Hanjie Li's research while affiliated with Chinese Academy of Sciences and other places

Publications (20)

Article
Full-text available
Lung cancer is the leading cause of cancer-related death worldwide. Cancer immunotherapy has shown great success in treating advanced-stage lung cancer but has yet been used to treat early-stage lung cancer, mostly due to lack of understanding of the tumor immune microenvironment in early-stage lung cancer. The immune system could both constrain an...
Article
Full-text available
The functional activity and differentiation potential of cells are determined by their interactions with surrounding cells. Approaches that allow unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a...
Article
Immunotherapies that were developed based on our understandings of tumor immunology have revolutionized cancer treatment. However, the success of immunotherapy is eclipsed by several grand challenges, including low response rate, intrinsic/acquired resistance and adverse effects. While a deeper understanding of the interaction between tumor and our...
Preprint
Full-text available
The functional activity and differentiation potential of cells is determined by their interaction with surrounding cells. Approaches that allow the unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by...
Article
Full-text available
Understanding the mechanism that leads to immune dysfunction in severe coronavirus disease 2019 (COVID-19) is crucial for the development of effective treatment. Here, using single-cell RNA sequencing, we characterized the peripheral blood mononuclear cells (PBMCs) from uninfected controls and COVID-19 patients and cells in paired broncho-alveolar...
Preprint
Full-text available
The functional activity and differentiation potential of cells is determined by their interaction with surrounding cells. Approaches that allow the unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by...
Preprint
Understanding the mechanism that leads to immune dysfunction induced by SARS-CoV2 virus is crucial to develop treatment for severe COVID-19. Here, using single cell RNA-seq, we characterized the peripheral blood mononuclear cells (PBMC) from uninfected controls and COVID-19 patients, and cells in paired broncho-alveolar lavage fluid (BALF). We foun...
Article
Full-text available
Multiple sclerosis (MS) is characterized by pathological inflammation that results from the recruitment of lymphoid and myeloid immune cells from the blood into the brain. Due to subset heterogeneity, defining the functional roles of the various cell subsets in acute and chronic stages of MS has been challenging. Here, we used index and transcripti...
Article
Viruses are a constant threat to global health as highlighted by the current COVID-19 pandemic. Currently, lack of data underlying how the human host interacts with viruses, including the SARS-CoV-2 virus, limits effective therapeutic intervention. We introduce Viral-Track, a computational method that globally scans unmapped scRNA-seq data for the...
Article
Full-text available
Single-cell RNA sequencing (scRNA-seq) is a powerful new technology allowing the analysis of transcriptomes from individual cell and is ideally suited to dissect immune cell heterogeneity. ScRNA-seq has already been applied to identify novel immune cell subsets, elaborate cellular differentiation trajectories, and elucidate immunopathogenic mechani...
Conference Paper
Checkpoint blockade therapies that aim to reactivate antitumor immune responses have revolutionized cancer treatment, resulting in durable responses in a significant proportion of patients with advanced tumor progression. Nevertheless, many patients fail to reach long-term clinical benefit due to lack of response or acquired resistance. Inconsisten...
Article
Tumor immune cell compositions play a major role in response to immunotherapy, but the heterogeneity and dynamics of immune infiltrates in human cancer lesions remain poorly characterized. Here, we identify conserved intratumoral CD4 and CD8 T cell behaviors in scRNA-seq data from 25 melanoma patients. We discover a large population of CD8 T cells...
Conference Paper
Checkpoint blockade therapies that aim to reactivate anti-tumor immune responses have revolutionized cancer treatment, resulting in durable responses in a significant proportion of patients with advanced disease. Nevertheless, many patients fail to reach long-term clinical benefit, and therefore, a better insight into the mechanisms underlying resp...
Article
Cellular functions are strongly dependent on surrounding cells and environmental factors. Current technologies are limited in characterizing the spatial location and unique gene-programs of cells in less structured and dynamic niches. Here we developed a method (NICHE-seq) that combines photoactivatable fluorescent reporters, two-photon microscopy...
Article
To guide the design of immunotherapy strategies for patients with early stage lung tumors, we developed a multiscale immune profiling strategy to map the immune landscape of early lung adenocarcinoma lesions to search for tumor-driven immune changes. Utilizing a barcoding method that allows a simultaneous single-cell analysis of the tumor, non-invo...

Citations

... Despite these advances, lung cancer continues to pose a significant public burden that is heightened by its dismal overall prognosis, poor clinical outcome, and a five-year survival rate of only 18% in the US, which is among the lowest across early-stage malignancies [13]. These sub-optimal outcomes are attributed to multiple factors, including low screening adherence (4-6% of potential eligible candidates in the United States) [14] as well as resistance of certain of patient subgroups to specific treatment strategies [15]. For instance, durable benefits in response to single-agent ICB are limited to a subset of patients, and this setback highlighted an urgent need to better identify biomarkers to stratify patients who are likely to respond to ICB and to determine the best window of time for therapeutic intervention [16]. ...
... [1][2] Bioorthogonal chemistry, reactions that use motifs that do not inherently react with cellular biomolecules, can be used to manipulate glycans, proteins, and nucleic acids in and on cells in a selective, chemically-regulated manner. 2 Key methods for chemical activation of biomolecules include reaction-driven decaging of extracellular ligands for receptors 3 as well as photochemical methods for internal compound release of signaling agents, drugs, or metabolites. 1,4,5 Among abiotic triggering methods greater challenges remain for activating bioorthogonal agents in live cells because reporter molecules must be cell permeable, non-toxic, and have resistance to intracellular reactivity including redox processes. Photochemistry using non-toxic wavelengths of light is a strategy to "trigger" chemical probe release with a critical benefit of spatiotemporal activation limited to those cells within the area and timeframe of light irradiation. ...
... Ultimately, all of these techniques (and others not listed here but reviewed elsewhere 48,49 ) deliver complementary capabilities with their own particular use cases and could even be coupled with SPACECAT to link cellular dynamics to end-state phenotype 49 . We envision SPACECAT serving as a strong small molecule addition to the set of recently developed methods for spatially informed assays that leverage photocaged olignucleotides 50 and nanobodies 51 . With a minimally perturbative, temporally stable, and spatially precise fluorescent-tagging signal, the SPACECAT protocol can be incorporated into existing sample workflows to increase information produced from an experiment, requiring only the addition of specific dyes described here and elsewhere and an active UV illumination source 19 . ...
... According to our findings, IL1R2 is a downregulated NP marker for COVID-19 patients. IL1R2, known as anti-inflammatory cytokines, is highly expressed in monocyte-macrophages from BALF and follicular regulatory T (TFR) cells; however, TFR cells have been reported to be significantly lower in hospitalized COVID-19 patients (Meckiff et al. 2020;Xu et al. 2020). LAMB3 which is present in anchoring junctions of epithelial cells was among NP-based diagnostic biomarkers. ...
... Several laboratory tests such as albumin (14), CRP (15), lymphocyte abundance (16)(17)(18)(19), , and the fibrin degradation product D-dimer (21) have been used to monitor COVID-19, with their levels variably associated with disease severity. While these routinely available assays may have some clinical use in disease prognostication, they depict an incomplete landscape of pathophysiological changes associated with COVID-19. ...
... Cryptococcus neoformans is an encapsulated yeast that causes disease mainly in immunosuppressed hosts, but the morbidity is also increasing in patients with normal immune function [1,2]. Cryptococcus infects the body through the inhalation of environmental spores or yeasts that are present in environmental sources, causing cryptococcal meningitis and cryptococcal pneumonia [3]. C. neoformans are responsible for over 180 thousand deaths yearly worldwide [4], which is a serious threat to human health. ...
... Previous studies disclosed that the hyperinflammatory phenotype was considerably higher in the bronchi than in the nasopharynx of the COVID-19 patients [101,102]. Oxidative stress in the lung tissues is a characteristic of infections caused by SARS-CoV-2 [103] and an important mechanism underlying fibrosis [104]. To study if ARND could prevent fibrosis, a H 2 O 2 -induced lung fibrosis cell model of the lower respiratory tract Calu-3 cells was established for investigation [105,106]. ...
... Many single-cell proteome and transcriptome studies have been performed on single-cell suspensions from dissociated tumors in order to analyze the heterogeneity of the immune microenvironment and how it relates to therapy responses [3]. For example, multiple single-cell studies, employing RNA sequencing and flow cytometry of isolated tumor infiltrating T cells, have demonstrated that T cell exhaustion in the TME can predict the response to immune checkpoint inhibition [4,5]. These single-cell approaches have led to the discovery of various tumor-specific cell types and activated transcriptional programs in the TME relevant to cancer evolution, cancer progression, or patients' treatment responses. ...
... The Tool-Like Receptors (TLRs) responsible for pathogen recognition and the induction of innate immune responses were related to regulating the activation of antigen-presenting cells and key cytokines in EAE, and the increased TLRs expression in the absence of any evidence of microbial presence could explain why some species where resistant to the induction of EAE, particularly TRL9 [16,17]. On the other hand, it was recently identified that Cxcl10 + and Saa3 + monocytic subsets were derived from early myeloid cell progenitors by Single Cell analysis and that the perspectives of therapeutic targets were both potential pathogenic triggers of CNS inflammation in MS findings [18]. The pathological mechanisms were the central point of discussion in the development of new therapies before starting essays on new treatments that explain these interests to better understand the preclinical model when looking for therapeutic targets. ...
... This method called Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) allows accurate characterization of both phenotype and transcriptome in a scRNAseq experiment. [293][294][295] All these data strongly support the accuracy of CYTOF/ CITE-seq and scRNAseq to analyse the effects of VitD on the whole PBMC population to improve our understanding of the pleiotropic effects of VitD while keeping detailed analysis of key populations modified by VitD. ...