Article
Cell Biology
Piniel Alphayo Kambey, Wen-Ya Liu, Jiao Wu, Bakwatanisa Bosco, Iqra Nadeem, Kouminin Kanwore, Dian-Shuai Gao
Summary: By using liquid chromatography coupled with tandem mass spectrometry, it was found that deficiency in nuclear receptor-related factor 1 (Nurr1) is associated with Parkinson's disease. Knocking down Nurr1 resulted in the high expression of 231 genes in dopaminergic neurons, with 14 genes linked to the Parkinson's disease pathway. Furthermore, Nurr1 deficiency led to an increase in Cd74 expression, causing the destruction of dopaminergic neurons and suggesting a potential therapeutic target for Parkinson's disease.
NEURAL REGENERATION RESEARCH
(2023)
Article
Multidisciplinary Sciences
Adib Miraki Feriz, Arezou Khosrojerdi, Mohammad Lotfollahi, Neusha Shamsaki, Mohammad GhasemiGol, Edris HosseiniGol, Mohammad Fereidouni, Mohammad Hossein Rohban, Ahmad Reza Sebzari, Samira Saghafi, Patrizia Leone, Nicola Silvestris, Hossein Safarpour, Vito Racanelli
Summary: Prostate cancer (PCa) is a solid malignancy with worse prognosis when there is a higher infiltration of T cells in the tumor microenvironment (TME). In this study, the focus was on dendritic cells (DCs), which are professional antigen-presenting cells. Tumor cells were found to stimulate the migration of immature DCs to the tumor site by inducing inflammatory chemokines. Various signaling pathways were up-regulated in DCs at the tumor location, while certain molecules on the surface of DCs decreased. The study also explored the communication between DCs and macrophages in the TME, identifying molecular pairs involved in the migration of DCs and disruption of their antigen-presenting function.
Article
Biochemistry & Molecular Biology
Mohamed Nabil Bakr, Haruko Takahashi, Yutaka Kikuchi
Summary: By using gene expression signature classification and Cox regression analyses, a prognosis-related gene signature for melanoma was established and validated in multiple datasets, showing potential for predicting prognosis in melanoma patients.
Article
Plant Sciences
Sampath Kumar Banoth, Harsh Chauhan
Summary: The growth and development of barley meristems are regulated by complex networks involving hormones, photoperiod, nutrient availability, and genetic makeup. The double ridge stage of meristems during the transition from vegetative to inflorescence meristem plays a significant role in spikelet and seed development and final crop yield. Early meristem development allows plants to complete their ontogeny faster and escape the negative effects of terminal heat stress. This study identified tolerant and sensitive cultivars to terminal heat stress conditions and explored the transcriptional reprogramming and developmental differences between them.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Endocrinology & Metabolism
Yourae Hong, Hyun Jung Kim, Seongyeol Park, Shinae Yi, Mi Ae Lim, Seong Eun Lee, Jae Won Chang, Ho-Ryun Won, Je-Ryong Kim, Hyemi Ko, Seon-Young Kim, Seon-Kyu Kim, Jong-Lyul Park, In-Sun Chu, Jin Man Kim, Kun Ho Kim, Jeong Ho Lee, Young Seok Ju, Minho Shong, Bon Seok Koo, Woong-Yang Park, Yea Eun Kang
Summary: This study used single-cell RNA sequencing to identify specific changes in gene expression in human thyroid cells during aging. It found that a subset of cells showed functional decline and increased expression of certain genes, suggesting their increased vulnerability during aging. This research provides evidence for understanding the changes in the human thyroid gland during aging.
Article
Biochemistry & Molecular Biology
Samantha Lapehn, Jonas A. Gustafson, Andrew E. Timms, Michael L. Cunningham, Alison G. Paquette
Summary: This study aimed to compare gene expression differences between patients with different phenotypes of single-suture craniosynostosis and controls, using primary calvarial cell lines. The results showed differentially expressed genes associated with each type of craniosynostosis, as well as differences between males and females. Pathway analysis also identified relevant signaling pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Urology & Nephrology
Jia Fu, Zeguo Sun, Xuan Wang, Tuo Zhang, Weijie Yuan, Fadi Salem, Samuel Mon-Wei Yu, Weijia Zhang, Kyung Lee, John Cijiang He
Summary: This article provides a comprehensive analysis of macrophage transcriptomic profiles in early DKD, highlighting the dynamic macrophage phenotypes in disease progression.
KIDNEY INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Xirong Zhang, Yini Li, Xiaopan Chen, Bihui Jin, Chongyi Shu, Wanmao Ni, Yinshen Jiang, Jing Zhang, Lijia Ma, Jing Shu
Summary: Infertility is a global social and medical problem, and thin endometrium (TE) poses a great challenge to infertility treatment. This study used single-cell RNA sequencing to construct a transcriptomic atlas and identified cellular and molecular heterogeneity in TE. Differential expressed genes (DEGs) were found to affect cell-type ratio and impair endometrial receptivity in TE.
Article
Immunology
M. Elizabeth Deerhake, Estefany Y. Reyes, Shengjie Xu-Vanpala, Mari L. Shinohara
Summary: Neutrophils play a critical role in acute pulmonary cryptococcosis by forming two distinct subsets during infection: Ox-PMN with oxidative stress signature and Cyt-PMN with enhanced cytokine gene expression. Ox-PMNs interact with the fungus to generate ROS, while Cyt-PMNs modulate cell-cell communication with dendritic cells and alveolar macrophages in response to Cn-derived ligands and cytokines. This suggests a division of labor in activated neutrophils during in vivo fungal infection.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Cell Biology
Gaetan Juban, Benedicte Chazaud
Summary: Efferocytosis, the engulfment of dead cells by macrophages, plays a crucial role in tissue repair post-injury by delineating the transition from the pro-inflammatory phase to the recovery phase. In the context of skeletal muscle regeneration, efferocytosis is essential for sterile tissue injury followed by complete regeneration, with molecular mechanisms and metabolic control playing a significant role in this process.
Review
Neurosciences
Kristen M. Pitts, Milica A. Margeta
Summary: The DAM signature is a microglial response common to various neurodegenerative diseases, sharing features with developmental microglia. Single cell RNA sequencing has revealed heterogeneity within the DAM signature, with contributions from yolk sac-derived microglia and bone marrow-derived macrophages. This review explores the role of DAM in retinal development and disease, focusing on crosstalk between resident microglia and infiltrating monocytes in age-related neurodegeneration.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2023)
Letter
Oncology
Si-Qing Liu, Zhi-Jie Gao, Juan Wu, Hong-Mei Zheng, Bei Li, Si Sun, Xiang-Yu Meng, Qi Wu
Summary: This study combines single-nucleus RNA sequencing and spatial transcriptomics to identify cell populations and their spatial distribution in breast cancer tissues. Malignant cells are clustered into distinct subpopulations with diverse features and functions, and their mapping in tissue regions shows differential enrichment of stromal cell types.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2022)
Review
Biochemical Research Methods
Xizhi Luo, Fei Qin, Feifei Xiao, Guoshuai Cai
Summary: This study developed a Bayesian method called BISC for accurately inferring the kinetics of transcriptional bursting and detecting differential bursting genes from single-cell transcriptomic data. It revealed the importance of bursting frequency in gene expression regulation and provided new mechanistic insights into the role of enhancers and superenhancers. BISC was also able to identify cell-type signature genes missed by differential expression analysis and tumor signature genes associated with alterations in bursting kinetics, demonstrating its value in understanding disease development.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Immunology
Tao Liu, Chao Li, Jiantao Zhang, Han Hu, Chenyao Li
Summary: In this study, a set of prognostic genes (EFRGs) were identified through RNA sequencing analysis of HCC patients. A prognostic model was established based on these genes, which can provide valuable support for decision-making in the context of immunotherapy and chemotherapy.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Sumeer Ahmad Khan, Alberto Maillo, Vincenzo Lagani, Robert Lehmann, Narsis A. Kiani, David Gomez-Cabrero, Jesper Tegner
Summary: The rise of single-cell genomics has provided an opportunity for machine learning algorithms. The scBERT method, inspired by the success of BERT in natural language processing, is a data-driven tool for annotating cell types in single-cell genomics data. However, the imbalance in cell-type distribution significantly affects the performance of scBERT, and careful consideration of data distribution and the introduction of subsampling techniques are necessary.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Surgery
Shuangjin Yu, Anil Dangi, Melanie Burnette, Michael M. Abecassis, Edward B. Thorp, Xunrong Luo
Summary: Acute CMV infection disrupts established transplantation tolerance in 50%-60% of recipients during the maintenance stage and leads to recipient allo-sensitization. This disruption reverts allo-specific T cells to a non-tolerant state and promotes their differentiation into allo-specific memory cells, resulting in accelerated rejection of a second same-donor islet allograft. Close monitoring for allo-sensitization is recommended in previously tolerant transplant recipients with disrupted tolerance maintenance due to acute CMV infection.
AMERICAN JOURNAL OF TRANSPLANTATION
(2021)
Editorial Material
Cardiac & Cardiovascular Systems
Paul W. Burridge, Edward B. Thorp
CIRCULATION RESEARCH
(2020)
Article
Urology & Nephrology
Longhui Qiu, Xingqiang Lai, Jiao-jing Wang, Xin Yi Yeap, Shulin Han, Feibo Zheng, Charlie Lin, Zhuoli Zhang, Daniele Procissi, Deyu Fang, Lin Li, Edward B. Thorp, Michael M. Abecassis, Yashpal S. Kanwar, Zheng J. Zhang
KIDNEY INTERNATIONAL
(2020)
Article
Multidisciplinary Sciences
Xiaolei Liu, Ester De la Cruz, Xiaowu Gu, Laszlo Balint, Michael Oxendine-Burns, Tamara Terrones, Wanshu Ma, Hui-Hsuan Kuo, Connor Lantz, Trisha Bansal, Edward Thorp, Paul Burridge, Zoltan Jakus, Joachim Herz, Ondine Cleaver, Miguel Torres, Guillermo Oliver
Article
Multidisciplinary Sciences
Tarun Pant, Anuradha Dhanasekaran, Ming Zhao, Edward B. Thorp, Joseph M. Forbess, Zeljko J. Bosnjak, Ivor J. Benjamin, Zhi-Dong Ge
Summary: This study identified five circulating lncRNAs that play a crucial role in the pathogenesis of diabetic cardiomyopathy, suggesting their high potential as diagnostic biomarkers for DCM.
SCIENTIFIC REPORTS
(2021)
Article
Medicine, Research & Experimental
Matthew DeBerge, Kristofor Glinton, Manikandan Subramanian, Lisa D. Wilsbacher, Carla Rothlin, Ira Tabas, Edward B. Thorp
Summary: In response to myocardial ischemia/reperfusion injury, AXL receptor in myeloid cells plays a maladaptive role leading to increased inflammation, adverse ventricular remodeling, and impaired contractile function. Inhibiting AXL alone can improve cardiac healing, and combination with blocking MerTK cleavage enhances the efficacy further, suggesting macrophage TAM receptors as potential therapeutic targets for myocardial infarction.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Cardiac & Cardiovascular Systems
Adovich S. Rivera, Arjun Sinha, Faraz S. Ahmad, Edward Thorp, Jane E. Wilcox, Donald M. Lloyd-Jones, Matthew J. Feinstein
Summary: The study revealed distinct patterns of left ventricular ejection fraction trajectories associated with specific individual CIDs among patients with HF, highlighting the diversity of HF subtypes and changes over time across different CIDs.
CIRCULATION-HEART FAILURE
(2021)
Article
Immunology
Matthew DeBerge, Connor Lantz, Shirley Dehn, David P. Sullivan, Anja M. van der Laan, Hans W. M. Niessen, Margaret E. Flanagan, Daniel J. Brat, Matthew J. Feinstein, Sunjay Kaushal, Lisa D. Wilsbacher, Edward B. Thorp
Summary: This study reveals the significant proinflammatory roles of myeloid cell expression of HIF-1α and HIF-2α during myocardial infarction. While HIF-2α suppresses anti-inflammatory macrophage mitochondrial metabolism, HIF-1α promotes cardioprotective factor MerTK cleavage through glycolytic reprogramming. The combined loss of myeloid HIF-1α and HIF-2α leads to catastrophic consequences, including macrophage necroptosis, impaired fibrogenesis, and cardiac rupture.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Endocrinology & Metabolism
Laurent Yvan-Charvet, Edward Benjamin Thorp
Summary: Glycolysis fuels inflammatory response in macrophages and produces pyruvate. However, a study in Nature Metabolism by Ran et al. shows that transporting pyruvate to the mitochondria for Krebs cycle is not necessary for inflammation.
Article
Medicine, Research & Experimental
Xingsheng Ren, Laura D. Manzanares, Enzo B. Piccolo, Jessica M. Urbanczyk, David P. Sullivan, Lenore K. Yalom, Triet M. Bui, Connor Lantz, Hinda Najem, Parambir S. Dulai, Amy B. Heimberger, Edward B. Thorp, Ronen Sumagin
Summary: Neutrophil mobilization to sites of injury is important for host defense and requires transendothelial migration. This study identifies a new mechanism where vessel-associated macrophages prime EC responses to form ICAM-1 hot spots, supporting PMN transendothelial migration.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Review
Medicine, Research & Experimental
Edward B. Thorp
Summary: Interest in cardioimmunology has grown as researchers explore the potential of immunotherapy for clinical care. The role of cardiac macrophages, which modulate cardiac function, has become a focus of study. After a heart attack, myeloid macrophages can both protect and harm the heart. The outcomes depend on factors such as myeloid ontogeny, heterogeneity, and cellular plasticity. The extracellular milieu and nutrient limitations also play a role.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Medicine, Research & Experimental
Kristofor E. Glinton, Wanshu Ma, Connor Lantz, Lubov S. Grigoryeva, Matthew DeBerge, Xiaolei Liu, Maria Febbraio, Mark Kahn, Guillermo Oliver, Edward B. Thorp
Summary: Clearance of dying cells by efferocytosis is crucial for cardiac repair after myocardial infarction (MI). In this study, it was found that defective efferocytosis by macrophages after MI led to a reduction in cardiac lymphangiogenesis and Vegfc expression. Cardiac macrophages promoted myocardial lymphangiogenesis and suppressed inflammatory cytokines through the production of Vegfc.
JOURNAL OF CLINICAL INVESTIGATION
(2022)