Biology subjects

Naderi, P.

Publications and source records attributed to Naderi, P..

3 recordsLinked to original sources

bioRxiv2026

MicroRNA correlates of resilience to Alzheimer's disease identify candidate therapeutic targets for neuroprotection

Many aged individuals accumulate advanced Alzheimers disease (AD) neuropathology without cognitive decline, signifying potent endogenous resilience mechanisms. Mimicking resilience to AD may offer new therapeutic opportunities by emulating endogenous neuroprotection, but the molecular pathways that underpin resilience remain largely unknown. MicroRNAs (miRNAs)--small noncoding RNA molecules that post-transcriptionally regulate gene expression--influence neuronal and glial processes associated with development, aging, and AD neurodegeneration but their role in resilience has not been characterized. We investigated resilience-associated miRNAs and their targeted programs in the dorsolateral prefrontal cortex of post-mortem human brains. We analyzed matched miRNA and messenger RNA (mRNA) expression across resilient, AD, and control subjects from the Religious Order Study and Memory and Aging Project (ROSMAP) cohort. Nine miRNAs were differentially expressed in resilience compared with AD, including previously unreported miR-362-3p and miR-433-3p and new resilience-associated roles for known AD-related miRNAs, including neuronal miR-132-3p and miR-129-5p. By analyzing miRNA activity across AD progression, we found additional cognitive-associated miRNAs (e.g., miR-335-5p and miR-19b) and one plaque-restricted miRNA (miR-199a-5p). Sex-specific miRNA dysregulation was observed: miR-7-5p showed male-specific upregulation in AD versus resilience and suggested sex-specific differences in AD patients. Integrated co-expression and target-enrichment analyses linked resilience-associated miRNAs to pathways that were associated with cognitive decline, including transforming growth factor {beta}, Rho guanosine triphosphatases, and neurotransmitter receptor regulation. We also report restricted co-activity in AD subjects for miR-362-3p with inflammatory pathways, including tumor necrosis factor and Toll-like receptor signaling. These results demonstrate systematic involvement of miRNAs across neuronal and glial programs of AD resilience, cognitive decline, and sex-specific regulation. Our study provides an important resource for discovery of actionable regulatory programs that could lead to new therapies, based on endogenous molecules, that emulate natural resilience to AD. Key pointsO_LINine distinct cortical microRNA (miRNA) signatures correlate with resilience to Alzheimers disease (AD)-related cognitive decline, pointing to endogenous regulatory programs that may help preserve cognitive function. C_LIO_LIAt the miRNA level, resilient brains show minimal or no detectable differences to healthy individuals, despite the profound pathological differences, supporting the idea that resilience reflects preserved molecular homeostasis rather than a separate disease state. C_LIO_LISome miRNA signatures are specific to a certain pathology (e.g., one linked to amyloid-{beta} plaques independently of tau pathology and cognitive decline), helping to disentangle the regulation of these processes. C_LIO_LISex-specific miRNA dysregulation in AD suggests that resilience-linked pathways may be regulated differently in males and females, reinforcing the value of sex-stratified analyses and the potential for differential therapeutic strategies. C_LIO_LIIntegrative miRNA-pathway analysis highlights candidate regulatory networks involved in inflammation, matrisome, and cellular stress responses, providing a framework for resilience-linked therapeutic targets. C_LI

neuroscience↗

bioRxiv2022

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.

genomics↗

bioRxiv2021

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63+ intrapulmonary basal-like progenitor (IPBLP) cells, similar to cells identified in H1N1 influenza, that may serve as an emergency cellular reserve for severely damaged alveoli. Together, these findings suggest the activation and failure of multiple avenues for regeneration of the epithelium in these terminal lungs. SARS-CoV-2 RNA reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.

genomics↗