaux Betz, Andréa Witz, Julie Dardare, Cassandra Michel, Vincent Massard, Romain Boidot, Pauline Gilson, Jean-Louis Merlin, Alexandre Harlé

Subjects: “…Mutational signature…”
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Survival outcome prediction of esophageal squamous cell carcinoma patients based on radiomics and mutation signature by Ting Yan, Zhenpeng Yan, Guohui Chen, Songrui Xu, Chenxuan Wu, Qichao Zhou, Guolan Wang, Ying Li, Mengjiu Jia, Xiaofei Zhuang, Jie Yang, Lili Liu, Lu Wang, Qinglu Wu, Bin Wang, Tianyi Yan

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Adenomas from individuals with pathogenic biallelic variants in the MUTYH and NTHL1 genes demonstrate base excision repair tumour mutational signature profiles similar to colorectal cancers, expanding potential diagnostic and variant classification applications by Romy Walker, Jihoon E. Joo, Khalid Mahmood, Mark Clendenning, Julia Como, Susan G. Preston, Sharelle Joseland, Bernard J. Pope, Ana B.D. Medeiros, Brenely V. Murillo, Nicholas Pachter, Kevin Sweet, Allan D. Spigelman, Alexandra Groves, Margaret Gleeson, Krzysztof Bernatowicz, Nicola Poplawski, Lesley Andrews, Emma Healey, Steven Gallinger, Robert C. Grant, Aung K. Win, John L. Hopper, Mark A. Jenkins, Giovana T. Torrezan, Christophe Rosty, Finlay A. Macrae, Ingrid M. Winship, Daniel D. Buchanan, Peter Georgeson

Subjects: “…Mutational signature…”
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Functional annotation of variants from healthy individuals by Jean Lee, Sung Eun Hong

“…The pathogenicity of the DNVs was not strongly elevated, reflecting the health status of the cohort. The mutational signatures were consistent with previous studies. …”
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The high cancer incidence in young people in Italy: do genetic signatures reveal their environmental causes? by Ruggero Ridolfi

“…Today, the whole genome sequencing techniques for human cancers can help to formulate a map of mutational signatures in individual tumours, and a list of mutational fingerprints showing exposure to specific environmental mutagens is being developed. …”
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Assessment of candidate high-grade serous ovarian carcinoma predisposition genes through integrated germline and tumour sequencing by Deepak N. Subramanian, Maia Zethoven, Kathleen I. Pishas, Evanny R. Marinović, Simone McInerny, Simone M. Rowley, Prue E. Allan, Lisa Devereux, Dane Cheasley, Paul A. James, Ian G. Campbell

“…PALB2 and ATM validate as HGSOC predisposition genes, with 6/8 germline carrier tumours exhibiting biallelic inactivation accompanied by characteristic mutational signatures. Among candidate genes, only LLGL2 consistently shows biallelic inactivation and protein expression loss, supporting it as a novel HGSOC susceptibility gene. …”
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Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer by Noah Sasa, Toshihiro Kishikawa, Masashi Mori, Rie Ito, Yumie Mizoro, Masami Suzuki, Hirotaka Eguchi, Hidenori Tanaka, Takahito Fukusumi, Motoyuki Suzuki, Yukinori Takenaka, Keisuke Nimura, Yukinori Okada, Hidenori Inohara

“…HPV+ HNSCCs exhibited almost no smoking-induced mutational signatures. Heterozygous loss of ataxia-telangiectasia mutated (ATM) was observed in 67% of tumors, with its downregulation confirmed by single-cell RNA sequencing and immunohistochemistry, suggesting ATM haploinsufficiency contributes to carcinogenesis. …”
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Prospective clinical performance of CoVarScan in identifying SARS-CoV-2 Omicron subvariants by Kenneth Zhu, Manoj Sah, Lenin Mahimainathan, Yan Liu, Chao Xing, Karen Roush, Andrew Clark, Jeffrey SoRelle

“…CoVarScan achieved 96.5% concordance with WGS and could detect unique mutational signatures for BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, XBB, and BA.2.86. …”
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Genome sequencing enhances the diagnostic yield and expands the genetic landscape of male breast cancer by Wen Wen, Sen Zhao, Yiwen Jiang, Chengzhu Ou, Changyuan Guo, Ziqi Jia, Jiayi Li, Yansong Huang, Hengyi Xu, Pengming Pu, Tongxuan Shang, Lin Cong, Xiang Wang, Nan Wu, Jiaqi Liu

“…Exome sequencing analysis further identified significant somatic oncogenic drivers and revealed a dominant mutational signature SBS3 across BRCA1/2-negative samples, reinforcing the contribution of omologous recombination deficiency underlying the MBC development. …”
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Widespread mutagenesis and chromosomal instability shape somatic genomes in systemic sclerosis by Sriram Vijayraghavan, Thomas Blouin, James McCollum, Latarsha Porcher, François Virard, Jiri Zavadil, Carol Feghali-Bostwick, Natalie Saini

“…In the genomes of patients with systemic sclerosis, we find evidence of somatic hypermutation or kategis (typically only seen in cancer genomes), we identify mutation signatures closely resembling the error-prone translesion polymerase Polη activity, and observe an activation-induced deaminase-like mutation signature, which overlaps with genomic regions displaying kataegis.…”
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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

“…Results: Patients in the high TMB group had better overall survival (OS) rates than patients in the low TMB group for both cohorts and TMB was associated with age, mutation signature 1 and mutation signature 17. The Cox regression analysis revealed that age, not TMB, was an independent prognosis factor. …”
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DNA replication initiation drives focal mutagenesis and rearrangements in human cancers by Pierre Murat, Guillaume Guilbaud, Julian E. Sale

“…Using ductal pancreatic adenocarcinoma as a cancer model, we demonstrate that the initiation of DNA synthesis is error-prone at G-quadruplex-forming sequences in tumours displaying markers of replication stress, resulting in a previously recognised but uncharacterised mutational signature. Finally, we demonstrate that replication origins serve as hotspots for genomic rearrangements, including structural and copy number variations. …”
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MASH as an emerging cause of hepatocellular carcinoma: current knowledge and future perspectives by Michael Karin, Ju Youn Kim

“…Here we review the literature on adipose tissues, liver‐related HCC etiologies and recently discovered genetic mutation signatures found in MAFLD‐driven HCC patients. …”
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Promoted read-through and mutation against pseudouridine-CMC by an evolved reverse transcriptase by Zhiyong He, Weiqi Qiu, Huiqing Zhou

“…We report a high-confidence list of Ψ sites in polyA-enriched RNAs from HEK-293T cells identified by orthogonal chemical treatments (CMC and bisulfite). The mutation signatures resolve the position of Ψ in UU-containing sequences, revealing diverse occurrence of Ψs in such sequences. …”
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Sex disparities in the association between rare earth elements exposure and genetic mutation frequencies in lung cancer patients by Mengyuan Liu, Jiali Zhang, Xiaohong Duan, Qiming Zhou, Jing Chen, Siyao Liu, Junyan Su, Li Han, Fan Yang, Niansong Qian

“…Additionally, plasma REE levels was associated with specific mutation types and variant allele frequencies (VAFs) of particular genes in a sex-dependent manner. Mutational signature analysis revealed sex-specific associations of La with indel signatures. …”
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Characterization of the genomic landscape in liver oligometastatic NSCLC by Rongxin Liao, Guangming Yi, Lu Shen, Xiao Xiao, Chuan Zeng, Liangzhong Liu, Hongjun Tang, Shunping Huang, Xiaoyue Zhang, Zaicheng Xu, Zhenzhou Yang, Yuan Peng

“…Age, APOBEC, homologous recombination deficiency (HRD) and deficient mismatch repair (dMMR) established the mutational signature of liver oligometastatic NSCLC. The median tumor mutation burden (TMB) was 4.8 mutations/Mb. …”
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Molecular dependencies and genomic consequences of a global DNA damage tolerance defect by Daniel de Groot, Aldo Spanjaard, Ronak Shah, Maaike Kreft, Ben Morris, Cor Lieftink, Joyce J. I. Catsman, Shirley Ormel, Matilda Ayidah, Bas Pilzecker, Olimpia Alessandra Buoninfante, Paul C. M. van den Berk, Roderick L. Beijersbergen, Heinz Jacobs

“…Conclusions Our data highlight the essential contribution of the DDT system to genome maintenance and type 3 deletions as mutational signature of replication stress. The unique characteristics of type 3 deletions implicate the existence of a novel deletion pathway in mice and humans that is counteracted by DDT. …”
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