Article
Genetics & Heredity
Xiaojing Ren, Sisi Tian, Qinghao Meng, Hyun-Min Kim
Summary: Histone methylation plays a crucial role in shaping the epigenetic configuration and regulating various nuclear processes. This study investigated the role of histone demethylase AMX-1 in C. elegans and uncovered how its absence leads to sterility in a p53/CEP-1 dependent manner, by regulating Piwi gene expression and transposon silencing.
FRONTIERS IN GENETICS
(2022)
Article
Hematology
Takashi Ishio, Sarvesh Kumar, Joji Shimono, Anusara Daenthanasanmak, Sigrid Dubois, Yuquan Lin, Bonita Bryant, Michael N. Petrus, Emmanuel Bachy, Da Wei Huang, Yandan Yang, Patrick L. Green, Hiroo Hasegawa, Michiyuki Maeda, Hideki Goto, Tomoyuki Endo, Takashi Yokota, Kanako C. Hatanaka, Yutaka Hatanaka, Shinya Tanaka, Yoshihiro Matsuno, Yibin Yang, Satoshi Hashino, Takanori Teshima, Thomas A. Waldmann, Louis M. Staudt, Masao Nakagawa
Summary: The study identifies CDK6 as a novel therapeutic target for adult T-cell leukemia/lymphoma (ATLL) and suggests the potential of combining CDK6 inhibitor palbociclib with mTORC1 inhibitors for treating this difficult malignancy.
Article
Genetics & Heredity
Yuki Date, Ichiro Taniuchi, Kosei Ito
Summary: This study reveals that Runx1 upregulates Myc to promote the development of p53-deficient thymic lymphoma, and depletion of Runx1 or Myc can prolong the lifespan of mice and suppress lymphoma development.
Article
Biochemistry & Molecular Biology
Fabiola N. Velazquez, Jeffrey L. Stith, Leiqing Zhang, Amira M. Allam, John Haley, Lina M. Obeid, Ashley J. Snider, Yusuf A. Hannun
Summary: This study suggests that targeting sphingosine kinase 1 (SK1), a key enzyme upregulated in various types of cancer, can effectively decrease tumor growth in lymphoma without functional p53. This positions SK1 as a potential therapeutic target for tumors that lack functional p53.
Article
Medicine, Research & Experimental
Ru-Chen Xu, Fu Wang, Jia-Lei Sun, Weinire Abuduwaili, Guang-Cong Zhang, Zhi-Yong Liu, Tao-Tao Liu, Ling Dong, Xi-Zhong Shen, Ji-Min Zhu
Summary: In this study, a novel genetic cHCC-ICC mouse model was generated, providing insights into the molecular features and related signaling pathways of cHCC-ICC and identifying LAMB1 as a potential therapeutic target.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Gerhild Euler, Jens Kockskaemper, Rainer Schulz, Mariana S. Parahuleva
Summary: HF and AF are major life-threatening diseases worldwide, and recent studies suggest JDP2 as a potential prognostic marker and therapeutic target for these diseases. Studies in genetically modified mice show impressive involvement of JDP2 in HF and AF.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Markus Schick, Le Zhang, Sabine Maurer, Hans Carlo Maurer, Konstandina Isaakaidis, Lara Schneider, Upayan Patra, Kathrin Schunck, Elena Rohleder, Julia Hofstetter, Apoorva Baluapuri, Anna Katharina Scherger, Julia Slotta-Huspenina, Franziska Hettler, Julia Weber, Thomas Engleitner, Roman Maresch, Jolanta Slawska, Richard Lewis, Rouzanna Istvanffy, Stefan Habringer, Katja Steiger, Armin Baiker, Robert A. J. Oostendorp, Cornelius Miething, Hans-Peter Lenhof, Florian Bassermann, Bjoern Chapuy, Matthias Wirth, Elmar Wolf, Roland Rad, Stefan Mueller, Ulrich Keller
Summary: Loss of the SUMO isopeptidase SENP6 leads to unrestricted SUMOylation and genomic instability, promoting lymphomagenesis and generating vulnerability to PARP inhibition.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Melinda L. Telli, Sara M. Tolaney, Geoffrey Shapiro, Mark Middleton, Simon R. Lord, Hendrik Tobias Arkenau, Andrew Tutt, Vandana Abramson, Emma Dean, Tufia C. Haddad, Robert Wesolowski, Jordi Ferrer-Playan, Thomas Goddemeier, Thomas Grombacher, Jennifer Dong, Patricia Fleuranceau-Morel, Ivan Diaz-Padilla, Ruth Plummer
Summary: This study reports an expansion cohort of a phase 1b trial investigating the combination of the ATR inhibitor berzosertib and cisplatin in patients with metastatic triple-negative breast cancer. The results show that berzosertib was well tolerated with a similar toxicity profile to previous reports, but the overall response rate was relatively low. Further studies combining ATR inhibitors and platinum compounds may be warranted in highly selected patient populations.
Article
Biochemical Research Methods
Valentine U. Nlebedim, Roy R. Chaudhuri, Kevin Walters
Summary: The study introduces a novel probabilistic Bayesian approach for classifying bacterial essential genes based on Tn5 transposon insertion density. Through analysis of simulated data and three bacterial datasets, the effectiveness of the method is demonstrated with high classification accuracy.
Article
Biochemistry & Molecular Biology
Jianan Zheng, Zhongwang Wang, Xiangyu Pan, Zhixin Zhang, He Li, Xintong Deng, Pengpeng Liu, Qi Zhang, Feifei Na, Chong Chen, Ting Niu, Yu Liu
Summary: This study found that mutations in the DNMT3A gene accelerate the development of angioimmunoblastic T-cell lymphoma (AITL) and lead to the expansion of malignant Tfh cells and aberrant B cells, resulting in shortened disease-free survival.
Article
Biochemistry & Molecular Biology
Hua Yang, Yanyan Liu, Jingyi Yang, Qing Zhang, Haoran Wang, Yu Chen, Keshu Zhou
Summary: This study revealed the biological roles of deubiquitinase USP25 in the tumorigenesis of DLBCL. USP25 was found to be frequently upregulated in DLBCL and associated with poor prognosis. Inhibition of USP25 suppressed DLBCL growth and migration, while increasing apoptosis. Mechanistically, USP25 stabilized MDM2 and subsequently decreased p53 expression, promoting DLBCL progression.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Hematology
Anya L. Levinson, Karensa Tjoa, Benjamin Huang, Lauren K. Meyer, Mi-Ok Kim, Samuel W. Brady, Jinghui Zhang, Kevin Shannon, Anica M. Wandler
Summary: The study reveals that JDP2 overexpression acts as a mechanism of adaptive glucocorticoid resistance in T-ALL and interacts with KDM6A inactivation. This finding sheds light on the additional mechanisms of glucocorticoid resistance and offers potential targets for therapy.
Article
Biochemistry & Molecular Biology
Meng Wang, Ying-Xian Goh, Cui Tai, Hui Wang, Zixin Deng, Hong-Yu Ou
Summary: VRprofile2 is an updated pipeline that rapidly identifies diverse mobile genetic elements in bacterial genome sequences. It provides user-friendly visualization to investigate the relationship between antibiotic resistance genes and various mobile elements. The pipeline also includes predicted strain's sequence typing, incompatibility group, and plasmid transferability to efficiently examine the relationship between antibiotic resistance genes, mobile elements, and host strains. VRprofile2 is freely available and comes with an updated backend database of active mobile elements.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Timothy J. Humpton, Koji Nomura, Julia Weber, Helge M. Magnussen, Andreas K. Hock, Colin Nixon, Sandeep Dhayade, David Stevenson, Danny T. Huang, Douglas Strathdee, Karen Blyth, Karen H. Vousden
Summary: The p53 tumor suppressor protein, which activates proliferative arrest and cell death, is regulated by MDM2 protein in normal cells. Blocking the interaction between MDM2 protein and E2/ubiquitin complex to enhance p53 response to DNA damage suggests a promising avenue for therapeutic development.
GENES & DEVELOPMENT
(2021)
Article
Biochemistry & Molecular Biology
Kenji Watanabe, Shuichi Shibuya, Yusuke Ozawa, Toshihiko Toda, Takahiko Shimizu
Summary: The study showed that p53 regulated ROS-mediated apoptotic cell death and tumorigenesis, but did not affect ROS-mediated tissue degeneration in SOD-deficient models.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Juncheng Wu, Anushka Rajesh, Yu-Ning Huang, Karishma Chhugani, Rajesh Acharya, Kerui Peng, Ruth D. Johnson, Andrada Fiscutean, Carla Daniela Robles-Espinoza, Francisco M. De la Vega, Riyue Y. Bao, Serghei Mangul
Summary: Post-pandemic, conference organizers need to adopt new approaches to increase accessibility, diversity, and inclusivity of conferences.
NATURE BIOTECHNOLOGY
(2022)
Editorial Material
Genetics & Heredity
Carla Daniela Robles-Espinoza
NATURE REVIEWS GENETICS
(2022)
Article
Genetics & Heredity
Rahia Mashoodh, Lisa C. Hulsmann, Frances L. Dearden, Nozomi Takahashi, Carol Edwards, Anne C. Ferguson-Smith
Summary: In this study, imprinting genes were used as a model system to investigate the relationship between the parental origin of chromosomes, the localization of genes within the cell nucleus, and their active expression. The results indicate that there is a small preference for the paternal chromosome to be closer to the periphery, but there is a significant correlation between transcription and distance to the edge of the nucleus for the Gtl2/Meg3 gene. Furthermore, a chromosome nearer the periphery is just as likely to express the gene as the chromosome further away. These findings suggest that the parental origin of the chromosome may not be as important as the transcription of the gene in defining the position of the imprinted region within the nucleus.
Article
Multidisciplinary Sciences
Estelle Vincendeau, Wenming Wei, Xuefei Zhang, Cyril Planchais, Wei Yu, Helene Lenden-Hasse, Thomas Cokelaer, Juliana Pipoli da Fonseca, Hugo Mouquet, David J. Adams, Frederick W. Alt, Stephen P. Jackson, Gabriel Balmus, Chloe Lescale, Ludovic Deriano
Summary: SHLD1 is a component of the Shieldin complex, playing a role in DNA repair via non-homologous end-joining (NHEJ), which is essential for lymphocyte development. However, it is dispensable for lymphocyte development and V(D)J recombination, but essential for class-switching recombination in activated B cells.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Carlos Cordova-Fletes, Horacio Rivera, Thania Alejandra Aguayo-Orozco, Lizeth Alejandra Martinez-Jacobo, Elvira Garza-Gonzalez, Carla Daniela Robles-Espinoza, Patricia Basurto-Lozada, Hector-Gerardo Avalos-Gomez, Eduardo Esparza-Garcia, Ma Guadalupe Dominguez-Quezada
Summary: Germline or constitutional chromoanagenesis-related complex chromosomal rearrangements (CCRs) are rare and catastrophic events that involve chromothripsis and chromoplexy. In this study, a patient with a phenotype resembling MRD44 was found to have a complex t(5;7;21)dn rearrangement involving multiple disordered breakpoints. Whole-genome sequencing revealed disruptions in several neurodevelopmental genes, with the disruption of TRIO most likely contributing to the patient's phenotype.
EUROPEAN JOURNAL OF MEDICAL GENETICS
(2022)
Article
Biochemical Research Methods
Chenxi Zhou, Shane A. McCarthy, Richard Durbin
Summary: YaHS is a user-friendly command-line tool that constructs chromosome-scale scaffolds from Hi-C data. It requires minimal input from users (an assembly file and an alignment file), can be run with a single-line command, and provides assembly results in multiple formats, enabling rapid and accurate construction of high-quality genome assemblies.
Article
Medical Informatics
Albert Burger, Richard A. Baldock, David J. Adams, Shahida Din, Irene Papatheodorou, Michael Glinka, Bill Hill, Derek Houghton, Mehran Sharghi, Michael Wicks, Mark J. Arends
Summary: This study describes a conceptual coordinate model for the Gut Cell Atlas, which represents the location of the human gut in 1D, 2D, and 3D models. It allows clinicians and pathologists to accurately describe gut locations and perform cell comparison analysis.
BMC MEDICAL INFORMATICS AND DECISION MAKING
(2023)
Article
Biochemistry & Molecular Biology
Vladimir Ovchinnikov, Marcela Uliano-Silva, Mark Wilkinson, Jonathan Wood, Michelle Smith, Karen Oliver, Ying Sims, James Torrance, Alexander Suh, Shane A. McCarthy, Richard Durbin, Mary J. O'Connell
Summary: We have sequenced the genomes of two limbless, soil-dwelling amphibians, Geotrypetes seraphini (3.8 Gb) and Microcaecilia unicolor (4.7 Gb). These species have reduced eyes and unique chemosensory tentacles. Our analysis identified unique gene groups related to olfaction and chemosensory perception in caecilians. We also found positive selection signatures on genes involved in organ development, sensory perception, immunity, and other functions in caecilians.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Carol A. Edwards, William M. D. Watkinson, Stephanie B. Telerman, Lisa C. Hulsmann, Russell S. Hamilton, Anne C. Ferguson-Smith, Deborah Bourc'his
Summary: In mice and humans, imprinting genes play important roles in development, behavior, and post-natal adaptations. Failure to properly imprint genes in humans is associated with various disorders and diseases. Researchers have used RNA-seq technologies and hybrid mouse strains to identify novel imprinted genes, leading to an increase in reported genes with parental origin-specific expression bias. However, validation experiments show that many of these genes are not genuine imprinted genes and that the mouse strain has a greater influence on expression biases than parental origin.
Article
Multidisciplinary Sciences
Abdelghani Mazouzi, Sarah C. Moser, Federico Abascal, Bram van den Broek, Martin Del Castillo Velasco-Herrera, Ingrid van der Heijden, Maarten Hekkelman, Anne Paulien Drenth, Eline van der Burg, Lona J. Kroese, Kees Jalink, David J. Adams, Jos Jonkers, Thijn R. Brummelkamp
Summary: DNA interstrand crosslinks (ICLs) can hinder DNA replication and transcription if not repaired. The cellular response to ICLs requires coordination of various DNA repair mechanisms. FIRRM/C1orf112 was identified as a crucial factor in maintaining genome stability. It controls MUS81 chromatin loading to affect resolution of HR intermediates and plays a critical role in the response to ICLs encountered during DNA replication.
Article
Cell Biology
Guia Cerretelli, Ying Zhou, Mike F. Muller, David J. Adams, Mark J. Arends
Summary: This study found that defective MMR interacts with acetaldehyde, enhancing colonic tumor formation. Loss of ALDH1B1 increases acetaldehyde levels and DNA damage that interacts with dMMR to accelerate colonic tumor formation.
DISEASE MODELS & MECHANISMS
(2023)
Review
Cell Biology
Christian Molina-Aguilar, C. Daniela Robles-Espinoza
Summary: The lack of diversity in current academic research is mainly due to insufficient support for studying non-European populations and unequal partnerships between scientists in different income countries. Expanding research funding, increasing the participation of underrepresented scientists, and properly acknowledging the contributions of researchers from low- and middle-income countries can promote equity and lead to more impactful research with diverse samples, improving our understanding of diseases and treatment.
DISEASE MODELS & MECHANISMS
(2023)
Article
Biochemistry & Molecular Biology
Stephen J. Pettitt, Nan Shao, Diana Zatreanu, Jessica Frankum, Ilirjana Bajrami, Rachel Brough, Dragomir B. Krastev, Theodoros I. Roumeliotis, Jyoti S. Choudhary, Sonja Lorenz, Alistair Rust, Johann S. de Bono, Timothy A. Yap, Andrew N. J. Tutt, Christopher J. Lord
Summary: Reduced expression of HUWE1 leads to increased levels of BRCA1- increment 11q and PARPi resistance. This effect is specific to cells able to express BRCA1- increment 11q and is not seen in other BRCA1 or BRCA2 mutant cells. HUWE1 silencing also restores RAD51 nuclear foci and platinum salt resistance, indicating its potential as a biomarker for PARPi resistance in future clinical trials.
Article
Multidisciplinary Sciences
Amir D. Hay, Noah J. Kessler, Daniel Gebert, Nozomi Takahashi, Hugo Tavares, Felipe K. Teixeira, Anne C. Ferguson-Smith
Summary: A study found that DNA methylation is generally stable at hypo- and hypermethylated sites, but not at intermediately methylated sites. The lack of clonal inheritance at these sites challenges the current model of epigenetic inheritance and has implications for the functional relevance and interpretability of DNA methylation as a stable epigenetic mark.
NATURE COMMUNICATIONS
(2023)
Letter
Biotechnology & Applied Microbiology
Douglas M. Fowler, David J. Adams, Anna L. Gloyn, William C. Hahn, Debora S. Marks, Lara A. Muffley, James T. Neal, Frederick P. Roth, Alan F. Rubin, Lea M. Starita, Matthew E. Hurles, Nadav Ahituv, Orli G. Bahcal, Dustin Baldridge, Jonathan S. Berg, Alice H. Berger, Aisha Haley Bianchi, Benedetta Bolognesi, Michael Boutros, Steven Brenner, Matthew H. Brush, Vanessa Bryant, Carol J. Bult, Martha Bulyk, Melissa Call, Hannah Carter, Melina Claussnitzer, Feng Chen, Melissa S. Cline, Josh T. Cuperus, Moez Dawood, Hannah N. De Jong, Mafalda Dias, Michael Dunn, Jesse Engreitz, Kyle Farh, Phillip G. Febbo, Stanley Fields, Gregory M. Findlay, Helen Firth, James S. Fraser, Jonathan Frazer, Mattia Frontini, Irene Gallego Romero, Andrew M. Glazer, Murat Gueler, Rasmus Hartmann-Petersen, Richard Houlston, Kuan-Lin Huang, Carolyn M. Hutter, Sujatha Jagannathan, Richard G. James, Martin Kampmann, Rachel Karchin, Justin B. Kinney, Alexis C. Komor, Sriram Kosuri, Ben Lehner, Kresten Lindorff-Larsen, Zane Lombard, Daniel G. MacArthur, Maria Martin, Ultan McDermott, Shannon M. McNulty, Alex N. Nguyen Ba, Anne O'Donnell-Luria, Brian J. O'Roak, Victoria N. Parikh, Leopold Parts, Michael J. Pazin, Tina Pesaran, Slave Petrovski, Christine Queitsch, David E. Root, Jay Shendure, Amanda B. Spurdle, Kevin L. Taylor, Clare Turnbull, Judit Villen, L. E. L. M. Vissers, Alex H. Wagner, Matthew J. Wakefield, Jochen Weile, Jenny Xiao
Summary: Sequencing has identified numerous genetic variants in humans, but their functional effects remain largely unknown, hindering precision medicine. However, multiplexed variant effect assays can assess large numbers of variants simultaneously, generating variant effect maps that reveal the functional impact of every possible single nucleotide change. Creating an "Atlas" of variant effect maps for all protein encoding genes and regulatory elements in the human genome would revolutionize our understanding of genetics and enable advancements in therapeutics, human evolution, and disease diagnosis and treatment.