Biology subjects

White, M. A.

Publications and source records attributed to White, M. A..

40 records · Page 3Linked to original sources

bioRxiv2019

High-Throughput Functional Annotation of Natural Products by Integrated Activity Profiling

Determining mechanism of action (MOA) is one of the biggest challenges in natural products discovery. Here, we report a comprehensive platform that uses Similarity Network Fusion (SNF) to improve MOA predictions by integrating data from the cytological profiling high-content imaging platform and the gene expression platform FUSION, and pairs these data with untargeted metabolomics analysis for de novo bioactive compound discovery. The predictive value of the integrative approach was assessed using a library of target-annotated small molecules as benchmarks. Using Kolmogorov-Smirnov (KS) tests to compare in-class to out-of-class similarity, we found that SNF retains the ability to identify significant in-class similarity across a diverse set of target classes, and could also find target classes that were not detectable in either platform alone. This confirmed that integration of expression-based and image-based phenotypes can accurately report on MOA. Furthermore, we integrated untargeted metabolomics of complex natural product fractions with the SNF network to map biological signatures to specific metabolites. Three examples are presented where SNF coupled with metabolomics was used to directly functionally characterize natural products and accelerate identification of bioactive metabolites, including the discovery of the novel azoxy-containing biaryl compounds parkamycins A and B. Our results support SNF integration of multiple phenotypic screening approaches along with untargeted metabolomics as a powerful approach for advancing natural products drug discovery. Significance statementNew data-driven methods to aid in the discovery and biological characterization of natural products are necessary to advance the field. Assigning the mechanism of action (MOA) to novel bioactive compounds is an essential step in drug discovery and a major challenge in chemical biology. Despite technological advances in isolation, synthesis and screening strategies that make many bioactive substances readily available, in most cases their biological targets remain unknown. Additionally, a major bottleneck in natural products discovery efforts is de-replication of the large number of known compounds that predominate in crude extracts and fraction libraries. Advances in metabolomics has provided a better understanding of the constituents present in these libraries, but is not sufficient in itself to drive the discovery of novel biologically active metabolites. Here we describe an unbiased, data-driven strategy which integrates phenotypic screening with metabolomics into a single platform that provides rapid identification and functional annotation of natural products. This approach can be applied to any cohort of uncharacterized chemicals and represents a strategy that could significantly accelerate the process of drug discovery.

pharmacology and toxicology↗

bioRxiv2019

The interplay between molten globule intermediates and heme disassociation characterizes human hemoglobin disassembly

Hemoglobin functions as an oxygen transport protein, with each subunit containing a heme cofactor. We have developed a global disassembly model for human hemoglobin, linking hemin (ferric heme) disassociation and apo(heme-free)-protein unfolding pathways. The model was based on the evaluation of circular dichroism and visible absorbance measurements of guanidine hydrochloride-induced disassembly of holo (heme-bound)-hemoglobin and previous measurements of apohemoglobin unfolding. The populations of holo-intermediates and equilibrium disassembly parameters were determined quantitatively for adult and fetal hemoglobins. The key stages for disassembly into unfolded monomers are characterized by hemichrome intermediates with molten globule characteristics. Hemichromes, which occur when both hemin iron axial sites coordinate amino acids, are not energetically favored in native human hemoglobins. However, these hexacoordinate iron complexes are important for preventing hemin disassociation from partially unfolded species during early disassembly and late stage assembly events. Both our model evaluation and independent small angle X-ray scattering measurements demonstrate that heme disassociation during early disassembly leads to loss of tetrameric structural integrity. Dimeric and monomeric hemichrome intermediates occur along the disassembly pathway inside red cells where the hemoglobin concentration is very high. This prediction explains why in the red cells of patients with unstable hemoglobinopathies, misassembled hemoglobins often get trapped as hemichromes that accumulate into insoluble Heinz bodies. These Heinz bodies become deposited on the cell membranes and can lead to hemolysis. Alternatively, when acellular hemoglobin is diluted into blood plasma after red cell lysis, the disassembly pathway is dominated by early hemin disassociation events, which leads to the generation of higher fractions of apo-subunits and free hemin known to damage to the integrity of blood vessel walls. Thus, our model illuminates the pathophysiology of hemoglobinopathies and other disease states associated with unstable globins and red cell lysis, and provides insights into the factors governing hemoglobin assembly during erythropoiesis.\n\nSignificanceOur deconvolution and global analysis of spectral data led to both the characterization of \"hidden\" hemichrome intermediates and the development of a quantitative model for human hemoglobin disassembly/assembly. The importance of this mechanism is several-fold. First, the hemoglobin system serves as a general biological model for understanding the role of oligomerization and cofactor binding in facilitating protein folding and assembly. Second, the fitted parameters provide: (a) estimates of hemin affinity for apoprotein states; (b) quantitative interpretations of the pathophysiology of hemoglobinopathies and other diseases associated with unstable globins and red cell lysis; (c) insights into the factors governing hemoglobin assembly during erythropoiesis; and (d) a framework for designing targeted hemoglobinopathy therapeutics.

biophysics↗

bioRxiv2019

METABOLIC DIVERSITY IN HUMAN NON-SMALL CELL LUNG CANCER CELLS

Intermediary metabolism in cancer cells is regulated by diverse cell-autonomous processes including signal transduction and gene expression patterns arising from specific oncogenotypes and cell lineages. Although it is well established that metabolic reprogramming is a hallmark of cancer, we lack a full view of the diversity of metabolic programs in cancer cells and an unbiased assessment of the associations between metabolic pathway preferences and other cell-autonomous processes. Here we quantified over 100 metabolic features, mostly from 13C enrichment of molecules from central carbon metabolism, in over 80 non-small cell lung cancer (NSCLC) cell lines cultured under identical conditions. Because these cell lines were extensively annotated for oncogenotype, gene expression, protein expression and therapeutic sensitivity, the resulting database enables the user to uncover new relationships between metabolism and these orthogonal processes.

cancer biology↗

bioRxiv2018

Fine-scale recombination landscapes between a freshwater and marine population of threespine stickleback fish

Meiotic recombination is a highly conserved process that has profound effects on genome evolution. Recombination rates can vary drastically at a fine-scale across genomes and often localize to small recombination \"hotspots\" with highly elevated rates surrounded by regions with little recombination. Hotspot targeting to specific genomic locations is variable across species. In some mammals, hotspots have divergent landscapes between closely related species which is directed by the binding of the rapidly evolving protein, PRDM9. In many species outside of mammals, hotspots are generally conserved and tend to localize to regions with open chromatin such as transcription start sites. It remains unclear if the location of recombination hotspots diverge in taxa outside of mammals. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using an LD-based approach, we found recombination rates varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had divergent landscapes between stickleback populations, where only ~15% were shared, though part of this divergence could be due to demographic history. Additionally, we did not detect a strong association of PRDM9 with recombination hotspots in threespine stickleback fish. Our results suggest fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish and argue for additional molecular characterization to verify the extent of the divergence.

genomics↗