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Sarwath, H.

Publications and source records attributed to Sarwath, H..

5 recordsLinked to original sources

NAD+ boosting by oral nicotinamide mononucleotide administration regulates key metabolic and immune pathways through SIRT1 dependent and independent mechanisms to mitigate diet-induced obesity and dyslipidemia in mice.

Sirtuins are NAD+-dependent histone deacetylases that play a key role in metabolism. Sirtuin activity is compromised in aging and metabolic disorders, and pharmacological strategies that promote sirtuin function including NAD+ boosting approaches show potential as therapeutics. To study the impact of nicotinamide mononucleotide (NMN) supplementation in mice in high fat diet (HFD) induced obesity and the role of SIRT1, a sirtuin family member, in mediating the NMN response, we administered NMN to mice in drinking water to boost NAD+ in control and in inducible SIRT1 knock-out mouse models and performed a combination of metabolic phenotyping, lipid profiling and plasma proteomics in these mice. We discovered that supplementation with NMN mitigated diet induced weight gain by enhancing energy expenditure, corrected dyslipidemia, and reversed perturbations in fasting blood glucose, all in a SIRT1-dependent manner. On the other hand, NMN-induced reductions in fat mass, fluid mass, eWAT and mesenteric WAT were SIRT1 independent. Proteomic approaches in plasma samples using O-Link and mass-spectrometry provided novel insights into key obesity- and NMN-dependent changes in circulating molecules with potential relevance to inflammation, liver function, and dyslipidemia. We discovered SIRT1 dependent and independent alterations in key circulating plasma proteins and identified key metabolic and molecular pathways that were significantly affected by HFD, several of which were reverted by oral NMN administration. Glucose metabolism, cholesterol metabolism and immune-related pathways are among the most significantly affected changes. Causal analysis of proteomic data suggests that observed effects could be mediated by transcription regulators FBXW7, ADIPOR2 and PRDM16. Collectively, our data supports the hypothesis that promoting SIRT1 function by boosting NAD+ levels in vivo may be a useful strategy to mitigate obesity and associated cardiovascular complications such as dyslipidemia.

physiology↗

A genome-wide association study of mass spectrometry proteomics using the Seer Proteograph platform

Genome-wide association studies (GWAS) with proteomics are essential tools for drug discovery. To date, most studies have used affinity proteomics platforms, which have limited discovery to protein panels covered by the available affinity binders. Furthermore, it is not clear to which extent protein epitope changing variants interfere with the detection of protein quantitative trait loci (pQTLs). Mass spectrometry-based (MS) proteomics can overcome some of these limitations. Here we report a GWAS using the MS-based Seer ProteographTM platform with blood samples from a discovery cohort of 1,260 American participants and a replication in 325 individuals from Asia, with diverse ethnic backgrounds. We analysed 1,980 proteins quantified in at least 80% of the samples, out of 5,753 proteins quantified across the discovery cohort. We identified 252 and replicated 90 pQTLs, where 30 of the replicated pQTLs have not been reported before. We further investigated 200 of the strongest associated cis-pQTLs previously identified using the SOMAscan and the Olink platforms and found that up to one third of the affinity proteomics pQTLs may be affected by epitope effects, while another third were confirmed by MS proteomics to be consistent with the hypothesis that genetic variants induce changes in protein expression. The present study demonstrates the complementarity of the different proteomics approaches and reports pQTLs not accessible to affinity proteomics, suggesting that many more pQTLs remain to be discovered using MS-based platforms. Graphical AbstractSummarizing the approach taken to identify potential epitope effects. O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/596028v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@34d11aorg.highwire.dtl.DTLVardef@18c0211org.highwire.dtl.DTLVardef@dbb003org.highwire.dtl.DTLVardef@1009fa7_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping

Genome-wide association studies (GWAS) with proteomics generate hypotheses on protein function and offer genetic evidence for drug target prioritization. Although most protein quantitative loci (pQTLs) have so far been identified by high-throughput affinity proteomics platforms, these methods also have some limitations, such as uncertainty about target identity, non-specific binding of aptamers, and inability to handle epitope-modifying variants that affect affinity binding. Mass spectrometry (MS) proteomics has the potential to overcome these challenges and broaden the scope of pQTL studies. Here, we employ the recently developed MS-based Proteograph workflow (Seer, Inc.) to quantify over 18,000 unique peptides from almost 3,000 proteins in more than 320 blood samples from a multi-ethnic cohort. We implement a bottom-up MS-proteomics approach for the detection and quantification of blood-circulating proteins in the presence of protein altering variants (PAVs). We identify 184 PAVs located in 137 genes that are significantly associated with their corresponding variant peptides in MS data (MS-PAVs). Half of these MS-PAVs (94) overlap with cis-pQTLs previously identified by affinity proteomics pQTL studies, thus confirming the target specificity of the affinity binders. An additional 54 MS-PAVs overlap with trans-pQTLs (and not cis-pQTLs) in affinity proteomics studies, thus identifying the putatively causal cis-encoded protein and providing experimental evidence for its presence in blood. The remaining 36 MS-PAVs have not been previously reported and include proteins that may be inaccessible to affinity proteomics, such as a variant in the incretin pro-peptide (GIP) that associates with type 2 diabetes and cardiovascular disease. Overall, our study introduces a novel approach for analyzing MS-based proteomics data within the GWAS context, provides new insights relevant to genetics-based drug discovery, and highlights the potential of MS-proteomics technologies when applied at population scale. HighlightsO_LIThis is the first pQTL study that uses the Proteograph (Seer Inc.) mass spectrometry-based proteomics workflow. C_LIO_LIWe introduce a novel bottom-up proteomics approach that accounts for protein altering variants in the detection of pQTLs. C_LIO_LIWe confirm the target and potential epitope effects of affinity binders for cis-pQTLs from affinity proteomics studies. C_LIO_LIWe establish putatively causal proteins for known affinity proteomics trans-pQTLs and confirm their presence in blood. C_LIO_LIWe identify novel protein altering variants in proteins of clinical relevance that may not be accessible to affinity proteomics. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/537640v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@5db14forg.highwire.dtl.DTLVardef@123c1edorg.highwire.dtl.DTLVardef@90ebb6org.highwire.dtl.DTLVardef@6320ff_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

Auto-Immunoproteomics Analysis of COVID-19 ICU Patients Revealed Increased Levels of Autoantibodies Related to Male Reproductive System

The role of autoantibodies in coronavirus disease (COVID-19) complications is not yet fully understood. The current investigation screened two independent cohorts of 97 COVID-19 patients (Discovery (Disc) cohort from Qatar (n = 49) and Replication (Rep) cohort from New York (n = 48)) utilizing high-throughput KoRectly Expressed (KREX) immunome protein-array technology. Autoantibody responses to 57 proteins were significantly altered in the COVID-19 Disc cohort compared to healthy controls (P [≤] 0.05). The Rep cohort had altered autoantibody responses against 26 proteins compared to non-COVID-19 ICU patients that served as controls. Both cohorts showed substantial similarities (r2 = 0.73) and exhibited higher autoantibodies responses to numerous transcription factors, immunomodulatory proteins, and human disease markers. Analysis of the combined cohorts revealed elevated autoantibody responses against SPANXN4, STK25, ATF4, PRKD2, and CHMP3 proteins in COVID-19 patients. KREX analysis of the specific IgG autoantibody responses indicates that the targeted host proteins are supposedly increased in COVID-19 patients. The autoantigen-autoantibody response was cross-validated for SPANXN4 and STK25 proteins using Uniprot BLASTP and sequence alignment tools. SPANXN4 is essential for spermiogenesis and male fertility, which may predict a potential role for this protein in COVID-19 associated male reproductive tract complications and warrants further research. Significance StatementCoronavirus disease (COVID-19), caused by the SARS-CoV-2 virus, has emerged as a global pandemic with a high morbidity rate and multiorgan complications. It is observed that the host immune system contributes to the varied responses to COVID-19 pathogenesis. Autoantibodies, immune system proteins that mistakenly target the bodys own tissue, may underlie some of this variation. We screened total IgG autoantibody responses against 1,318 human proteins in two COVID-19 patient cohorts. We observed several novel markers in COVID-19 patients that are associated with male fertility, such as sperm protein SPANXN4, STK25, and the apoptotic factor ATF4. Particularly, elevated levels of autoantibodies against the testicular tissue-specific protein SPANXN4 offer significant evidence of anticipating the protein role in COVID-19 associated male reproductive complications.

immunology↗

Connecting genetic risk to disease endpoints through the human blood plasma proteome

Genome-wide association studies (GWAS) with intermediate phenotypes, like changes in metabolite and protein levels, provide functional evidence for mapping disease associations and translating them into clinical applications. However, although hundreds of genetic risk variants have been associated with complex disorders, the underlying molecular pathways often remain elusive. Associations with intermediate traits across multiple chromosome locations are key in establishing functional links between GWAS-identified risk-variants and disease endpoints. Here, we describe a GWAS performed with a highly multiplexed aptamer-based affinity proteomics platform. We quantified associations between protein level changes and gene variants in a German cohort and replicated this GWAS in an Arab/Asian cohort. We identified many independent, SNP-protein associations, which represent novel, inter-chromosomal links, related to autoimmune disorders, Alzheimer's disease, cardiovascular disease, cancer, and many other disease endpoints. We integrated this information into a genome-proteome network, and created an interactive web-tool for interrogations. Our results provide a basis for new approaches to pharmaceutical and diagnostic applications.

genetics↗