Article
Biology
Ibrahim Ahmed, Shen-Hsi Yang, Samuel Ogden, Wei Zhang, Yaoyong Li, Andrew D. Sharrocks, William C. Hahn
Summary: This article utilizes RNA-seq data and open chromatin maps to identify potential enhancer RNAs and associated enhancer regions in oesophageal adenocarcinoma. It discovers OAC-specific enhancers and uncovers new cellular pathways operative in OAC. The study also demonstrates the clinical utility of the dataset for disease stage identification and patient prognosis.
Article
Hematology
Tasneem Khanam, Sarah Sandmann, Jochen Seggewiss, Charlotte Ruether, Martin Zimmermann, Allison B. Norvil, Christoph Bartenhagen, Gerrit Randau, Stephanie Mueller, Heidi Herbrueggen, Per Hoffmann, Stefan Herms, Lanying Wei, Marius Woeste, Christian Wuensch, Humaira Gowher, Ilske Oschlies, Wolfram Klapper, Wilhelm Woessmann, Martin Dugas, Birgit Burkhardt
Summary: T-cell lymphoblastic lymphoma (T-LBL) is a rare and heterogeneous malignancy with NOTCH1 and KMT2D identified as prognostic markers. These findings offer new insights into the pathogenesis of T-LBL.
Article
Biochemistry & Molecular Biology
Alba Machado-Lopez, Roberto Alonso, Victor Lago, Jorge Jimenez-Almazan, Marta Garcia, Javier Monleon, Susana Lopez, Francisco Barcelo, Amparo Torroba, Sebastian Ortiz, Santiago Domingo, Carlos Simon, Aymara Mas
Summary: The absence of standardized molecular profiling to differentiate uterine leiomyosarcomas from leiomyomas is a current diagnostic challenge. In this study, artificial intelligence was used to search for a differential molecular signature for these myometrial tumors. Differential exome and transcriptome-wide research revealed higher tumor mutation burden in leiomyosarcomas compared to leiomyomas, as well as alterations in specific copy number variant regions and differentially expressed genes. A machine learning approach based on differentially expressed genes was developed to differentiate both tumor types with high sensitivity and specificity. These findings provide a novel molecular signature for the diagnosis of leiomyoma and leiomyosarcoma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Siddhartha Devarakonda, Yize Li, Fernanda Martins Rodrigues, Sumithra Sankararaman, Humam Kadara, Chandra Goparaju, Irena Lanc, Kymberlie Pepin, Saiama N. Waqar, Daniel Morgensztern, Jeffrey Ward, Ashiq Masood, Robert Fulton, Lucinda Fulton, Michael A. Gillette, Shankha Satpathy, Steven A. Carr, Ignacio Wistuba, Harvey Pass, Richard K. Wilson, Li Ding, Ramaswamy Govindan
Summary: The study analyzed genomic and transcriptomic data from never-smoker lung adenocarcinoma samples, finding a high prevalence of clinically actionable driver alterations and potential role of germline variants in DNA repair genes and passive exposure to cigarette smoke in the pathogenesis of a subset of never-smoker LUADs. The findings also highlight the importance of obtaining biopsies with adequate cellularity for clinical genomic testing in these patients.
JOURNAL OF CLINICAL ONCOLOGY
(2021)
Article
Hematology
Qian Wang, Wen-zhi Cai, Qin-rong Wang, Ming-qing Zhu, Ling-zhi Yan, Yan Yu, Xie-bing Bao, Hong-jie Shen, Hong Yao, Jun-dan Xie, Tong-tong Zhang, Ling Zhang, Xiao-yu Xu, Zhe Shan, Hong Liu, Jian-nong Cen, Dan-dan Liu, Jin-lan Pan, Da-ru Lu, Jia Chen, Yang Xu, Ri Zhang, Ying Wang, Sheng-li Xue, Miao Miao, Yue Han, Xiao-wen Tang, Hui-ying Qiu, Ai-ning Sun, Jin-yan Huang, Hai-ping Dai, De-pei Wu, Su-ning Chen
Summary: Mixed phenotype acute leukemia (MPAL) is a rare and heterogeneous subtype of leukemia. In this study, the genetic features of 176 MPAL patients were explored using integrated genomic and transcriptomic approaches, leading to the identification of eight molecular subgroups. Furthermore, single-cell RNA sequencing analysis revealed distinct gene expression signatures in different subgroups. These findings contribute to the precise diagnosis and treatment of MPAL.
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Article
Oncology
Kangle Kong, Shan Hu, Jiaqi Yue, Ziheng Yang, Salma K. Jabbour, Yu Deng, Bo Zhao, Fan Li
Summary: This study performed comprehensive genomic profiling of lymph node metastasis in small cell lung cancer (SCLC) using whole-exome sequencing and RNA sequencing. The study identified differentially expressed genes and significantly mutated genes associated with lymph node metastasis, which are important for early detection and reliable therapeutic targets.
TRANSLATIONAL LUNG CANCER RESEARCH
(2023)
Article
Immunology
Binfeng Liu, Chenbei Li, Chengyao Feng, Hua Wang, Haixia Zhang, Chao Tu, Shasha He, Zhihong Li
Summary: Given the poor prognosis of soft tissue sarcoma (STS), this study aimed to explore the association of angiogenesis-related genes (ARGs) with STS and establish a novel angiogenesis-related signature (ARSig). The ARSig was validated as a promising prognostic factor for STS and was found to be relevant to the tumor immune microenvironment, tumor mutational burden (TMB), and therapeutic response. In vitro experiments further confirmed the dysregulation of signature ARGs and their role in the malignant progression of STS cells. This study provides a new strategy for prognostic assessment and personalized treatment of STS.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biology
Fang-Jie Hu, Ying-Jie Li, Li Zhang, Deng-Bo Ji, Xin-Zhi Liu, Yong-Jiu Chen, Lin Wang, Ai-Wen Wu
Summary: A single-cell RNA sequencing analysis reveals molecular differences between mucinous adenocarcinoma and classical adenocarcinoma, providing insight into these two subtypes of colorectal cancer. Mucinous adenocarcinoma, a unique histological subtype, responds poorly to chemoradiotherapy and its prognosis compared to classical adenocarcinoma is controversial. The study findings show that mucinous adenocarcinoma cells exhibit goblet cell-like properties and express higher levels of goblet cell markers than classical adenocarcinoma cells. TFF3 and possibly RPS4X play essential roles in the transcriptional regulation of these molecules and the development of the mucinous adenocarcinoma mucus phenotype.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ziyang Liu, Anqiang Wang, Yingying Pu, Zhongwu Li, Ruidong Xue, Chong Zhang, Xiao Xiang, E. Jian-Yu, Zhaode Bu, Fan Bai, Jiafu Ji
Summary: Hepatoid adenocarcinoma of the stomach (HAS) is a rare subtype of gastric cancer with high mortality rate. Research suggests that HAS may originate from pluripotent precursor cells and has high stemness and methionine cycle activity. Genes involved in the methionine cycle, such as MAT2A and AHCY, are potential targets for HAS treatment.
Article
Oncology
Qiong Shi, Lin Liu, Jianru Chen, Weigang Zhang, Weinan Guo, Xiao Wang, Huina Wang, Sen Guo, Qiao Yue, Jingjing Ma, Yu Liu, Guannan Zhu, Tao Zhao, Jianhong Zhao, Ying Liu, Tianwen Gao, Chunying Li
Summary: This study conducted genomic research on acral melanoma in Asian populations, identifying mutated genes associated with the disease and analyzing its pathogenesis and therapeutic targets. Additionally, it reconstructed the mutational processes of the samples and identified early mutational events. This study provides a foundation for the development of personalized strategies for treating acral melanoma in Asian populations.
CLINICAL CANCER RESEARCH
(2022)
Article
Oncology
FeiYan Ai, Wenhao Wang, Shaojun Liu, Decai Zhang, Zhenyu Yang, Fen Liu
Summary: This study aimed to develop a gene signature for predicting the prognosis of colon adenocarcinoma (COAD). Through analyzing the proteomic and genomic data, 86 genes related to recurrence were identified, and an 8-gene signature was developed to separate patients into high- and low-risk groups. The validation and analysis showed that these gene signatures might serve as effective prognostic predictors and promising therapeutic targets for COAD patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Hui Li, Linyan Chen, Hao Zeng, Qimeng Liao, Jianrui Ji, Xuelei Ma
Summary: The study found that histopathological image features have the ability to predict survival in COAD patients. An integrative prognostic model based on histopathological images and genomic features could improve prognosis prediction in COAD, potentially assisting clinical decision-making in the future.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Manuel Cabeza-Segura, Valentina Gambardella, Francisco Gimeno-Valiente, Juan Antonio Carbonell-Asins, Lorena Alarcon-Molero, Arturo Gonzalez-Vilanova, Sheila Zuniga-Trejos, Pilar Rentero-Garrido, Rosana Villagrasa, Mireia Gil, Ana Dura, Paula Richart, Noelia Alonso, Marisol Huerta, Susana Rosello, Desamparados Roda, Noelia Tarazona, Carolina Martinez-Ciarpaglini, Josefa Castillo, Andres Cervantes, Tania Fleitas
Summary: This study investigates the immune microenvironment features related to sensitivity or resistance to immune checkpoint inhibitors (CPIs) in advanced gastro-oesophageal cancer (GEA). Through transcriptomic analysis, the researchers identified a cluster of tumors with high gene signatures related to immunomodulatory pathways and immunotherapy response, suggesting that these tumors may benefit the most from CPIs. The findings were validated in an external population, highlighting the potential of using transcriptomic classification to improve precision immunotherapy for GEA patients.
BRITISH JOURNAL OF CANCER
(2022)
Article
Microbiology
Alejandro Palomo, Arnaud Dechesne, Anders G. Pedersen, Barth F. Smets
Summary: This study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira.
Article
Medicine, General & Internal
Abdessamad El Kaoutari, Nicolas A. Fraunhoffer, Luc Camoin, Yolande Berthois, Odile Gayet, Julie Roques, Martin Bigonnet, Claire Bongrain, Joseph Ciccolini, Juan L. Iovanna, Nelson J. Dusetti, Philippe Soubeyran
Summary: Through specific proteomic tools and bioinformatics analysis, we established the ubiquitin dependent proteome of 60 PDAC, identifying 38 ubiquitination site profiles correlated with tumor phenotype and having prognostic capabilities. These findings have potential application in predicting chemotherapy response and personalized treatment in clinical settings.
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
Colin Y. C. Lee, Adriaan Olivier, Judith Honing, Anne-Marie Lydon, Susan Richardson, Maria O'Donovan, Marc Tischkowitz, Rebecca C. Fitzgerald, Massimiliano di Pietro
Summary: Hereditary diffuse gastric cancer, caused by CDH1 gene mutations, is characterized by early-onset signet ring cell carcinoma. Prophylactic total gastrectomy is the recommended treatment. This study assessed different sampling strategies for detecting signet ring cell carcinoma and identified criteria for characterizing endoscopic lesions in hereditary diffuse gastric cancer.
Article
Oncology
Judith Honing, Rebecca C. Fitzgerald
Summary: Barrett's esophagus is a precancerous condition that can progress to esophageal adenocarcinoma. Surveillance is needed to detect progression, but current methods are limited. This commentary proposes incorporating new risk factors and tools, such as nonendoscopic triage and commercial biomarker panels, into clinical practice for better risk stratification.
CANCER PREVENTION RESEARCH
(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)
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
Biochemistry & Molecular Biology
Arianne C. Richard, Claire Y. Ma, John C. Marioni, Gillian M. Griffiths
Summary: This study investigates the impact of transcriptomic changes on the killing ability of effector cytotoxic T lymphocytes (CTLs). The results show that while transcription is required for the expression of cytokines/chemokines and transcriptional machinery, it is relatively robust to transcription blockade for cytotoxic protein expression and cytolytic activity. Additionally, the study reveals a cell-intrinsic transcriptional requirement for infiltration.
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
Genetics & Heredity
Emma Dann, Ana-Maria Cujba, Amanda J. Oliver, Kerstin B. Meyer, Sarah A. Teichmann, John C. Marioni
Summary: Joint analysis of diseased tissues and healthy reference data can reveal altered cell states. Using a reference atlas for latent space learning followed by differential analysis against controls improves identification of disease-associated cells, especially with multiple perturbed cell types. Reducing control sample numbers does not increase false discovery rates.
Article
Multidisciplinary Sciences
Ha-Linh Nguyen, Tatjana Geukens, Marion Maetens, Samuel Aparicio, Ayse Bassez, Ake Borg, Jane Brock, Annegien Broeks, Carlos Caldas, Fatima Cardoso, Maxim De Schepper, Mauro Delorenzi, Caroline A. Drukker, Annuska M. Glas, Andrew R. Green, Edoardo Isnaldi, Jorunn Eyfjoro, Hazem Khout, Stian Knappskog, Savitri Krishnamurthy, Sunil R. Lakhani, Anita Langerod, John W. M. Martens, Amy E. McCart Reed, Leigh Murphy, Stefan Naulaerts, Serena Nik-Zainal, Ines Nevelsteen, Patrick Neven, Martine Piccart, Coralie Poncet, Kevin Punie, Colin Purdie, Emad A. Rakha, Andrea Richardson, Emiel Rutgers, Anne Vincent-Salomon, Peter T. Simpson, Marjanka K. Schmidt, Christos Sotiriou, Paul N. Span, Kiat Tee Benita Tan, Alastair Thompson, Stefania Tommasi, Karen Van Baelen, Marc Van de Vijver, Steven Van Laere, Laura van't Veer, Giuseppe Viale, Alain Viari, Hanne Vos, Anke T. Witteveen, Hans Wildiers, Giuseppe Floris, Abhishek D. Garg, Ann Smeets, Diether Lambrechts, Elia Biganzoli, Francois Richard, Christine Desmedt
Summary: Obesity is associated with an increased risk of developing breast cancer and worse prognosis in breast cancer patients. This study investigates the biological differences in untreated primary breast cancer according to patients' body mass index (BMI). The study finds several genomic alterations that are differentially prevalent in overweight or obese patients compared to lean patients. It also reveals an elevated and unresolved inflammation of the breast cancer tumor microenvironment associated with obesity. The findings suggest that patient adiposity may play a significant role in the heterogeneity of breast cancer and should be considered for tailored treatment.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Kieran Foley, David Shorthouse, Eric Rahrmann, Lizhe Zhuang, Ginny Devonshire, Rebecca C. OCCAMS Consortium, Rebecca C. Fitzgerald, Benjamin A. Hall
Summary: Metastasis in oesophageal adenocarcinoma (OAC) is a crucial factor affecting survival. Radiological staging is commonly used to assess metastases, but its accuracy is limited. This study analyzed lymph node metastases and identified new roles of genes SMAD4 and KCNQ3 in metastasis. The findings suggest that both genes could serve as novel biomarkers for metastatic risk and offer potential new targets for drug treatment.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2024)