Biology subjects

Sagar, S.

Publications and source records attributed to Sagar, S..

15 recordsLinked to original sources

bioRxiv2026

M-CSF drives alveolar macrophage plasticity during development and cytomegalovirus infection

Alveolar macrophages (AM), the most frequent resident immune cells of the lung, are at the first line of defence against respiratory pathogens and instruct structural lung cells, e.g. in tissue repair. They are long-lived and receive their terminal phenotypic imprint through signals originating from the unique location at the tissue-air interface, as well as through cytokines like granulocyte-macrophage colony-stimulating factor (GM-CSF) and transforming growth factor-{beta} (TGF-{beta}). However, the regulatory mechanisms governing their phenotypic plasticity, which is conceptually critical for their positioning and differentiation in early life and for their functional adaptation during infection, remain poorly defined. Here we explored respiratory tract infection with cytomegalovirus (CMV), which is closely linked to mammalian immune evolution. Complementary host-pathogen fate-mapping strategies revealed AM to constitute the bottleneck for efficient mouse (M)CMV infection. MCMV infection induced macrophage colony-stimulating factor (M-CSF) in the alveolar space, and culturing of AM in M-CSF led to a profound remodelling of morphology, immunophenotype, and transcriptional identity, e.g. it increased the expression of interferon-stimulated genes (ISG), which modulated susceptibility to infection. Notably, already at baseline recently differentiated neonatal AM across species retained an M-CSF-associated transcriptional program. This was linked to reduced permissiveness to respiratory MCMV infection in vivo. Overall, our findings identify the role of M-CSF-dependent signalling in conferring plasticity to AM, when it is most needed, particularly during early-life establishment and in response to viral infection.

immunology↗

bioRxiv2026

Postnatal Maturation of Dendritic Epidermal T Cells and Langerhans Cells Follows Distinct Differentiation Trajectories Independent of Microbiota

The mouse epidermis harbors two key resident immune populations--dendritic epidermal T cells (DETCs), a subset of invariant {gamma}{delta} T cells, and Langerhans cells (LCs), specialized tissue-resident macrophages--both of which play critical roles in immune surveillance, barrier integrity, and tissue homeostasis. While the fetal origin of both cell types has been defined, the cellular and molecular mechanisms that govern their postnatal fates following colonization of the epidermis around birth remain incompletely understood. Here, we present a combination of immunophenotyping- and transcriptome-resolved single-cell map of DETC and LC development in the mouse epidermis from late embryogenesis through adulthood. We delineate differentiation trajectories for both cell types, marked by distinct changes in morphology, proliferation, and transcriptional programming. Using mice deficient in {gamma}{delta} T cells, which lack canonical DETCs, we demonstrate that LCs develop independently of canonical DETCs likely due to the presence of {beta}DETCs. Moreover, analysis of germ-free mice and wildlings reveals that the postnatal development of both DETCs and LCs is independent of microbial colonization. Together, our findings define the core principles underlying the establishment of the mouse epidermal immune niche. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/716534v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@18088a0org.highwire.dtl.DTLVardef@189e0f2org.highwire.dtl.DTLVardef@10f37d6org.highwire.dtl.DTLVardef@1ad59c_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

GFI1 as a novel regulator of γδ T cell development and the IL-17/IFNγ lineage commitment

GFI1 is a DNA-binding zinc finger transcription factor regulating the commitment of hematopoietic precursors to myeloid and lymphoid lineages. Here we report that GFI1 is expressed in {gamma}{delta} T cells and restricts the cellularity of ROR{gamma}t+V{gamma}6+ {gamma}{delta}T cells that produce high levels of IL-17A, while promoting the expansion of V{gamma}1+ and V{gamma}4+ {gamma}{delta}T cells. Absence of GFI1 results in a pronounced bias toward the production of {gamma}{delta}T17 cells, commencing post-birth. Additionally, we observe an expansion of ROR{gamma}t+/MAF+ cells within the thymic DN1e population of GFI1-deficient mice. The DN1e population, along with other DN subsets in GFI1 knock-out (KO) mice, exhibits a distinctive {gamma}{delta}T17 cell-specific transcriptomic profile. Specifically, DN1, DN3, and {gamma}{delta} T cells lacking GFI1 show upregulation of the B-ZIP transcription factor MAF, which regulates genes critical for {gamma}{delta}T cells, such as Il17a, Il22, and Blk that are all induced in Gfi1 deficient cells. The Maf gene is occupied by GFI1 in DN pre-T cells at cognate binding sites in its promoter region, suggesting that GFI1 acts as a direct repressor of Maf. We conclude that GFI1 functions as a novel regulator of V{gamma}6+ {gamma}{delta}T17 precursor cells restricting their peripheral expansion by acting upstream of a MAF dependent regulatory network. Highlights- GFI1 controls the expansion of {gamma}{delta} T cells in peripheral lymphoid organs and in barrier tissues. - GFI1 specifically restricts expansion of {gamma}{delta} T cells secreting IL-17 by acting upstream of a MAF dependent transcriptional regulatory network. - GFI1 plays a cell intrinsic role in controlling the generation of {gamma}{delta}T cells through the repression of Maf. - GFI1 controls a MAF+/ROR{gamma}t+ {gamma}{delta}T cell precursor cell population within the DN1e cell subset.

immunology↗

bioRxiv2026

Effector dsRNA delivery via MgFe-layered double hydroxide nanocarriers confers prolonged protection against powdery mildew in pea

Layered double hydroxides (LDHs) have emerged as promising nanocarriers for RNA interference (RNAi)-based crop protection due to their ability to stabilize and effectively deliver pathogen-specific double-stranded RNA (dsRNA). However, their potential against obligate biotrophic pathogens like powdery mildews remains unexplored. In this study, we investigated Magnesium Iron-LDH (MgFe-LDH) nanomaterials as carriers of fungal effector dsRNA (Ef-dsRNA) and evaluated the efficacy of the resulting complex in suppressing Erysiphe pisi (powdery mildew) infection in pea (Pisum sativum) via foliar spray application. The synthesized LDH nanomaterial exhibits strong leaf adherence, biocompatibility, and high dsRNA loading capacity, protects the dsRNA against RNase-mediated degradation, and facilitates its sustained release over time. Foliar spray application of the Ef-dsRNA-LDH complex on intact pea plants results in enhanced gene silencing of the target fungal effector and confers greater and prolonged local and systemic powdery mildew disease protection compared to treatments with dsRNA or LDH alone. Following spray application, the LDH nanomaterial is rapidly taken up by intact pea leaf cells and from the plant into E. pisi hyphae via haustoria, enabling efficient dsRNA delivery and silencing of the target gene up to 15 days post-application. Overall, our Ef-dsRNA-LDH formulation offers a robust, sustainable, and targeted approach for RNAi-mediated control of powdery mildews.

plant biology↗

bioRxiv2025

Colibactin-producing E. coli promote carcinogenesis of gastroesophageal adenocarcinoma and simultaneously induce autophagy and differentiation

Background & AimsGastroesophageal adenocarcinoma (GEAC) is a malignancy of the gastroesophageal junction (GEJ) and is associated with reflux of gastroduodenal contents and Barretts Esophagus (BE). A shift towards gram-negative bacteria in the microbiota of the GEJ additionally promotes inflammation and likely carcinogenesis. Enterobacteriaceae are enriched in advanced stages of GEAC development, and members of this family can produce colibactin, a genotoxin implicated in DNA damage and tumor progression. We aimed to validate these observations and investigate the effect of E. coli with or without colibactin production on GEAC-carcinogenesis. MethodsBacteria were profiled in human biopsies with imaging and 16S rRNA gene sequencing. Organoids of our L2-IL1B mouse model of GEAC were exposed to E. coli with colibactin (CoPEC) and without colibactin production (noCoPEC) via organoid microinjection. The phenotypic and transcriptomic changes in the organoids after the coculture with E. coli were evaluated via histology and single-cell RNA sequencing. ResultsIn human specimens, we observed an infiltration of bacteria in GEJ-tissue upon tumor formation and detected Enterobacteriaceae in one third of BE-patients. CoPEC-injected organoids exhibited high rates of proliferation and DNA damage, and an upregulation of cancer-associated genes and pathways. Furthermore, genes and pathways associated with immune activation, defense mechanisms, metabolic reprogramming, autophagy and differentiation were upregulated in CoPEC-injected organoids. ConclusionIn addition to the enrichment of Enterobacteriaceae in the GEJ-tissue of patients at late stages of GEAC, we show that the exposure of colibactin-producing E. coli to murine BE-organoids promotes genetic instability and proliferation, and the activation of cancer-associated pathways, while also activating autophagy and enhancing intercellular homeostasis. This indicates that colibactin-producing E. coli have a dual effect on early stages of GEAC-carcinogenesis. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/687579v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1281a14org.highwire.dtl.DTLVardef@1c83c91org.highwire.dtl.DTLVardef@10088d2org.highwire.dtl.DTLVardef@1698a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

An immunobiliary single-cell atlas resolves crosstalk of type 2 cDCs and γδT cells in cholangitis

Background and aimsThe immunobiliary niche serves as a reservoir of tissue-resident immune cells, yet the role of unconventional T cells during cholangitis remains poorly understood. Here, we connect cell state dynamics of type 2 conventional dendritic cells (cDC2) in cholangitis with site-specific{gamma}{delta} T17 responses in liver and draining lymph nodes (LN). MethodsThe 0.1% Diethoxycarbonyl-1,4-Dihydrocollidine (DDC) diet was used to generate an immunobiliary DC- and{gamma}{delta} T-enriched mouse liver and LN single-cell RNA-sequencing (scRNA-seq) atlas covering temporal disease dynamics, resolution and cDC2B depletion. cDC2 trajectories were inferred using VarID2 and{gamma}{delta} T cell transcription factor (TF) regulon activity was predicted by SCENIC. The human biliary niche was resolved by integrating human liver scRNA-seq data with available spatial transcriptomics data. Functional studies were conducted using Tcrd knockout, Il17a/f knockout and Tcrd reporter mice. ResultsA disease trajectory of Mgl2+ cDC2B was identified connecting DC maturation, homing and the expression of Il17-inducing genes. Disease progression was associated with numeric exhaustion of mature cDC2B and recruitment of DC precursors.{gamma}{delta} T cells were the main Il17 producers and were subtyped into Il17ahigh Scart1+ V{gamma}6+ and Il17low Scart2+ V{gamma}4+ populations exhibiting cDC2-directed communication and divergent TF regulon activity. Spatial proximity and conserved molecular interactions of cDC2 and{gamma}{delta} T cells were confirmed in human cholangitis. Il17-deficiency resulted in reduced liver fibrosis in mice, while cDC2B depletion attenuated{gamma}{delta} T17 cell states. ConclusionsIn cholangitis, a profibrogenic function of{gamma}{delta} T cells is contingent on the induction by peribiliary cDC2B, thereby highlighting relevant disease determinants within the immunobiliary and liver-draining LN niche. Impact and ImplicationsThe immunobiliary niche contains rare immune cells such as conventional dendritic cells and unconventional T cells, however, the function of these cell types in liver inflammation remains poorly understood. Mirroring human biliary diseases such as primary sclerosing cholangitis, we induced experimental cholangitis in a mouse model to generate a site-specific single-cell sequencing atlas resource resolving underexplored cell populations. Our data capture a profibrotic hepatic disease state trajectory of Mgl2+ cDC2B inducing a{gamma}{delta} T cell-specific Il17-response, which is attenuated upon cDC2B depletion and in DC precursors, which are characterized by reduced genomic accessibility of{gamma}{delta} T cell-interacting genes. These results highlight the importance of portal niche residing underexplored immune cell populations and the necessity to further resolve immunobiliary niche responses and crosstalk in inflammatory settings such as in cholangitis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/664083v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d21193org.highwire.dtl.DTLVardef@7ff3dcorg.highwire.dtl.DTLVardef@630c78org.highwire.dtl.DTLVardef@c79f9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Mycobacterial infection uncovers plasticity of Kupffer cells

Bona fide Kupffer cells (KCs) are prenatally seeded and show unique functional and immunophenotypic features among tissue macrophages. They are considered as terminally differentiated, and adaptability in disease is attributed to recruited, monocyte-derived KCs. Here, we investigated the extent of KC plasticity and the impact of origin in mycobacterial infections that target macrophages and can persist for months. Fate-mapping combined with high-resolution imaging revealed the emergence of a unique, infection specific KC subset which downregulated the signature markers CLEC4F and VSIG4 ("KClow"). KClow were derived from bona fide KCs and located exclusively to granuloma cores. In contrast, monocyte-derived macrophages were contained at the granuloma borders and contributed to this tissue reaction. ATAC and single-cell RNA sequencing identified a specific signature of KClow with high antimycobacterial activity and specialization to a hypoxic microenvironment. Despite their fundamental deviation from the classical KC phenotype, KClow showed remarkable adaptability, and were capable to return to a homeostatic-like KC state. Accordingly, mycobacterial infections unmask KCs as highly plastic cells, capable of responding to extreme environmental changes.

immunology↗

bioRxiv2024

Suppression of meiotic crossovers in pericentromeric heterochromatin requires synaptonemal complex and meiotic recombination factors in Drosophila melanogaster

The centromere effect (CE) is a meiotic phenomenon that ensures meiotic crossover suppression in pericentromeric regions. Despite being a critical safeguard against nondisjunction, the mechanisms behind the CE remain unknown. Previous studies have shown that various regions of the Drosophila pericentromere, encompassing proximal euchromatin, beta and alpha heterochromatin, undergo varying levels of crossover suppression, raising the question of whether distinct mechanisms establish the CE in these different regions. To address this question, we asked whether different pericentromeric regions respond differently to mutations that impair various features that may play a role in the CE. In flies with a mutation that affects the synaptonemal complex (SC), a structure is hypothesized to have important roles in recombination and crossover patterning, we observed a significant redistribution of pericentromeric crossovers from proximal euchromatin towards beta heterochromatin but not alpha heterochromatin, indicating a role for the SC in suppressing crossovers in beta heterochromatin. In flies mutant for mei-218 or rec, which encode components of a critical pro-crossover complex, there was a more extreme redistribution of pericentromeric crossovers towards both beta and alpha heterochromatin, suggesting an important role for these meiotic recombination factors in suppressing heterochromatic crossovers. Lastly, we mapped crossovers in flies mutant for Su(var)3-9. Although we expected a strong alleviation of crossover suppression in heterochromatic regions, no changes in pericentromeric crossover distribution were observed in this mutant, indicating that this vital heterochromatin factor is dispensable to prevent crossovers in heterochromatin. Our results indicate that the meiotic machinery plays a bigger role in suppressing crossovers than the chromatin state.

genetics↗

bioRxiv2024

Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance

In a subset of SARS-CoV-2 infected individuals treated with the oral antiviral nirmatrelvir-ritonavir, the virus rebounds following treatment. The mechanisms driving this rebound are not well understood. We used a mathematical model to describe the longitudinal viral load dynamics of 51 individuals treated with nirmatrelvir-ritonavir, 20 of whom rebounded. Target cell preservation, either by a robust innate immune response or initiation of nirmatrelvir-ritonavir near the time of symptom onset, coupled with incomplete viral clearance, appear to be the main factors leading to viral rebound. Moreover, the occurrence of viral rebound is likely influenced by time of treatment initiation relative to the progression of the infection, with earlier treatments leading to a higher chance of rebound. Finally, our model demonstrates that extending the course of nirmatrelvir-ritonavir treatment, in particular to a 10-day regimen, may greatly diminish the risk for rebound in people with mild-to-moderate COVID-19 and who are at high risk of progression to severe disease. Altogether, our results suggest that in some individuals, a standard 5-day course of nirmatrelvir-ritonavir starting around the time of symptom onset may not completely eliminate the virus. Thus, after treatment ends, the virus can rebound if an effective adaptive immune response has not fully developed. These findings on the role of target cell preservation and incomplete viral clearance also offer a possible explanation for viral rebounds following other antiviral treatments for SARS-CoV-2. ImportanceNirmatrelvir-ritonavir is an effective treatment for SARS-CoV-2. In a subset of individuals treated with nirmatrelvir-ritonavir, the initial reduction in viral load is followed by viral rebound once treatment is stopped. We show the timing of treatment initiation with nirmatrelvir-ritonavir may influence the risk of viral rebound. Nirmatrelvir-ritonavir stops viral growth and preserves target cells but may not lead to full clearance of the virus. Thus, once treatment ends, if an effective adaptive immune response has not adequately developed, the remaining virus can lead to rebound. Our results provide insights into the mechanisms of rebound and can help develop better treatment strategies to minimize this possibility.

immunology↗

bioRxiv2021

Obesity impairs therapeutic efficacy of mesenchymal stem cells by inhibiting cardiolipin-dependent mitophagy and intercellular mitochondrial transfer in mouse models of airway allergic inflammation

Mesenchymal stem cell (MSC) transplantation alleviates metabolic defects in diseased recipient cells by intercellular mitochondrial transport (IMT). However, the effect of host metabolic conditions on MSCs in general, and IMT in particular, has largely remained unexplored. This study has identified a molecular pathway that primarily governs the metabolic function and IMT of MSCs. We found underlying mitochondrial dysfunction, impaired mitophagy, and reduced IMT in MSCs derived from high-fat diet (HFD)-induced obese mice (MSC-Ob). Mechanistically, MSC-Ob failed to sequester their damaged mitochondria into LC3-dependent autophagosomes due to decrease in mitochondrial cardiolipin content, which we propose as a putative mitophagy receptor for LC3 in MSCs. Functionally, MSC-Ob exhibited diminished potential to rescue metabolic deficits and cell death in stress-induced epithelial cells. In a small molecule screen, we found pyrroloquinoline quinone (PQQ) as a regulator of mitophagy and IMT. Long-term culture of MSC-Ob with PQQ (MSC-ObPQQ) restored cardiolipin content and sequestration of mitochondria to autophagosomes with concomitant activation of mitophagy. Upon co-culture, MSC-ObPQQ rescued cell death in stress-induced epithelial cells by enhancing IMT. The beneficial effect of PQQ was also evident in MSCs derived from human subjects in an in vitro model. In two independent mice models, the transplantation of MSC-ObPQQ restored IMT to airway epithelial cells, improved their mitochondrial metabolism and attenuated features of allergic airway inflammation (AAI). However, unmodulated MSC-Ob failed to do so. In summary, we uncover the molecular mechanism leading to the therapeutic decline of obese-derived MSCs and highlight the importance of pharmacological modulation of these cells for therapeutic intervention.

cell biology↗

bioRxiv2020

Bromelain Inhibits SARS-CoV-2 Infection in VeroE6 Cells

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The initial interaction between Transmembrane Serine Protease 2 (TMPRSS2) primed SARS-CoV-2 spike (S) protein and host cell receptor angiotensin-converting enzyme 2 (ACE-2) is a pre-requisite step for this novel coronavirus pathogenesis. Here, we expressed a GFP-tagged SARS-CoV-2 S-Ectodomain in Tni insect cells. That contained sialic acid-enriched N- and O-glycans. Surface resonance plasmon (SPR) and Luminex assay showed that the purified S-Ectodomain binding to human ACE-2 and immunoreactivity with COVID-19 positive samples. We demonstrate that bromelain (isolated from pineapple stem and used as a dietary supplement) treatment diminishes the expression of ACE-2 and TMPRSS2 in VeroE6 cells and dramatically lowers the expression of S-Ectodomain. Importantly, bromelain treatment reduced the interaction between S-Ectodomain and VeroE6 cells. Most importantly, bromelain treatment significantly diminished the SARS-CoV-2 infection in VeroE6 cells. Altogether, our results suggest that bromelain or bromelain rich pineapple stem may be used as an antiviral against COVID-19. Highlights O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/297366v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@b7afb0org.highwire.dtl.DTLVardef@16f8185org.highwire.dtl.DTLVardef@1a07df8org.highwire.dtl.DTLVardef@1ae33fa_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIBromelain inhibits / cleaves the expression of ACE-2 and TMPRSS2 C_LIO_LIBromelain cleaves / degrades SARS-CoV-2 spike protein C_LIO_LIBromelain inhibits S-Ectodomain binding and SARS-CoV-2 infection C_LI

microbiology↗

bioRxiv2020

Spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation

Anterior mesoderm (AM) and definitive endoderm (DE) progenitors represent the earliest embryonic cell types that are specified during germ layer formation at the primitive streak (PS) of the mouse embryo. Genetic experiments indicate that both lineages segregate from Eomes expressing progenitors in response to different NODAL signaling levels. However, the precise spatiotemporal pattern of the emergence of these cell types and molecular details of lineage segregation remain unexplored. We combined genetic fate labeling and imaging approaches with scRNA-seq to follow the transcriptional identities and define lineage trajectories of Eomes dependent cell types. All cells moving through the PS during the first day of gastrulation express Eomes. AM and DE specification occurs before cells leave the PS from discrete progenitor populations that are generated in distinct spatiotemporal patterns. Importantly, we dont find evidence for the existence of progenitors that co-express markers of both cell lineages suggesting an immediate and complete separation of AM and DE lineages. Summary statementCells lineages are specified in the mouse embryo already within the primitive streak where Mesp1+ mesoderm and Foxa2+ endoderm are generated in a spatial and temporal sequence from unbiased progenitors.

developmental biology↗

bioRxiv2020

Adhatoda Vasica ameliorates cellular hypoxia dependent mitochondrial dysfunction in acute and severe asthmatic mice.

Severe asthma is a chronic airway disease that exhibits poor response to conventional asthma therapies. Growing evidence suggests that elevated hypoxia increases the severity of asthmatic inflammation among patients and in model systems. In this study, we elucidate the therapeutic effects and mechanistic basis of Adhatoda Vasica (AV) aqueous extract on mouse models of acute allergic as well as severe asthma subtypes at physiological, histopathological, and molecular levels. Oral administration of AV extract attenuates the increased airway resistance and inflammation in acute allergic asthmatic mice and alleviates the molecular signatures of steroid (dexamethasone) resistance like IL-17A, KC, and HIF-1 (hypoxia inducible factor-1alpha) in severe asthmatic mice. AV inhibits HIF-1 levels through restoration of expression of its negative regulator-PHD2 (prolyl hydroxylase domain-2). Alleviation of hypoxic response mediated by AV is further confirmed in the acute and severe asthma model. AV reverses cellular hypoxia-induced mitochondrial dysfunction in human bronchial epithelial cells - evident from bioenergetic profiles and morphological analysis of mitochondria. In silico docking of AV constituents reveal higher negative binding affinity for C and O-glycosides for HIF-1, IL-6, Janus kinase 1/3, TNF- and TGF-{beta}-key players of hypoxia-inflammation. This study for the first time provides a molecular basis of action and effect of AV whole extract that is widely used in Ayurveda practice for diverse respiratory ailments. Further, through its effect on hypoxia-induced mitochondrial dysfunction, the study highlights its potential to treat severe steroid-resistant asthma. Significance StatementSevere asthma is a global health concern with a large fraction unresponsive to current treatment modalities involving corticosteroids. Recent findings suggest that elevated hypoxia has a critical role in severity of asthma. Here, we report therapeutic treatment with aqueous extract of Adhatoda Vasica (AV), an ayurvedic medicine, attenuates sever steroid insensitive asthmatic features in mice. The observed effects of AV are through inhibition of hypoxic response, both in vivo and in vitro. AV also reverses mitochondrial dysfunction, a key consequence associated with hypoxia, and asthma. This study highlights the translational potential of AV for the treatment of severe asthma and provides opportunities for its usage in other disease conditions where hypoxia is pertinent.

immunology↗

bioRxiv2018

Deciphering the Regulatory Landscape of γδ T Cell Development by Single-Cell RNA-Sequencing

Recent studies have established{gamma}{delta} T cells as critical players in a broad range of infections, antitumor surveillance, autoimmune diseases and tissue homeostasis. However, differentiation of{gamma}{delta} T cells in the adult thymus remains poorly understood, due to the rare frequency of this lineage. Here, we infer high-resolution developmental trajectories of this rare population by single-cell RNA-sequencing. We reveal previously unknown subtypes and identify the transcription factor c-MAF as a novel key regulator of IL-17-producing{gamma}{delta} T cell ({gamma}{delta}T17) differentiation. c-MAF knockout mice exhibit a complete block in{gamma}{delta} T17 differentiation, absence of these cells from peripheral organs, and protection from an autoimmune phenotype in a psoriasis model. Single-cell RNA-sequencing of Sox13 and Rorc knockout mice pinpoints c-MAF as an essential missing link between these lineage-specifying factors. These findings significantly enhance our understanding of{gamma}{delta} T cell ontogeny. Our experimental strategy provides a blueprint for deciphering differentiation of rare cell types.

immunology↗

bioRxiv2017

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

Differentiation of multipotent cells is a complex process governed by interactions of thousands of genes subject to substantial expression fluctuations. Resolving cell state heterogeneity arising during this process requires quantification of gene expression within individual cells. However, computational methods linking this heterogeneity to biases towards distinct cell fates are not well established. Here, we perform deep single-cell transcriptome sequencing of ~2,000 bone-marrow derived mouse hematopoietic progenitors enriched for lymphoid lineages. To resolve subtle transcriptome priming indicative of distinct lineage biases, we developed FateID, an iterative supervised learning algorithm for the probabilistic quantification of cell fate bias. FateID delineates domains of fate bias within progenitor populations and permits the derivation of high-resolution differentiation trajectories, revealing a common progenitor population of B cells and plasmacytoid dendritic cells, which we validated by in vitro differentiation assays. We expect that FateID will enhance our understanding of the process of cell fate choice in complex multi-lineage differentiation systems.

bioinformatics↗