Article
Biochemistry & Molecular Biology
Samantha Lapehn, Jonas A. Gustafson, Andrew E. Timms, Michael L. Cunningham, Alison G. Paquette
Summary: This study aimed to compare gene expression differences between patients with different phenotypes of single-suture craniosynostosis and controls, using primary calvarial cell lines. The results showed differentially expressed genes associated with each type of craniosynostosis, as well as differences between males and females. Pathway analysis also identified relevant signaling pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Maria-Veronica Teleanu, Carmina T. Fuss, Nagarajan Paramasivam, Sebastian Pirmann, Andreas Mock, Christoph Terkamp, Stefan Kircher, Laura-Sophie Landwehr, Christina Lenschow, Nicolas Schlegel, Albrecht Stenzinger, Arne Jahn, Martin Fassnacht, Hanno Glimm, Daniel Huebschmann, Stefan Froehling, Matthias Kroiss
Summary: We performed whole-genome and RNA sequencing on four advanced parathyroid carcinoma patients to identify molecular alterations for clinical management. Two experimental therapies, immune checkpoint inhibition with pembrolizumab and multi-receptor tyrosine kinase inhibition with lenvatinib, showed promising results. Our data also provided new insights into the molecular landscape of parathyroid carcinoma.
MOLECULAR ONCOLOGY
(2023)
Article
Cell Biology
Pauline Sararols, Isabelle Stevant, Yasmine Neirijnck, Diane Rebourcet, Annalucia Darbey, Michael K. Curley, Francoise Kuhne, Emmanouil Dermitzakis, Lee B. Smith, Serge Nef
Summary: FLCs and ALCs exhibit significant differences in transcriptional and functional features, including gene expression variations and non-transcriptional events such as intron retention. The FLC-specific expression of Crhr1 and Mc2r receptors suggests a dual regulation of steroidogenesis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Minyoung Youn, Stephanie M. Smith, Alex Gia Lee, Hee-Don Chae, Elizabeth Spiteri, Jason Erdmann, Ilana Galperin, Lara Murphy Jones, Michele Donato, Parveen Abidi, Henrique Bittencourt, Norman Lacayo, Gary Dahl, Catherine Aftandilian, Kara L. Davis, Jairo A. Matthews, Steven M. Kornblau, Min Huang, Nathan Sumarsono, Michele S. Redell, Cecilia H. Fu, I-Ming Chen, Todd A. Alonzo, Elizabeth Eklund, Jason Gotlib, Purvesh Khatri, E. Alejandro Sweet-Cordero, Nobuko Hijiya, Kathleen M. Sakamoto
Summary: A study compared the transcriptomic signature of pediatric and adult chronic myeloid leukemia (CML) cells, identifying unique molecular characteristics in pediatric CML, such as dysregulation of the Rho pathway. Understanding the biology of CML across different ages may inform future treatment approaches for pediatric and adult patients with CML.
Article
Multidisciplinary Sciences
Hower Lee, Sergio Marco Salas, Daniel Gyllborg, Mats Nilsson
Summary: Highly multiplexed spatial mapping of transcripts allows for investigation of transcriptomic and cellular diversity. This study explores a new direct RNA detection approach, which significantly improves transcript detection efficiency and validates its multiplexing capabilities.
SCIENTIFIC REPORTS
(2022)
Article
Urology & Nephrology
J. Alberto Nakauma-Gonzalez, Maud Rijnders, Job van Riet, Michiel S. van der Heijden, Jens Voortman, Edwin Cuppen, Niven Mehra, Sandra van Wilpe, Sjoukje F. Oosting, L. Lucia Rijstenberg, Hans M. Westgeest, Ellen C. Zwarthoff, Ronald de Wit, Astrid A. M. van der Veldt, Harmen J. G. van de Werken, Martijn P. J. Lolkema, Joost L. Boormans
Summary: This study analyzed the molecular and genetic features of metastatic urothelial carcinoma (mUC) and identified different genomic and transcriptomic subtypes, providing potential therapeutic options for individualized treatment. The findings have significant clinical implications.
Article
Orthopedics
Nathaniel P. Disser, Alexander N. Piacentini, Andrea J. De Micheli, Martin M. Schonk, Vincent J. H. Yao, Xiang-Hua Deng, David J. Oliver, Scott A. Rodeo
Summary: This study investigated the transcriptomic and mechanical properties of a single Achilles tendon and found region-specific gene expression signatures and mechanical properties. The proximal region displayed gene expression resembling a tendon phenotype and increased expression of nerve cell markers, while the distal region showed increased expression of genes involved in extracellular matrix synthesis and remodeling, immune cell regulation, and a phenotype similar to cartilage and bone. There was a significant increase in Young modulus from the proximal to middle region and an additional increase from the middle to distal region.
AMERICAN JOURNAL OF SPORTS MEDICINE
(2022)
Article
Veterinary Sciences
Cecilia Gola, Diana Giannuzzi, Andrea Rinaldi, Selina Iussich, Paola Modesto, Emanuela Morello, Paolo Buracco, Luca Aresu, Raffaella De Maria
Summary: The study aims to determine variants, putative driver genes, and gene expression aberrations in canine OSA cell lines, revealing a mean tumor mutational burden of 9.6 mutations/Mb. Known oncogenes and tumor suppressor genes were identified as likely players in canine OSA, with mutations in genes like TP53 retrieved in the cell lines. The findings provide molecular characterization for potential therapeutic targets and biomarkers in canine OSA.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Environmental Sciences
Miodrag Stojkovic, Francisco Manuel Ortuno Guzman, Dongjun Han, Petra Stojkovic, Joaquin Dopazo, Konstantina M. Stankovic
Summary: Plastic pollution is rapidly increasing, but its impact on human health is poorly understood. This study demonstrates the use of human cellular models to identify molecular biomarkers of environmental pollution and potentially decipher the origins of environmental diseases.
ENVIRONMENTAL POLLUTION
(2023)
Article
Agronomy
Liangjing Cao, Mingjie Lyu, Jingyi Wang, Xuan Wang, Xinchang Li, Ruilian Jing, Jun Liu, Xinwen Hu
Summary: This study identified a large number of gene polymorphisms and mutations in two popular winter wheat cultivars and found time-point specific and cultivar-preferential responsive gene expression patterns related to abiotic stress response. Unexpected pathways associated with stress responses were also discovered.
Article
Medicine, Research & Experimental
Onat Kadioglu, Mohamed E. M. Saeed, Nuha Mahmoud, Shaymaa S. Hussein Azawi, Martina Rincic, Thomas Liehr, Thomas Efferth
Summary: Several genes were found to be overexpressed in B16-F10 cells, including Nr5a1/sf1 and Hoxb8 which are known to be linked with tumor progression and metastasis. Additionally, B16-F10 cells acquired additional chromosomal aberrations compared to B16-F1 cells. The study identified numerous novel genes and genomic aberrations that may serve as potential targets for future treatment strategies.
Article
Obstetrics & Gynecology
Wen-bi Zhang, Qing Li, Hu Liu, Wei-jian Chen, Chun-lei Zhang, He Li, Xiang Lu, Jun-ling Chen, Lu Li, Han Wu, Xiao-xi Sun
Summary: The study defined the transcriptomic signature of endometrial receptivity in Chinese women and developed a bioinformatic predictor for endometrial dating with high accuracy. This method can be used to monitor the window of implantation and predict the personal window of implantation for Chinese women, providing a new approach for evaluating endometrial status in this population.
FERTILITY AND STERILITY
(2021)
Article
Biochemistry & Molecular Biology
Uwe Schwartz, Maria Llamazares Prada, Stephanie T. Pohl, Mandy Richter, Raluca Tamas, Michael Schuler, Corinna Keller, Vedrana Mijosek, Thomas Muley, Marc A. Schneider, Karsten Quast, Joschka Hey, Claus P. Heussel, Arne Warth, Hauke Winter, Oezdemirhan Sercin, Harry Karmouty-Quintana, Soma S. K. Jyothula, Manish K. Patel, Felix Herth, Ina Koch, Giuseppe Petrosino, Alexandru Titimeaua, Balca R. Mardin, Dieter Weichenhan, Tomasz P. Jurkowski, Charles D. Imbusch, Benedikt Brors, Vladimir Benes, Birgit Jung, David Wyatt, Heiko F. Stahl, Christoph Plass, Renata Z. Jurkowska
Summary: Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. We hypothesized that COPD is associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps of primary human lung fibroblasts (HLFs) across COPD stages and found early epigenetic changes in COPD, predominantly in regulatory regions. Dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization were observed. Furthermore, we identified candidate regulators and demonstrated the potential for novel therapeutic avenues for COPD patients.
Review
Cell Biology
Stefania Kokkali, Eleni Georgaki, Georgios Mandrakis, Claudia Valverde, Stamatios Theocharis, Filomena De Nigris
Summary: The clinical utility of next-generation sequencing (NGS) in the treatment of soft tissue sarcoma (STS) is still controversial, with limited retrospective studies providing data on the use and efficacy of targeted treatment. Despite detailed reports on different gene mutations, fusions, or amplifications, there is a lack of information on the effectiveness of targeted therapies in STS.
Article
Immunology
Qixia Shen, Lisha Teng, Yucheng Wang, Luying Guo, Feng Xu, Hongfeng Huang, Wenqing Xie, Qin Zhou, Ying Chen, Junwen Wang, Youying Mao, Jianghua Chen, Hong Jiang
Summary: This study identifies novel genes related to the recurrence of FSGS after kidney transplantation, with MDH2 being a susceptibility gene for FSGS recurrence. The MDH2 c.26C >T mutation may contribute to progressive podocyte injury in these patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Patrick Sven Plum, Heike Loeser, Thomas Zander, Ahlem Essakly, Christiane J. Bruns, Axel M. Hillmer, Hakan Alakus, Wolfgang Schroeder, Reinhard Buttner, Florian Gebauer, Alexander Quaas
Summary: The study found amplification of GATA6 in 9.9% of esophageal adenocarcinoma cases, with a higher rate of 12.3% in patients after neoadjuvant treatment. Additionally, a simultaneous amplification of PIK3CA and GATA6 was observed, not detected in other genes analyzed.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2021)
Article
Genetics & Heredity
Carina Heydt, Christina B. Woelwer, Oscar Velazquez Camacho, Svenja Wagener-Ryczek, Roberto Pappesch, Janna Siemanowski, Jan Rehker, Florian Haller, Abbas Agaimy, Karl Worm, Thomas Herold, Nicole Pfarr, Wilko Weichert, Thomas Kirchner, Andreas Jung, Joerg Kumbrink, Wolfgang Goering, Irene Esposito, Reinhard Buettner, Axel M. Hillmer, Sabine Merkelbach-Bruse
Summary: Gene fusions are important targets for cancer therapy in lung cancer. RNA-based parallel sequencing methods are potent tools for reliable detection of targetable gene fusions in clinical diagnostics. DNA-based methods also show promise but may result in more false positive results.
BMC MEDICAL GENOMICS
(2021)
Article
Dermatology
Elaine G. Y. Chew, Tze Chiun Lim, Meng Fatt Leong, Xingliang Liu, Yee Yen Sia, See Ting Leong, Benjamin C. Yan-Jiang, Celine Stoecklin, Rosa Borhan, Stefanie Heilmann-Heimbach, Markus M. Nothen, Virgile Viasnoff, Ng Shyh-Chang, Andrew C. A. Wan, Michael P. Philpott, Axel M. Hillmer
Summary: Using a three-dimensional culture model, this study examined the pathogenesis of androgenetic alopecia (AGA) in males and found that balding DP cells exhibited mitochondrial dysfunction, increased oxidative stress, and impaired metabolite uptake.
EXPERIMENTAL DERMATOLOGY
(2022)
Letter
Oncology
Kian Leong Lee, Tun Kiat Ko, Nicole Y. L. Saw, Asif Javed, Axel M. Hillmer, Charles Chuah, Vaidehi Krishnan, S. Tiong Ong
Article
Oncology
M. Janning, J. Sueptitz, C. Albers-Leischner, P. Delpy, A. Tufman, J-L Velthaus-Rusik, M. Reck, A. Jung, D. Kauffmann-Guerrero, I Bonzheim, S. Braendlein, H-D Hummel, M. Wiesweg, H-U Schildhaus, J. A. Stratmann, M. Sebastian, J. Alt, J. Buth, I Esposito, J. Berger, L. Toegel, F. C. Saalfeld, M. Wermke, S. Merkelbach-Bruse, A. M. Hillmer, F. Klauschen, C. Bokemeyer, R. Buettner, J. Wolf, S. Loges
Summary: This retrospective multicenter study investigated the response of atypical EGFR mutations in different systemic treatments. The study found that uncommon mutations responded well to EGFR-TKI, while exon 20 insertions were insensitive to EGFR-TKI. Very rare point and compound mutations also showed sensitivity to TKI, but treatment responses varied greatly. Co-occurring TP53 mutations may have a detrimental effect on treatment outcome in certain cases.
ANNALS OF ONCOLOGY
(2022)
Article
Gastroenterology & Hepatology
Julia Schroeder, Laura Chegwidden, Carlo Maj, Jan Gehlen, Jan Speller, Anne C. Boehmer, Oleg Borisov, Timo Hess, Nicole Kreuser, Marino Venerito, Hakan Alakus, Andrea May, Christian Gerges, Thomas Schmidt, Rene Thieme, Dominik Heider, Axel M. Hillmer, Julian Reingruber, Orestis Lyros, Arne Dietrich, Albrecht Hoffmeister, Matthias Mehdorn, Florian Lordick, Gertraud Stocker, Michael Hohaus, Daniel Reim, Jennis Kandler, Michaela Mueller, Alanna Ebigbo, Claudia Fuchs, Christiane J. Bruns, Arnulf H. Holscher, Hauke Lang, Peter P. Grimminger, Dani Dakkak, Yogesh Vashist, Sandra May, Siegfried Gorg, Andre Franke, David Ellinghaus, Sara Galavotti, Lothar Veits, Josef Weismuller, Jens Dommermuth, Udo Benner, Thomas Roesch, Helmut Messmann, Brigitte Schumacher, Horst Neuhaus, Carsten Schmidt, Thaddaus T. Wissinowski, Markus M. Noethen, Jing Dong, Jue-Sheng Ong, Matthew F. Buas, Aaron P. Thrift, Thomas L. Vaughan, Ian Tomlinson, David C. Whiteman, Rebecca Claire Fitzgerald, Janusz Jankowski, Michael Vieth, Andreas Mayr, Puya Gharahkhani, Stuart MacGregor, Ines Gockel, Claire Palles, Johannes Schumacher
Summary: This study utilized GWAS, genetic correlation analysis, and polygenic risk modeling to investigate the genetic causes of BE/EA. The findings identified new risk loci and candidate genes associated with BE/EA development. The study also revealed differences in the etiology of BE and EA and demonstrated improved risk prediction models when combining PRS with risk factors. These findings provide valuable insights into the mechanisms underlying BE/EA and improve our understanding of the disease.
Article
Oncology
Shinichi Namba, Yuki Saito, Yasunori Kogure, Tatsuo Masuda, Melissa L. Bondy, Puya Gharahkhani, Ines Gockel, Dominik Heider, Axel Hillmer, Janusz Jankowski, Stuart MacGregor, Carlo Maj, Beatrice Melin, Quinn T. Ostrom, Claire Palles, Johannes Schumacher, Ian Tomlinson, David C. Whiteman, Yukinori Okada, Keisuke Kataoka
Summary: Aggregation of genome-wide common risk variants can measure genetic susceptibility to cancer. Our results suggest that common germline cancer risk variants are associated with earlier cancer onset and lower burden of somatic alterations.
Article
Oncology
Sascha Hoppe, Lydia Meder, Florian Gebauer, Roland T. Ullrich, Thomas Zander, Axel M. Hillmer, Reinhard Buettner, Patrick Plum, Julian Puppe, Wolfram Malter, Alexander Quaas
Summary: This study found that TROP2 is widely expressed in esophageal adenocarcinoma and is associated with the treatment response to sacituzumab govitecan. Tumors with high TROP2 expression were more sensitive to SG, while tumors with negative TROP2 expression were not sensitive.
Correction
Genetics & Heredity
Huipeng Li, Elise T. Courtois, Debarka Sengupta, Yuliana Tan, Kok Hao Chen, Jolene Jie Lin Goh, Say Li Kong, Clarinda Chua, Lim Kiat Hon, Wah Siew Tan, Mark Wong, Paul Jongjoon Choi, Lawrence J. K. Wee, Axel M. Hillmer, Iain Beehuat Tan, Paul Robson, Shyam Prabhakar
Article
Oncology
Martin Thelen, Diandra Keller, Jonas Lehmann, Kerstin Wennhold, Hendrik Weitz, Eugen Bauer, Birgit Gathof, Monika Brueggemann, Michaela Kotrova, Alexander Quaas, Christoph Mallmann, Seung-Hun Chon, Axel M. Hillmer, Christiane Bruns, Michael von Bergwelt-Baildon, Maria Alejandra Garcia-Marquez, Hans Anton Schloesser
Summary: We investigated the role of tumor-associated antigens (TAAs) in esophago-gastric adenocarcinoma (EGA) and found a correlation between TAAs and T-cell abundance and antigen presentation genes. These findings suggest that TAAs could be used as monitoring markers and therapeutic targets in clinical trials.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Oncology
Christoph Arolt, Franziska Hoffmann, Lisa Nachtsheim, Marcel Mayer, Orlando Guntinas-Lichius, Reinhard Buettner, Ferdinand von Eggeling, Jens Peter Klussmann, Axel Hillmer, Alexander Quaas, Sebastian Klein, Philipp Wolber
Summary: This study characterized the extracellular matrix (ECM) landscape of salivary gland carcinomas (SGCs) and identified two fundamental SGC ECM classes. Three biologically distinct protein modules associated with ECM were described, and their differential expression across ECM classes and cell types had a prognostic impact on different SGC types. Putative therapeutic targets for SGC were also identified based on the proteomic expression profile.
JOURNAL OF PATHOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Philipp Mueller, Oscar Velazquez Camacho, Ali M. Yazbeck, Christina Woelwer, Weiwei Zhai, Johannes Schumacher, Dominik Heider, Reinhard Buettner, Alexander Quaas, Axel M. Hillmer
Summary: The loss of the Y chromosome (LoY) is often observed in somatic cells of older men, but is significantly increased in tumor tissue and has a negative impact on prognosis. The underlying causes and effects of LoY are still largely unknown. In this study, genomic and transcriptomic data from 2375 cancer patients of 13 different types were analyzed, and tumors of male patients were categorized based on loss or retention of the Y chromosome. LoY was found to be associated with genomic instability, aneuploidy, and higher mutation burden. Additionally, certain tumor suppressor genes and oncogenes were more frequently mutated or amplified in LoY tumors. Transcriptomic analysis revealed differential expression of genes involved in invasion and tumor suppression. Furthermore, a mutation signature related to smoking was enriched in LoY tumors of head and neck and lung cancer. The incidence rates of LoY were also found to correlate with sex-specific bias in cancer types, suggesting that LoY may contribute to increased cancer risk in males.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Meeting Abstract
Oncology
Heather Scharpenseel, Florian Malchers, Inken Terjung, Axel Hillmer, Sabine Merkelbach-Bruse, Andreas H. Scheel, Janna Siemanowski, Matthias Scheffler, Richard Riedel, Anna Eisert, Sebastian Yves Friedrich Michels, Rieke Nila Fischer, Jan-Philip Weber, Theresa Westphal, Anna Kron, Juliane Sueptitz, Roman K. Thomas, Reinhard Buettner, Juergen Wolf, Lucia Nogova
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Meeting Abstract
Oncology
M. Scheffler, M. Dugan, M. M. Saleh, S. Koleczko, J. Bragelmann, C. Arolt, L. Nogova, R. Riedel, S. Michels, A. Eisert, R. Fischer, H. Scharpenseel, J. P. Weber, A. H. Scheel, S. Merkelbach-Bruse, R. Buttner, F. Lafleur, R. Wild, L. Catanzariti, A. M. Hillmer, J. Wolf
JOURNAL OF THORACIC ONCOLOGY
(2022)
Article
Medicine, Research & Experimental
Neslihan A. Kaya, Jianbin Chen, Hannah Lai, Hechuan Yang, Liang Ma, Xiaodong Liu, Jacob Santiago Alvarez, Jin Liu, Axel M. Hillmer, David Tai, Joe Yeong Poh Sheng, Zheng Hu, Yun Shen Chan, Pierce K. H. Chow, Yuguang Mu, Torsten Wuestefeld, Weiwei Zhai
Summary: This study integrated HCC genomes from different countries and compared the genomic differences between Asians and Europeans. The study identified new candidate driver genes and found higher genomic instability in Asians. Furthermore, survival models were more accurate in predicting patient prognosis in Asians, suggesting a higher potential for precision medicine applications in Asia.