Article
Oncology
Jun Wang, Thomas Kunzke, Verena M. Prade, Jian Shen, Achim Buck, Annette Feuchtinger, Ivonne Haffner, Birgit Luber, Drolaiz H. W. Liu, Rupert Langer, Florian Lordick, Na Sun, Axel Walch
Summary: This study used high mass resolution imaging mass spectrometry to perform spatial metabolomics in 362 patients with gastric cancer. The study identified three tumor-specific subtypes and three stroma-specific subtypes, linked with clinicopathological characteristics and molecular features. The findings suggest that tissue-based spatial metabolomics could provide valuable additional information for existing gastric cancer molecular classification systems.
CLINICAL CANCER RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ruiyang Ge, Roberto Sassi, Lakshmi N. N. Yatham, Sophia Frangou
Summary: This study classified mood and anxiety disorders in youth aged 9-10 years into three subtypes using multimodal neuroimaging data. These subtypes showed differences in brain development and functioning, and were closely associated with family conflict and social adversity.
MOLECULAR PSYCHIATRY
(2023)
Article
Oncology
Jiwei Bai, Jianxin Shi, Yazhuo Zhang, Chuzhong Li, Yujia Xiong, Hela Koka, Difei Wang, Tongwu Zhang, Lei Song, Wen Luo, Bin Zhu, Belynda Hicks, Amy Hutchinson, Erin Kirk, Melissa A. Troester, Mingxuan Li, Yutao Shen, Tianshun Ma, Junmei Wang, Xing Liu, Shuai Wang, Songbai Gui, Mary L. McMaster, Stephen J. Chanock, Dilys M. Parry, Alisa M. Goldstein, Xiaohong R. Yang
Summary: This study identified two molecular subtypes of skull-base chordoma and found that one subtype is associated with somatic mutations and reduced expression in chromatin remodeling genes, while the other subtype is characterized by the upregulation of genes in epithelial-mesenchymal transition and Sonic Hedgehog pathways. Immunohistochemical staining showed that the expression of certain markers is significantly associated with survival outcomes. These findings contribute to a better understanding of chordoma tumorigenesis and provide potential targets for clinical prognostication and treatment.
CLINICAL CANCER RESEARCH
(2023)
Article
Oncology
Gehong Dong, Xuxiang Liu, Lifu Wang, Wenjuan Yin, Alyssa Bouska, Qiang Gong, Kunal Shetty, Lu Chen, Sunandini Sharma, Jibin Zhang, Carmen Lome-Maldonado, Leticia Quintanilla-Martinez, Yuping Li, Joo Y. Song, Wenyan Zhang, Yunfei Shi, Jinhui Wang, Lingbo Kong, Xiwei Wu, Jingwen Wang, Hong-Gang Liu, Lingfei Kong, Wenyong Sun, Weiping Liu, Lili Wang, Timothy W. McKeithan, Javeed Iqbal, Wing C. Chan
Summary: This study provides a comprehensive genomic analysis and clinical study of extra-nodal NK/T-cell lymphoma, nasal type (ENKTCL). It identifies factors associated with overall survival, reveals frequent oncogenic activation of the JAK/STAT3 pathway, and identifies genetic clusters associated with different clinical outcomes. The study also highlights a novel functional cooperation between activating STAT3 mutations and loss of the TSG, PRDM1.
Article
Cell Biology
Cameron J. Cardona, Evan R. Hermann, Kate N. Kouplen, Steven D. Hartson, McKale R. Montgomery
Summary: This study reveals the differences in cellular response to iron restriction among different TP53 mutation subtypes, and suggests that mutant TP53-dependent sensitivities to iron restriction are driven by differences in cellular antioxidant and lipid handling protein expression.
Article
Multidisciplinary Sciences
Karama Asleh, Gian Luca Negri, Sandra E. Spencer Miko, Shane Colborne, Christopher S. Hughes, Xiu Q. Wang, Dongxia Gao, C. Blake Gilks, Stephen K. L. Chia, Torsten O. Nielsen, Gregg B. Morin
Summary: Proteomic analysis of breast cancer surgical specimens identifies distinct subtypes, immune features, and survival outcomes.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Erez Dror, Luca Fagnocchi, Vanessa Weqert, Stefanos Apostle, Brooke Grimaldi, Tim Gruber, Ilaria Panzeri, Steffen Heyne, Kira Daniela Hoeffler, Victor Kreiner, Reagan Ching, Tess Tsai-Hsiu Lu, Ayush Semwal, Ben Johnson, Parijat Senapati, Adelheid Lempradl, Dustin Schones, Axel Imhof, Hui Shen, John Andrew Pospisilik
Summary: This study identifies two major subtypes of pancreatic β cells, βHI and βLO, based on histone mark heterogeneity. These two subtypes show differences in histone modification, gene expression, cell morphology, mitochondrial activity, insulin secretion, and are enriched in individuals with type 2 diabetes. The findings suggest that epigenetic dosage regulates cell subtype specification and has implications for understanding the mechanisms of β cell function and dysfunction.
Article
Gastroenterology & Hepatology
Dmitri Mouradov, Paul Greenfield, Shan Li, Eun-Jung In, Claire Storey, Anuratha Sakthianandeswaren, Peter Georgeson, Daniel D. Buchanan, Robyn L. Ward, Nicholas J. Hawkins, Iain Skinner, Ian T. Jones, Peter Gibbs, Chenkai Ma, Yi Jin Liew, Kim Y. C. Fung, Oliver M. Sieber
Summary: By profiling the tumor and normal mucosa of 423 colorectal cancer patients, it was found that tumors can be classified into three distinct microbiota-based subtypes with different clinicomolecular features and outcomes. These findings provide new insights and a framework for microbiota-based stratification of colorectal cancer.
Article
Multidisciplinary Sciences
Xizhao Chen, Mansheng Li, Songbiao Zhu, Yang Lu, Shuwei Duan, Xu Wang, Yong Wang, Pu Chen, Jie Wu, Di Wu, Zhe Feng, Guangyan Cai, Yunping Zhu, Haiteng Deng, Xiangmei Chen
Summary: We constructed a quantitative proteome atlas for IgA nephropathy (IgAN) and identified three subtypes based on proteomic profiles. We found differences in protein expression, subcellular injury, and extracellular accumulation among the subtypes. The complement mitochondrial extracellular (CME) pathway showed high diagnostic potential in distinguishing IgAN subtypes. Moreover, proteins related to glial cells, endothelial cells, and tubular interstitial fibrosis were highly expressed in certain subtypes and associated with worse prognosis.
Article
Multidisciplinary Sciences
Yafei Jiang, Jinzeng Wang, Mengxiong Sun, Dongqing Zuo, Hongsheng Wang, Jiakang Shen, Wenyan Jiang, Haoran Mu, Xiaojun Ma, Fei Yin, Jun Lin, Chongren Wang, Shuting Yu, Lu Jiang, Gang Lv, Feng Liu, Linghang Xue, Kai Tian, Gangyang Wang, Zifei Zhou, Yu Lv, Zhuoying Wang, Tao Zhang, Jing Xu, Liu Yang, Kewen Zhao, Wei Sun, Yujie Tang, Zhengdong Cai, Shengyue Wang, Yingqi Hua
Summary: In this study, genomic, transcriptomic, and epigenomic data from 121 osteosarcoma patients were comprehensively analyzed, leading to the identification of osteosarcoma subtypes related to treatment outcome. Each subtype has distinct molecular features and clinical prognosis, and potential therapeutic targets were identified. The findings contribute to a deeper understanding of osteosarcoma and may guide future precision treatment strategies.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Ramya Thota, Mingli Yang, Lance Pflieger, Michael J. Schell, Malini Rajan, Thomas B. Davis, Heiman Wang, Angela Presson, Warren Jack Pledger, Timothy J. Yeatman
Summary: The study aims to use APC and TP53 mutations to refine the classification of CRC patients, in order to better identify subpopulations sensitive to cetuximab therapy. Results show that tumors harboring combined AP mutations are predominantly enriched in the CMS2 class and have significantly higher cetuximab sensitivity scores across all CMS classes.These findings suggest that the AP mutation signature may serve as a convenient biomarker to predict sensitivities to EGFR targeted therapies in CRC patients.
Article
Genetics & Heredity
Alba Rodriguez-Meira, Ruggiero Norfo, Sean Wen, Agathe L. Chedeville, Haseeb Rahman, Jennifer O'Sullivan, Guanlin Wang, Eleni Louka, Warren W. Kretzschmar, Aimee Paterson, Charlotte Brierley, Jean-Edouard Martin, Caroline Demeule, Matthew Bashton, Nikolaos Sousos, Daniela Moralli, Lamia Subha Meem, Joana Carrelha, Bishan Wu, Angela Hamblin, Helene Guermouche, Florence Pasquier, Christophe Marzac, Francois Girodon, William Vainchenker, Mark Drummond, Claire Harrison, J. Ross Chapman, Isabelle Plo, Sten Eirik W. Jacobsen, Bethan Psaila, Supat Thongjuea, Ileana Antony-Debre, Adam J. Mead
Summary: This study analyzes hematopoietic stem/progenitor cells from patients with secondary acute myeloid leukemia (sAML) transforming from myeloproliferative neoplasm. They find that chronic inflammation suppresses TP53 wild-type cells while enhancing the fitness advantage of TP53-mutant cells, promoting genetic evolution. These findings will aid in the development of risk-stratification, early detection, and treatment strategies for TP53-mutant leukemia.
Article
Cell Biology
Ujjwal Mukund Mahajan, Ahmed Alnatsha, Qi Li, Bettina Oehrle, Frank-Ulrich Weiss, Matthias Sendler, Marius Distler, Waldemar Uhl, Tim Fahlbusch, Elisabetta Goni, Georg Beyer, Ansgar Chromik, Markus Bahra, Fritz Klein, Christian Pilarsky, Robert Gruetzmann, Markus M. Lerch, Kirsten Lauber, Nicole Christiansen, Beate Kamlage, Ivonne Regel, Julia Mayerle
Summary: The study identified three metabolic PDAC subtypes associated with distinct complex lipid patterns through plasma metabolome analysis, revealing the heterogeneity of PDAC patients and laying the foundation for sphingolipid metabolism research in PDAC.
Article
Clinical Neurology
Peter S. Myers, Joshua J. Jackson, Amber K. Clover, Christina N. Lessov-Schlaggar, Erin R. Foster, Baijayanta Maiti, Joel S. Perlmutter, Meghan C. Campbell
Summary: Parkinson disease clinical subtypes show clear and temporally distinct patterns of symptom progression, particularly in cognitive and psychiatric features. Comprehensive clinical examinations are crucial as the order of symptom presentation impacts clinical prognosis.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2021)
Article
Pathology
Chan Xiang, Chunyu Ji, Yiran Cai, Haohua Teng, Yulu Wang, Ruiying Zhao, Zhanxian Shang, Lianying Guo, Shengnan Chen, Analyn Lizaso, Jing Lin, Haozhe Wang, Bing Li, Zhou Zhang, Jikai Zhao, Jinzhi Wei, Jiaxin Liu, Lei Zhu, Wentao Fang, Yuchen Han
Summary: This study analyzed the clinical, histopathological, and molecular data of Chinese patients with preinvasive to invasive lung adenocarcinoma (LUAD). The findings revealed distinct molecular features between preinvasive lesions and invasive tumors, including specific gene mutations. The study also demonstrated different mutational features for subtypes of oncogene mutations favored by different invasion patterns in adenocarcinomas.