Article
Allergy
Alain Lefevre-Utile, Melissa Saichi, Peter Olah, Marc Delord, Bernhard Homey, Vassili Soumelis
Summary: The study identified 4 endotypes of AD and discovered key gene sets associated with specific biological pathways. There were significant differences in disease severity and S. aureus colonization between different clusters. These findings could potentially provide new insights into personalized treatment strategies.
Article
Allergy
Michael Fricker, Ling Qin, Stephany Sanchez-Ovando, Jodie L. Simpson, Katherine J. Baines, Carlos Riveros, Hayley A. Scott, Lisa G. Wood, Peter AB. Wark, Nazanin Z. Kermani, Kian Fan Chung, Peter G. Gibson
Summary: In this study, RNASeq analysis was conducted on sputum macrophages from NA and NNA patients, revealing transcriptomic differences in NA macrophages. Pathway analysis indicated activation of inflammatory programs in NA macrophages, supporting NA as a specific endotype characterized by transcriptional activation of inflammatory pathways in cell types other than neutrophils.
Article
Critical Care Medicine
Hector R. Wong, Kimberly W. Hart, Christopher J. Lindsell, Timothy E. Sweeney
Summary: This study analyzed publicly available transcriptomic data and found that corticosteroid exposure may be associated with increased mortality among pediatric septic shock endotype A patients.
CRITICAL CARE MEDICINE
(2021)
Article
Critical Care Medicine
Nadir Yehya, Julie C. Fitzgerald, Katie Hayes, Donglan Zhang, Jenny Bush, Natalka Koterba, Fang Chen, Florin Tuluc, David T. Teachey, Fran Balamuth, Simon F. Lacey, Jan Joseph Melenhorst, Scott L. Weiss
Summary: Trajectory-defined sub-phenotypes based on temperature can help categorize critically ill septic children, with hypothermic patients exhibiting lower levels of inflammatory cytokines and chemokines.
Article
Pharmacology & Pharmacy
Yanwei Cheng, Xue Cao, Jiange Zhang, Dong Chen, Juan Zhu, Lijun Xu, Lijie Qin
Summary: In sepsis, the systematic dysregulation of lncRNAs is closely associated with the remodeling of gene expression regulatory network. The lncRNA-mRNA expression network may be utilized to refine biomarker predictions for developing novel therapeutic approaches in sepsis.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Immunology
Jessica M. Povroznik, Halima Akhter, Jordan K. Vance, Madhavi Annamanedi, Sebastian A. Dziadowicz, Lei Wang, Ashley M. Divens, Gangqing Hu, Cory M. Robinson
Summary: Human newborns have increased vulnerability and risk of mortality from infection due to differences in immune responses compared to adults. The immune suppressive cytokine, IL-27, is elevated in neonatal cells and tissues. In a mouse model, deficient IL-27 signaling results in reduced mortality and better control of bacteria with less inflammation. The absence of IL-27 signaling leads to differential gene expression associated with inflammation and cytokine signaling, particularly in macrophages.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jian Ma, Jingjing Guo, Zhiwei Fan, Weiling Zhao, Xiaobo Zhou
Summary: In this study, a tool called CVAM was developed to infer the CNA profile from spatial transcriptome data, which performed better in identifying CNA events compared to existing tools. Co-occurrence and mutual exclusion between CNA events in tumor clusters were also analyzed, providing insights into potential interactions between mutated genes. Additionally, Ripley's K-function was applied for CNA multi-distance spatial pattern analysis to understand the spatial distribution differences of different gene CNA events, enabling more effective treatment measures based on spatial characteristics of genes.
Review
Pathology
Evdoxia Kyriazopoulou, Evangelos J. Giamarellos-Bourboulis
Summary: This review summarizes the progress in biomarker development for classifying the immune response of septic hosts in the past decade, focusing on immunosuppression and hyperinflammation. It discusses biomarkers such as ferritin, sCD163, and IL-18 for diagnosing complications in sepsis, as well as novel approaches like MDSC and specific endotypes. The future target includes developing specific sepsis endotypes for personalized treatment incorporating biomarkers.
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
(2021)
Article
Immunology
Maxime Bodinier, Estelle Peronnet, Karen Brengel-Pesce, Filippo Conti, Thomas Rimmele, Julien Textoris, Christophe Vedrine, Laurence Quemeneur, Andrew D. Griffiths, Lionel K. Tan, Fabienne Venet, Delphine Maucort-Boulch, Guillaume Monneret
Summary: Sepsis, a life-threatening condition caused by a dysregulated host response to infection, often involves dysregulation of the immune system. This study identifies four distinctive trajectories of monocyte HLA-DR expression in septic patients during the first week, highlighting the potential for early risk stratification using mHLA-DR measurements on the initial and third day. This research sheds light on the heterogeneity of immune response following sepsis onset, providing insights for potential immunomodulatory treatments to improve outcomes.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Nancy Liliana Tateosian, Maria Paula Morelli, Joaquin Miguel Pellegrini, Veronica Edith Garcia
Summary: Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), has resulted in the death of almost one billion people in the past 200 years. TB remains a significant global health concern, ranking among the top thirteen leading causes of death worldwide. TB infection in humans can manifest in different stages with varying symptoms, immune responses, and pathology profiles. Active Mtb infection can lead to the development of diverse immune endotypes in TB patients due to individual immunological profiles influenced by various factors. Understanding the factors involved in shaping the immunological status of TB patients during active Mtb infection can contribute to the development of Host Directed Therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Dijoia B. Darden, Gabriela L. Ghita, Zhongkai Wang, Julie A. Stortz, Maria-Cecilia Lopez, Michael C. Cox, Russell B. Hawkins, Jaimar C. Rincon, Lauren S. Kelly, Brittany P. Fenner, Tezcan Ozrazgat-Baslanti, Christiaan Leeuwenburgh, Azra Bihorac, Tyler J. Loftus, Frederick A. Moore, Scott C. Brakenridge, Henry Baker, Rhonda Bacher, Alicia M. Mohr, Lyle L. Moldawer, Philip A. Efron
Summary: The study found that sepsis survivors have unique blood leukocyte transcriptomes in late sepsis, indicating ongoing immune dyscrasia which could help understand the prognosis of sepsis patients with CCI.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Plant Sciences
Lingtao Su, Chunhui Xu, Shuai Zeng, Li Su, Trupti Joshi, Gary Stacey, Dong Xu
Summary: This study analyzed large-scale soybean transcriptome samples and identified tissue-specific highly expressed genes using an adversarial deconfounding autoencoder model and an unsupervised autoencoder model. Tissue-specific gene regulatory networks and differential correlation networks were constructed to identify key transcription factors and hub genes in each tissue. The results were validated through literature and gene enrichment analysis, confirming the presence of tissue-specific genes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Chunman Zuo, Luonan Chen
Summary: The study introduces a single-cell multimodal variational autoencoder model that effectively integrates transcriptomic and chromatin accessibility information, accurately representing the multilayer profiles of cells and demonstrating good capabilities in dissecting cellular heterogeneity, denoising and imputing data, as well as constructing associations between multilayer omics data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Cell Biology
Fabiano Pinheiro da Silva, Andre Nicolau Aquime Goncalves, Amaro Nunes Duarte-Neto, Thomaz Luescher Dias, Hermes Vieira Barbeiro, Cristiane Naffah Souza Breda, Leandro Carvalho Dantas Breda, Niels Olsen Saraiva Camara, Helder I. Nakaya
Summary: Septic shock is a life-threatening condition characterized by a robust immune inflammatory response to infection. The lungs and colon are the most affected organs, and gene activation dominates in septic shock. However, inhibitory signals are also detected, particularly in the lungs. The disease is highly heterogeneous, both between individuals and within different tissues of the same patient. Tissue specificity, particularly in respiratory electron transport and metabolic functions, is a hallmark of sepsis. Additionally, evident signals of accelerated ageing are found in sepsis population.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2023)
Article
Medicine, Research & Experimental
Ren-qi Yao, Zhi-xuan Li, Li-xue Wang, Yu-xuan Li, Li-yu Zheng, Ning Dong, Yao Wu, Zhao-fan Xia, Timothy R. Billiar, Chao Ren, Yong-ming Yao
Summary: In this study, the heterogeneity of immune cell subsets during sepsis was analyzed using single-cell RNA sequencing. A unique subcluster of dendritic cells called "mregDC" was identified and its presence and function in the disease were confirmed. Furthermore, the study found that the mregDC program was initiated through specific intracellular signaling pathways within 24 hours of septic challenge.
Article
Health Care Sciences & Services
Zhongheng Zhang, Xiaodian Zhang, Shenhong Gu, Xiaoqing Xu, Wei Jiang, Chuanzhu Lv, Shaojiang Zheng
Summary: This article illustrates how to apply dynamic programming in a clinical scenario of Sepsis resuscitation, optimizing treatment policies to adapt to patients' different conditions, and finding the best treatment strategy based on current states and previous conditions.
ANNALS OF PALLIATIVE MEDICINE
(2021)
Article
Immunology
Lin Chen, Senjun Jin, Min Yang, Chunmei Gui, Yingpu Yuan, Guangtao Dong, Weizhong Zeng, Jing Zeng, Guoxin Hu, Lujun Qiao, Jinhua Wang, Yonglin Xi, Jian Sun, Nan Wang, Minmin Wang, Lifeng Xing, Yi Yang, Yan Teng, Junxia Hou, Qiaojie Bi, Huabo Cai, Gensheng Zhang, Yucai Hong, Zhongheng Zhang
Summary: This study systematically explored the potential mechanisms of the immunomodulatory effects of Ulinastatin (UTI) in sepsis by integrating bulk and single cell RNA-seq data. The results indicate that UTI regulates neutrophil activity to achieve immunomodulation and leads to significant expansion of Myeloid-derived suppressor cells (MDSC) in sepsis. Further analysis revealed signaling pathways that may be involved in the immunomodulatory effects of UTI.
FRONTIERS IN IMMUNOLOGY
(2022)
Editorial Material
Medicine, General & Internal
Zhongheng Zhang, Rahul Kashyap, Nan Liu, Longxiang Su, Qinghe Meng
FRONTIERS IN MEDICINE
(2022)
Article
Public, Environmental & Occupational Health
Ping Xu, Lin Chen, Yuanfang Zhu, Shuai Yu, Rangui Chen, Wenbin Huang, Fuli Wu, Zhongheng Zhang
Summary: This study establishes a clinical database for patients with infections, incorporating high-granularity data from various sources. The database can be utilized for a variety of clinical studies, filling a gap in this area for Chinese adult patients.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Multidisciplinary Sciences
Lin Chen, Kun Chen, Yucai Hong, Lifeng Xing, Jianjun Zhang, Kai Zhang, Zhongheng Zhang
Summary: This study for the first time described isoform switching in sepsis, including differential expression of isoform fractions between patients with and without sepsis and survivors and non-survivors. The study identified the biological consequences of isoform switching, such as changes in protein domains and intron retention. Many genes showed significant isoform switching even without differences in gene expression.
SCIENTIFIC REPORTS
(2022)
Article
Medicine, General & Internal
Tsung-Ming Yang, Lin Chen, Chieh-Mo Lin, Hui-Ling Lin, Tien-Pei Fang, Huiqing Ge, Huabo Cai, Yucai Hong, Zhongheng Zhang
Summary: This study identified four subclusters of PMV patients based on trajectories of RSBI and developed a machine learning model to predict the cluster membership using baseline variables. The results showed that these clusters could be easily predicted with baseline clinical variables.
FRONTIERS IN MEDICINE
(2022)
Article
Health Care Sciences & Services
Zhongheng Zhang, Lin Chen, Ping Xu, Qing Wang, Jianjun Zhang, Kun Chen, Casey M. Clements, Leo Anthony Celi, Vitaly Herasevich, Yucai Hong
Summary: This study demonstrates the beneficial effect of using an automated alerting system in the management of sepsis, especially for patients in the emergency department and ward. Machine learning-based prediction methods are more effective in reducing mortality compared to rule-based methods.
NPJ DIGITAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Yucai Hong, Lin Chen, Jian Sun, Lifeng Xing, Yi Yang, Xiaohong Jin, Huabo Cai, Lianlian Dong, Liping Zhou, Zhongheng Zhang
Summary: This study used single-cell RNA sequencing to analyze nearly 300,000 human peripheral blood cells and identified four subtypes of neutrophils, with Neu1 being significantly associated with septic shock and showing high predictive ability. The findings provide a crucial framework for studying neutrophil-related mechanisms, predicting biomarkers, and potential therapeutic targets for septic shock.
Letter
Medicine, General & Internal
Weimin Zhang, Zhongheng Zhang, Maofeng Wang, Xinling Pan, Xuandong Jiang
ANNALS OF INTERNAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Senjun Jin, Lin Chen, Kun Chen, Chaozhou Hu, Sheng'an Hu, Zhongheng Zhang
Summary: The medical specialty of critical care provides emergency medical care to patients with life-threatening complications and injuries, generating a large amount of data. In-depth mining of this data could provide insights into underlying diseases and healthcare practices. Establishing an openly accessible critical care database is crucial for research purposes in China, considering its large patient population and potential for generating large healthcare databases.
Editorial Material
Medicine, General & Internal
Zhongheng Zhang, Rahul Kashyap, Longxiang Su, Qinghe Meng
FRONTIERS IN MEDICINE
(2022)
Article
Critical Care Medicine
Zhongheng Zhang, Lin Chen, Xiaoli Liu, Jie Yang, Jiajie Huang, Qiling Yang, Qichao Hu, Ketao Jin, Leo Anthony Celi, Yucai Hong
Summary: Cluster analysis of sepsis patients across different cohorts showed modest reproducibility. Sepsis heterogeneity is better characterized through continuous disease axes that coexist to varying degrees within the same individual, rather than mutually exclusive subtypes.
INTENSIVE CARE MEDICINE
(2023)
Article
Critical Care Medicine
Zhongheng Zhang, Lin Chen, Huiheng Liu, Yujing Sun, Pengfei Shui, Jian Gao, Decong Wang, Huilin Jiang, Yanling Li, Kun Chen, Yucai Hong
Summary: This study classified sepsis-induced acute kidney injury and analyzed the changes in transcriptional profiles. The SVM model developed using gene signature showed better performance in predicting renal function trajectories.
Correction
Critical Care Medicine
Lu Ke, Jiajia Lin, Gordon S. Doig, Arthur R. H. van Zanten, Yang Wang, Juan Xing, Zhongheng Zhang, Tao Chen, Lixin Zhou, Dongpo Jiang, Qindong Shi, Jiandong Lin, Jun Liu, Aibin Cheng, Yafeng Liang, Peiyang Gao, Junli Sun, Wenming Liu, Zhenyu Yang, Rumin Zhang, Wei Xing, An Zhang, Zhigang Zhou, Tingfa Zhou, Yang Liu, Fei Tong, Qiuhui Wang, Aijun Pan, Xiaobo Huang, Chuming Fan, Weihua Lu, Dongwu Shi, Lei Wang, Wei Li, Liming Gu, Yingguang Xie, Rongqing Sun, Feng Guo, Lin Han, Lihua Zhou, Xiangde Zheng, Feng Shan, Jianbo Liu, Yuhang Ai, Yan Qu, Liandi Li, Hailing Li, Zhiguo Pan, Donglin Xu, Zhiqiang Zou, Yan Gao, Chunli Yang, Qiuye Kou, Xijing Zhang, Jinglan Wu, Chuanyun Qian, Weixing Zhang, Minjie Zhang, Yuan Zong, Bingyu Qin, Fusen Zhang, Zhe Zhai, Yun Sun, Ping Chang, Bo Yu, Min Yu, Shiying Yuan, Yijun Deng, Liyun Zhao, Bin Zang, Yuanfei Li, Fachun Zhou, Xiaomei Chen, Min Shao, Weidong Wu, Ming Wu, Zhaohui Zhang, Yimin Li, Qiang Guo, Zhiyong Wang, Yuanqi Gong, Yunlin Song, Kejian Qian, Yongjian Feng, Baocai Fu, Xueyan Liu, Zhiping Li, Chuanyong Gong, Cheng Sun, Jian Yu, Zhongzhi Tang, Linxi Huang, Biao Ma, Zhijie He, Qingshan Zhou, Rongguo Yu, Zhihui Tong, Weiqin Li
Article
Critical Care Medicine
Lu Ke, Jiajia Lin, Gordon S. Doig, Arthur R. H. van Zanten, Yang Wang, Juan Xing, Zhongheng Zhang, Tao Chen, Lixin Zhou, Dongpo Jiang, Qindong Shi, Jiandong Lin, Jun Liu, Aibin Cheng, Yafeng Liang, Peiyang Gao, Junli Sun, Wenming Liu, Zhenyu Yang, Rumin Zhang, Wei Xing, An Zhang, Zhigang Zhou, Tingfa Zhou, Yang Liu, Fei Tong, Qiuhui Wang, Aijun Pan, Xiaobo Huang, Chuming Fan, Weihua Lu, Dongwu Shi, Lei Wang, Wei Li, Liming Gu, Yingguang Xie, Rongqing Sun, Feng Guo, Lin Han, Lihua Zhou, Xiangde Zheng, Feng Shan, Jianbo Liu, Yuhang Ai, Yan Qu, Liandi Li, Hailing Li, Zhiguo Pan, Donglin Xu, Zhiqiang Zou, Yan Gao, Chunli Yang, Qiuye Kou, Xijing Zhang, Jinglan Wu, Chuanyun Qian, Weixing Zhang, Minjie Zhang, Yuan Zong, Bingyu Qin, Fusen Zhang, Zhe Zhai, Yun Sun, Ping Chang, Bo Yu, Min Yu, Shiying Yuan, Yijun Deng, Liyun Zhao, Bin Zang, Yuanfei Li, Fachun Zhou, Xiaomei Chen, Min Shao, Weidong Wu, Ming Wu, Zhaohui Zhang, Yimin Li, Qiang Guo, Zhiyong Wang, Yuanqi Gong, Yunlin Song, Kejian Qian, Yongjian Feng, Baocai Fu, Xueyan Liu, Zhiping Li, Chuanyong Gong, Cheng Sun, Jian Yu, Zhongzhi Tang, Linxi Huang, Biao Ma, Zhijie He, Qingshan Zhou, Rongguo Yu, Zhihui Tong, Weiqin Li
Summary: This large-scale multicenter trial found that active implementation of an evidence-based feeding guideline reduced the time to commencement of enteral nutrition and overall parenteral nutrition use, but did not result in a reduction in mortality among critically ill patients.