Article
Oncology
Apexa Modi, Gonzalo Lopez, Karina L. Conkrite, Chun Su, Tsz Ching Leung, Sathvik Ramanan, Elisabetta Manduchi, Matthew E. Johnson, Daphne Cheung, Samantha Gadd, Jinghui Zhang, Malcolm A. Smith, Jaime M. Guidry Auvil, Soheil Meshinchi, Elizabeth J. Perlman, Stephen P. Hunger, John M. Maris, Andrew D. Wells, Struan F. A. Grant, Sharon J. Diskin
Summary: This study curated and analyzed RNA sequencing data for 1,044 pediatric leukemia and solid tumors, revealing stable expression of lncRNAs in six pediatric cancers and their association with key processes such as proliferation, metabolism, and DNA damage. By integrating various analyses, several lncRNAs were prioritized for experimental validation.
Article
Genetics & Heredity
Angela Verdoni, Jie Hu, Urvashi Surti, Melanie Babcock, Elizabeth Sheehan, Michele Clemens, Sarah Drewes, Leslie Walsh, Rebecca Clark, Sunita Katari, Joe Sanfilippo, Devereux N. Saller, Aleksandar Rajkovic, Svetlana A. Yatsenko
Summary: Patients with reciprocal balanced translocations (RBT) are at risk for recurrent pregnancy losses (RPL), affected children, and infertility. Factors such as chromosome-specific factors, female gender, age, and history of RPL influence pregnancy and in vitro fertilization success in RBT patients. Chromosomal microarray analysis of products of conception (POC) is necessary for accurate and timely diagnosis of patients with adverse reproductive outcomes.
GENETICS IN MEDICINE
(2021)
Article
Multidisciplinary Sciences
Gita A. Pathak, Kritika Singh, Tyne W. Miller-Fleming, Frank Wendt, Nava Ehsan, Kangcheng Hou, Ruth Johnson, Zeyun Lu, Shyamalika Gopalan, Loic Yengo, Pejman Mohammadi, Bogdan Pasaniuc, Renato Polimanti, Lea K. Davis, Nicholas Mancuso
Summary: This study integrates genome-wide association study data with mRNA expression, splicing, and protein levels to identify genes and pathways related to COVID-19 hospitalization, highlighting putative causal genes impacting disease severity and symptomology.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Enrico Berrino, Laura Annaratone, Sara Erika Bellomo, Giulio Ferrero, Amedeo Gagliardi, Alberto Bragoni, Dora Grassini, Simonetta Guarrera, Caterina Parlato, Laura Casorzo, Mara Panero, Ivana Sarotto, Silvia Giordano, Matteo Cereda, Filippo Montemurro, Riccardo Ponzone, Nicola Crosetto, Alessio Naccarati, Anna Sapino, Caterina Marchio
Summary: HLBCs have distinct genomic features compared to HER2-positive and HER2-negative BCs, with differences across IHC classes. HLBC-2E category has the most distinctive features, while HLBC-1 is nearly identical to HER2-negative disease. Further studies are needed to determine whether the four genomic-driver classes of the LAURA classification have prognostic and/or predictive implications.
Article
Obstetrics & Gynecology
Elisa Spataro, Adalgisa Cordisco, Carlo Luchi, Gilda Rosaria Filardi, Giulia Masini, Lucia Pasquini
Summary: The objective of this study was to determine the residual risk of morbidity-related outcome in fetuses with nuchal translucency (NT) of 3.5 mm or more after normal genetic testing and mid-trimester anomaly scan. The results showed that the residual risk of morbidity-related outcome was 24.64% for NT 3.5-4.5 mm, 25% for NT 4.5-6 mm, and 76.47% for NT more than 6 mm. After a normal RASopathy testing and mid-trimester anomaly scan, the residual risks decreased to 7.14%, 8.69%, and 33.3% in the three groups, respectively.
INTERNATIONAL JOURNAL OF GYNECOLOGY & OBSTETRICS
(2023)
Article
Biology
Guangyue Li, Gongbo Su, Yunxuan Wang, Wenmeng Wang, Jinming Shi, Dangdang Li, Guangchao Sui
Summary: G-quadruplexes in promoters play a regulatory role in DNA replication and gene transcription. They exhibit selective constraint and contribute to active gene expression by enriching gene activation histone marks, chromatin remodeler and transcription factor binding sites.
COMMUNICATIONS BIOLOGY
(2023)
Article
Oncology
Binjie Cao, Haijian Sun, Zhehao Fan, Muhammad Babar Khawar, Liangliang Cai, Shiyi Yu, Zhengyan Liang, Dan Lv, Ning Wang, Caili Bi, Haibo Sun
Summary: This study explored the transcriptome and immunological features of patients with Ewing sarcoma (ES) using publicly available microarray data. The analysis identified differentially expressed genes (DEGs) related to bone and muscle functioning, cellular metabolism pathways, and immune infiltration patterns in ES. Furthermore, several identified DEGs were associated with survival outcomes, and silencing of specific up-regulated genes inhibited ES cell proliferation and colony formation.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Oncology
Yoann Pradat, Julien Viot, Andrey A. Yurchenko, Konstantin Gunbin, Luigi Cerbone, Marc Deloger, Guillaume Grisay, Loic Verlingue, Veronique Scott, Ismael Padioleau, Leonardo Panunzi, Stefan Michiels, Antoine Hollebecque, Gerome Jules-Clement, Laura Mezquita, Antoine Laine, Yohann Loriot, Benjamin Besse, Luc Friboulet, Fabrice Andre, Paul-Henry Cournede, Daniel Gautheret, Sergey I. Nikolaev
Summary: Metastatic relapse after treatment is the main cause of cancer mortality, with unknown resistance mechanisms for most treatments. To address this issue, a pan-cancer cohort (META-PRISM) of 1,031 refractory metastatic tumors was analyzed. META-PRISM tumors, especially prostate, bladder, and pancreatic types, exhibited the most transformed genomes compared to untreated tumors. Standard-of-care resistance biomarkers were identified in only 9.6% of META-PRISM tumors, indicating a lack of clinical validation for resistance mechanisms. However, investigational and hypothetical resistance mechanisms were enriched in treated patients, supporting their potential role in treatment resistance. Furthermore, molecular markers improved 6-month survival prediction, particularly for advanced breast cancer patients. The META-PRISM cohort proves valuable for studying resistance mechanisms and conducting predictive analysis in cancer.
Article
Multidisciplinary Sciences
Liam McAllan, Damir Baranasic, Sergio Villicana, Scarlett Brown, Weihua Zhang, Benjamin Lehne, Marco Adamo, Andrew Jenkinson, Mohamed Elkalaawy, Borzoueh Mohammadi, Majid Hashemi, Nadia Fernandes, Nathalie Lambie, Richard Williams, Colette Christiansen, Youwen Yang, Liudmila Zudina, Vasiliki Lagou, Sili Tan, Juan Castillo-Fernandez, James W. D. King, Richie Soong, Paul Elliott, James Scott, Inga Prokopenko, Ines Cebola, Marie Loh, Boris Lenhard, Rachel L. Batterham, Jordana T. Bell, John C. Chambers, Jaspal S. Kooner, William R. Scott
Summary: This study reveals that DNA methylation variations are associated with human obesity and may play a causal role in disease pathogenesis, impacting adipocyte functions through regulating gene transcription.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Yizhou Huang, Jie Luo, Yue Zhang, Tao Zhang, Xiangwei Fei, Liqing Chen, Yingfan Zhu, Songyue Li, Caiyun Zhou, Kaihong Xu, Yunlong Ma, Jun Lin, Jianhong Zhou
Summary: Using integrative analysis of large-scale genome-wide association studies and blood-based eQTL dataset, we identified 14 genes associated with the risk of endometriosis. Functional enrichment analysis revealed their involvement in metabolic and immune-related pathways. Differential gene expression analysis confirmed abnormal expression levels of several genes in peripheral blood samples and ectopic endometrium. Functional experiments further validated MKNK1 and TOP3A as novel risk-related genes for endometriosis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Genetics & Heredity
Ida C. Bay Lund, Naja Becher, Jesper Graakjaer, Dorte L. Lildballe, Niels Uldbjerg, Pauline Bogaard, Astrid Petersen, Else M. Vestergaard, Ida Vogel
Summary: This study compared mosaicism in prenatal chorionic villus samples with corresponding postpartum placental samples and found that some aberrations detected prenatally were confirmed in the postpartum placenta. It indicates that chromosomal aneuploidies constitute a significant proportion in placental mosaicism.
PRENATAL DIAGNOSIS
(2021)
Article
Multidisciplinary Sciences
Carles A. Boix, Benjamin T. James, Yongjin P. Park, Wouter Meuleman, Manolis Kellis
Summary: Annotating the molecular basis of human disease using EpiMap, a compendium of 10,000 epigenomic maps, has revealed the importance of dense, rich, high-resolution epigenomic annotations for investigating complex traits. The study used EpiMap to annotate genetic loci associated with traits and predict trait-relevant tissues and candidate target genes, showing extensive pleiotropy in top-scoring loci.
Article
Oncology
Sheetal Parida, Sumit Siddharth, Yuqing Xia, Dipali Sharma
Summary: Racial disparities in breast cancer are evident, with Black women having a lower risk of incidence but the highest mortality. This study investigates the genomic and metagenomic features of breast tumors from Asian, Black and white women, revealing distinctive microbial compositions and tumor immune microenvironment-related traits. The findings provide a comprehensive understanding of racial disparities in breast cancer and suggest potential race-specific microbial biomarkers.
Article
Multidisciplinary Sciences
Ziad Bakouny, David A. Braun, Sachet A. Shukla, Wenting Pan, Xin Gao, Yue Hou, Abdallah Flaifel, Stephen Tang, Alice Bosma-Moody, Meng Xiao He, Natalie Vokes, Jackson Nyman, Wanling Xie, Amin H. Nassar, Sarah Abou Alaiwi, Ronan Flippot, Gabrielle Bouchard, John A. Steinharter, Pier Vitale Nuzzo, Miriam Ficial, Miriam Sant'Angelo, Juliet Forman, Jacob E. Berchuck, Shaan Dudani, Kevin Bi, Jihye Park, Sabrina Camp, Maura Sticco-Ivins, Laure Hirsch, Sylvan C. Baca, Megan Wind-Rotolo, Petra Ross-Macdonald, Maxine Sun, Gwo-Shu Mary Lee, Steven L. Chang, Xiao X. Wei, Bradley A. McGregor, Lauren C. Harshman, Giannicola Genovese, Leigh Ellis, Mark Pomerantz, Michelle S. Hirsch, Matthew L. Freedman, Michael B. Atkins, Catherine J. Wu, Thai H. Ho, W. Marston Linehan, David F. McDermott, Daniel Y. C. Heng, Srinivas R. Viswanathan, Sabina Signoretti, Eliezer M. Van Allen, Toni K. Choueiri
Summary: Sarcomatoid and rhabdoid renal cell carcinomas are highly aggressive tumors that exhibit high responsiveness to immune checkpoint inhibitors. Molecular characterization in this study revealed specific alterations and an immune-inflamed phenotype in these tumors.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Donatella Conconi, Serena Redaelli, Andrea Alberto Lissoni, Chiara Cilibrasi, Patrizia Perego, Eugenio Gautiero, Elena Sala, Mariachiara Paderno, Leda Dalpra, Fabio Landoni, Marialuisa Lavitrano, Gaia Roversi, Angela Bentivegna
Summary: The study analyzed the genomic and epigenomic profiles of uterine smooth muscle tumors, finding similarities between STUMPs and LMSs. Some genes with potential prognostic value, previously not associated with STUMP, were identified. Methylation data showed promise, especially in samples with divergent profiles, and Gene Ontology analysis highlighted cancer genes that may serve as prognostic markers in the future.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Jos B. Poell, Leon J. Wils, Arjen Brink, Ralf Dietrich, Christine Krieg, Eunike Velleuer, Ilkay Evren, Elisabeth R. Brouns, Jan G. de Visscher, Elisabeth Bloemena, Bauke Ylstra, Ruud H. Brakenhoff
Summary: This study developed a noninvasive genetic assay to detect genetically altered fields in the oral cavity. The assay demonstrated high accuracy and predicted the development of oral squamous cell carcinoma in high-risk individuals. This method can be used for cancer screening in high-risk populations and to map the extent of lesions beyond what is visible.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Hematology
Jakoba J. Eertink, Gerben J. C. Zwezerijnen, Sanne E. Wiegers, Simone Pieplenbosch, Martine E. D. Chamuleau, Pieternella J. Lugtenburg, Daphne de Jong, Bauke Ylstra, Matias Mendeville, Ulrich Duehrsen, Christine Hanoun, Andreas Huettmann, Julia Richter, Wolfram Klapper, Yvonne W. S. Jauw, Otto S. Hoekstra, Henrica C. W. de Vet, Ronald Boellaard, Josee M. Zijlstra
Summary: This study investigated whether combining clinical, molecular genotype, and radiomics features can improve the outcome prediction of patients with aggressive B-cell lymphoma. The results showed that adding radiomics features improved the model performance and positive predictive values, aiding in the identification of poor prognosis patients.
Article
Oncology
Sanne ten Hoorn, Linda Mol, Dirkje W. Sommeijer, Lisanne Nijman, Tom van den Bosch, Tim R. de Back, Bauke Ylstra, Erik van Dijk, Carel J. M. van Noesel, Roy J. Reinten, Iris D. Nagtegaal, Miriam Koopman, Cornelis J. A. Punt, Louis Vermeulen
Summary: We evaluated the potential efficacy of adding anti-EGFR therapy to anti-VEGF therapy in a subgroup of patients with metastatic colorectal cancer. The retrospective study (CAIRO2 trial, n = 736) showed no benefit of anti-EGFR addition within the subgroup, but an overall survival increase of 6.5 months compared to the original trial.
CLINICAL COLORECTAL CANCER
(2023)
Article
Oncology
G. Tjitske Los-de Vries, Phylicia Stathi, Ryanne Rutkens, Nathalie J. Hijmering, Jeroen A. C. W. Luijks, Patricia J. T. A. Groenen, Daphne de Jong, Bauke Ylstra, Margaretha G. M. Roemer
Summary: Primary and relapsed LBCL-IP have a common set of genetic alterations that support survival and proliferation, providing insight into the disease progression.
Article
Gastroenterology & Hepatology
Maarten te Groen, Lauranne A. A. P. Derikx, Lisa van Lierop, Bauke Ylstra, Frank Hoentjen, Iris D. Nagtegaal, Femke Simmer
Summary: The presence of previous colorectal neoplasia is the most significant indicator for the development of pouch neoplasia in inflammatory bowel disease. However, the underlying mechanism remains unknown. Our study found evidence of clonality between colorectal and pouch neoplasia in 30% of patients, suggesting that most pouch neoplasia develops independently from prior colorectal lesions.
INFLAMMATORY BOWEL DISEASES
(2023)
Article
Oncology
Leon Emanuel Schnoeller, Daniel Piehlmaier, Peter Weber, Nikko Brix, Daniel Felix Fleischmann, Alexander Edward Nieto, Martin Selmansberger, Theresa Heider, Julia Hess, Maximilian Niyazi, Claus Belka, Kirsten Lauber, Kristian Unger, Michael Orth
Summary: Despite previous efforts, glioblastoma remains a highly devastating disease with poor prognosis. In this study, we integrated data from multiple molecular levels to identify therapy resistance and potential targets for treatment. Our findings suggest new candidates for combination therapy and provide proof-of-concept for multi-level data integration. The generated dataset offers valuable resources for researchers in the field of glioblastoma therapy resistance.
RADIATION ONCOLOGY
(2023)
Article
Oncology
Sebastian Burkart, Christopher Weusthof, Karam Khorani, Sonja Steen, Fabian Stoegbauer, Kristian Unger, Julia Hess, Horst Zitzelsberger, Claus Belka, Ina Kurth, Jochen Hess
Summary: In this study, a new subgroup of UCHL1-related cancers was identified across multiple solid tumor entities and characterized by increased genomic instability and vulnerability to DNA-damaging treatment, with a favorable prognosis after radiotherapy. A novel classification model was established for accurate identification of UCHL1-related cancers, providing a basis for further research.
Article
Oncology
Anna Lena van Gulik, Ellen Sluydts, Liesbet Vervoort, Mark Kockx, Pim Kortman, Bauke Ylstra, Stephen P. Finn, Lukas Bubendorf, Idris Bahce, Daoud Sie, Teodora Radonic, Birgit Lissenberg-Witte, Erik Thunnissen
Summary: This study investigates the impact of cell size and ploidy on FISH results. The results show that in liver cell nuclei, the number of FISH signals increases with nuclear size and section thickness. In non-small cell lung cancer cases, tumor cells with higher ploidy levels and nuclear size have an increased chance of single signals. In addition, no rearrangements were found in lung cancer samples with borderline ALK FISH results, proving a false positive result.
TRANSLATIONAL LUNG CANCER RESEARCH
(2023)
Letter
Hematology
Wendy B. C. Stevens, G. Tjitske Los-de Vries, Carole Langois-Jacques, Andrew J. Clear, Phylicia Stathi, Birgitta Sander, Andreas Rosenwald, Maria Calaminici, Eva Hoster, Wolfgang Hiddemann, Philippe Gaulard, Gilles Salles, Wolfram Klapper, Luc Xerri, Catherine Burton, Reuben M. Tooze, Alexandra G. Smith, Christian Buske, David W. Scott, Yasodha Natkunam, Ranjana Advani, Laurie H. Sehn, John Raemaekers, John Gribben, Sandra Lockmer, Eva Kimby, Marie Jose Kersten, Delphine Maucort-Boulch, Bauke Ylstra, Erik van Dijk, Daphne de Jong
Article
Hematology
Patricia Johansson, Stefan Alig, Julia Richter, Christine Hanoun, Jan Rekowski, Jan Duerig, Bauke Ylstra, Daphne de Jong, Wolfram Klapper, Ash A. Alizadeh, Ulrich Duehrsen, Andreas Huettmann
Summary: In DLBCL, a positive interim PET scan predicts treatment failure, and combining it with the presence of an IgM gammopathy can improve prediction. The combination of interim PET and IgM gammopathy can dichotomize the population into high-risk and low-risk groups with significantly different outcomes. Only the interim PET result and IgM gammopathy status were significantly associated with outcome, making them important factors in risk-adapted treatment strategies.
ANNALS OF HEMATOLOGY
(2023)
Editorial Material
Hematology
Bauke Ylstra, Daphne de Jong
Summary: In this study, the authors demonstrate the usefulness of a dark zone signature (DZsig) for diagnosing aggressive B-cell lymphoma with DLBCL morphology, and highlight its strong prognostic value.
Article
Pathology
Tanya T. D. Soeratram, Hedde D. Biesma, Jacqueline M. P. Egthuijsen, Elma Meershoek-Klein Kranenbarg, Henk H. Hartgrink, Cornelis J. H. van de Velde, Aart Mookhoek, Erik van Dijk, Yongsoo Kim, Bauke Ylstra, Hanneke W. M. van Laarhoven, Nicole C. T. van Grieken
Summary: Tumor-infiltrating lymphocytes are important for the survival of gastric cancer patients, and T-cell densities in different regions of the tumor can serve as prognostic markers. CD8OIM and FOXP3TC are identified as key factors for survival, and the combination of their densities can stratify patients into distinct subgroups with different prognosis. These immune subgroups are independent predictors for cancer-specific survival in resectable gastric cancer.
Article
Multidisciplinary Sciences
Margaretha G. M. Roemer, Tim van de Brug, Erik Bosch, Daniella Berry, Nathalie Hijmering, Phylicia Stathi, Karin Weijers, Jeannette Doorduijn, Jacoline Bromberg, Mark van de Wiel, Bauke Ylstra, Daphne de Jong, Yongsoo Kim
Summary: In order to understand the clinical relevance of the tumor microenvironment (TME), it is important to study the interactions between malignant and non-malignant cells in clinical samples. Researchers have developed a computational framework to comprehensively analyze the spatial context of the TME, including close and long-distance interactions between different cell types. This framework was applied to imaging data from 88 primary central nervous system lymphomas, revealing significant prognostic subgroups mainly determined by the spatial context. The results highlight the importance of spatial context in predicting patient survival, particularly in relation to macrophage infiltration near specific cell types.
Letter
Hematology
Esther E. E. Drees, Yvonne W. S. Jauw, Erik van Dijk, Sven Borchmann, Sandra A. W. M. Verkuijlen, Phylicia Stathi, Nils J. Groenewegen, Nathalie J. Hijmering, Daniella R. A. I. Berry, Eric J. Meershoek, Danielle Hoogmoed, Anne Kwakman, Tessa J. Molenaar, Dirk M. Pegtel, Bauke Ylstra, Daphne de Jong, Josee M. Zijlstra, Margaretha G. M. Roemer
Article
Hematology
G. Tjitske Los-deVries, Wendy B. C. Stevens, Erik van Dijk, Carole Langois-Jacques, Andrew J. Clear, Phylicia Stathi, Margaretha G. M. Roemer, Matias Mendeville, Nathalie J. Hijmering, Birgitta Sander, Andreas Rosenwald, Maria Calaminici, Eva Hoster, Wolfgang Hiddemann, Philippe Gaulard, Gilles Salles, Heike Horn, Wolfram Klapper, Luc Xerri, Catherine Burton, Reuben M. Tooze, Alexandra G. Smith, Christian Buske, David W. Scott, Yasodha Natkunam, Ranjana Advani, Laurie H. Sehn, John Raemaekers, John Gribben, Eva Kimby, Marie Jose Kersten, Delphine Maucort-Boulch, Bauke Ylstra, Daphne de Jong
Summary: The genomic and immune microenvironmental features of follicular lymphoma (FL) differ between stage I and stage III/IV, with distinct differences in cell populations and mutations. This exploratory study provides new insights into the heterogeneity of FL and its underlying oncogenic pathways.
