Zha0rong

Zha0rong

Professional Bioinformatician with 7 years of experience in industry and academia

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AHR signaling is induced by infection with coronaviruses

Published in Nature Communications, 2021

Coronavirus infection in humans is usually associated to respiratory tract illnesses, ranging in severity from mild to life-threatening respiratory failure. The aryl hydrocarbon receptor (AHR) was recently identified as a host factor for Zika and dengue viruses; AHR antagonists boost antiviral immunity, decrease viral titers and ameliorate Zika-induced pathology in vivo. Here we report that AHR is activated by infection with different coronaviruses, potentially impacting antiviral immunity and lung epithelial cells. Indeed, the analysis of single-cell RNA-seq from lung tissue detected increased expression of AHR and AHR transcriptional targets, suggesting AHR signaling activation in SARS-CoV-2-infected epithelial cells from COVID-19 patients. Moreover, we detected an association between AHR expression and viral load in SARS-CoV-2 infected patients. Finally, we found that the pharmacological inhibition of AHR suppressed the replication in vitro of one of the causative agents of the common cold, HCoV-229E, and the causative agent of the COVID-19 pandemic, SARS-CoV-2. Taken together, these findings suggest that AHR activation is a common strategy used by coronaviruses to evade antiviral immunity and promote viral replication, which may also contribute to lung pathology. Future studies should further evaluate the potential of AHR as a target for host-directed antiviral therapy.

Recommended citation: Giovannoni, F., Li, Z., Remes-Lenicov, F., Davola, M. E., Elizalde, M., Paletta, A., ... & Quintana, F. J. (2021). AHR signaling is induced by infection with coronaviruses. Nature communications, 12(1), 5148.
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Disease-associated astrocyte epigenetic memory promotes CNS pathology

Published in Nature, 2024

Disease-associated astrocyte subsets contribute to the pathology of neurologic diseases, including multiple sclerosis and experimental autoimmune encephalomyelitis (EAE), an experimental model for multiple sclerosis. However, little is known about the stability of these astrocyte subsets and their ability to integrate past stimulation events. Here we report the identification of an epigenetically controlled memory astrocyte subset that exhibits exacerbated pro-inflammatory responses upon rechallenge. Specifically, using a combination of single-cell RNA sequencing, assay for transposase-accessible chromatin with sequencing, chromatin immunoprecipitation with sequencing, focused interrogation of cells by nucleic acid detection and sequencing, and cell-specific in vivo CRISPR–Cas9-based genetic perturbation studies we established that astrocyte memory is controlled by the metabolic enzyme ATP-citrate lyase (ACLY), which produces acetyl coenzyme A (acetyl-CoA) that is used by histone acetyltransferase p300 to control chromatin accessibility. The number of ACLY+p300+ memory astrocytes is increased in acute and chronic EAE models, and their genetic inactivation ameliorated EAE. We also detected the pro-inflammatory memory phenotype in human astrocytes in vitro; single-cell RNA sequencing and immunohistochemistry studies detected increased numbers of ACLY+p300+ astrocytes in chronic multiple sclerosis lesions. In summary, these studies define an epigenetically controlled memory astrocyte subset that promotes CNS pathology in EAE and, potentially, multiple sclerosis. These findings may guide novel therapeutic approaches for multiple sclerosis and other neurologic diseases.

Recommended citation: Lee, H. G., Rone, J. M., Li, Z., Akl, C. F., Shin, S. W., Lee, J. H., ... & Quintana, F. J. (2024). Disease-associated astrocyte epigenetic memory promotes CNS pathology. Nature, 627(8005), 865-872.
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Identification of environmental factors that promote intestinal inflammation

Published in The Journal of Immunology, 2024

Genome-wide association studies have identified risk loci linked to inflammatory bowel disease (IBD)—a complex chronic inflammatory disorder of the gastrointestinal tract. The increasing prevalence of IBD in industrialized countries and the augmented disease risk observed in migrants who move into areas of higher disease prevalence suggest that environmental factors are also important determinants of IBD susceptibility and severity. However, the identification of environmental factors relevant to IBD and the mechanisms by which they influence disease has been hampered by the lack of platforms for their systematic investigation. To overcome this limitation, we developed an integrated systems approach which combines publicly available databases, zebrafish chemical screens, machine learning, and mouse preclinical models to identify environmental factors that control intestinal inflammation. Using this approach we established that the herbicide propyzamide increases inflammation in the small and large intestine. Moreover, we found that an AHR–NF-κB–C/EBPβ signalling axis operates in T cells and dendritic cells to promote intestinal inflammation, and is targeted by propyzamide. In conclusion, we developed a pipeline for the identification of environmental factors and mechanisms of pathogenesis in IBD and, potentially, other inflammatory diseases.

Recommended citation: Sanmarco, L. M., Chao, C. C., Wang, Y. C., Kenison, J. E., Li, Z., Rone, J. M., ... & Quintana, F. J. (2022). Identification of environmental factors that promote intestinal inflammation. Nature, 611(7937), 801-809.
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Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq

Published in Nature Protocle, 2024

Cell–cell interactions are essential for the function and contextual regulation of biological tissues. We present a platform for high-throughput microfluidics-supported genetic screening of functional regulators of cell–cell interactions. Systematic perturbation of encapsulated associated cells followed by sequencing (SPEAC-seq) combines genome-wide CRISPR libraries, cell coculture in droplets and microfluidic droplet sorting based on functional read-outs determined by fluorescent reporter circuits to enable the unbiased discovery of interaction regulators. This technique overcomes limitations of traditional methods for characterization of cell–cell communication, which require a priori knowledge of cellular interactions, are highly engineered and lack functional read-outs. As an example of this technique, we describe the investigation of neuroinflammatory intercellular communication between microglia and astrocytes, using genome-wide CRISPR–Cas9 inactivation libraries and fluorescent reporters of NF-κB activation. This approach enabled the discovery of thousands of microglial regulators of astrocyte NF-κB activation important for the control of central nervous system inflammation. Importantly, SPEAC-seq can be adapted to different cell types, screening modalities, cell functions and physiological contexts, only limited by the ability to fluorescently report cell functions and by droplet cultivation conditions. Performing genome-wide screening takes less than 2 weeks and requires microfluidics capabilities. Thus, SPEAC-seq enables the large-scale investigation of cell–cell interactions.

Recommended citation: Faust Akl, C., Linnerbauer, M., Li, Z., Lee, H. G., Clark, I. C., Wheeler, M. A., & Quintana, F. J. (2025). Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq. Nature protocols, 20(2), 440-461.
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CLEC16A in astrocytes promotes mitophagy and limits pathology in a multiple sclerosis mouse model

Published in Nature Neuroscience, 2025

Astrocytes promote neuroinflammation and neurodegeneration in multiple sclerosis (MS) through cell-intrinsic activities and their ability to recruit and activate other cell types. In a genome-wide CRISPR-based forward genetic screen investigating regulators of astrocyte proinflammatory responses, we identified the C-type lectin domain-containing 16A gene (CLEC16A), linked to MS susceptibility, as a suppressor of nuclear factor-κB (NF-κB) signaling. Gene and small-molecule perturbation studies in mouse primary and human embryonic stem cell-derived astrocytes in combination with multiomic analyses established that CLEC16A promotes mitophagy, limiting mitochondrial dysfunction and the accumulation of mitochondrial products that activate NF-κB, the NLRP3 inflammasome and gasdermin D. Astrocyte-specific Clec16a inactivation increased NF-κB, NLRP3 and gasdermin D activation in vivo, worsening experimental autoimmune encephalomyelitis, a mouse model of MS. Moreover, we detected disrupted mitophagic capacity and gasdermin D activation in astrocytes in samples from individuals with MS. These findings identify CLEC16A as a suppressor of astrocyte pathological responses and a candidate therapeutic target in MS.

Recommended citation: Kadowaki, A., Wheeler, M. A., Li, Z., Andersen, B. M., Lee, H. G., Illouz, T., ... & Quintana, F. J. (2025). CLEC16A in astrocytes promotes mitophagy and limits pathology in a multiple sclerosis mouse model. Nature Neuroscience, 28(3), 470-486.
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ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets

Published in Frontiers in Bioinformatics, 2025

Gene signature extraction from transcriptomics datasets has been instrumental to identify sets of co-regulated genes, identify associations with prognosis, and for biomarker discovery. Independent component analysis (ICA) is a powerful tool to extract such signatures to uncover hidden patterns in complex data and identify coherent gene sets. The ICARus package offers a robust pipeline to perform ICA on transcriptome datasets. While other packages perform ICA using one value of the main parameter (i.e., the number of signatures), ICARus identifies a range of near-optimal parameter values, iterates through these values, and assesses the robustness and reproducibility of the signature components identified. To test the performance of ICARus, we analyzed transcriptome datasets obtained from COVID-19 patients with different outcomes and from lung adenocarcinoma. We identified several reproducible gene expression signatures significantly associated with prognosis, temporal patterns, and cell type composition. The GSEA of these signatures matched findings from previous clinical studies and revealed potentially new biological mechanisms. ICARus with a vignette is available on Github https://github.com/Zha0rong/ICArus.

Recommended citation: Li, Z., & Fuxman Bass, J. I. (2025). ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets. Frontiers in Bioinformatics, 5, 1604418.
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Barcoded viral tracing identifies immunosuppressive astrocyte–glioma interactions

Published in Nature, 2025

Glioblastoma (GBM) is the most lethal primary brain malignancy1. Immunosuppression in the GBM tumour microenvironment (TME) is an important barrier to immune-targeted therapies, but our understanding of the mechanisms of immune regulation in the GBM TME is limited2. Here we describe a viral barcode interaction-tracing approach3 to analyse TME cell–cell communication in GBM clinical samples and preclinical models at single-cell resolution. We combine it with single-cell and bulk RNA-sequencing analyses, human organotypic GBM cultures, in vivo cell-specific CRISPR–Cas9-driven genetic perturbations as well as human and mouse experimental systems to identify an annexin A1–formyl peptide receptor 1 (ANXA1–FPR1) bidirectional astrocyte–GBM communication pathway that limits tumour-specific immunity. FPR1 inhibits immunogenic necroptosis in tumour cells, and ANXA1 suppresses NF-κB and inflammasome activation in astrocytes. ANXA1 expression in astrocytes and FPR1 expression in cancer cells are associated with poor outcomes in individuals with GBM. The inactivation of astrocyte–glioma ANXA1–FPR1 signalling enhanced dendritic cell, T cell and macrophage responses, increasing infiltration by tumour-specific CD8+ T cells and limiting T cell exhaustion. In summary, we have developed a method to analyse TME cell–cell interactions at single-cell resolution in clinical samples and preclinical models, and used it to identify bidirectional astrocyte–GBM communication through ANXA1–FPR1 as a driver of immune evasion and tumour progression.

Recommended citation: Andersen, B. M., Faust Akl, C., Wheeler, M. A., Li, Z., Diebold, M., Kilian, M., ... & Quintana, F. J. (2025). Barcoded viral tracing identifies immunosuppressive astrocyte–glioma interactions. Nature, 644(8078), 1097-1106.
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Glioblastoma-instructed astrocytes suppress tumour-specific T cell immunity

Published in Nature, 2025

Glioblastoma is the most common and aggressive primary brain cancer and shows minimal response to therapies. The immunosuppressive tumour microenvironment in glioblastoma contributes to the limited therapeutic response. Astrocytes are abundant in the central nervous system and have important immunoregulatory roles. However, little is known about their role in the immune response to glioblastoma1. Here we used single-cell and bulk RNA sequencing of clinical glioblastoma samples and samples from preclinical models, multiplexed immunofluorescence, in vivo CRISPR-based cell-specific genetic perturbations and in vitro mouse and human experimental systems to address this gap in knowledge. We identified an astrocyte subset that limits tumour immunity by inducing T cell apoptosis through the death receptor ligand TRAIL. Moreover, we identified that IL-11 produced by tumour cells is a driver of STAT3-dependent TRAIL expression in astrocytes. Astrocyte signalling through STAT3 and TRAIL expression were associated with a shorter time to recurrence and overall decreased survival in patients with glioblastoma. Genetic inactivation of the IL-11 receptor or TRAIL in astrocytes extended survival in mouse models of glioblastoma and enhanced T cell and macrophage responses. Finally, treatment with an oncolytic HSV-1 virus engineered to express a TRAIL-blocking single-chain antibody in the tumour microenvironment extended survival and enhanced tumour-specific immunity in preclinical models of glioblastoma. In summary, we establish that IL-11–STAT3-driven astrocytes suppress glioblastoma-specific protective immunity by inducing TRAIL-dependent T cell apoptosis, and engineered therapeutic viruses can be used to target this mechanism of astrocyte-driven tumour immunoevasion.

Recommended citation: Faust Akl, C., Andersen, B. M., Li, Z., Giovannoni, F., Diebold, M., Sanmarco, L. M., ... & Quintana, F. J. (2025). Glioblastoma-instructed astrocytes suppress tumour-specific T cell immunity. Nature, 643(8070), 219-229.
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Eradicating Drug-tolerant Persister Cells in EGFR-Mutated Non–Small Cell Lung Cancer by Targeting TROP2 with CAR-T Cellular Therapy

Published in Cancer Discovery, 2025

EGFR tyrosine kinase inhibitors have dramatically improved outcomes for patients with EGFR-mutated non–small cell lung cancer (NSCLC), but relapse frequently occurs because of drug-tolerant persister (DTP) cells that can evolve and develop diverse mechanisms of drug resistance. In samples from patients with EGFR-mutated NSCLC treated with EGFR tyrosine kinase inhibitors in the neoadjuvant setting, we observed enriched expression of the cell surface protein TROP2, a target of clinically active antibody–drug conjugates (ADC). We confirmed these findings across multiple EGFR-mutated NSCLC cell line and patient-derived xenograft models treated with osimertinib in vivo. Treatment with the TROP2 ADC sacituzumab govitecan at the time of osimertinib-induced minimal residual disease only modestly delayed tumor recurrence in vivo, whereas a single infusion of sacituzumab-based TROP2-directed chimeric antigen receptor (CAR) T cells significantly prolonged relapse-free survival, with evidence of cure. These data highlight the potential of engineering TROP2 CAR T-cell therapy to eliminate EGFR DTPs in patients.

Recommended citation: Baldacci, S., Brea, E. J., Facchinetti, F., Li, Z., Ngo, K., Malhotra, S., ... & Barbie, D. A. (2025). Eradicating Drug-tolerant Persister Cells in EGFR-Mutated Non–Small Cell Lung Cancer by Targeting TROP2 with CAR-T Cellular Therapy. Cancer discovery, 15(11), 2235-2250.
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Retargeted oncolytic viruses engineered to remodel the tumor microenvironment for glioblastoma immunotherapy

Published in Nature Cancer, 2025

Glioblastoma (GBM) is an aggressive, immunotherapy-resistant brain tumor. Here, we engineered an oncolytic virus platform based on herpes simplex virus 1 for GBM viroimmunotherapy. We mutated the highly cytopathic MacIntyre strain to increase spread and oncolytic activity, limit genetic drift, prevent neuron infection and enable PET tracing. We incorporated microRNA target cassettes to attenuate replication in healthy brain cells. Moreover, we engineered the gD envelope protein to specifically target GBM using EGFR-specific or integrin-specific binders. Lastly, we incorporated five immunomodulators to remodel the tumor microenvironment (TME) by locally expressing IL-12, anti-PD1, a bispecific T cell engager, 15-hydroxyprostaglandin dehydrogenase and anti-TREM2 to target T cells and myeloid cells in the GBM TME. A single intratumoral injection increased survival in GBM preclinical models, while promoting tumor-specific T cell, natural killer cell and myeloid cell responses in the TME. In summary, we engineered a retargeted, safe and traceable oncolytic virus with strong cytotoxic and immunostimulatory activities for GBM immunotherapy.

Recommended citation: Giovannoni, F., Strathdee, C. A., Faust Akl, C., Andersen, B. M., Li, Z., Lee, H. G., ... & Quintana, F. J. (2025). Retargeted oncolytic viruses engineered to remodel the tumor microenvironment for glioblastoma immunotherapy. Nature Cancer, 6(12), 1994-2010.
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talks

teaching

Teaching experience 1

Undergraduate course, University 1, Department, 2014

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Teaching experience 2

Workshop, University 1, Department, 2015

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