Biology subjects

Singh, R. B.

Publications and source records attributed to Singh, R. B..

4 recordsLinked to original sources

bioRxiv2026

IL-27 Signaling Protects Against Influenza-Associated Pulmonary Aspergillosis Through Inhibition of Type 2 Immunity and Enhanced Antifungal Immunity

Influenza-associated pulmonary aspergillosis (IAPA) is a severe complication of influenza infection associated with substantial mortality. Influenza disrupts pulmonary host defenses and alters innate immune responses, predisposing patients to invasive fungal infection. Interleukin-27 (IL-27) is an immunoregulatory cytokine with context-dependent antiviral and antifungal effects; however, its role during IAPA remains undefined. A mouse model of IAPA was established by infecting wild-type and IL-27 receptor -deficient (Il27ra-/-) mice with influenza A, followed by Aspergillus fumigatus challenge. IL-27 and IL-27R expression were increased during IAPA. Single-cell RNA sequencing identified monocytes as the primary source of IL-27 and T cells as major IL-27r-expressing cells. Il27ra-/- mice exhibited significantly increased pulmonary fungal and influenza viral burden, enhanced type 2 immune responses characterized by elevated IL-4, IL-5, IL-9, IL-13, eosinophils, Th2 cells, pathogenic Th2 cells, and ILC2s. Despite increased eosinophil abundance, eosinophil-mediated conidial killing was impaired in Il27ra-/- mice. IL-27R deficiency also reduced macrophage abundance and impaired macrophage conidial uptake. Conversely, timed administration of rIL-27 enhanced fungal clearance, improved survival, and increased macrophage conidial uptake and augmented eosinophil killing capacity during IAPA. IL-27 signaling is a protective immunoregulatory cytokine during IAPA that limits pathological type 2 inflammation and enhances antifungal effector function of both eosinophils and macrophages. These findings identify IL-27 as a potential therapeutic in IAPA.

immunology↗

bioRxiv2026

Broad remodeling of the pulmonary immune landscape occurs during IAPA with specific functional deficits of neutrophil subsets

BackgroundInfluenza-associated pulmonary aspergillosis (IAPA) is a severe complication of influenza infection associated with prolonged intensive care unit stay and increased mortality. Although impaired antifungal immunity has been implicated in IAPA pathogenesis, the cell type-specific immune mechanisms driving susceptibility remain incompletely understood. We aimed to characterize the pulmonary immune landscape during IAPA using single-cell transcriptomics and functional neutrophil assays. MethodsMale C57BL/6 mice were assigned to naive control, influenza A/PR/8/34 (H1N1) infection, A. fumigatus (ATCC 42202) infection, or IAPA groups. Lung CD45+ immune cells underwent single-cell RNA sequencing with downstream clustering and CellChat ligand-receptor interaction analysis. Differential gene expression analyses were performed across myeloid, lymphoid, and neutrophil populations. Functional neutrophil responses were evaluated using flow cytometry, myeloperoxidase activity assays, and FLARE (fluorescent Aspergillus reporter) conidia to assess fungal conidia uptake and killing. Cross-species validation was performed using gene set enrichment analysis compared with published human IAPA transcriptomic datasets. ResultsIAPA broadly remodeled the pulmonary immune landscape across myeloid, lymphoid, and neutrophil compartments. Myeloid cells showed coordinated suppression of fungal pattern recognition receptors, lysosomal biogenesis programs, and inflammatory signaling. Lymphoid populations exhibited transcriptional signatures of T cell exhaustion and Th17 suppression. Within the neutrophil compartment, we identified two transcriptionally and functionally distinct populations, conventional and inflammatory neutrophils, with divergent antifungal effector capacities. Inflammatory neutrophils showed selective killing defects, while both subsets exhibited impaired phagocytic uptake during IAPA. Murine transcriptomic findings demonstrated strong concordance with immune dysfunction signatures identified in human IAPA. ConclusionIAPA susceptibility arises from coordinated transcriptional dysfunction spanning innate and adaptive immune compartments. Distinct neutrophil subset dysfunction, impaired fungal recognition pathways, and T-cell exhaustion signatures collectively contribute to defective fungal clearance, providing mechanistic insight into IAPA susceptibility and potential therapeutic targets.

immunology↗

bioRxiv2019

Pathological circadian rhythm states driven by CK2 and noise

Circadian rhythm maintains sleep-wake cycle in living systems. Disruption of this rhythm may cause diseases. We propose an extended Drosophila circadian rhythm model incorporating cross-talk of CK2 with Per protein. We studied the model using stochastic simulation algorithm, and the behavior of the amplitude, time period and permutation entropy us identify three distinct circadian states namely, active, weak activity, active, weak activity and rhythmic death all driven by CK2. These states may correspond to distinct pathological cellular states of the living system. Noise, an important factor, has ability to switch normal circadian rhythm to any of the three aforementioned circadian states. Fluctuations in systems size, can help us in deterning the extent of noise present. We also highlighted that disruption in circadian rhythm may lead to various diseases including cancer. We present various cellular pathways driven by per mutant genes and their pathological states.\n\nStatement of significanceCircadian rhythm, which is one of the most important biological rhythm, regulates and intervenes various cellular processes. Significant changes in the rhythmic dynamics may lead to pathological states which may trigger various diseases. In this work, the impact of CK2 via per gene mutants on rhythmic dynamics is investigated, and found three distinct states, namely, active, weak activity and rhythmic death driven by CK2 which may correspond to various cellular states. Noise due to intrinsic random molecular events and cellular size variability is found to have the capability of regulating and controlling rhythmic properties, and can trigger to the three rhythmic states. We then listed various possible pathways which are regulated by per gene mutants and corresponding various possible pathological states.

systems biology↗

bioRxiv2019

First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis)

This study reports the first haplotype phased reference quality genome assembly of Murrah an Indian breed of river buffalo. A mother-father-progeny trio was used for sequencing so that the individual haplotypes could be assembled in the progeny. Parental DNA samples were sequenced on the Illumina platform to generate a total of 274 Gb paired-end data. The progeny DNA sample was sequenced using PacBio long reads and 10x Genomics linked reads at 166x coverage along with 802Gb of optical mapping data. Trio binning based FALCON assembly of each haplotype was scaffolded with 10x Genomics reads and super-scaffolded with BioNano Maps to build reference quality assembly of sire and dam haplotypes of 2.63Gb and 2.64Gb with just 59 and 64 scaffolds and N50 of 81.98Mb and 83.23Mb, respectively. BUSCO single copy core gene set coverage was > 91.25%, and gVolante-CEGMA completeness was >96.14% for both haplotypes. Finally, RaGOO was used to order and build the chromosomal level assembly with 25 scaffolds and N50 of 117.48 Mb (sire haplotype) and 118.51 Mb (dam haplotype). The improved haplotype phased genome assembly of river buffalo may provide valuable resources to discover molecular mechanisms related to milk production and reproduction traits.

genomics↗