Samah Shah
YOU?
Author Swipe
View article: A multi-omics analysis of human fibroblasts overexpressing an Alu transposon reveals widespread disruptions in aging-associated pathways
A multi-omics analysis of human fibroblasts overexpressing an Alu transposon reveals widespread disruptions in aging-associated pathways Open
During aging and cellular senescence, repetitive elements are frequently transcriptionally derepressed across species and cell types. Among these, the most abundant repeats by copy number in the human genome are Alu retrotransposons. Thoug…
View article: A multi-omics analysis of human fibroblasts overexpressing an <i>Alu</i> transposon reveals widespread disruptions in aging-associated pathways
A multi-omics analysis of human fibroblasts overexpressing an <i>Alu</i> transposon reveals widespread disruptions in aging-associated pathways Open
During aging and cellular senescence, repetitive elements are frequently transcriptionally derepressed across species and cell types. Among these, the most abundant repeats by copy number in the human genome are Alu retrotransposons. Thoug…
View article: A Fibroblast State Choreographs an Epithelial YAP-dependent Regenerative Program Essential to (Pre)malignancy via ECM-mediated Mechanotransduction
A Fibroblast State Choreographs an Epithelial YAP-dependent Regenerative Program Essential to (Pre)malignancy via ECM-mediated Mechanotransduction Open
Chronic lung injury generates metaplasia which occasionally, but ominously, progresses to squamous dysplasia and squamous lung cancer. To identify mechanisms through which disrupted tissue homeostasis contributes to malignant initiation an…
View article: Sirtuin-5 Is Recruited to Hepatic Peroxisomes in Mice Fed Dodecanedioic Acid but Has Little Impact on the Peroxisomal Succinylome
Sirtuin-5 Is Recruited to Hepatic Peroxisomes in Mice Fed Dodecanedioic Acid but Has Little Impact on the Peroxisomal Succinylome Open
Lysine succinylation, and its reversal by sirtuin-5 (SIRT5), is known to modulate mitochondrial fatty acid β-oxidation (FAO). We recently showed that feeding mice dodecanedioic acid, a 12-carbon dicarboxylic acid (DC12) that can be chain-s…
View article: Sirtuin‐5 Is Recruited to Hepatic Peroxisomes in Mice Fed Dodecanedioic Acid but Has Little Impact on the Peroxisomal Succinylome
Sirtuin‐5 Is Recruited to Hepatic Peroxisomes in Mice Fed Dodecanedioic Acid but Has Little Impact on the Peroxisomal Succinylome Open
Lysine succinylation, and its reversal by sirtuin-5 (SIRT5), is known to modulate mitochondrial fatty acid β-oxidation (FAO). We recently showed that feeding mice dodecanedioic acid, a 12-carbon dicarboxylic acid (DC12) that can be chain-s…
View article: Dietary dicarboxylic acids provide a nonstorable alternative fat source that protects mice against obesity
Dietary dicarboxylic acids provide a nonstorable alternative fat source that protects mice against obesity Open
Dicarboxylic fatty acids are generated in the liver and kidney in a minor pathway called fatty acid ω-oxidation. The effects of consuming dicarboxylic fatty acids as an alternative source of dietary fat have not been explored. Here, we fed…
View article: KIBRA repairs synaptic plasticity and promotes resilience to tauopathy-related memory loss
KIBRA repairs synaptic plasticity and promotes resilience to tauopathy-related memory loss Open
Synaptic plasticity is obstructed by pathogenic tau in the brain, representing a key mechanism that underlies memory loss in Alzheimer's disease (AD) and related tauopathies. Here, we found that reduced levels of the memory-associated prot…
View article: Neuronal Glycogen Breakdown Mitigates Tauopathy via Pentose Phosphate Pathway-Mediated Oxidative Stress Reduction
Neuronal Glycogen Breakdown Mitigates Tauopathy via Pentose Phosphate Pathway-Mediated Oxidative Stress Reduction Open
Tauopathies encompass a range of neurodegenerative disorders, such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). Unfortunately, current treatment approaches for tauopathies have yielded limited success, underscoring the pr…
View article: Ketogenic diet administration later in life improves memory and regulates the synaptic cortical proteome through the cAMP/PKA signaling pathway in aging mice
Ketogenic diet administration later in life improves memory and regulates the synaptic cortical proteome through the cAMP/PKA signaling pathway in aging mice Open
Summary Aging is a complex biological process that compromises brain function and neuronal network activity, leading to cognitive decline and synaptic dysregulation. In recent years, a cyclic Ketogenic Diet (KD) has emerged as a potential …
View article: KIBRA repairs synaptic plasticity and promotes resilience to tauopathy-related memory loss
KIBRA repairs synaptic plasticity and promotes resilience to tauopathy-related memory loss Open
Synaptic plasticity is obstructed by pathogenic tau in the brain, representing a key mechanism that underlies memory loss in Alzheimer’s disease (AD) and related tauopathies. Here, we define a mechanism for plasticity repair in vulnerable …
View article: Concerted epithelial and stromal changes during progression of Barrett’s Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis
Concerted epithelial and stromal changes during progression of Barrett’s Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis Open
Esophageal adenocarcinoma arises from Barrett’s esophagus, a precancerous metaplastic replacement of squamous by columnar epithelium in response to chronic inflammation. Multi-omics profiling, integrating single-cell transcriptomics, extra…
View article: Coenzyme A binding sites induce proximal acylation across protein families
Coenzyme A binding sites induce proximal acylation across protein families Open
Lysine Nɛ-acylations, such as acetylation or succinylation, are post-translational modifications that regulate protein function. In mitochondria, lysine acylation is predominantly non-enzymatic, and only a specific subset of the proteome i…
View article: Data‐independent acquisition and quantification of extracellular matrix from human lung in chronic inflammation‐associated carcinomas
Data‐independent acquisition and quantification of extracellular matrix from human lung in chronic inflammation‐associated carcinomas Open
Early events associated with chronic inflammation and cancer involve significant remodeling of the extracellular matrix (ECM), which greatly affects its composition and functional properties. Using lung squamous cell carcinoma (LSCC), a ch…
View article: TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies
TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies Open
In spite of its central role in biology and disease, protein turnover is a largely understudied aspect of most proteomic studies due to the complexity of computational workflows that analyze in vivo turnover rates. To address this need, we…
View article: SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein
SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein Open
SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-…
View article: A novel splice variant of Elp3/Kat9 regulates mitochondrial tRNA modification and function
A novel splice variant of Elp3/Kat9 regulates mitochondrial tRNA modification and function Open
Post-translational modifications, such as lysine acetylation, regulate the activity of diverse proteins across many cellular compartments. Protein deacetylation in mitochondria is catalyzed by the enzymatic activity of the NAD + -dependent…
View article: Data-Independent Acquisition and Quantification of Extracellular Matrix from Human Lung in Chronic Inflammation-Associated Carcinomas
Data-Independent Acquisition and Quantification of Extracellular Matrix from Human Lung in Chronic Inflammation-Associated Carcinomas Open
Early events associated with chronic inflammation and cancer involve significant remodeling of the extracellular matrix (ECM), which greatly affects its composition and functional properties. Using lung squamous cell carcinoma (LSCC), a ch…
View article: Coenzyme A binding sites induce proximal acylation across protein families
Coenzyme A binding sites induce proximal acylation across protein families Open
Lysine Nε-acylations, such as acetylation or succinylation, are post-translational modifications that regulate protein function. In mitochondria, lysine acylation is predominantly non-enzymatic, and only a specific subset of the proteome i…
View article: Human Elp3/Kat9 is a mitochondrial tRNA modifying enzyme
Human Elp3/Kat9 is a mitochondrial tRNA modifying enzyme Open
Post-translational modifications, such as lysine acetylation, regulate the activity of diverse proteins across many cellular compartments. Protein deacetylation in mitochondria is catalyzed by the enzymatic activity of the NAD+-dependent d…
View article: Human Elp3/Kat9 is a mitochondrial tRNA modifying enzyme
Human Elp3/Kat9 is a mitochondrial tRNA modifying enzyme Open
Post-translational modifications, such as lysine acetylation, regulate the activity of diverse proteins across many cellular compartments. Protein deacetylation in mitochondria is catalyzed by the enzymatic activity of the NAD+-dependent d…
View article: SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein
SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein Open
SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-…
View article: Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications
Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications Open
Research into the basic biology of human health and disease, as well as translational human research and clinical applications, all benefit from the growing accessibility and versatility of mass spectrometry (MS)-based proteomics. Although…
View article: Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization Open
Studying multiple post-translational modifications (PTMs) of proteins is a crucial step to understand PTM crosstalk and gain more holistic insights into protein function. Despite the importance of multi-PTM enrichment studies, few studies …
View article: Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization Open
Studying multiple post-translational modifications (PTMs) of proteins is a crucial step to understand PTM crosstalk and gain more holistic insights into protein function. Despite the importance of multi-PTM enrichment studies, few studies …
View article: A proteomic atlas of senescence-associated secretomes for aging biomarker development
A proteomic atlas of senescence-associated secretomes for aging biomarker development Open
The senescence-associated secretory phenotype (SASP) has recently emerged as a driver of and promising therapeutic target for multiple age-related conditions, ranging from neurodegeneration to cancer. The complexity of the SASP, typically …
View article: A Proteomic Atlas of Senescence-Associated Secretomes for Aging Biomarker Development
A Proteomic Atlas of Senescence-Associated Secretomes for Aging Biomarker Development Open
The senescence-associated secretory phenotype (SASP) has recently emerged as a driver of, and promising therapeutic target for, multiple age-related conditions, ranging from neurodegeneration to cancer. The complexity of the SASP, typicall…