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Articles by Junbin Qian
16-h fasting optimizes cancer immunotherapy in mice and humans
Keywords diet intervention immune checkpoint therapy immunometabolism tumor metabolism tumor microenvironment Introduction The tumor microenvironment (TME) is a metabolically competitive niche where malignant cells outcompete immune cells for limited nutrients, including carbohydrates, amino acids, and lipids.1,2 During cancer progression, tumor cells exploit metabolic plasticity to upregulate diverse metabolic pathways, such as glycolysis, glutaminolysis, and lipid metabolism.3,4,5 However,...
Exercise-induced histone lactylation in monocyte-derived macrophages restores cardiac immune homeostasis and function in sepsis-induced cardiomyopathy | Nature Communications
Abstract An active lifestyle protects against cardiovascular diseases, yet its mechanisms in modulating the cardiac immune environment and preserving cardiac function remain unclear. Here, we identify a subpopulation of monocyte-derived cardiac macrophages, termed iNOS+Arg1+ macrophages, which simultaneously express pro-inflammatory and pro-reparative genes in exercised male mice.
Decoding tumor heterogeneity: A spatially informed pan-cancer analysis of the tumor microenvironment
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Keywords single-cell RNA sequencing scRNA-seq tumor microenvironment TME pan-cancer immune checkpoint blockade ICB tertiary lymphoid structure TLS Introduction Tumor infiltrating T cells are key functional components of the tumor microenvironment (TME) that have demonstrated anti-cancer efficacy in multiple clinical settings, including immune checkpoint blockade (ICB).
By Francesca Lodi, Duojiao Chen, Bram Boeckx, Frederik Peeters, Luuk Harbers, Liselore Loverix, Yiduo Zhou, Michel Bila, Ayse Bassez, Sarah Cappuyns, Tom Venken, Siel Olbrecht, Amelie Franken, Rogier Schepers, Thomas Van Brussel, Gino Philips, Hanne Vos, Machteld Keupers, Frederik De Smet, Sabine Tejpar, Oliver Bechter, Gabriele Bergers, Ann Smeets, PAUL CLEMENT, Els Wauters, Jeroen Dekervel, Toon Van Gorp, Junbin Qian, Jean-Christophe Marine, Diether Lambrechts, Sam Vanmassenhove, Lucas Ferreira Maciel, Elena Donders, Heesoo Song, Pierre Van Mol
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Cell Reports Medicine
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Forsythoside a as a potential therapeutic agent for non-alcoholic fatty liver disease: from target identification to in vitro and in vivo validation
Abstract Non-alcoholic fatty liver disease (NAFLD) is a long-term metabolic condition marked by unusual fat buildup in the liver, with an increasing occurrence worldwide. Forsythoside A (FA), a bioactive component of Forsythia suspensa, has anti-inflammatory, antioxidative, and hepatoprotective effects. This study investigates the mechanisms by which FA may treat NAFLD. Using bioinformatics tools, 35 potential targets of FA were identified, and a protein-protein interaction network was constructed.
Reference-informed evaluation of batch correction for single-cell omics data with overcorrection awareness - Communications Biology
Abstract Batch effect correction (BEC) is fundamental to integrate multiple single-cell RNA sequencing datasets, and its success is critical to empower in-depth interrogation for biological insights. However, no simple metric is available to evaluate BEC performance with sensitivity to data overcorrection, which erases true biological variations and leads to false biological discoveries. Here, we propose RBET, a reference-informed statistical framework for evaluating the success of BEC.
Case-specific selection of batch correction methods for integrating single-cell transcriptomic data from different sources
Abstract Integrating single-cell RNA-sequencing datasets from different sources is a common practice to empower in-depth interrogation for biological insights, where batch effect correction (BEC) is of vital importance. However, an inappropriate BEC may lead to overcorrection and report misleading results on downstream analyses including cell anno-tation, trajectory inference and cell-cell communication.
RBET guides case-specific choice of batch correction methods for single-cell transcriptomic data with overcorrection awareness and large batch effect robustness
Abstract Integrating single-cell RNA-sequencing datasets from different sources is a common practice to empower in-depth interrogation for biological insights, where batch effect correction (BEC) is of vital importance. However, an inappropriate BEC may lead to overcorrection and report misleading results on downstream analyses including cell anno-tation, trajectory inference and cell-cell communication.
PD-1- CD45RA+ effector-memory CD8 T cells and CXCL10+ macrophages are associated with response to atezolizumab plus bevacizumab in advanced hepatocellular carcinoma | Nature Communications
Abstract The combination of atezolizumab plus bevacizumab (atezo/bev) has dramatically changed the treatment landscape of advanced HCC (aHCC), achieving durable responses in some patients. Using single-cell transcriptomics, we characterize the intra-tumoural and peripheral immune context of patients with aHCC treated with atezo/bev.
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification
Siel Olbrecht ORCID: orcid.org/0000-0001-9452-59051,2,3, Pieter Busschaert2, Junbin Qian3,4, 1,2, Liselore Loverix1,2,3, Toon Van Gorp1,2, 1,2, Sileny Han1,2, 2, An Coosemans5, 6,7, Diether Lambrechts3,4 & Ignace Vergote1,2 Genome Medicine volume 13, Article number: 111 (2021) Cite this article Abstract Background High-grade serous tubo-ovarian cancer (HGSTOC) is characterised by extensive inter- and intratumour heterogeneity, resulting in persistent therapeutic resistance and poor disease...
An Attachment-Independent Biochemical Timer of the Spindle Assembly Checkpoint
Publication HistoryPublished: November 9, 2017Accepted: October 11, 2017; Received in revised form: August 24, 2017; Received: March 29, 2017;
The Importance of Kinase-Phosphatase Integration: Lessons from Mitosis
Although individual phosphorylated molecules often behave like binary switches, multiple copies of each binary switch can be used to output complex biological responses. Kinase and phosphatases work together to shape how these multiple substrate copies behave in time and space. This ‘cooperativity’ is critical for determining three key properties of a signal response: amplitude, localisation, and timing.
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