Biology subjects

Naikawadi, R. P.

Publications and source records attributed to Naikawadi, R. P..

4 recordsLinked to original sources

bioRxiv2026

Comparative molecular analysis of histopathologic subtypes reveals shared epithelial remodeling yet distinct fibroblast programs in scleroderma lung disease

Rationale: Interstitial lung disease (ILD) drives mortality in systemic sclerosis (SSc), with a subset developing progressive pulmonary fibrosis (PPF) resembling idiopathic pulmonary fibrosis (IPF). Despite recognition of two distinct histopathologic patterns, the cellular basis of nonspecific interstitial pneumonia (NSIP) and usual interstitial pneumonia (UIP) remains poorly understood. Objectives: To define shared and distinct cellular and molecular features of SSc-NSIP and SSc-UIP compared to IPF. Methods: Single-nucleus RNA sequencing and spatial transcriptomics were performed on explanted lungs from patients with SSc-NSIP (n=6), SSc-UIP (n=6), or IPF (n=6), and control donors (n=12) with immunohistochemistry and western blot validation. Main Results: Across 120,254 nuclei from 35 cell types, there was striking similarity across fibrotic subgroups in epithelial, endothelial, and immune compartments, including alveolar type 1 cell loss, pathologic alveolar type 2 (AT2) gene expression, and expansion of COL15A1 endothelial cells and profibrotic macrophages. Diseased AT2s showed activation of the p53/DNA damage pathway. Aberrant basaloid (AB) cells were present in both SSc-ILD subtypes and transcriptionally similar to IPF ABs. They consistently neighbored profibrotic CTHRC1 fibroblasts, even in SSc-NSIP, despite lacking fibroblast foci. Fibroblast heterogeneity differentiated the histopathologic subtypes. Inflammatory fibroblasts were enriched in SSc-NSIP and CTHRC1 fibroblasts in UIP. AB-to-pathologic fibroblast crosstalk was defined by profibrotic signaling, with amplified TGF-{beta} signaling in UIP. Conclusions: Convergent epithelial remodeling is a hallmark of PPF in SSc-ILD and IPF. Fibroblast heterogeneity characterized by altered TGF-beta signaling distinguishes SSc-NSIP from SSc-UIP and IPF. Accelerated aging, DNA damage, and p53-dependent senescence pathways may represent shared drivers of PPF.

genomics↗

bioRxiv2026

NINTEDANIB AND PIRFENIDONE AFFECT GROWTH AND DIFFERENTIATION OF HUMAN ALVEOLAR TYPE 2 CELLS

BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease characterized by epithelial cell senescence. Pirfenidone and nintedanib are approved drugs for the treatment of IPF. They significantly slow disease progression, but their mechanisms of action, especially on alveolar type 2 (AT2) cells, are poorly understood. We addressed this question by evaluating colony formation and growth of human AT2 cells co-cultured with fibroblasts in organoid culture in the presence of pirfenidone and nintedanib. We further evaluated molecular changes induced by these drugs via single cell RNA-seq of treated organoids. MethodsAT2 cells isolated from normal donor lungs or IPF patients were mixed with human fibroblasts in 3D culture and grown in the absence or presence of pirfenidone or nintedanib. After 14 days in culture, the organoids were quantified and cells extracted from Matrigel for single cell RNA-seq. ResultsAT2 cell organoids cultured in the presence of pirfenidone or nintedanib resulted in increased colony formation and, in the case of nintedanib, in larger colonies. We observed that untreated or pirfenidone treated AT2 cells lost surfactant protein C (SFTPC) expression and acquired an expression profile consistent with keratin (KRT)17high/KRT5- basaloid cells, whereas a larger proportion of nintedanib treated cells retained SFTPC expression. In contrast, AT2 cells treated with TGF{beta} inhibitor exhibited intermediate (SFTPC-/KRT17low) gene expression profile. ConclusionThese results suggest that nintedanib maintains an AT2-like expression state in culture and acts proximal to TGF{beta}. Conflict of Interest StatementPJW was supported by grants from Boehringer Ingelheim, Roche, Sanofi, Pliant and Arda Therapeutics and received personal fees from Boehringer Ingelheim and Sanofi. None of these companies had a role in the design or analysis of the study or in the writing of the manuscript. ASM, GP, JRR and DG are employees of Genetech. The other authors have no conflicts of interest to declare.

cell biology↗

bioRxiv2025

Cellular profiling identifies an early profibrotic alveolar type 2 cell signature in lung fibrosis

RationaleIdiopathic pulmonary fibrosis (IPF) is a progressive, age-associated, lung disease characterized by short telomeres in alveolar type 2 (AT2) cells, epithelial remodeling, and fibrosis. ObjectivesThis study investigated how telomere dysfunction in AT2 cells lacking Telomere Repeat Binding Factor 1 (TRF1) drives lung remodeling in SPC-creTRF1flox/flox mice and its relevance to IPF. MethodsMouse model of telomere dysfunction was used to conditionally delete TRF1 in AT2 cells. SPC-creTRF1flox/flox mouse lung epithelial cells were used to perform single cell RNA sequencing. AT2 cells from IPF lungs were analyzed by single cell RNA sequencing in an organoid model. Measurements and Main ResultsSingle cell RNA-sequencing revealed distinct pathological AT2 cells enriched in DNA damage, senescence, oxidative stress, and pro-fibrotic genes, along with fewer "normal" AT2 cells and increased club cells in SPC-creTRF1flox/flox mice. Pathological AT2 cells showed different early and late-stage gene signatures, with a prominent p53 signature at both time-points. Genetic deletion of p53 in SPC-creTRF1flox/flox AT2 cells improved survival and prevented lung fibrosis. p53 deletion or inhibition improved organoid formation, surfactant protein C expression, and reduced pro-fibrotic gene expression in AT2 cells isolated from SPC-creTRF1flox/flox mice or IPF lungs. ConclusionsThese data suggest that the DNA damage response to AT2 cell telomere dysfunction, driven by enhanced p53 activity, mediates early AT2 cell transdifferentiation and senescence, leading to epithelial cell remodeling and fibrosis and that reversing this reprogramming is a potential therapeutic approach for managing IPF.

cell biology↗

bioRxiv2019

Telomere Dysfunction Drives Chronic Lung Allograft Dysfunction Pathology

RationaleTelomere dysfunction is associated with multiple fibrotic lung processes, including chronic lung allograft dysfunction (CLAD) which is a major limitation to long-term survival following lung transplantation. Although shorter donor telomere lengths are associated with an increased risk of CLAD, it is unknown whether short telomeres are a cause or consequence of CLAD pathology.\n\nObjectiveOur objective was to test whether telomere dysfunction contributes to pathologic changes seen in CLAD.\n\nMethods and ResultsHistopathologic and molecular analysis of human CLAD lungs demonstrated shortened telomeres in lung epithelial cells quantified by teloFISH, increased numbers of surfactant protein C immunoreactive type II alveolar epithelial cells (AECs), and increased expression of senescence markers (beta-galactosidase, p16, p53 and p21) in lung epithelial cells. Telomere repeat binding factor 1 flox/flox (TRF1F/F) mice were crossed with tamoxifen inducible SCGB1a1-cre mice to generate SCGB1a1-creTRF1 F/F mice. Following 9 months of tamoxifen-induced deletion of TRF1 in club cells, mice developed mixed obstructive and restrictive lung physiology, small airway obliteration on micro-computed tomography, a 4-fold decrease in telomere length in airway epithelial cells, collagen deposition around bronchioles and adjacent lung parenchyma, increased type II AEC numbers, expression of senescence-associated beta-galactosidase in epithelial cells and decreased SCGB1a1 expression in airway epithelial cells.\n\nConclusionsThese findings demonstrate that telomere dysfunction isolated to club cells leads to airway-centric lung remodeling and fibrosis similar to that observed in patients with CLAD and suggest that lung epithelial cell telomere dysfunction may be a molecular driver of CLAD.

cell biology↗