Biology subjects

Crawford, D.

Publications and source records attributed to Crawford, D..

5 recordsLinked to original sources

bioRxiv2023

Cell Surface β-Lactamase Recruitment: A Facile Selection to Identify Protein-Protein Interactions

Protein-protein interactions are central to many cellular processes, and the identification of novel protein-protein interactions is a critical step in the discovery of protein therapeutics. Simple methods to identify naturally existing or laboratory evolved protein-protein interactions are therefore valuable research tools. We have developed a facile selection that links protein-protein interaction-dependent {beta}-lactamase recruitment on the surface of E. coli with resistance to ampicillin. Bacteria displaying a protein which form a complex with a specific protein-{beta}-lactamase fusion are protected from ampicillin-dependent cell death. In contrast, bacteria that do not recruit {beta}-lactamase to the cell surface are killed by ampicillin. Given its simplicity and tunability, we anticipate this selection will be a valuable addition to the palette of methods for illuminating and interrogating protein-protein interactions.

biochemistry↗

bioRxiv2023

Trans-Acting Genotypes Drive mRNA Expression Affecting Metabolic And Thermal Tolerance Traits

AO_SCPLOWBSTRACTC_SCPLOWEvolutionary processes driving physiological trait variation depend on the underlying genomic mechanisms. Evolution of these mechanisms depends on whether traits are genetically complex (involving many genes) and how gene expression that impact the traits is converted to phenotype. Yet, genomic mechanisms that impact physiological traits are diverse and context dependent (e.g., vary by environment or among tissues), making them difficult to discern. Here we examine the relationships between genotype, mRNA expression, and physiological traits to discern the genetic complexity and whether the gene expression effecting the physiological traits is primarily cis or trans-acting. We use low-coverage whole genome sequencing and tissue specific mRNA expression among individuals to identify polymorphisms directly associated with physiological traits and expressed quantitative trait loci (eQTL) driving variation in six temperature specific physiological traits (standard metabolic rate, thermal tolerance, and four substrate specific cardiac metabolic rates). Not surprisingly, there were few, only five, SNPs directly associated with physiological traits. Yet, by focusing on a select set of mRNAs belonging to co-expression modules that explain up to 82% of temperature specific (12{degrees}C or 28{degrees}C) metabolism and thermal tolerance, we identified hundreds of significant eQTL for mRNA whose expression affects physiological traits. Surprisingly, most eQTL (97.4% for heart and 96.7% for brain) of eQTL were trans-acting. This could be due to higher effect size or greater importance of trans versus cis acting eQTLs for mRNAs that are central to co-expression modules. That is, we may have enhanced the identification of trans-acting factors by looking for SNPs associated with mRNAs in co-expression modules that are known to be correlated with the expression of 10s or 100s of other genes, and thus have identified eQTLs with widespread effects on broad gene expression patterns. Overall, these data indicate that the genomic mechanism driving physiological variation across environments is driven by trans-acting tissue specific mRNA expression. AO_SCPLOWUTHORC_SCPLOW SO_SCPLOWUMMARYC_SCPLOWIn the salt marsh killifish Fundulus heteroclitus there is amazingly large variation in physiological traits assumed to be under stabilizing selection, which should reduce their variation. To discern the heritability of this physiological variation we took an innovative approach to define the DNA variation that drives mRNA expression linked to physiological variation. This indirect approach revealed many DNA sequence variants associated with physiological variation via their effect on mRNA expression. Surprisingly, these changes were not in the mRNAs themselves, but in unlinked distant genes which regulate mRNA expression. That is, the vast majority (>95%) were trans-acting. This is surprising because trans-acting effects are found less often than DNA variants within or close to mRNA expression genes. Our results are likely related to the select subset of mRNAs across environments that are linked to physiological variation.

genetics↗

bioRxiv2021

Melanoma Addiction to GCDH is Mediated by NRF2 Tumor Suppressor Function

Tumor dependency on specific metabolic signals has guided numerous therapeutic approaches. Here we identify melanoma addiction to the mitochondrial protein Glutaryl-CoA dehydrogenase (GCDH), a component in lysine metabolism which controls protein glutarylation. GCDH knockdown promoted apoptotic Unfolded Protein Response signaling and cell death in melanoma cells, an activity blocked by knockdown of the upstream lysine catabolism enzyme DHTKD1. Correspondingly, reduced GCDH expression correlated with improved survival of melanoma patients. A key mediator of GCDH-dependent melanoma cell death programs is the transcription factor NRF2, which induces ATF3, CHOP, and CHAC1 transcription linking lysine catabolism with the UPR signaling. NRF2 glutarylation upon GCDH KD increased its stability and DNA binding activity, which coincided with increased transcriptional activity, promoting apoptotic UPR signaling and tumor suppression. In vivo, genetic GCDH inhibition effectively inhibited melanoma tumor growth. Overall, these findings demonstrate an addiction of melanoma cells to GCDH, which by controlling NRF2 glutarylation limits apoptotic UPR signaling. Inhibiting the GCDH pathway could represent a novel therapeutic modality to treat melanoma.

cancer biology↗

bioRxiv2021

Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS

The tumor microenvironment (TME) is a complex mixture of cell types whose interactions affect tumor growth and clinical outcome. To discover such interactions, we developed CODEFACS (COnfident DEconvolution For All Cell Subsets), a tool deconvolving cell-type-specific gene expression in each sample from bulk expression, and LIRICS (LIgand Receptor Interactions between Cell Subsets), a statistical framework prioritizing clinically relevant ligand-receptor interactions between cell types from the deconvolved data. We first demonstrate the superiority of CODEFACS versus the state-of-the-art deconvolution method, CIBERSORTx. Second, analyzing the TCGA, we uncover cell-type-specific interactions of mismatch-repair-deficient tumors that are associated with their higher anti-PD1 response rates, including specific T-cell co-stimulating interactions that enhance immunotherapy response independently of the tumors mutation burden levels. Finally, we identify a subset of ligand-receptor interactions in the melanoma TME that predict patient response to anti-PD1 therapy better than recently published transcriptomics-based methods.

bioinformatics↗

bioRxiv2018

Genome-wide association meta-analysis of PR interval identifies 47 novel loci associated with atrial and atrioventricular electrical activity

Electrocardiographic PR interval measures atrial and atrioventricular depolarization and conduction, and abnormal PR interval is a risk factor for atrial fibrillation and heart block. We performed a genome-wide association study in over 92,000 individuals of European descent and identified 44 loci associated with PR interval (34 novel). Examination of the 44 loci revealed known and novel biological processes involved in cardiac atrial electrical activity, and genes in these loci were highly over-represented in several cardiac disease processes. Nearly half of the 61 independent index variants in the 44 loci were associated with atrial or blood transcript expression levels, or were in high linkage disequilibrium with one or more missense variants. Cardiac regulatory regions of the genome as measured by cardiac DNA hypersensitivity sites were enriched for variants associated with PR interval, compared to non-cardiac regulatory regions. Joint analyses combining PR interval with heart rate, QRS interval, and atrial fibrillation identified additional new pleiotropic loci. The majority of associations discovered in European-descent populations were also present in African-American populations. Meta-analysis examining over 105,000 individuals of African and European descent identified additional novel PR loci. These additional analyses identified another 13 novel loci. Together, these findings underscore the power of GWAS to extend knowledge of the molecular underpinnings of clinical processes.

genetics↗