Review
Genetics & Heredity
Malgorzata Drzewiecka, Gabriela Barszczewska-Pietraszek, Piotr Czarny, Tomasz Skorski, Tomasz Sliwinski
Summary: Research studies on synthetic lethality in human cells aim to develop effective and safe anti-cancer chemotherapy. DNA repair factors, especially those involved in double-strand break repair, are the primary targets for inducing the synthetic lethality effect. Inhibition of RAD52 and/or PARP1 has shown promise as a potential target for inducing synthetic lethality in tumor cells with deficiencies in the canonical repair pathways. However, resistance to PARP1 inhibitors poses a major obstacle to successful treatment protocols. DNA polymerase theta (Pol theta) plays a key role in an alternative DSB repair pathway and its inhibition holds potential for inducing synthetic lethality in tumors with homologous recombination repair deficiencies.
Review
Genetics & Heredity
Karl E. Zahn, Ryan B. Jensen
Summary: The POLQ gene encodes DNA polymerase theta, which plays a critical role in DNA repair and over-expression may lead to abnormal DNA repair in cancer cells. Specific inhibitors targeting polymerase theta could be a novel strategy to treat BRCA-mutant cancers and overcome resistance to PARP inhibitors.
Article
Biochemistry & Molecular Biology
Mengfan Tang, Guangsheng Pei, Dan Su, Chao Wang, Xu Feng, Mrinal Srivastava, Zhen Chen, Zhongming Zhao, Junjie Chen
Summary: The study identified that CCNC is a critical survival target in cells with BRCA2 loss, potentially contributing to PARPi resistance.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Alina Thokkadam, Truc Do, Xinchun Ran, Mark P. Brynildsen, Zhongyue J. Yang, A. James Link
Summary: The Burkholderia cepacia complex (Bcc) is a group of bacteria that can cause serious infections in immunocompromised individuals and cystic fibrosis patients. Ubonodin, a lasso peptide, has shown potential in inhibiting Bcc species by targeting RNA polymerase. Through a high-throughput screening and next-generation sequencing, a library of over 90,000 ubonodin variants was created, providing valuable insights into the structure-activity relationship of ubonodin. One variant with improved activity and a submicromolar minimum inhibitory concentration (MIC) against Burkholderia cenocepacia, a Bcc member, was identified. Additionally, some variants had lower MICs against certain Bcc strains compared to clinically approved antibiotics. The large library size also allowed the development of DeepLasso, a deep learning model for predicting the RNAP inhibitory activity of ubonodin variants.
ACS CENTRAL SCIENCE
(2023)
Article
Multidisciplinary Sciences
Rafaela S. Fernandes, Gabriela D. Noske, Victor O. Gawriljuk, Ketllyn I. Z. de Oliveira, Andre S. Godoy, Nathalya C. M. R. Mesquita, Glaucius Oliva
Summary: The discovery of antiviral drugs requires the development of reliable biochemical and cellular assays that can be performed in high-throughput screening formats. NS3 and NS5 are the most studied enzymes of the flavivirus replication complex, playing crucial roles in viral genome replication and therefore constituting the main targets for drug development.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
Alexandra Vaisman, John P. McDonald, Mallory R. Smith, Sender L. Aspelund, Thomas C. Evans, Roger Woodgate
Summary: Y-family DNA polymerases consist of six phylogenetically separate subfamilies, with representatives found in all three domains of life. Different evolutionary diversity exists within eukaryotes, with different species possessing varying numbers and types of Y-family pols. The Y-family pols from Thermomyces lanuginosus show increased thermostability and share major biochemical properties with their human counterparts, displaying low fidelity during DNA synthesis.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Alessandra Brambati, Olivia Sacco, Sarina Porcella, Joshua Heyza, Mike Kareh, Jens C. Schmidt, Agnel Sfeir
Summary: Nonhomologous end-joining (NHEJ) and homologous recombination (HR) are the primary pathways for repairing DNA double-strand breaks (DSBs) during interphase. Microhomology-mediated end-joining (MMEJ) has been identified as a backup mechanism for repairing DSBs. Our study identifies the 9-1-1 complex and its interacting partner, RHINO, as crucial factors for MMEJ, and reveals the unexpected function of RHINO in restricting MMEJ to mitosis.
Article
Multidisciplinary Sciences
Wenshan Zheng, Shijie Zhao, Yehang Yin, Huidan Zhang, David M. Needham, Ethan D. Evans, Chengzhen L. Dai, Peter J. Lu, Eric J. Alm, David A. Weitz
Summary: This article presents a high-throughput method called Microbe-seq, which allows the genomes of individual microbes to be obtained from complex microbial communities. It explores the human gut microbiome and reveals insights into microbial interactions and horizontal gene transfer. Microbe-seq offers a culture-free approach to investigate the genomic blueprints of complex microbial communities with single-cell resolution.
Article
Multidisciplinary Sciences
Daniel S. Park, Son C. Nguyen, Randi Isenhart, Parisha P. Shah, Wonho Kim, R. Jordan Barnett, Aditi Chandra, Jennifer M. Luppino, Jailynn Harke, May Wai, Patrick J. Walsh, Richard J. Abdill, Rachel Yang, Yemin Lan, Sora Yoon, Rebecca Yunker, Masato T. Kanemaki, Golnaz Vahedi, Jennifer E. Phillips-Cremins, Rajan Jain, Eric F. Joyce
Summary: Researchers developed a high-throughput DNA or RNA labeling technology called HiDRO, enabling the quantitative measurement of chromatin interactions in single cells. By screening the human druggable genome, they identified over 300 factors that influence genome folding during interphase, with 43 genes validated to increase or decrease interactions between topologically associating domains. Inhibition of the kinase GSK3A was found to increase long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These findings highlight the importance of GSK3A signaling in nuclear architecture and demonstrate the utility of HiDRO for identifying mechanisms of spatial genome organization.
Article
Cell Biology
Anna Schrempf, Sara Bernardo, Emili A. Arasa Verge, Miguel A. Ramirez Otero, Jordan Wilson, Dominik Kirchhofer, Gerald Timelthaler, Anna M. Ambros, Atilla Kaya, Marcus Wieder, Gerhard F. Ecker, Georg E. Winter, Vincenzo Costanzo, Joanna I. Loizou
Summary: Polymerase theta (POLO) is an error-prone DNA polymerase that is synthetically lethal in cancer cells with BRCA1/2 mutations. The study shows that POLO processes single-stranded DNA gaps in the absence of BRCA1, promoting replication fork progression and survival of BRCA1 mutant cells. The research also uncovers suppressors of the POLO-BRCA1 interaction, including NBN and CDK6, which contribute to ssDNA gap formation and exacerbate replication stress in BRCA1-deficient cells.
Article
Microbiology
Michelle K. Scotland, Caleb Homiski, Mark D. Sutton
Summary: Specialized DNA polymerases (Pols) capable of translesion synthesis (TLS) generate mutations that contribute to bacterial virulence, pathoadaptation, and antimicrobial resistance. The mechanism by which bacterial TLS Pol IV gains access to the DNA involves exchanging places with bacterial Pol III replicase via a Pol III-Pol IV switch, which may be regulated by multiple interactions between Pol III and Pol IV. Furthermore, several additional E. coli Pol-Pol interactions have been described, suggesting their fundamental roles in coordinating bacterial DNA replication, DNA repair, and TLS.
JOURNAL OF BACTERIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Gabriela Barszczewska-Pietraszek, Malgorzata Drzewiecka, Piotr Czarny, Tomasz Skorski, Tomasz Sliwinski
Summary: DNA polymerase theta (Pol theta)-mediated end joining (TMEJ) is a crucial mechanism for repairing DNA double-strand breaks (DSBs), and its inhibition has potential therapeutic value in cancer treatment. Pol theta has synthetic lethal interactions with other DNA repair mechanisms and is being studied as a target in cancer research. Different methods, including RNA interference and small molecule inhibitors, have been used to inhibit Pol theta. This review provides an overview of Pol theta and its role in DNA repair, discusses the current state of Pol theta inhibitors, and highlights the promise of Pol theta as a therapeutic target.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Mateusz Kciuk, Adrianna Gielecinska, Somdutt Mujwar, Mariusz Mojzych, Renata Kontek
Summary: Synthetic lethal interactions involving CDKs with MYC, PARP-1, and TP53 are emerging as potential targets for selectively targeting tumor cells with DNA repair defects. These interactions reveal the crucial roles of cell cycle regulatory proteins in the DNA damage response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Hannah E. Neiger, Emily L. Siegler, Yihui Shi
Summary: BRCA1 and BRCA2 are tumor suppressor genes crucial in DNA repair mechanisms. Synthetic lethality, caused by simultaneous perturbations of two genes, can help identify new therapeutic options for BRCA1/2 mutations. PARP inhibitor Olaparib has shown success as the first synthetic lethality-based therapy for BRCA1/2 breast and ovarian cancer, but drug resistance poses a challenge for targeted cancer therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Computer Science, Information Systems
Takuya Fujihashi, Toshiaki Koike-Akino, Philip Orlik, Takashi Watanabe
Summary: Screen-camera communications using LCD screen and camera can achieve high transmission rates, with methods like nonlinear channel equalization and nonbinary channel coding found to be effective in improving performance. Experimental results show that our proposed scheme outperforms existing schemes in terms of transmission rates.
IEEE TRANSACTIONS ON MOBILE COMPUTING
(2021)
Article
Biochemistry & Molecular Biology
Lilas Courtot, Elodie Bournique, Chrystelle Maric, Laure Guitton-Sert, Miguel Madrid-Mencia, Vera Pancaldi, Jean-Charles Cadoret, Jean-Sebastien Hoffmann, Valerie Bergoglio
Summary: This study reveals that low replication stress can lead to advanced DNA replication timing, which is cell-type specific and involves large heterochromatin domains. These advanced events can be inherited by the next generation of cells, leading to changes in chromatin accessibility, replication origin landscape, and gene expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Jeremy Setton, Michael Zinda, Nadeem Riaz, Daniel Durocher, Michal Zimmermann, Maria Koehler, Jorge S. Reis-Filho, Simon N. Powell
Summary: Synthetic lethality (SL) provides a theoretical framework for targeting loss-of-function mutations in tumor suppressor genes and DNA repair genes, as well as amplification and/or overexpression of genes that cannot be directly targeted. The emergence of next generation tumor-specific alterations targetable through SL from high-throughput CRISPR technology presents new opportunities for drug development, but also brings important challenges in developing optimal predictive biomarkers.
Article
Biochemistry & Molecular Biology
Marina Dall'Osto, Laura Pierini, Nicolas Valery, Jean-Sebastien Hoffmann, Marie-Jeanne Pillaire
Summary: The study revealed a new role of Pol kappa in controlling the stability and abundance of checkpoint kinase 1 (Chk1), where loss of Pol kappa decreases Chk1 protein levels and protects it from proteasome degradation. Additionally, the fork restart defects in Pol kappa-depleted cells can be overcome by the reexpression of Chk1.
MOLECULAR AND CELLULAR BIOLOGY
(2021)
Article
Biology
Solenne Gaillard, Virginie Charasson, Cyril Ribeyre, Kader Salifou, Marie-Jeanne Pillaire, Jean-Sebastien Hoffmann, Angelos Constantinou, Didier Trouche, Marie Vandromme
Summary: KDM5A and KDM5B histone-demethylases play crucial roles in replication stress response and tolerance, positively regulating RRM2 and activated Chk1. They are major players in RS management, and drugs targeting their enzymatic activity may not fully address all cancer-related consequences of their overexpression.
Review
Oncology
Paula Pellenz Tomasini, Temenouga Nikolova Guecheva, Natalia Motta Leguisamo, Sarah Pericart, Anne-Cecile Brunac, Jean Sebastien Hoffmann, Jenifer Saffi
Summary: Colorectal cancer is a common cancer that currently relies on conventional chemotherapy for treatment, but targeting DNA repair and replication stress response may offer new therapeutic opportunities. Synthetic lethal mechanisms targeting DNA damage response pathways have not been systematically explored in CRC, presenting a potential area for further research and clinical trials.
Article
Oncology
Pascale Palassin, Marion Lapierre, Samuel Pyrdziak, Antoine Wagner, Regine Stehle, Carole Corsini, Jacqueline Duffour, Sandrine Bonnet, Abdelhay Boulahtouf, Carmen Rodriguez, Alexandre Ho-Pun-Cheung, Evelyne Lopez-Crapez, Florence Boissiere-Michot, Frederic Bibeau, Simon Thezenas, Nabila Elarouci, Janick Selves, Jean-Sebastien Hoffmann, Paul Roepman, Thibault Mazard, Olivier Buhard, Alex Duval, Stephan Jalaguier, Vincent Cavailles, Audrey Castet-Nicolas
Summary: Microsatellite instability (MSI) is closely related to alterations in mismatch repair (MMR) genes and is important in the pathogenesis of colorectal cancer (CRC). The transcription factor NRIP1 is involved in intestinal tumorigenesis and can induce the transcription of MMR genes MSH2 and MSH6, reducing MSI and potentially affecting patient survival outcomes in CRC. A dominant-negative truncated mutant of NRIP1 may amplify MMR deficiency and play a role in advanced MSI CRC progression and prognosis.
Article
Oncology
Jian Li, Josephine Mun-Yee Ko, Wei Dai, Valen Zhuoyou Yu, Hoi Yan Ng, Jean-Sebastien Hoffmann, Maria Li Lung
Summary: High expression of POLQ in esophageal squamous cell carcinoma is associated with unfavorable prognosis, contributing to malignant phenotypes through promoting genome stability, suggesting it as a potential therapeutic target.
Article
Biology
Johnny M. Tkach, Reuben Philip, Amit Sharma, Jonathan Strecker, Daniel Durocher, Laurence Pelletier
Summary: Centrosomes play a crucial role as the main microtubule organizing center in metazoans. Recent research has discovered that the E3 ligase TRIM37 is important for cell cycle arrest in acentrosomal cells. In this study, genome-wide CRISPR/Cas9 screens were conducted to identify factors involved in growth arrest triggered by PLK4 inhibition. The results showed that TRIM37 is a key mediator of this growth arrest, and PLK4 activity is more correlated with growth arrest than mitotic length or centrosome number.
Article
Biochemistry & Molecular Biology
Cherine Sifri, Lisa Hoeg, Daniel Durocher, Dheva Setiaputra
Summary: 53BP1 is a chromatin-binding protein that recruits downstream effectors RIF1, shieldin, and CST to promote DNA double-strand break repair. The structural details of protein-protein interactions within the 53BP1-RIF1-shieldin-CST pathway, essential for DNA repair, are largely unknown. In this study, we used AlphaFold2-Multimer (AF2) to predict and provide structural models for seven previously characterized interactions in this pathway. Our analysis also revealed a novel binding interface between RIF1 and SHLD3. Experimental validation demonstrated that the RIF1-SHLD3 binding is crucial for shieldin recruitment, antibody class switch recombination, and PARP inhibitor sensitivity, highlighting the essential role of this interaction in the 53BP1-RIF1-shieldin-CST pathway activity.
Editorial Material
Multidisciplinary Sciences
Yibo Xue, Daniel Durocher
Summary: Two studies reveal the mechanism by which shattered chromosomes are passed on to daughter cells and reassembled, benefiting cancer cells.
Article
Microbiology
Remy Betous, Anthony Emile, Hua Che, Eva J. Guchen, Didier Concordet, Thavy Long, Sandra Noack, Paul M. Selzer, Roger Prichard, Anne Lespine
Summary: Nematode parasites enter their definitive host as infectious larvae and DAF-12 plays a role in their development to adulthood. The filarial nematodes' DAF-12 exhibit higher sensitivity to ligands and can be specifically activated by mammalian sera. These findings suggest that filarial nematodes have evolved to sense and adapt to their host environment to resume larval development.
Article
Genetics & Heredity
Daniel de Barcellos Azambuja, Helena de Castro e Gloria, Gabriel e Silva Montenegro, Antonio Nocchi Kalil, Jean-Sebastien Hoffmann, Natalia Motta Leguisamo, Jenifer Saffi
Summary: Through evaluating the gene expression in tumor specimens and healthy tissues of 63 colorectal cancer (CRC) patients, it was found that the MRE11 homologous recombination repair gene is significantly overexpressed in CRC, particularly in primary tumors of higher stages, and mostly in right-side CRC, which has the worst prognosis. Furthermore, high MRE11 expression is associated with shorter overall survival and higher risk of death. Therefore, monitoring MRE11 expression could serve as both a predictor of outcome and a marker for selecting treatments for CRC patients.
Article
Biochemistry & Molecular Biology
Guillaume Labrousse, Pierre Vande Perre, Genis Parra, Marion Jaffrelot, Laura Leroy, Frederic Chibon, Frederic Escudie, Janick Selves, Jean-Sebastien Hoffmann, Rosine Guimbaud, Malik Lutzmann
Summary: The exonuclease domain of DNA polymerases epsilon's catalytic subunit (POLE) plays a role in proofreading by removing misincorporated nucleotides. Certain mutations in the POLE exonuclease domain, such as N363K, not only increase single nucleotide substitutions but also cause DNA damage and chromosome instability. This study highlights the importance of assessing both the mutational potential and genetic instability for the classification and treatment of POLE-mutated tumors.
Article
Oncology
Pascale Palassin, Marion Lapierre, Sandrine Bonnet, Marie-Jeanne Pillaire, Balazs Gyorffy, Catherine Teyssier, Stephan Jalaguier, Jean-Sebastien Hoffmann, Vincent Cavailles, Audrey Castet-Nicolas
Summary: This study reveals that RIP140 plays a role in maintaining microsatellite stability through positively regulating the expression of the POLK gene. The regulation of POLK gene expression by RIP140 involves the p53 tumor suppressor. The correlation between RIP140 and POLK gene expression was observed in CRC patient samples. Furthermore, it was found that cells lacking the Rip140 gene had an increased cellular response to methyl methane sulfonate.
CANCER DRUG RESISTANCE
(2022)
Meeting Abstract
Oncology
Audrey Lumeau, Nicolas Bery, Cyril Ribeyre, Samad Elkaoutari, Guillaume Labrousse, Miguel Madrid-Mencia, Vera Pancaldi, Marie-Jeanne Pillaire, Valerie Bergoglio, Nelson Dusseti, Jean-Sebastien Hoffmann, Louis Buscail, Malik Lutzmann, Pierre Cordelier