Biology subjects

Holcomb, N. P.

Publications and source records attributed to Holcomb, N. P..

7 recordsLinked to original sources

bioRxiv2026

A Bioactive Phospholipid Promotes Rapid Progenitor Lung Progenitor Activation via AP-1

Upon injury to the distal lung, alveolar type 2 cells (AT2s) must make a discrete switch from surfactant factories to stem cells capable of regeneration, which involves both proliferation and differentiation into oxygen-exchanging alveolar type 1 (AT1) cells. However, the discrete signals and molecular pathways facilitating this fundamental switch in AT2 functionality are uncertain. Here we demonstrate that the bioactive lipid lysophosphatidic acid (LPA), typically associated with driving fibrosis, is an extremely efficient inducer of this state change in comparison to previously implicated signals IL-1{beta} and p53 stabilization. We observed endogenous production and accumulation of LPA in influenza-injured murine lungs, creating a microenvironment that facilitates AT2 progenitor switching. Multiple transcriptomic approaches reveal elevation of Fosl1 and Jun, core members of the Activator Protein 1 (AP-1) transcription factor family, in response to LPA. Using novel genetic models combined with influenza injury, we demonstrate that AP-1 activity in AT2s is necessary for effective alveolar regeneration at both the cellular and physiologic levels. These findings unveil a critical relationship between paracrine LPA and cell-intrinsic AP-1 in facilitating effective lung alveolar regeneration. HighlightsO_LILPA facilitates progenitor switching in lung regeneration via initiation of a discrete transcriptomic state C_LIO_LILPA promotes AT2 state switching via Jun (AP-1) C_LIO_LIImpaired AP-1 signaling significantly restricts recovery from influenza infection C_LI

cell biology↗

bioRxiv2026

Influenza-induced tuft cell expansion alters ILC-mediated inflammation

Tuft cells act as sentinels that amplify type 2 inflammation primarily by activating type 2 innate lymphoid cells (ILC2s). Although normally absent from the distal lung, ectopic tuft cells form after severe lung injury including influenza infection in mice. Here, we investigated the function of these ectopic tuft cells in shaping innate immunity following influenza injury. We observed that IFN{gamma} restrains tuft cell differentiation, whereas ILC2s drive tuft cell expansion, establishing a reciprocal regulatory axis. Tuft cell-deficient mice exhibited reduced eosinophilic inflammation and expansion of ILC1s and ILC3s after influenza injury resolution. Single-cell RNA-seq of influenza infected whole lung revealed transcriptional signatures consistent with type 1 pathway activation, type 2 suppression and oxidative stress. Following influenza injury and subsequent Alternaria alternata challenge, tuft cell-deficient mice also showed neutrophilic and ILC3 expansion. Together, these data identify a distal-airway tuft-cell-ILC2 circuit that helps maintain a balanced inflammatory environment in response to viral injury and aeroallergens.

molecular biology↗

bioRxiv2026

Dysplastic Epithelial Repair Propagates Chronic Pathology Through the Paracrine Transformation of Pulmonary Fibroblasts

Severe lung injury promotes the ectopic accumulation of basal cells in the alveoli and the presence of these dysplastic epithelial cells are strongly associated with regions of pulmonary fibrosis (PF) in diseased lungs. Recent studies have identified a unique subset of "inflammatory" fibroblasts expressing pro-inflammatory genes, especially cytokines involved in monocyte recruitment, that are also enriched in disease and thought to contribute to the onset and progression of PF. Here we show that these two injury-induced cell types are intricately connected, in that dysplastic basal cells generate diffusible signals to robustly induce the inflammatory phenotype in pulmonary fibroblasts. Capitalizing on transcriptomic analysis, we identify the enriched inflammatory signaling pathways in treated fibroblasts and specifically demonstrate that IL-1 secreted by dysplastic basal cells is responsible for this fibroblastic transformation. IL-1 neutralization in vivo is sufficient to significantly reduce the inflammatory fibroblast burden in regions of alveolar bronchiolization, and the resolution of inflammatory fibroblasts in turn reduces CCR2+ immune cell recruitment to these areas. These results suggest dysplastic basal cells play an indirect role in chronic inflammation and fibrotic remodeling through the induction of a proinflammatory fibroblast phenotype and subsequent recruitment of immune cells, establishing a chronic wound healing microenvironment that prolongs localized pathologic remodeling.

cell biology↗

bioRxiv2024

Disruption of Immune Responses By Type I Diabetes Exacerbates SARS-CoV-2 Mediated Lung Injury

COVID-19 commonly presents as pneumonia, with those most severely affected progressing to respiratory failure. Patient responses to SARS-CoV-2 infection are varied, with comorbidities acting as major contributors to varied outcomes. Focusing on one such major comorbidity, we assessed whether pharmacological induction of Type I Diabetes Mellitus (T1DM) would increase the severity of lung injury in a murine model of COVID-19 pneumonia utilizing wild type mice infected with mouse-adapted SARS-CoV-2. Hyperglycemic mice exhibited increased weight loss and reduced blood oxygen saturation in comparison to their euglycemic counterparts, suggesting that these animals indeed experienced more severe lung injury. Transcriptomic analysis revealed a significant impairment of the adaptive immune response in the lungs of diabetic mice compared to those of control. In order to expand the limited options available for tissue analysis due to biosafety restrictions, we also employed a novel technique to digest highly fixed tissue into a single cell suspension, which allowed for flow cytometric analysis as well as single cell RNA sequencing. Flow immunophenotyping and scRNA-Seq confirmed impaired recruitment of T cells into the lungs of T1DM animals. Additionally, scRNA-Seq revealed a distinct, highly inflammatory macrophage profile in the diabetic cohort that correlates with the more severe infection these mice experienced clinically, allowing insight into a possible mechanism for this phenomenon. Recognizing the near certainty that respiratory viruses will continue to present significant public health concerns for the foreseeable future, our study provides key insights into how T1DM results in a much more severe infection and identifies possible targets to ameliorate comorbidity-associated severe disease. NEW AND NOTEWORTHYWe define the exacerbating effects of Type I Diabetes Mellitus (T1DM) on COVID-19 pneumonia severity in mice. Hyperglycemic mice experienced increased weight loss and reduced oxygen saturation. Transcriptomic analysis revealed impaired immune responses in diabetic mice, while flow cytometry and single-cell RNA sequencing confirmed reduced T cell recruitment and an inflammatory macrophage profile. Additionally, we introduced a novel technique for tissue analysis, enabling flow cytometric analysis and single-cell RNA sequencing on highly fixed tissue samples.

immunology↗

bioRxiv2023

Vascular Endothelial-derived SPARCL1 Exacerbates Viral Pneumonia Through Pro-Inflammatory Macrophage Activation

Inflammation upon infectious lung injury is a double-edged sword: while tissue-infiltrating immune cells and cytokines are necessary to control infection, these same factors often aggravate injury. Full appreciation of both the sources and targets of inflammatory mediators is required to facilitate strategies to maintain antimicrobial effects while minimizing off-target epithelial and endothelial damage. Recognizing that the vasculature is centrally involved in tissue responses to injury and infection, we observed that pulmonary capillary endothelial cells (ECs) exhibit dramatic transcriptomic changes upon influenza injury punctuated by profound upregulation of Sparcl1. Endothelial deletion and overexpression of SPARCL1 implicated this secreted matricellular protein in driving key pathophysiologic symptoms of pneumonia, which we demonstrate result from its effects on macrophage polarization. SPARCL1 induces a shift to a pro-inflammatory "M1-like" phenotype (CD86+CD206-), thereby increasing associated cytokine levels. Mechanistically, SPARCL1 acts directly on macrophages in vitro to induce the pro-inflammatory phenotype via activation of TLR4, and TLR4 inhibition in vivo ameliorates inflammatory exacerbations caused by endothelial Sparcl1 overexpression. Finally, we confirmed significant elevation of SPARCL1 in COVID-19 lung ECs in comparison with those from healthy donors. Survival analysis demonstrated that patients with fatal COVID-19 had higher levels of circulating SPARCL1 protein compared to those who recovered, indicating the potential of SPARCL1 as a biomarker for prognosis of pneumonia and suggesting that personalized medicine approaches might be harnessed to block SPARCL1 and improve outcomes in high-expressing patients.

immunology↗

bioRxiv2022

Injury-induced pulmonary tuft cells are heterogenous, arise independent of key Type 2 cytokines, and are dispensable for dysplastic repair

While the lung bears significant regenerative capacity, severe viral pneumonia can chronically impair lung function by triggering dysplastic remodeling. The connection between these enduring changes and chronic disease remains poorly understood. We recently described the emergence of tuft cells within Krt5+ dysplastic regions after influenza injury. Using bulk and single cell transcriptomics, we characterized and delineated multiple distinct tuft cell populations that arise following influenza clearance. Distinct from intestinal tuft cells which rely on Type 2 immune signals for their expansion, neither IL-25 nor IL-4R signaling are required to drive tuft cell development in dysplastic/injured lungs. Furthermore, tuft cells were also observed upon bleomycin injury, suggesting that their development may be a general response to severe lung injury. While intestinal tuft cells promote growth and differentiation of surrounding epithelial cells, in the lungs of tuft cell deficient mice, Krt5+ dysplasia still occurs, goblet cell production is unchanged, and there remains no appreciable contribution of Krt5+ cells into more regionally appropriate alveolar Type 2 cells. Together, these findings highlight unexpected differences in signals necessary for lung tuft cell amplification and establish a framework for future elucidation of tuft cell functions in pulmonary health and disease.

cell biology↗

bioRxiv2022

ΔNp63 drives dysplastic alveolar remodeling and restricts epithelial plasticity upon severe lung injury

Unlike many mammalian vital organs, the lung exhibits a robust, multifaceted regenerative response to severe injuries such as influenza infection, which primarily targets epithelial cells in the airways and alveoli. Quiescent lung-resident epithelial progenitors proliferate, migrate, and differentiate following lung injury, participating in two distinct reparative pathways: functionally beneficial regeneration and dysplastic tissue remodeling. Intrapulmonary airway-resident basal-like p63+ progenitors are one such progenitor cell type that migrates from the airways to form ectopic bronchiolar tissue in the alveoli, generating honeycomb-like cysts that fail to resolve after injury. Though this phenomenon is now well described, the cell-autonomous signals that drive dysplastic alveolar remodeling remain uncertain, a question made especially salient by observations that p63+ progenitors also expand dramatically upon diffuse alveolar damage in humans resulting from a variety of insults including SARS-CoV-2-induced ARDS. Here we show that the master basal cell transcription factor {Delta}Np63 is required for the immense migratory capacity of intrapulmonary p63+ progenitors and consequently for the dysplastic repair pathway manifest by these cells. We further demonstrate that {Delta}Np63 restricts the fate plasticity of intrapulmonary p63+ progenitors by regulating their epigenetic landscape, and that loss of {Delta}Np63 alters the deposition of active and repressive histone modifications at key differentiation gene loci, allowing {Delta}Np63KO progenitors to proceed towards airway or alveolar differentiation depending on their surrounding environment. These insights into the regulatory mechanisms of dysplastic repair and intrapulmonary p63+ progenitor fate choice highlight potential therapeutic targets to promote more effective alveolar regeneration following severe lung injuries.

molecular biology↗