Article
Genetics & Heredity
Sara Hagg, Juulia Jylhava, Yunzhang Wang, Kamila Czene, Felix Grassmann
Summary: This study investigated the factors influencing mitochondrial DNA (mtDNA) abundance, revealing that it is higher in women compared to men and negatively correlated with age, smoking exposure, BMI, frailty index, and certain blood biochemistry markers. Genome-wide association study identified 50 regions significantly associated with mtDNA abundance, indicating the involvement of genes related to immunity, cancer, and mitochondrial function. The SNP-heritability of mtDNA abundance was estimated to be around 8%, and mtDNA abundance was found to be associated with leukemia, hematologic diseases, and hypertension.
Article
Plant Sciences
Maria Duk, Alexander Kanapin, Tatyana Rozhmina, Mikhail Bankin, Svetlana Surkova, Anastasia Samsonova, Maria Samsonova
Summary: The study provides a comprehensive analysis of the core collection of flax maintained by the Russian Federal Research Center for Bast Fiber Crops, revealing significant population differentiation between oilseed and fiber flax, as well as genetic evidence supporting the hypothesis of kryazh's mixed origin.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Oncology
Haruhiko Takeda, Atsushi Takai, Yuji Eso, Ken Takahashi, Hiroyuki Marusawa, Hiroshi Seno
Summary: This article summarizes the genomic landscape and intratumor heterogeneity of liver cancer, providing insights into early genetic alterations in hepatocarcinogenesis, including early HCC and noncancerous liver tissues. It also discusses the multistep accumulation of genetic aberrations throughout cancer progression and the potential clinical application of this genetic information.
Article
Cardiac & Cardiovascular Systems
Zhijian Yang, Erin Macdonald-Dunlop, Jiantao Chen, Ranran Zhai, Ting Li, Anne Richmond, Lucija Klaric, Nicola Pirastu, Zheng Ning, Chenqing Zheng, Yipeng Wang, Tingting Huang, Yazhou He, Huiming Guo, Kejun Ying, Stefan Gustafsson, Bram Prins, Anna Ramisch, Emmanouil T. Dermitzakis, Grace Png, Niclas Eriksson, Jeffrey Haessler, Xiaowei Hu, Daniela Zanetti, Thibaud Boutin, Shih-Jen Hwang, Eleanor Wheeler, Maik Pietzner, Laura M. Raffield, Anette Kalnapenkis, James E. Peters, Ana Vinuela, Arthur Gilly, Solve Elmstahl, George Dedoussis, John R. Petrie, Ozren Polasek, Lasse Folkersen, Yan Chen, Chen Yao, Urmo Vosa, Erola Pairo-Castineira, Sara Clohisey, Andrew D. Bretherick, Konrad Rawlik, Tonu Esko, Stefan Enroth, Asa Johansson, Ulf Gyllensten, Claudia Langenberg, Daniel Levy, Caroline Hayward, Themistocles L. Assimes, Charles Kooperberg, Ani W. Manichaikul, Agneta Siegbahn, Lars Wallentin, Lars Lind, Eleftheria Zeggini, Jochen M. Schwenk, Adam S. Butterworth, Karl Michaelsson, Yudi Pawitan, Peter K. Joshi, J. Kenneth Baillie, Anders Malarstig, Alexander P. Reiner, James F. Wilson, Xia Shen
Summary: In this study, genetic correlations between plasma ACE2 levels and cardiovascular disease, COVID-19, and other related diseases were identified. Mendelian randomization analysis showed a causal effect of elevated ACE2 levels on COVID-19 severity, hospitalization, and infection. The study also revealed that ACE2 regulatory variants were enriched for DNA methylation sites in blood immune cells.
Article
Cardiac & Cardiovascular Systems
Rahul Goli, Jian Li, Jeff Brandimarto, Lisa D. Levine, Valerie Riis, Quentin McAfee, Steven DePalma, Alireza Haghighi, J. G. Seidman, Christine E. Seidman, Daniel Jacoby, George Macones, Daniel P. Judge, Sarosh Rana, Kenneth B. Margulies, Thomas P. Cappola, Rami Alharethi, Julie Damp, Eileen Hsich, Uri Elkayam, Richard Sheppard, Jeffrey D. Alexis, John Boehmer, Chizuko Kamiya, Finn Gustafsson, Peter Damm, Anne S. Ersboll, Sorel Goland, Denise Hilfiker-Kleiner, Dennis M. McNamara, Zolt Arany
Summary: The study found that 10.4% of women with PPCM carried TTNtvs, and there was a significant increase in truncating variants in FLNC, DSP, and BAG3. Women with TTNtvs had lower left ventricular ejection fraction on presentation, but did not differ significantly in timing of presentation after delivery, prevalence of preeclampsia, or rates of clinical recovery compared to those without TTNtvs.
Article
Biochemistry & Molecular Biology
Christoph B. Messner, Vadim Demichev, Julia Muenzner, Simran K. Aulakh, Natalie Barthel, Annika Roehl, Lucia Herrera-Dominguez, Anna-Sophia Egger, Stephan Kamrad, Jing Hou, Guihong Tan, Oliver Lemke, Enrica Calvani, Lukasz Szyrwiel, Michael Muelleder, Kathryn S. Lilley, Charles Boone, Georg Kustatscher, Markus Ralser
Summary: Functional genomic strategies are crucial for gene function annotation and regulatory network analysis. In this study, we integrated functional genomics with proteomics to quantify protein abundances in a large-scale knockout library of Saccharomyces cerevisiae using data-independent acquisition mass spectrometry. Our findings indicate that global protein expression is influenced by a complex interplay of biological and functional properties, and functional proteomics can complement current gene annotation strategies. This study provides insights into the principles governing protein expression and offers a valuable resource for functional annotation.
Review
Oncology
Fernando Augusto Batista Campos, Etienne Rouleau, Giovana Tardin Torrezan, Dirce Maria Carraro, Jose Claudio Casali da Rocha, Higor Kassouf Mantovani, Leonardo Roberto da Silva, Cynthia Aparecida Bueno de Toledo Osorio, Solange Moraes Sanches, Sandrine M. Caputo, Elizabeth Santana dos Santos
Summary: Male breast cancer is a rare disease, with distinct genetic background compared to female breast cancer. Common genetic and epigenetic features of female breast cancer are not shared with male breast cancer. Inherited germline variants likely play a significant role in the tumorigenesis of male breast cancer.
Article
Oncology
Yasuhide Takeuchi, Kenichi Yoshida, Adriane Halik, Annegret Kunitz, Hiromichi Suzuki, Nobuyuki Kakiuchi, Yusuke Shiozawa, Akira Yokoyama, Yoshikage Inoue, Tomonori Hirano, Tetsuichi Yoshizato, Kosuke Aoki, Yoichi Fujii, Yasuhito Nannya, Hideki Makishima, Berit Maria Pfitzner, Lars Bullinger, Masahiro Hirata, Keita Jinnouchi, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Takeshi Okamoto, Hironori Haga, Seishi Ogawa, Frederik Damm
Summary: Myxofibrosarcoma (MFS) is a rare subtype of sarcoma with complex genetic basis. This study analyzed 69 MFS cases and identified various genetic abnormalities, including mutations and copy number alterations in known disease drivers, as well as previously unknown gene aberrations. Longitudinal analysis revealed an increase in mutation number and significant changes in clonal composition over time.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Multidisciplinary Sciences
Matthew Naish, Michael Alonge, Piotr Wlodzimierz, Andrew J. Tock, Bradley W. Abramson, Anna Schmuecker, Terezie Mandakova, Bhagyshree Jamge, Christophe Lambing, Pallas Kuo, Natasha Yelina, Nolan Hartwick, Kelly Colt, Lisa M. Smith, Jurriaan Ton, Tetsuji Kakutani, Robert A. Martienssen, Korbinian Schneeberger, Martin A. Lysak, Frederic Berger, Alexandros Bousios, Todd P. Michael, Michael C. Schatz, Ian R. Henderson
Summary: The study used long-read sequencing to assemble the Arabidopsis genome and resolve all five centromeres. It found that centromeres consist of megabase-scale tandemly repeated satellite arrays and are invaded by retrotransposons. The centromeres are evolving through cycles of satellite homogenization and retrotransposon-driven diversification.
Article
Multidisciplinary Sciences
Tirthankar Mohanty, Christofer A. Q. Karlsson, Yashuan Chao, Erik Malmstrom, Eleni Bratanis, Andrietta Grentzmann, Martina Morch, Victor Nizet, Lars Malmstrom, Adam Linder, Oonagh Shannon, Johan Malmstrom
Summary: This study used pharmacoproteomics to evaluate the time-dependent treatment effects of meropenem and methylprednisolone on a murine Escherichia coli sepsis model. Three distinct proteome response patterns were identified, which depended on the underlying proteotype for each organ. The findings provide insights for guiding treatment timing, dosage, and potential combination therapies.
NATURE COMMUNICATIONS
(2023)
Article
Critical Care Medicine
Qi Liu, Yuan Zhou, Joy D. Cogan, Daphne B. Mitchell, Quanhu Sheng, Shilin Zhao, Youhuang Bai, Kristen K. Ciombor, Carleen M. Sabusap, M. Merced Malabanan, Cheryl R. Markin, Katrina Douglas, Guixiao Ding, Nicholas E. Banovich, Deborah A. Nickerson, Elizabeth E. Blue, Michael J. Bamshad, Kevin K. Brown, David A. Schwartz, John A. Phillips, Ruben Martinez-Barricarte, Margaret L. Salisbury, Yu Shyr, James E. Loyd, Jonathan A. Kropski, Timothy S. Blackwell
Summary: In this study, the genetic risk of familial pulmonary fibrosis (FPF) was comprehensively evaluated, and it was found that about 14.9-23.4% of the genetic risk in kindreds could be explained by rare variants in genes previously linked to FPF. New candidate genes and pathways relevant to FPF were identified, and tools were developed for evaluating and prioritizing genes containing rare variants. However, no new genes containing rare variants shared across multiple kindreds were identified, suggesting that heterogeneous genetic variants involving various genes and pathways mediate the genetic risk in most FPF kindreds.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Article
Biodiversity Conservation
Iris Reinula, Sabrina Trager, Ignacio M. Hernandez-Agramonte, Aveliina Helm, Tsipe Aavik
Summary: The study found that the genetic diversity within populations of Primula veris was related to the extent of grassland loss over the past 80 years, the historical grassland edge density in the surrounding landscape, and the historical proportion of grasslands between populations. Despite drastic changes in landscape over the past century, the genetic diversity and gene flow patterns of Primula veris still largely reflect the effects of historical landscape composition, providing a potential for preserving genetic diversity through immediate restoration activities.
DIVERSITY AND DISTRIBUTIONS
(2021)
Article
Cell Biology
Belen Garcia Bohorquez, Elena Aller, Ana Rodriguez Munoz, Teresa Jaijo, Gema Garcia Garcia, Jose M. Millan
Summary: Inherited retinal dystrophies (IRD) are a group of diseases with high genetic and clinical variability, making genetic diagnosis challenging. Next generation sequencing has greatly improved diagnostic accuracy, identifying novel mutations and enabling accurate genetic counseling. The study identified multiple pathogenic variants and highlighted the importance of including deep-intronic regions in gene panel design for effective genetic diagnosis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Oncology
Marian Constantin, Cristina Matanie, Livia Petrescu, Alexandra Bolocan, Octavian Andronic, Coralia Bleotu, Mihaela Magdalena Mitache, Sorin Tudorache, Corneliu Ovidiu Vrancianu
Summary: An analysis of the presence of mutations in appendiceal cancers reveals the importance of inactivating tumor suppressor genes like TP53 and activating oncogenic genes such as KRAS, GNAS, and BRAF. Mucinous neoplasms of the appendix show the most mutated genes, while the RAS-RAF-MEK-ERK signaling pathway is frequently affected in appendiceal goblet cell adenocarcinomas and mucinous adenocarcinomas. Microsatellite instability is rare in appendix cancers. The review discusses the main genetic mutations involved in appendix tumors and their roles in various tumor processes.
Article
Immunology
Rosalyn W. Sayaman, Mohamad Saad, Vesteinn Thorsson, Donglei Hu, Wouter Hendrickx, Jessica Roelands, Eduard Porta-Pardo, Younes Mokrab, Farshad Farshidfar, Tomas Kirchhoff, Randy F. Sweis, Oliver F. Bathe, Carolina Heimann, Michael J. Campbell, Cynthia Stretch, Scott Huntsman, Rebecca E. Graff, Najeeb Syed, Laszlo Radvanyi, Simon Shelley, Denise Wolf, Francesco M. Marincola, Michele Ceccarelli, Jerome Galon, Elad Ziv, Davide Bedognetti
Summary: Understanding the host's genetic background's contribution to cancer immunity has significant impact on the composition and functional orientation of the tumor immune microenvironment, with certain genes potentially acting as immune modulators. Investigating the effects of germline variants on immune traits provides a resource toward further understanding tumor-immune interactions.
Article
Pathology
Scott H. Greenwald, Jeremy R. Charette, Magdalena Staniszewska, Lan Ying Shi, Steve D. M. Brown, Lisa Stone, Qin Liu, Wanda L. Hicks, Gayle B. Collin, Michael R. Bowl, Mark P. Krebs, Patsy M. Nishina, Eric A. Pierce
AMERICAN JOURNAL OF PATHOLOGY
(2016)
Article
Biochemistry & Molecular Biology
G. V. Walls, M. Stevenson, K. E. Lines, P. J. Newey, A. A. C. Reed, M. R. Bowl, J. Jeyabalan, B. Harding, K. J. Bradley, S. Manek, J. Chen, P. Wang, B. O. Williams, B. T. Teh, R. V. Thakker
Article
Multidisciplinary Sciences
Michael R. Bowl, Michelle M. Simon, Neil J. Ingham, Simon Greenaway, Luis Santos, Heather Cater, Sarah Taylor, Jeremy Mason, Natalja Kurbatova, Selina Pearson, Lynette R. Bower, Dave A. Clary, Hamid Meziane, Patrick Reilly, Osamu Minowa, Lois Kelsey, Glauco P. Tocchini-Valentini, Xiang Gao, Allan Bradley, William C. Skarnes, Mark Moore, Arthur L. Beaudet, Monica J. Justice, John Seavitt, Mary E. Dickinson, Wolfgang Wurst, Martin Hrabe de Angelis, Yann Herault, Shigeharu Wakana, Lauryl M. J. Nutter, Ann M. Flenniken, Colin McKerlie, Stephen A. Murray, Karen L. Svenson, Robert E. Braun, David B. West, K. C. Kent Lloyd, David J. Adams, Jacqui White, Natasha Karp, Paul Flicek, Damian Smedley, Terrence F. Meehan, Helen E. Parkinson, Lydia M. Teboul, Sara Wells, Karen P. Steel, Ann-Marie Mallon, Steve D. M. Brown
NATURE COMMUNICATIONS
(2017)
Article
Multidisciplinary Sciences
Arnaud P. J. Giese, Yi-Quan Tang, Ghanshyam P. Sinha, Michael R. Bowl, Adam C. Goldring, Andrew Parker, Mary J. Freeman, Steve D. M. Brown, Saima Riazuddin, Robert Fettiplace, William R. Schafer, Gregory I. Frolenkov, Zubair M. Ahmed
NATURE COMMUNICATIONS
(2017)
Article
Endocrinology & Metabolism
K. E. Lines, P. J. Newey, C. J. Yates, M. Stevenson, R. Dyar, G. V. Walls, M. R. Bowl, R. V. Thakker
JOURNAL OF ENDOCRINOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Mattea J. Finelli, Davide Aprile, Enrico Castroflorio, Alexander Jeans, Matteo Moschetta, Lauren Chessum, Matteo T. Degiacomi, Julia Grasegger, Alexis Lupien-Meilleur, Andrew Bassett, Elsa Rossignol, Philippe M. Campeau, Michael R. Bowl, Fabio Benfenati, Anna Fassio, Peter L. Oliver
HUMAN MOLECULAR GENETICS
(2019)
Article
Multidisciplinary Sciences
Lauren Chessum, Maggie S. Matern, Michael C. Kelly, Stuart L. Johnson, Yoko Ogawa, Beatrice Milon, Mark McMurray, Elizabeth C. Driver, Andrew Parker, Yang Song, Gemma Codner, Christopher T. Esapa, Jack Prescott, Graham Trent, Sara Wells, Abigail K. Dragich, Gregory I. Frolenkov, Matthew W. Kelley, Walter Marcotti, Steve D. M. Brown, Ran Elkon, Michael R. Bowl, Ronna Hertzano
Article
Cell Biology
Thomas Agnew, Michelle Goldsworthy, Carlos Aguilar, Anna Morgan, Michelle Simon, Helen Hilton, Chris Esapa, Yixing Wu, Heather Cater, Liz Bentley, Cheryl Scudamore, Joanna Poulton, Karl J. Morten, Kyle Thompson, Langping He, Steve D. M. Brown, Robert W. Taylor, Michael R. Bowl, Roger D. Cox
Article
Medicine, Research & Experimental
Michael R. Bowl, Sally J. Dawson
COLD SPRING HARBOR PERSPECTIVES IN MEDICINE
(2019)
Article
Medicine, Research & Experimental
Lucy A. Dunbar, Pranav Patni, Carlos Aguilar, Philomena Mburu, Laura Corns, Helena R. R. Wells, Sedigheh Delmaghani, Andrew Parker, Stuart Johnson, Debbie Williams, Christopher T. Esapa, Michelle M. Simon, Lauren Chessum, Sherylanne Newton, Joanne Dorning, Prashanthini Jeyarajan, Susan Morse, Andrea Lelli, Gemma F. Codner, Thibault Peineau, Suhasini R. Gopal, Kumar N. Alagramam, Ronna Hertzano, Didier Dulon, Sara Wells, Frances M. Williams, Christine Petit, Sally J. Dawson, Steve D. M. Brown, Walter Marcotti, Aziz El-Amraoui, Michael R. Bowl
EMBO MOLECULAR MEDICINE
(2019)
Article
Endocrinology & Metabolism
Katie U. Gaynor, Irina Grigorieva, Samantha M. Mirczuk, Sian Piret, Kreepa G. Kooblall, Mark Stevenson, Karine Rizzoti, Mike R. Bowl, M. Andrew Nesbit, Paul T. Christie, William D. Fraser, Tertius Hough, Michael P. Whyte, Robin Lovell-Badge, Rajesh Thakker
ENDOCRINE CONNECTIONS
(2020)
Article
Neurosciences
Jing-Yi Jeng, Stuart L. Johnson, Adam J. Carlton, Lara De Tomasi, Richard J. Goodyear, Francesca De Faveri, David N. Furness, Sara Wells, Steve D. M. Brown, Matthew C. Holley, Guy P. Richardson, Mirna Mustapha, Michael R. Bowl, Walter Marcotti
JOURNAL OF PHYSIOLOGY-LONDON
(2020)
Article
Neurosciences
Jing-Yi Jeng, Federico Ceriani, Jennifer Olt, Steve D. M. Brown, Matthew C. Holley, Michael R. Bowl, Stuart L. Johnson, Walter Marcotti
JOURNAL OF PHYSIOLOGY-LONDON
(2020)
Article
Medicine, Research & Experimental
Vincent Michel, Kevin T. Booth, Pranav Patni, Matteo Cortese, Hela Azaiez, Amel Bahloul, Kimia Kahrizi, Menelik Labbe, Alice Emptoz, Andrea Lelli, Julie Degardin, Typhaine Dupont, Asadollah Aghaie, Danuta Oficjalska-Pham, Serge Picaud, Hossein Najmabadi, Richard J. Smith, Michael R. Bowl, Steven D. M. Brown, Paul Avan, Christine Petit, Aziz El-Amraoui
EMBO MOLECULAR MEDICINE
(2017)