Efficacy of platinum-based chemotherapy in metastatic breast cancer and HRD biomarkers: utility of exome sequencing by Loïck Galland, Elise Ballot, Hugo Mananet, Romain Boidot, Julie Lecuelle, Juliette Albuisson, Laurent Arnould, Isabelle Desmoulins, Didier Mayeur, Courèche Kaderbhai, Silvia Ilie, Audrey Hennequin, Anthony Bergeron, Valentin Derangère, François Ghiringhelli, Caroline Truntzer, Sylvain Ladoire

“…The real benefit of these treatments is uncertain at advanced stages of the disease and in non-triple-negative subtypes. Since homologous recombination deficiency (HRD) could inform about tumor sensitivity to DNA-damaging agents, we aimed to determine biomarkers of genomic instability, and their link with platinum efficacy. …”
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Pan-cancer integrated bioinformatics analysis reveals cuproptosis related gene FDX1 is a potential prognostic and immunotherapeutic biomarker for lower-grade gliomas by Wei Huang, Yuliang Wu, Yuliang Wu, Jihui Zhu, Ning Luo, Chunyan Wang, Shupeng Liu, Zhongping Cheng

“…Additionally, positive correlations were observed between FDX1 and immune cells infiltration, immune checkpoints, tumor stemness, homologous recombination deficiency (HRD), and TMB in LGG in the pan-cancer analysis. …”
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SIRT6 is a DNA double-strand break sensor by Lior Onn, Miguel Portillo, Stefan Ilic, Gal Cleitman, Daniel Stein, Shai Kaluski, Ido Shirat, Zeev Slobodnik, Monica Einav, Fabian Erdel, Barak Akabayov, Debra Toiber

“…It activates downstream signaling for DSB repair by triggering ATM recruitment, H2AX phosphorylation and the recruitment of proteins of the homologous recombination and non-homologous end joining pathways. …”
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TCGA Pan-Cancer Genomic Analysis of Alternative Lengthening of Telomeres (ALT) Related Genes by Isaac Armendáriz-Castillo, Andrés López-Cortés, Jennyfer García-Cárdenas, Patricia Guevara-Ramírez, Paola E. Leone, Andy Pérez-Villa, Verónica Yumiceba, Ana K. Zambrano, Santiago Guerrero, César Paz-y-Miño

“…Finally, we made a protein-protein interaction network and enrichment analysis to observe the main pathways of these genes and discuss their role in ALT-related processes, like homologous recombination and homology directed repair. Overall, due to the lack of understanding of the molecular mechanisms of ALT cancers, we proposed a group of genes, which after ex vivo validations, could represent new potential therapeutic markers in the study of ALT.…”
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Multidrug Resistance Genes Carried by a Novel Transposon Tn7376 and a Genomic Island Named MMGI-4 in a Pathogenic Morganella morganii Isolate by Xing-Wei Luo, Pei-Yi Liu, Qing-Qing Miao, Rong-Jia Han, Hua Wu, Jian-Hua Liu, Dan-Dan He, Gong-Zheng Hu

“…Sequence analysis suggested that the Tn7376 could be generated through homologous recombination between two different IS26-bounded translocatable units (TUs), namely, module A (IS26-Hp-IS26-mph(A)-mrx(A)-mphR-IS6100-chrA-sul1-qacEΔ1) and module B (ISCR1-sul1-qacEΔ1-cmlA1-aadA1-aadB-intI1-IS26), and the genomic island named MMGI-4 might derive from a partial structure of different original genomic islands that also carried IS26-mediated TUs. …”
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Systematic Analysis of Two Tandem GGDEF/EAL Domain Genes Regulating Antifungal Activities in <i>Pseudomonas glycinae</i> MS82 by Jinsheng Lin, Shaoxuan Qu, Xianyi Chen, Huiping Li, Lijuan Hou, Shi-En Lu, Ping Xu, Ning Jiang, Lin Ma

“…Individual deletion mutants of <i>PafQ</i> and <i>PafR</i> were constructed in <i>P. glycinae</i> MS82 through biparental conjugation and homologous recombination. Subsequently, antifungal activity, biofilm formation, motility, and expression of the genes related to antifungal substance synthesis were examined and contrasted with those of wild-type <i>P. glycinae</i> MS82. …”
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Identification of tumor mutation burden-associated molecular and clinical features in cancer by analyzing multi-omics data by Mengyuan Li, Mengyuan Li, Xuejiao Gao, Xuejiao Gao, Xiaosheng Wang

“…Nine cancer-associated pathways correlated positively with TMB in various cancers, including nucleotide excision repair, DNA replication, homologous recombination, base excision repair, mismatch repair, cell cycle, spliceosome, proteasome, and RNA degradation. …”
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Exploration and validation of a combined Hypoxia and m6A/m5C/m1A regulated gene signature for prognosis prediction of liver cancer by Min ren, Bei Fan, Guangcai Cao, Rongrong Zong, Liaoliao Feng, Huiru Sun

“…The high-risk group exhibited more genome changes and higher homologous recombination deficiency scores and stemness scores. …”
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Discovery of a small-molecule inhibitor that traps Polθ on DNA and synergizes with PARP inhibitors by William Fried, Mrityunjay Tyagi, Leonid Minakhin, Gurushankar Chandramouly, Taylor Tredinnick, Mercy Ramanjulu, William Auerbacher, Marissa Calbert, Timur Rusanov, Trung Hoang, Nikita Borisonnik, Robert Betsch, John J. Krais, Yifan Wang, Umeshkumar M. Vekariya, John Gordon, George Morton, Tatiana Kent, Tomasz Skorski, Neil Johnson, Wayne Childers, Xiaojiang S. Chen, Richard T. Pomerantz

“…Abstract The DNA damage response (DDR) protein DNA Polymerase θ (Polθ) is synthetic lethal with homologous recombination (HR) factors and is therefore a promising drug target in BRCA1/2 mutant cancers. …”
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Multi-omics analyses of tumor-associated immune-infiltrating cells with the novel immune checkpoint protein tyrosine phosphatase 1B (PTP1B) in extracellular matrix of brain-lower-g... by Kun-Hao Bai, Kun-Hao Bai, Ming-Jiao Zhu, Yi-Yang Zhang, Yi-Yang Zhang, Xue-Ping Li, Xue-Ping Li, Si-Liang Chen, Da-Wei Wang, Yu-Jun Dai, Yu-Jun Dai

“…The methylation status of PTP1B in these four tumors exhibited hypomethylation and mutation landscape showed that PTP1B had its specific characteristics in genomic instability and heterogeneity. The homologous recombination deficiency (HRD) and loss of heterozygosity (LOH) were positive related to PTP1B expression in liver-hepatocellular-carcinoma (LIHC) and kidney-chromophobe (KICH), while the immunescore and immune infiltration displayed a significant positive correlation with PTP1B expression in LGG and UVM. …”
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Differential Recruitment of DNA Repair Proteins KU70/80 and RAD51 upon Microbeam Irradiation with α-Particles by Laure Bobyk, François Vianna, Juan S. Martinez, Gaëtan Gruel, Marc Benderitter, Céline Baldeyron

“…In mammalian cells, DNA DSBs can be repaired by two major pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). Here, we investigated their dynamics in mouse NIH-3T3 cells through the recruitment of key proteins, such as the KU heterodimer for NHEJ and RAD51 for HR upon localized α-particle irradiation. …”
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The fructose-bisphosphate, Aldolase A (ALDOA), facilitates DNA-PKcs and ATM kinase activity to regulate DNA double-strand break repair by Thais Sobanski, Amila Suraweera, Joshua T. Burgess, Iain Richard, Chee Man Cheong, Keyur Dave, Maddison Rose, Mark N. Adams, Kenneth J. O’Byrne, Derek J. Richard, Emma Bolderson

“…Consistent with this, cells depleted of ALDOA exhibited decreased DNA DSB repair via non-homologous end-joining and homologous recombination. In support of the defective repair observed in its absence, ALDOA was found to associate with the major DSB repair effector kinases, DNA-dependent Protein Kinase (DNA-PK) and Ataxia Telangiectasia Mutated (ATM) and their autophosphorylation was decreased when ALDOA was depleted. …”
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Molecular intrinsic subtypes, genomic, and immune landscapes of BRCA-proficient but HRD-high ER-positive/HER2-negative early breast cancers by Elise Ballot, Loïck Galland, Hugo Mananet, Romain Boidot, Laurent Arnould, Isabelle Desmoulins, Didier Mayeur, Courèche Kaderbhai, Silvia Ilie, Audrey Hennequin, Anthony Bergeron, Valentin Derangère, François Ghiringhelli, Caroline Truntzer, Sylvain Ladoire

“…Abstract Purpose The vast majority of research studies that have described the links between DNA damage repair or homologous recombination deficiency (HRD) score, and tumor biology, have concerned either triple negative breast cancers or cancers with mutation of BRCA 1/2. …”
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Micronuclei Formation upon Radioiodine Therapy for Well-Differentiated Thyroid Cancer: The Influence of DNA Repair Genes Variants by Luís S. Santos, Octávia M. Gil, Susana N. Silva, Bruno C. Gomes, Teresa C. Ferreira, Edward Limbert, José Rueff

“…We, therefore, sought to evaluate the induction and 2-year persistence of micronuclei (MN) in lymphocytes from 26 ¹³¹I-treated DTC patients and the potential impact of nine homologous recombination (HR), non-homologous end-joining (NHEJ), and mismatch repair (MMR) polymorphisms on MN levels. …”
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Circ_0008657 regulates lung DNA damage induced by hexavalent chromium through the miR-203a-3p/ATM axis by Wei Chen, Zehao Chen, Yangyang Jia, Yaozheng Guo, Liting Zheng, Shuwei Yao, Yueting Shao, Meizhen Li, Rulin Mao, Yiguo Jiang

“…Mechanistically, we found that circ_0008657 binds to microRNA (miR)-203a-3p and subsequently regulates ATM serine/threonine kinase (ATM), a key protein involved in homologous recombination repair downstream of miR-203a-3p, thereby regulating DNA damage induced by Cr (VI). …”
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Identification and Evolutionary Analysis of Cotton (<i>Gossypium hirsutum</i>) <i>WOX</i> Family Genes and Their Potential Function in Somatic Embryogenesis by Ruibin Sun, Xue Zhang, Dan Ma, Chuanliang Liu

“…Co-expression analysis showed that the cotton <i>WOXs</i> co-expressed with genes involved in extensive genetic information processing, including DNA replication, DNA repair, homologous recombination, RNA transport, protein processing, and several signaling and metabolism pathways, in which plant hormones signal transduction, MAPK signaling pathways, phosphatidylinositol signaling systems, and ABC transporters, as well as the metabolism of fatty acid; valine, leucine, and isoleucine biosynthesis; and cutin, suberine, and wax biosynthesis, were most significantly enriched. …”
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Pan-cancer analysis of genomic scar patterns caused by homologous repair deficiency (HRD) by E. Rempel, K. Kluck, S. Beck, I. Ourailidis, D. Kazdal, O. Neumann, A. L. Volckmar, M. Kirchner, H. Goldschmid, N. Pfarr, W. Weichert, D. Hübschmann, S. Fröhling, C. Sutter, C. P. Schaaf, P. Schirmacher, V. Endris, A. Stenzinger, J. Budczies

“…We developed a tumor classification system based on the loss of function of genes in the homologous recombination repair (HRR) pathway. To this end, somatic and germline alterations in BRCA1/2 and 140 other HRR genes were included and assessed for the impact on gene function. …”
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Prominent transcriptomic changes in Mycobacterium intracellulare under acidic and oxidative stress by Hyun-Eui Park, Kyu-Min Kim, Jeong-Ih Shin, Jeong-Gyu Choi, Won-Jun An, Minh Phuong Trinh, Kyeong-Min Kang, Jung-Wan Yoo, Jung-Hyun Byun, Myung Hwan Jung, Kon-Ho Lee, Hyung-Lyun Kang, Seung Cheol Baik, Woo-Kon Lee, Min-Kyoung Shin

“…In functional analysis, oxidative stress conditions activate DNA replication, nucleotide excision repair, mismatch repair, homologous recombination, and tuberculosis pathways. Additionally, our results demonstrate that DNA replication and repair system genes, such as dnaB, dinG, urvB, uvrD2, and recA, are indispensable for resistance to oxidative stress. …”
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β-Hemolysin, not agrA mutation, inhibits the hemolysis of α-hemolysin in Staphylococcus aureus laboratory and clinical strains by Lin Liu, Hemu Zhuang, Yanfei Wang, Yuexing Tu, Yunsong Yu, Yan Chen, Xueqing Wu

“…We created hlb knockout and complementary mutants via homologous recombination in RN4220 and NRS049, two strains that normally produce β-hemolysin and carry agrA mutation. …”
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Mutational signature-based identification of DNA repair deficient gastroesophageal adenocarcinomas for therapeutic targeting by Aurel Prosz, Pranshu Sahgal, Brandon M. Huffman, Zsofia Sztupinszki, Clare X. Morris, David Chen, Judit Börcsök, Miklos Diossy, Viktoria Tisza, Sandor Spisak, Pornlada Likasitwatanakul, Orsolya Rusz, Istvan Csabai, Michael Cecchini, Yasmine Baca, Andrew Elliot, Peter Enzinger, Harshabad Singh, Jessalyn Ubellaker, Jean-Bernard Lazaro, James M. Cleary, Zoltan Szallasi, Nilay S. Sethi

“…Abstract Homologous recombination (HR) and nucleotide excision repair (NER) are the two most frequently disabled DNA repair pathways in cancer. …”
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