Article
Cell Biology
Xiaolei Yao, Fengzhe Li, Zongyou Wei, M. A. EI-Samahy, Xu Feng, Fan Yang, Feng Wang
Summary: This study investigates the role of DNA methylation in regulating phenotypic variation in Hu sheep. The results show that DNA methylation influences gene expression in the ovaries, affecting the sheep's propensity for prolificacy.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Isabelle Bichindaritz, Guanghui Liu, Christopher Bartlett
Summary: The study proposes an adaptive multi-task learning method for survival prediction of breast cancer patients using multi-modal learning, achieving more effective results compared to existing approaches. By combining different gene features, reducing dimensions, and introducing auxiliary loss, an ordinal Cox hazards model is built to predict patients' survival risk.
Article
Dentistry, Oral Surgery & Medicine
Monnat Pongpanich, Sirima Sanguansin, Sudaporn Kengkarn, Arkom Chaiwongkot, Boworn Klongnoi, Nakarin Kitkumthorn
Summary: This study identified a group of novel genes that may be regulated by DNA methylation, potentially leading to new insights into the pathology and invasion mechanism of ameloblastoma.
Article
Oncology
Yicheng Wang, Haoling Xie, Xiaohong Chang, Wenqi Hu, Mengyao Li, Yi Li, Huiping Liu, Hongyan Cheng, Shang Wang, Ling Zhou, Danhua Shen, Sha Dou, Ruiqiong Ma, Yunuo Mao, Honglan Zhu, Xiaobo Zhang, Yuxuan Zheng, Xue Ye, Lu Wen, Kehkooi Kee, Heng Cui, Fuchou Tang
Summary: This study provides insights into the molecular characteristics of high-grade serous ovarian cancer through integrated analysis of multiomic changes and epigenetic regulation. It reveals the upregulation of interferon signaling and metallothioneins, which are influenced by demethylation and hypomethylation. The study also suggests the potential preexistence of metastatic cells in the subclones of primary tumors.
Article
Oncology
Xiaoqing Yu, Ling Cen, Y. Ann Chen, Joseph Markowitz, Timothy Shaw, Kenneth Y. Tsai, Jose R. Conejo-Garcia, Xuefeng Wang
Summary: DNA methylation signatures can be used as reliable biomarkers to predict patient prognosis and immune status in tumors. This study introduces the concept of tumor-based expression quantitative trait methylation (eQTM) for the identification of predictive biomarkers. eQTM CpGs and genes represent new and efficient candidate targets for prognosis and immune status monitoring.
Article
Oncology
Marcus J. J. Brookes, Corey D. D. Chan, Timothy P. P. Crowley, Maniram Ragbir, Thomas Beckingsale, Kanishka M. M. Ghosh, Kenneth S. S. Rankin
Summary: Sarcomas are rare, aggressive cancers that often spread to the lungs. Indeterminate pulmonary nodules (IPNs) may indicate the spreading of high-grade sarcomas. This study identifies characteristics of IPNs that are more likely to be cancerous.
Article
Oncology
Catherine Sarre-Lazcano, Sinziana Dumitra, Marco Fiore
Summary: Pelvic soft tissue sarcomas (PSTS) are a rare and heterogeneous group of tumors that differ from retroperitoneal sarcomas (RPS). Adequate imaging and preoperative biopsy are crucial for differential diagnosis and treatment planning. Surgical approach and multidisciplinary teamwork are essential due to anatomic constraints and potential complications. Early referral to specialized centers is recommended for optimal resection and improved survival. International consensus on PSTS treatment is needed, similar to recent efforts for RPS.
Article
Biochemical Research Methods
Manqi Cai, Molin Yue, Tianmeng Chen, Jinling Liu, Erick Forno, Xinghua Lu, Timothy Billiar, Juan Celedon, Chris McKennan, Wei Chen, Jiebiao Wang
Summary: This study focuses on using cellular deconvolution methods to extract cell-type-specific signals from tissue-level omics data. However, different methods produce different results under various real data settings. The study proposes EnsDeconv, an ensemble deconvolution method that synthesizes the results from multiple single deconvolution methods to achieve robust and accurate estimation of cellular fractions.
Article
Endocrinology & Metabolism
Yunjin Yao, Peiwei Xu, Tianxing Ying, Yue Wang, Xumeng Wang, Liqi Shu, Zhe Mo, Zhijian Chen, Xiaofeng Wang, Weibin Wang, Lisong Teng, Xiaoming Lou
Summary: This study conducted an integrative analysis of DNA methylation and RNA array data to identify thyroid cancer-specific DNA methylation markers, providing potential molecular markers for early diagnosis.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Multidisciplinary Sciences
Ana Cristina Vargas, Lesley-Ann Gray, Christine L. White, Fiona M. Maclean, Peter Grimison, Nima Mesbah Ardakani, Fiona Bonar, Elizabeth M. Algar, Alison L. Cheah, Peter Russell, Annabelle Mahar, Anthony J. Gill
Summary: The study used Illumina Infinium Methylation array to investigate genome-wide methylation changes in soft tissue sarcomas during metastatic and recurrent disease, finding differential methylation in all matched samples and identifying novel genes involved in sarcoma progression. These findings suggest the presence of epigenetic differences across primary and metastatic/recurrent human tissue samples previously unreported.
SCIENTIFIC REPORTS
(2021)
Article
Immunology
Lin Qi, Ruiling Xu, Xiaolei Ren, Wenchao Zhang, Zhimin Yang, Chao Tu, Zhihong Li
Summary: This study identified necroptosis-related genes (NRGs) in soft tissue sarcomas (STSs) and found their potential role in prognosis. The results showed that the risk score based on the necroptosis-related gene signature could serve as an independent prognostic factor and could also predict immune infiltration. Furthermore, the necroptosis-related gene signature was validated in other malignancies, indicating its potential as a prognostic indicator in different types of cancer.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Patrick Groothuis, Nicola Penel, Antoine Italiano, Nuria Kotecki, Fred Dijcks, Wim Dokter
Summary: Soft tissue sarcoma (STS) is a difficult-to-treat malignancy originating from mesenchymal or connective tissues. The molecule 5T4/trophoblast glycoprotein is found to be prominently expressed on the cell surface of many STS subtypes, making it a potential target for targeted therapies. Further investigation is warranted to determine whether this antigen could trigger an anti-tumor immune response or serve as a target for delivering more potent toxins through antibody drug conjugates, as it is expressed in more than 50% of other STS subtypes.
Article
Oncology
Hideyuki Kinoshita, Takeshi Ishii, Hiroto Kamoda, Yoko Hagiwara, Toshinori Tsukanishi, Masahiro Inoue, Toru Ueta, Seiji Ohtori, Tsukasa Yonemoto
Summary: The study found that postoperative radiotherapy did not significantly impact local recurrence-free survival in high-grade infiltrative soft tissue sarcomas. Important prognostic factors affecting LRFS include patient age at diagnosis and tumor growth pattern.
ANTICANCER RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Jiwon Lim, Yerim Heo, Sun Shim Choi
Summary: DNAm is important for regulating cellular activities, and this study investigated its alterations in obesity. Using methylome and transcriptome data, differentially methylated probes (DMPs) were identified between adipocytes and preadipocytes, as well as between obese and lean adipocytes. The study also examined the impact of hyper and hypomethylation on gene expression changes. Interestingly, greater DNAm alterations were observed during adipocyte differentiation under lean conditions compared to obese conditions. Overall, complex methylation changes affected adipogenesis-related genes, leading to differences in gene expression between lean and obese adipocytes.
Article
Agronomy
Ningning Wang, Yanan Yu, Di Zhang, Zhibin Zhang, Zhenhui Wang, Hongwei Xun, Guo Li, Bao Liu, Jian Zhang
Summary: Tissue culture is an important experimental technique that can induce somaclonal variation in plant cells. In this study, the researchers investigated the molecular basis of somaclonal variation and plant cell response to tissue culture in rice plants. They found widespread changes in gene expression, DNA methylation, and small RNA accumulation in regenerated plants compared to wild-type plants. These changes were associated with significant phenotypic alterations under abiotic stress conditions.
Correction
Biotechnology & Applied Microbiology
Sergei Yakneen, Sebastian M. Waszak, Michael Gertz, Jan O. Korbel, Brice Aminou, Javier Bartolome, Keith A. Boroevich, Rich Boyce, Angela N. Brooks, Alex Buchanan, Ivo Buchhalter, Adam P. Butler, Niall J. Byrne, Andy Cafferkey, Peter J. Campbell, Zhaohong Chen, Sunghoon Cho, Wan Choi, Peter Clapham, Brandi N. Davis-Dusenbery, Francisco M. De La Vega, Jonas Demeulemeester, Michelle T. Dow, Lewis Jonathan Dursi, Juergen Eils, Roland Eils, Kyle Ellrott, Claudiu Farcas, Francesco Favero, Nodirjon Fayzullaev, Vincent Ferretti, Paul Flicek, Nuno A. Fonseca, Josep Ll. Gelpi, Gad Getz, Bob Gibson, Robert L. Grossman, Olivier Harismendy, Allison P. Heath, Michael C. Heinold, Julian M. Hess, Oliver Hofmann, Jongwhi H. Hong, Thomas J. Hudson, Barbara Hutter, Carolyn M. Hutter, Daniel Hubschmann, Seiya Imoto, Sinisa Ivkovic, Seung-Hyup Jeon, Wei Jiao, Jongsun Jung, Rolf Kabbe, Andre Kahles, Jules N. A. Kerssemakers, Hyung-Lae Kim, Hyunghwan Kim, Jihoon Kim, Youngwook Kim, Kortine Kleinheinz, Michael Koscher, Antonios Koures, Milena Kovacevic, Chris Lawerenz, Ignaty Leshchiner, Jia Liu, Dimitri Livitz, George L. Mihaiescu, Sanja Mijalkovic, Ana Mijalkovic Lazic, Satoru Miyano, Naoki Miyoshi, Hardeep K. Nahal-Bose, Hidewaki Nakagawa, Mia Nastic, Steven J. Newhouse, Jonathan Nicholson, Brian D. O'Connor, David Ocana, Kazuhiro Ohi, Lucila Ohno-Machado, Larsson Omberg, B. F. Francis Ouellette, Nagarajan Paramasivam, Marc D. Perry, Todd D. Pihl, Manuel Prinz, Montserrat Puiggros, Petar Radovic, Keiran M. Raine, Esther Rheinbay, Mara Rosenberg, Romina Royo, Gunnar Ratsch, Gordon Saksena, Matthias Schlesner, Solomon I. Shorser, Charles Short, Heidi J. Sofia, Jonathan Spring, Lincoln D. Stein, Adam J. Struck, Grace Tiao, Nebojsa Tijanic, David Torrents, Peter Van Loo, Miguel Vazquez, David Vicente, Jeremiah A. Wala, Zhining Wang, Sebastian M. Waszak, Joachim Weischenfeldt, Johannes Werner, Ashley Williams, Youngchoon Woo, Adam J. Wright, Qian Xiang, Liming Yang, Denis Yuen, Christina K. Yung, Junjun Zhang, Jan O. Korbel
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Marina Laplana, Matthias Bieg, Christian Faltus, Svitlana Melnik, Olga Bogatyrova, Zuguang Gu, Thomas Muley, Michael Meister, Hendrik Dienemann, Esther Herpel, Christopher Amos, Matthias Schlesner, Roland Eils, Christoph Plass, Angela Risch
Summary: This study utilized a targeted sequencing approach to investigate DNA methylation changes in NSCLC patients, identifying differential methylation regions and confirming potential regulatory elements. The research contributes to understanding the mechanisms of lung cancer initiation and progression, and offers new potential targets for cancer treatment.
Article
Biotechnology & Applied Microbiology
Evgeniya Denisova, Dana Westphal, Harald M. Surowy, Friedegund Meier, Barbara Hutter, Julia Reifenberger, Arno Rutten, Alexander Schulz, Mildred Sergon, Mirjana Ziemer, Benedikt Brors, Regina C. Betz, Silke Redler
Summary: The study of the mutational landscape of EP revealed a high overall mutation rate attributed to processes related to UV exposure, APOBEC enzyme dysregulation, and defective homologous double-strand break repair. Recurrent driving somatic alterations were detected in EP candidate driver genes and chromosomal regions, with a reduction or loss of BRCA2 protein in 50% of EP tumors. The results suggest that defective homologous double-strand break repair and the p53 pathway play important roles in EP etiology, indicating potential treatment strategies targeting these pathways.
CANCER GENE THERAPY
(2022)
Article
Biotechnology & Applied Microbiology
J. Loske, J. Roehmel, S. Lukassen, S. Stricker, Vg Magalhaes, J. Liebig, Rl Chua, L. Thurmann, M. Messingschlager, A. Seegebarth, B. Timmermann, S. Klages, M. Ralser, B. Sawitzki, Le Sander, Vm Corman, C. Conrad, S. Laudi, M. Binder, S. Trump, R. Eils, M. A. Mall, I Lehmann
Summary: Children exhibit higher basal expression of relevant pattern recognition receptors in airway immune cells, resulting in stronger early innate antiviral responses to SARS-CoV-2 infection compared to adults. Unique immune cell subpopulations, including cytotoxic T cells and memory CD8+ T cells, predominantly occur in children.
NATURE BIOTECHNOLOGY
(2022)
Article
Hematology
Nicola Giesen, Nagarajan Paramasivam, Umut H. Toprak, Daniel Huebschmann, Jing Xu, Sebastian Uhrig, Mehmet Samur, Stella Baehr, Martina Froehlich, Sadaf S. Mughal, Elias K. Mai, Anna Jauch, Carsten Muller-Tidow, Benedikt Brors, Nikhil Munshi, Hartmut Goldschmidt, Niels Weinhold, Matthias Schlesner, Marc S. Raab
Summary: This study provides comprehensive genomic characterization of heavily pretreated relapsed/refractory multiple myeloma patients, revealing a complex mutational landscape and potential therapeutic targets. The findings highlight the impact of specific gene mutations on patient survival and suggest potential therapeutic implications.
Article
Urology & Nephrology
Daniel Burns, Ezequiel Anokian, Edward J. Saunders, Robert G. Bristow, Michael Fraser, Juri Reimand, Thorsten Schlomm, Guido Sauter, Benedikt Brors, Jan Korbel, Joachim Weischenfeldt, Sebastian M. Waszak, Niall M. Corcoran, Chol-Hee Jung, Bernard J. Pope, Chris M. Hovens, Geraldine Cancel-Tassin, Olivier Cussenot, Massimo Loda, Chris Sander, Vanessa M. Hayes, Karina Dalsgaard Sorensen, Yong-Jie Lu, Freddie C. Hamdy, Christopher S. Foster, Vincent Gnanapragasam, Adam Butler, Andy G. Lynch, Charlie E. Massie, Dan J. Woodcock, Colin S. Cooper, David C. Wedge, Daniel S. Brewer, Zsofia Kote-Jarai, Rosalind A. Eeles
Summary: This study identified rare genetic mutations that can predict the time to biochemical recurrence in prostate cancer patients after hormonal treatment and revealed the genetic factors associated with such progression.
Review
Computer Science, Information Systems
Mikael Beyene, Philipp A. Toussaint, Scott Thiebes, Matthias Schlesner, Benedikt Brors, Ali Sunyaev
Summary: This review uncovers the current state of research on the application of Distributed Ledger Technology (DLT) in genomics, identifying focal research themes and directions for future research. The analysis resulted in 7 themes, including data economy and sharing, data management, data protection, and ethical implications. The review also presents 7 future research directions, such as exploring alternative consensus mechanisms and investigating data storage models appropriate for DLT.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2022)
Article
Multidisciplinary Sciences
Josefine Radke, Naveed Ishaque, Randi Koll, Zuguang Gu, Elisa Schumann, Lina Sieverling, Sebastian Uhrig, Daniel Huebschmann, Umut H. Toprak, Cristina Lopez, Xavier Pastor Hostench, Simone Borgoni, Dilafruz Juraeva, Fabienne Pritsch, Nagarajan Paramasivam, Gnana Prakash Balasubramanian, Matthias Schlesner, Shashwat Sahay, Marc Weniger, Debora Pehl, Helena Radbruch, Anja Osterloh, Agnieszka Korfel, Martin Misch, Julia Onken, Katharina Faust, Peter Vajkoczy, Dag Moskopp, Yawen Wang, Andreas Joedicke, Lorenz Truemper, Ioannis Anagnostopoulos, Dido Lenze, Ralf Kueppers, Michael Hummel, Clemens A. Schmitt, Otmar D. Wiestler, Stephan Wolf, Andreas Unterberg, Roland Eils, Christel Herold-Mende, Benedikt Brors, Reiner Siebert, Stefan Wiemann, Frank L. Heppner
Summary: This study profiles the genomic and transcriptomic landscape of primary lymphomas of the central nervous system (PCNSL) and identifies common mutations in immune pathways and upregulated TERT gene expression. It also reveals distinct pathway differences between PCNSL and other primary CNS lymphomas, as well as DLBCL.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Anita Balazs, Pamela Millar-Buechner, Michael Muelleder, Vadim Farztdinov, Lukasz Szyrwiel, Annalisa Addante, Aditi Kuppe, Tihomir Rubil, Marika Drescher, Kathrin Seidel, Sebastian Stricker, Roland Eils, Irina Lehmann, Birgit Sawitzki, Jobst Roehmel, Markus Ralser, Marcus A. Mall
Summary: The nasal epithelium acts as the first line of defense against inhaled pathogens, allergens, and irritants, and plays a crucial role in the development of various respiratory diseases. This study aims to investigate the age-related differences in the structure and function of the nasal epithelium. The results showed intrinsic, age-related differences in the structure and function of the nasal epithelium, which may contribute to the development of age-dependent respiratory diseases.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Cell & Tissue Engineering
Ruzhica Bogeska, Ana-Matea Mikecin, Paul Kaschutnig, Malak Fawaz, Marleen Buechler-Schaeff, Duy Le, Miguel Ganuza, Angelika Vollmer, Stella Paffenholz, Noboru Asada, Esther Rodriguez-Correa, Felix Frauhammer, Florian Buettner, Melanie Ball, Julia Knoch, Sina Staeble, Dagmar Walter, Amelie Petri, Martha J. Carreno-Gonzalez, Vinona Wagner, Benedikt Brors, Simon Haas, Daniel B. Lipka, Marieke A. G. Essers, Vivienn Weru, Tim Holland-Letz, Jan-Philipp Mallm, Karsten Rippe, Stephan Kraemer, Matthias Schlesner, Shannon McKinney Freeman, Maria Carolina Florian, Katherine Y. King, Paul S. Frenette, Michael A. Rieger, Michael D. Milsom
Summary: Infection or inflammation may lead to irreversible depletion of functional hematopoietic stem cells, resulting in long-term effects on tissue maintenance and regeneration.
Article
Multidisciplinary Sciences
Jason A. Carter, Leonie Stroemich, Matthew Peacey, Sarah R. Chapin, Lars Velten, Lars M. Steinmetz, Benedikt Brors, Sheena Pinto, Hannah Meyer
Summary: This study reveals the transcriptomic diversity of mTECs in the thymus and establishes a web portal for querying their transcriptome, which may aid in identifying the drivers of autoimmune diseases.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Dania Riegel, Elena Romero-Fernandez, Malte Simon, Akinbami Raphael Adenugba, Katrin Singer, Roman Mayr, Florian Weber, Mark Kleemann, Charles D. Imbusch, Marina Kreutz, Benedikt Brors, Ines Ugele, Jens M. Werner, Peter J. Siska, Christian Schmidl
Summary: By integrating single-cell chromatin accessibility and RNA-seq data, we identified the heterogeneous functional and dysfunctional states of CD8+ tumor-infiltrating lymphocytes and revealed common chromatin remodeling and key regulatory factors involved in this process.
Meeting Abstract
Oncology
Tom T. Fischer, Kendra K. Maass, Pitithat Puranachot, Agnes M. E. Finster, Markus Mieskolainen, Paulina S. Schad, Martin Sill, Fabian Rosing, Tatjana Wedig, Nathalie Schwarz, Florian Iser, Jochen Meyer, Felix Sahm, Benedikt Brors, Hannu Haapasalo, Stefan M. Pfister, Joonas Haapasalo, Kristian W. Pajtler, Kristiina Nordfors
Article
Biochemistry & Molecular Biology
Philipp Georg, Rosario Astaburuaga-Garcia, Lorenzo Bonaguro, Sophia Brumhard, Laura Michalick, Lena J. Lippert, Tomislav Kostevc, Christiane Gaebel, Maria Schneider, Mathias Streitz, Vadim Demichev, Ioanna Gemuend, Matthias Barone, Pinkus Tober-Lau, Elisa T. Helbig, David Hillus, Lev Petrov, Julia Stein, Hannah-Philine Dey, Daniela Paclik, Christina Iwert, Michael Muelleder, Simran Kaur Aulakh, Sonja Djudjaj, Roman D. Buelow, Henrik E. Mei, Axel R. Schulz, Andreas Thiel, Stefan Hippenstiel, Antoine-Emmanuel Saliba, Roland Eils, Irina Lehmann, Marcus A. Mall, Sebastian Stricker, Jobst Roehmel, Victor M. Corman, Dieter Beule, Emanuel Wyler, Markus Landthaler, Benedikt Obermayer, Saskia von Stillfried, Peter Boor, Munevver Demir, Hans Wesselmann, Norbert Suttorp, Alexander Uhrig, Holger Mueller-Redetzky, Jacob Nattermann, Wolfgang M. Kuebler, Christian Meisel, Markus Ralser, Joachim L. Schultze, Anna C. Aschenbrenner, Charlotte Thibeault, Florian Kurth, Leif E. Sander, Nils Bluethgen, Birgit Sawitzki
Summary: Severe COVID-19 is associated with highly activated CD16(+) T cells that exhibit cytotoxic functions and contribute to endothelial injury. These CD16(+) T cells can degranulate and induce cytotoxicity through immune-complex-mediated mechanisms independent of the T cell receptor, which is not observed in other diseases. The presence of activated CD16(+) T cells and elevated levels of complement proteins upstream of C3a are associated with a fatal outcome of COVID-19, indicating the pathological role of enhanced cytotoxicity and complement activation in the disease.
Article
Medical Informatics
Jakob Steinfeldt, Thore Buergel, Lukas Loock, Paul Kittner, Greg Ruyoga, Julius Upmeier zu Belzen, Simon Sasse, Henrik Strangalies, Lara Christmann, Noah Hollmann, Benedict Wolf, Brian Ference, John Deanfield, Ulf Landmesser, Roland Eils
Summary: In this study, a neural network-based risk model (NeuralCVD) was developed and validated to estimate cardiovascular risk for primary prevention. The model integrates polygenic and clinical predictors and improves risk discrimination compared to established clinical scores and a Cox model. The findings highlight the importance of genetic information in identifying individuals with a high genetic predisposition for preventive interventions.
LANCET DIGITAL HEALTH
(2022)