Article
Immunology
Tao Wang, Tianye Li, Baiqing Li, Jiahui Zhao, Zhi Li, Mingyi Sun, Yan Li, Yanjiao Zhao, Shidi Zhao, Weiguang He, Xiao Guo, Rongjing Ge, Lian Wang, Dushan Ding, Saisai Liu, Simin Min, Xiaonan Zhang
Summary: Breast cancer has different immune subtypes with diverse characteristics and clinical prognostications. Patients with a high immunotherapeutic benefit score (ITBscore) have better response to immunotherapy, while those with a low ITBscore have poor immunotherapeutic efficacy. This study provides insights into the immune phenotypes in the tumor microenvironment and guides precision immuno-oncology and immunotherapy strategies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Xinting Yang, Jun Yan, Yu Xue, Qing Sun, Yun Zhang, Ru Guo, Chaohong Wang, Xuelian Li, Qingtao Liang, Hangyu Wu, Chong Wang, Xinlei Liao, Sibo Long, Maike Zheng, Rongrong Wei, Haoran Zhang, Yi Liu, Nanying Che, Laurence Don Wai Luu, Junhua Pan, Guirong Wang, Yi Wang
Summary: Using single-cell RNA sequencing, researchers found that tuberculosis pleural effusion (TPE) displayed significant differences in cell types compared to other types of effusion (TSPE and MPE), and these differences were associated with disease type. CD4 lymphocytes in TPE favored a Th1 and Th17 response, and immune exhaustion in NK cells was a prominent feature. Myeloid cells in TPE exhibited stronger functional capacity for phagocytosis, antigen presentation, and IFN-γ response. Additionally, macrophages drove the systemic elevation of inflammatory response genes and pro-inflammatory cytokines in TPE patients.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Genetics & Heredity
Arash Nabbi, Pengbo Beck, Alberto Delaidelli, Derek A. Oldridge, Sumedha Sudhaman, Kelsey Zhu, S. Y. Cindy Yang, David T. Mulder, Jeffrey P. Bruce, Joseph N. Paulson, Pichai Raman, Yuankun Zhu, Adam C. Resnick, Poul H. Sorensen, Martin Sill, Sebastian Brabetz, Sander Lambo, David Malkin, Pascal D. Johann, Marcel Kool, David T. W. Jones, Stefan M. Pfister, Natalie Jaeger, Trevor J. Pugh
Summary: We identified four immune clusters within paediatric solid tumours, namely Paediatric Inflamed (10%), Myeloid Predominant (30%), Immune Neutral (43%), and Immune Desert (17%). Our findings suggest that personalized immunogenomic profiling is necessary to guide the selection of immunotherapeutic strategies.
Article
Multidisciplinary Sciences
Shinichi Mizuno, Rui Yamaguchi, Takanori Hasegawa, Shuto Hayashi, Masashi Fujita, Fan Zhang, Youngil Koh, Su-Yeon Lee, Sung-Soo Yoon, Eigo Shimizu, Mitsuhiro Komura, Akihiro Fujimoto, Momoko Nagai, Mamoru Kato, Han Liang, Satoru Miyano, Zemin Zhang, Hidewaki Nakagawa, Seiya Imoto
Summary: The study analyzed 2834 whole genome and RNA sequencing datasets across 31 distinct tumor types, investigating the contribution of selective copy number changes in immune-related genes to immune escape, and developed an immunoediting history index for evaluating each tumor's immunoediting history.
SCIENTIFIC REPORTS
(2021)
Article
Critical Care Medicine
Kezhong Chen, Jing Bai, Alexandre Reuben, Heng Zhao, Guannan Kang, Chunliu Zhang, Qingyi Qi, Yaping Xu, Shawna Hubert, Lianpeng Chang, Yanfang Guan, Lin Feng, Kai Zhang, Kaitai Zhang, Xin Yi, Xuefeng Xia, Shujun Cheng, Fan Yang, Jianjun Zhang, Jun Wang
Summary: Through studying the molecular and immune characteristics of GGO-associated lung nodules, it was found that compared to solid nodules, GGO-associated lung cancers have a lower tumor mutation burden, less active immune environment, lower T-cell expansion, and less frequent HLA loss of heterozygosity, which may explain their indolent clinical course.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Gianlucca G. Nicastro, A. Maxwell Burroughs, Lakshminarayan M. Iyer, L. Aravind
Summary: Recent findings have revealed immune effectors that target nucleotides and the cellular energy currency-free nucleotides. Comparative genomics and sequence-structure analysis have identified several distinct effector domains, which are widely present in prokaryotic immune systems. This study establishes nucleotide-degrading effectors as an emerging immune paradigm and traces their origins back to homologous domains in housekeeping systems.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Peng Qin, Hongwei Lu, Huilong Du, Hao Wang, Weilan Chen, Zhuo Chen, Qiang He, Shujun Ou, Hongyu Zhang, Xuanzhao Li, Xiuxiu Li, Yan Li, Yi Liao, Qiang Gao, Bin Tu, Hua Yuan, Bingtian Ma, Yuping Wang, Yangwen Qian, Shijun Fan, Weitao Li, Jing Wang, Min He, Junjie Yin, Ting Li, Ning Jiang, Xuewei Chen, Chengzhi Liang, Shigui Li
Summary: The study assembled high-quality genomes of genetically diverse rice accessions, discovering a large number of structural variations and gene copy number variations. By using a graph-based genome, the research explored the impact of these variations on rice domestication and environmental adaptation.
Article
Immunology
Xiaowu Bai, Weixin Liu, Hongxia Chen, Tao Zuo, Xiaojian Wu
Summary: By analyzing RNA-seq data from patients with IBD (including CD and UC) and healthy individuals, this study revealed increased numbers of immune cells in different intestinal regions and disease-specific immune features in CD and UC. These findings provide important insights into the pathogenesis of IBD and serve as a valuable resource for future targeted studies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Zhao Zhang, Zhijie Zhu, Xincheng Liu, Zhenzhou Mi, Huiren Tao, Hongbin Fan
Summary: This study explores the significance of anoikis-related genes (ANRGs) in osteosarcoma and their impact on the immune landscape. It establishes a prognostic signature based on ANRGs and develops a model for predicting survival probability in osteosarcoma patients. The study also identifies chemotherapeutic agents suitable for different subtypes of osteosarcoma.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Yannick Audet-Delage, Julie St-Pierre
Summary: The study reveals how nutrient availability in the metastatic niche of breast cancer cells shapes their growth signaling, suggesting potential avenues for therapeutic interventions.
Article
Medicine, Research & Experimental
Xin Chen, Tianqi Liu, Jianqi Wu, Chen Zhu, Gefei Guan, Cunyi Zou, Qing Guo, Xiaolin Ren, Chen Li, Peng Cheng, Wen Cheng, Anhua Wu
Summary: This study extracted genetic and epigenetic features of TP53mut tumors and identified five different subtypes of TP53mut patients. These subtypes have distinct characteristics in terms of genomic alterations, clinical relevance, microenvironment dysregulation, and potential therapeutics. Among the subtypes, COCA3 was identified as having the worst prognosis, while olaparib showed promising therapeutic efficacy.
Article
Immunology
Leire Pedrosa, Carles Foguet, Helena Oliveres, Ivan Archilla, Marta Garcia de Herreros, Adela Rodriguez, Antonio Postigo, Daniel Benitez-Ribas, Jordi Camps, Miriam Cuatrecasas, Antoni Castells, Aleix Prat, Timothy M. Thomson, Joan Maurel, Marta Cascante
Summary: In this study, researchers developed an immune-metabolic signature suitable for personalized immune checkpoint inhibitor therapies. The signature classified tumors into three distinct immune-metabolic clusters, providing a new predictive tool for patient selection for specific immune-metabolic therapeutic approaches.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Xiaoyu Yang, Bo Song, Jie Cui, Lina Wang, Shuoshuo Wang, Linlin Luo, Lei Gao, Beixin Mo, Yu Yu, Lin Liu
Summary: This study reveals that translational reprogramming plays an important role in rice's response to salt stress, with the salt-tolerant cultivar SR86 adopting a more flexible translational adaptive strategy compared to the salt-sensitive cultivar NB. The differences in translational dynamics under salt stress between NB and SR86 may be due to their varying levels of ribosome stalling.
Article
Multidisciplinary Sciences
Evan A. Boyle, Winston R. Becker, Hua B. Bai, Janice S. Chen, Jennifer A. Doudna, William J. Greenleaf
Summary: Through high-throughput experiments, researchers observed significant variations in binding and cleavage efficacy, as well as specificity, of Cas9 ribonucleoproteins (RNPs) across different guide RNAs. Canonical guide sequences often exhibit unusually high specificity, and the sequence context surrounding the target modulates the Cas9 on-rate. Furthermore, Cas9 RNPs may trap targets in non-productive states that contribute to proofreading capability.
Article
Oncology
Neal Akhave, Jiexin Zhang, Erin Bayley, Meredith Frank, Shin-Heng Chiou, Carmen Behrens, Runzhe Chen, Xin Hu, Edwin Roger Parra, Won-Chul Lee, Stephen Swisher, Luisa Solis, Annikka Weissferdt, Cesar Moran, Neda Kalhor, Jianhua Zhang, Paul Scheet, Ara A. Vaporciyan, Boris Sepesi, Don L. Gibbons, John V. Heymach, Jack J. Lee, Ignacio I. Wistuba, P. Andrew Futreal, Jianjun Zhang, Junya Fujimoto, Alexandre Reuben
Summary: In this study, the relationship between growth patterns of early-stage lung adenocarcinoma (LUAD) and the tumor immune microenvironment was investigated. The poorly differentiated tumors were found to have a distinct immunogenic tumor microenvironment, which predicts a response to immune agents, including checkpoint inhibitors, in early-stage lung adenocarcinoma. These findings are important for the design of immunotherapy studies in LUAD.
Review
Oncology
Felix Sahm, Sebastian Brandner, Luca Bertero, David Capper, Pim J. French, Dominique Figarella-Branger, Felice Giangaspero, Christine Haberler, Monika E. Hegi, Bjarne W. Kristensen, Kathreena M. Kurian, Matthias Preusser, Bastiaan B. J. Tops, Martin van den Bent, Wolfgang Wick, Guido Reifenberger, Pieter Wesseling
Summary: In the 5th edition of the WHO CNS tumor classification, molecular characteristics have become important diagnostic criteria for many CNS tumor types. This guideline focuses on the methods used for diagnosing gliomas, glioneuronal, and neuronal tumors using informative molecular markers. Various molecular methods are discussed, including next-generation sequencing, methylation profiling, and immunohistochemistry. The guideline also covers the analysis of MGMT promoter methylation status, and provides an overview of the advantages, limitations, and requirements of different assays. The importance of molecular diagnostic testing in neuro-oncology is emphasized, along with discussions on clinical relevance, accessibility, cost, and ethical aspects.
Article
Oncology
Vladimir Wischnewski, Roeltje R. Maas, Paola Guerrero Aruffo, Klara Soukup, Giovanni Galletti, Mara Kornete, Sabine Galland, Nadine Fournier, Johanna Lilja, Pratyaksha Wirapati, Joao Lourenco, Alice Scarpa, Roy T. Daniel, Andreas F. Hottinger, Jean-Philippe Brouland, Agnese Losurdo, Emanuele Voulaz, Marco Alloisio, Monika E. Hegi, Enrico Lugli, Johanna A. Joyce
Summary: The authors used T cell profiling in brain tumor samples to understand the biology and therapeutic relevance of the brain tumor microenvironment. They found a tissue-specific conflict between immune suppression and immune activation in brain tumors, which can inform stratification for immunotherapy. Their analysis revealed differences in T cell biology between individuals, with a subgroup of brain metastases showing accumulation of potentially tumor-reactive T cells.
Article
Biochemistry & Molecular Biology
Roeltje R. Maas, Klara Soukup, Nadine Fournier, Matteo Massara, Sabine Galland, Mara Kornete, Vladimir Wischnewski, Joao Lourenco, Davide Croci, Angel F. Alvarez-Prado, Damien N. Marie, Johanna Lilja, Rachel Marcone, Gabriel F. Calvo, Rui Santalla Mendez, Pauline Aubel, Leire Bejarano, Pratyaksha Wirapati, Ivan Ballesteros, Andres Hidalgo, Andreas F. Hottinger, Jean-Philippe Brouland, Roy T. Daniel, Monika E. Hegi, Johanna A. Joyce
Summary: This study reveals that tumor-associated neutrophils (TANs) in tumor tissues differ significantly from blood neutrophils, and have immune-suppressive and pro-angiogenic capabilities. TANs exhibit distinct inflammatory features in brain metastasis and glioma, and together with tumor-associated myeloid cells, form a critical myeloid niche regulating overall immune suppression in human brain tumors.
Article
Oncology
Thi Tham Nguyen, Premnath Rajakannu, Minh Dieu Thanh Pham, Leo Weman, Alexander Jucht, Michelle C. Buri, Kristof Van Dommelen, Monika E. Hegi
Summary: Glioblastoma, a highly malignant brain tumor, exhibits characteristic epigenetic alterations, including the recurrent silencing of the HTATIP2 gene, which affects the nuclear localization of the DNA repair enzyme MPG. The reduced nuclear localization of MPG leads to decreased repair of treatment-induced DNA lesions, contributing to treatment resistance in glioblastoma.
MOLECULAR ONCOLOGY
(2023)
Article
Oncology
Federico Saltarin, Adrian Wegmuller, Leire Bejarano, Ece Su Ildiz, Pascale Zwicky, Andrej Vianin, Florentin Spadin, Klara Soukup, Vladimir Wischnewski, Britta Engelhardt, Urban Deutsch, Ines J. Marques, Martin Frenz, Johanna A. Joyce, Ruth Lyck
Summary: In this study, the researchers investigated the molecular and cellular mechanisms underlying melanoma cell extravasation across the blood-brain barrier (BBB) to prevent brain metastasis formation. They found that melanoma cells exclusively use the junctional pathway to intercalate into the BBB and that proteases play a crucial role in this process. The compromised BBB barrier properties were shown to facilitate melanoma cell extravasation both in vitro and in vivo. Preserving BBB integrity is an important measure to limit the formation of melanoma-brain metastasis.
Article
Oncology
Jun Wang, Na Sun, Thomas Kunzke, Jian Shen, Philipp Zens, Verena M. Prade, Annette Feuchtinger, Sabina Berezowska, Axel Walch
Summary: Molecular subtyping of lung squamous cell carcinoma (LUSC) has been performed, but stratification based on tissue metabolomics is lacking. In this study, different tumor and stroma subtypes with distinct metabolite patterns were identified in LUSC patients. The subtypes were associated with specific immunological features and metabolic pathways, and may contribute to personalized therapy.
NPJ PRECISION ONCOLOGY
(2023)
Article
Pathology
Andrew Janowczyk, Inti Zlobec, Cedric Walker, Sabina Berezowska, Viola Huschauer, Marianne Tinguely, Joel Kupferschmid, Thomas Mallet, Doron Merkler, Mario Kreutzfeldt, Radivoje Gasic, Tilman T. Rau, Luca Mazzucchelli, Isgard Eyberg, Gieri Cathomas, Kirsten D. Mertz, Viktor H. Koelzer, Davide Soldini, Wolfram Jochum, Matthias Roessle, Maurice Henkel, Rainer Grobholz
Summary: The integration of digital pathology (DP) into clinical diagnostic workflows is being emphasized as new hardware and software become available. To facilitate DP adoption, the Swiss Digital Pathology Consortium (SDiPath) organized a Delphi process and generated a series of recommendations for DP integration. Through the collaboration of four working groups, the process produced 83 consensus statements, providing up-to-date resources and best practices to ensure safe and efficient DP usage for national and international hospitals, researchers, and device manufacturers.
Review
Cell Biology
Sabina Berezowska, Marie Maillard, Mark Keyter, Bettina Bisig
Summary: Squamous cell carcinoma (SCC) is a type of lung cancer that can be divided into keratinising, non-keratinising, and basaloid SCC. Histomorphology alone can be used to diagnose keratinising SCC, but immunohistochemical analyses should be used for non-keratinising and basaloid tumors to confirm the diagnosis and exclude other possibilities. In cases where the morphology is ambiguous, a diagnosis of SCC can be made based on squamous immunophenotype. Most SCCs are associated with smoking and have specific molecular characteristics, but there are rare cases in younger and non-smoking patients. Lymphoepithelial carcinoma (LEC) is a poorly differentiated SCC with lymphoplasmacytic infiltrate and often associated with Epstein-Barr virus (EBV). This article describes the morphological and molecular characteristics of SCC and LEC and discusses the important differential diagnoses.
