Biology subjects

Ranade, S. S.

Publications and source records attributed to Ranade, S. S..

7 recordsLinked to original sources

bioRxiv2026

A Compact Regulatory Logic Governs Fibroblast Cell State Plasticity in Fibrosis

Fibroblast activation drives organ failure across human diseases, yet its regulatory basis remains largely undefined. Here, we repressed 280 conserved disease-activated enhancers using CRISPR droplet sequencing (CROP-seq) in ~550,000 fibroblasts, constructing a regulome of 15 gene programs governing the profibrotic state. Systematic TF perturbation converged on MEOX1 as a central regulator, and fibroblast-specific Meox1 deletion in mice improved cardiac function, reduced fibrosis, and rewired profibrotic fibroblasts toward quiescence in heart failure. Effector gene perturbation in human cardiac fibroblasts revealed distinct regulators of contractility, migration, and inflammatory signaling, and these programs were conserved across profibrotic states in human lung, liver, and skin. Simultaneous repression of just six enhancers using a multiplexed dCas12a-KRAB system collapsed the profibrotic network, suppressed migration and contraction, and rewired fibroblast paracrine signaling to attenuate macrophage inflammation. These findings define the regulatory logic of fibroblast plasticity and establish a new framework for reprogramming profibrotic cell states in disease.

genomics↗

bioRxiv2026

Autophagy flux during human aging is sex- and cell type-specific, and is associated with physical fitness

Autophagy is widely proposed to decline with age; however, direct evidence for this across cell and tissue types in humans remains limited. Furthermore, it remains unknown whether interventions that improve physiological health during aging can modify autophagic activity in humans. Here, we performed transcriptomic and functional autophagy analyses across subject-matched human cell types from a healthy aging cohort spanning the adult lifespan. RNA-seq of primary dermal fibroblasts and induced neurons (iNs) revealed increased transcription of many autophagy-related genes with age, most markedly in fibroblasts. The impact of age on autophagic activity, measured using autophagy flux assays, was cell type- and sex-dependent, and uncoupled from autophagy-gene transcription. Autophagy flux decreased with age in male fibroblasts, was unchanged in female fibroblasts, and increased in female iNs. In freshly isolated peripheral blood mononuclear cells (PBMCs), autophagy flux became more heterogeneous with age and trended higher in older individuals, independent of sex. Although autophagy flux levels did not match across different cell types, higher autophagy flux in all cell types was associated with reduced physical function in older adults ([≥]70 years). Importantly, autophagy flux decreased following 12 weeks of mild exercise in parallel with improved physical function. These findings indicate that autophagy is regulated in a cell type-, sex-and physiological function-dependent manner during human aging, and highlight PBMC autophagy flux as a potentially modifiable, blood-accessible readout of physiological state in older adults.

cell biology↗

bioRxiv2024

In silico characterisation of PAL homologs and metabolomic profiling of shade response indicates potential presence of PTALs and Tyr as a probable precursor of lignin biosynthesis in conifers

Norway spruce and Scots pine show enhanced lignin synthesis under shade along with differential expression of defense-related genes that renders disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants and tyrosine (Tyr) forms an additional lignin precursor in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed a relatively higher amount of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggests potential presence of PTALs in conifers, which is novel. Exome sequence analysis revealed latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and PTAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.

plant biology↗

bioRxiv2022

QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)

Pendula-phenotyped Norway spruce has a potential forestry interest for high density plantations. This phenotype is believed to be caused by a dominant single mutation. Despite the availability of RAPD markers linked to the trait, the nature of the mutation is yet unknown. We performed a Quantitative Trait Loci (QTL) mapping based on two different progenies of F1 crosses between pendula and normal crowned trees using NGS technologies. Approximately 25 % of all gene bearing scaffolds of Picea abies genome assembly v1.0 were mapped to 12 linkage groups and a single QTL, positioned near the center of LG VI, was found in both crosses. The closest probe-markers placed on the maps were positioned 0.82 cM and 0.48 cM away from the Pendula marker in two independent pendula-crowned x normal-crowned wildtype crosses, respectively. We have identified genes close to the QTL region with differential mutations on coding regions and discussed their potential role in changing branch architecture.

genomics↗

bioRxiv2022

Natural variation in PHY causes differential response to R/FR light following a latitudinal cline in Norway spruce

Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively and, play a fundamental role in regulating the light pathway in plants contributing to plant growth and development. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth, thus showing differential response to light quality. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled from different latitudes across Sweden that differ in exposure to photoperiod and FR light received during the growing season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. Asn835Ser in PHYO displayed the steepest cline among all other polymorphisms. We propose that these variations represent signs of local adaptation to light quality in Norway spruce.

genomics↗

bioRxiv2020

A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease

In diseased organs, stress-activated signaling cascades alter chromatin, triggering broad shifts in transcription and cell state that exacerbate pathology. Fibroblast activation is a common stress response that worsens lung, liver, kidney and heart disease, yet its mechanistic basis remains poorly understood1,2. Pharmacologic inhibition of the BET family of transcriptional coactivators alleviates cardiac dysfunction and associated fibrosis, providing a tool to mechanistically interrogate maladaptive fibroblast states and modulate their plasticity as a potential therapeutic approach3-8. Here, we leverage dynamic single cell transcriptomic and epigenomic interrogation of heart tissue with and without BET inhibition to reveal a reversible transcriptional switch underlying stress-induced fibroblast activation. Transcriptomes of resident cardiac fibroblasts demonstrated robust and rapid toggling between the quiescent fibroblast and activated myofibroblast state in a manner that directly correlated with BET inhibitor exposure and cardiac function. Correlation of single cell chromatin accessibility with cardiac function revealed a novel set of reversibly accessible DNA elements that correlated with disease severity. Among the most dynamic elements was an enhancer regulating the transcription factor MEOX1, which was specifically expressed in activated myofibroblasts, occupied putative regulatory elements of a broad fibrotic gene program, and was required for TGF{beta}-induced myofibroblast activation. CRISPR interference of the most dynamic cis-element within the enhancer, marked by nascent transcription, prevented TGF{beta}-induced activation of Meox1. These findings identify MEOX1 as a central regulator of stress-induced myofibroblast activation associated with cardiac dysfunction. The plasticity and specificity of the BET-dependent regulation of MEOX1 in endogenous tissue fibroblasts provides new trans- and cis- targets for treating fibrotic disease.

molecular biology↗

bioRxiv2018

Oligogenic inheritance of congenital heart disease involving a NKX2-5 modifier

Complex genetic inheritance is thought to underlie many human diseases, yet experimental proof of this model has been elusive. Here, we show that a human congenital heart defect, left ventricular non-compaction (LVNC), can be caused by a combination of rare, inherited heterozygous missense single nucleotide variants. Whole exome sequencing of a nuclear family revealed novel single nucleotide variants of MYH7 and MKL2 in an asymptomatic father while the offspring with severe childhood-onset LVNC harbored an additional missense variant in the cardiac transcription factor, NKX2-5, inherited from an unaffected mother. Mice bred to compound heterozygosity for the orthologous missense variants in Myh7 and Mkl2 had mild cardiac pathology; the additional inheritance of the Nkx2-5 variant yielded a more severe LVNC-like phenotype in triple compound heterozygotes. RNA sequencing identified genes associated with endothelial and myocardial development that were dysregulated in hearts from triple heterozygote mice and human induced pluripotent stem cell-derived cardiomyocytes harboring the three variants, with evidence for NKX2-5s contribution as a modifier on the molecular level. These studies demonstrate that the deployment of efficient gene editing tools can provide experimental evidence for complex inheritance of human disease.\n\nOne sentence summaryA combination of three inherited heterozygous missense single nucleotide variants underlying a familial congenital heart defect.

genetics↗