Biology subjects

Stein, B. D.

Publications and source records attributed to Stein, B. D..

5 recordsLinked to original sources

bioRxiv2023

Lineage-specific intolerance to oncogenic drivers restricts histological transformation

Lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC) are thought to originate from different epithelial cell types in the lung. Intriguingly, LUAD can histologically transform into SCLC following treatment with targeted therapies. Here we designed models to follow the conversion of LUAD to SCLC and found the barrier to histological transformation converges on tolerance to Myc, which we implicate as a lineage-specific driver of the pulmonary neuroendocrine cell. Histological transformations are frequently accompanied by activation of the Akt pathway. Manipulating this pathway permitted tolerance to Myc as an oncogenic driver, producing rare, stem-like cells, transcriptionally resembling the pulmonary basal lineage. These findings suggest histological transformation may require the plasticity inherent to the basal stem cell, enabling tolerance to previously incompatible oncogenic driver programs. One-Sentence SummaryBy modeling histological transformation of lung cancer, we uncover neuroendocrine-specific tolerance to Myc as an oncogenic driver.

cancer biology↗

bioRxiv2023

Submitochondrial Protein Translocation Upon Stress Inhibits Thermogenic Energy Expenditure

Mitochondria-rich brown adipocytes dissipate cellular energy as heat. Excessive nutrition or prolonged cold exposure suppress thermogenesis, but the mechanisms remain incompletely understood. Here we report that excessive cold or metabolic stress-induced proton leak into the matrix interface of mitochondrial innermembrane (IM) mobilizes 73 proteins from IM into matrix, which in turn alter mitochondrial bioenergetics. Interactome analysis indicates that key subunits of the electron transport chain and the mitochondrial calcium uniporter provide histidine-rich IM docking sites for 40 translocating proteins via pH-dependent protein-protein interactions. We further determine that 34% of translocating proteins correlate with obesity in human subcutaneous adipose tissue among which the top factor, acyl-CoA thioesterase 9 (ACOT9), enzymatically deactivates and prevents the utilization of acetyl-CoA in thermogenesis and promotes obesity. Overall, this study introduces stress-induced submitochondrial protein translocation as a new mitochondrial mechanism. One-Sentence SummaryMitochondrial stress regulates energy utilization by forcing translocation of IM-bound proteins into the matrix.

molecular biology↗

bioRxiv2021

Non-conserved metabolic regulation by LKB1 distinguishes human and mouse lung adenocarcinoma

KRAS is the most frequently mutated oncogene in human lung adenocarcinomas (hLUAD) and activating mutations in KRAS frequently co-occur with loss-of-function mutations in the tumor suppressor genes, TP53 or STK11/LKB1. However, mutation of all three genes is rarely observed in hLUAD, even though engineered mutations of all three genes produces a highly aggressive lung adenocarcinoma in mice (mLUAD). Here we provide an explanation of this difference between hLUAD and mLUAD by uncovering an evolutionary divergence in regulation of the glycolytic enzyme triosephosphate isomerase (TPI1). Using KRAS/TP53 mutant hLUAD cell lines, we show that TPI1 enzymatic activity can be altered via phosphorylation at Ser21 by the Salt Inducible Kinases (SIKs) in an LKB1-dependent manner; this allows modulation of glycolytic flux between completion of glycolysis and production of glycerol lipids. This metabolic flexibility appears to be critical in rapidly growing cells with KRAS and TP53 mutations, explaining why loss of LKB1 creates a metabolic liability in these tumors. In mice, the amino acid at position 21 of TPI1 is a Cys residue which can be oxidized to alter TPI1 activity, allowing regulation of glycolytic flux balance without a need for SIK kinases or LKB1. Our findings reveal an unexpected role for TPI1 in metabolic reprogramming and suggest that LKB1 and SIK family kinases are potential targets for treating KRAS/TP53 mutant hLUAD. Our data also provide a cautionary example of the limits of genetically engineered murine models as tools to study human diseases such as cancers.

cancer biology↗

bioRxiv2021

Diverse Hotspot Thermal Profiling Methods Detect Phosphorylation-Dependent Changes in Protein Stability

Hotspot thermal profiling (HTP) methods utilize modified-peptide level information in order to interrogate proteoform-specific stability inside of live cells. The first demonstration of HTP involved the integration of phosphopeptide enrichment into a TMT-based, single-LC separation thermal profiling workflow1. Here we present a new label-fractionate-enrich (LFE)-HTP method that involves high-pH reverse phase fractionation of TMT-labeled peptides prior to phosphopeptide enrichment, followed by peptide detection and quantitation using multi-notch LC-MS3. We find that LFE-HTP, while more resource intensive, improves the depth and precision of (phospho)proteoform coverage relative to the initial published HTP workflow. The fraction of detected phosphorylation sites that are significantly perturbed in this new dataset are consistent with those seen in our previous study, as well as those published by others, when compared head-to-head with the same analysis pipelines. Likewise, many hotspot phosphorylation sites identified in our paper are consistently reproduced by LFE-HTP as well as other modified HTP methods. The LFE-HTP dataset contains many novel hotspot phosphorylation sites that regulate the stability of diverse proteins, including phosphosites in the central glycolytic enzyme Aldolase A that are associated with monomer-to-oligomer formation, enzymatic activity and metabolic regulation in cancer cells. Our comparative analyses confirm that several variants of the HTP method can track modified proteoforms in live cells to detect and prioritize PTM-dependent changes in protein stability that may be associated with function.

biochemistry↗

bioRxiv2018

Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria

In diverse bacteria, proper cellular physiology requires the utilization of protein- or membrane-bound compartments that afford specific metabolic capabilities. One such compartment is the light-harvesting intracytoplasmic membrane (ICM) of purple nonsulfur bacteria (PNSB). Here we reveal that ICMs are subject to differential spatial organization among PNSB. We visualized ICMs in live cells of fourteen PNSB species by exploiting the natural autofluorescence of the photosynthetic machinery. We then quantitatively characterized ICM localization using automated computational analysis of autofluorescence patterns within single cells across the population. Our studies revealed that ICMs are localized in distinct subcellular patterns that differ between species; some PNSB elaborate ICMs throughout the cell, while others spatially restrict ICM to varying degrees. The most highly-restricted ICMs were localized in a specific pattern corresponding to progression of cell growth and division. An identical pattern of ICM restriction was conserved across at least two genera. Phylogenetic and phenotypic comparisons established that ICM localization and ICM architecture are not strictly interdependent and that neither trait fully correlates with the evolutionary relatedness of the species. This discovery of new diversity in bacterial cell organization has implications for understanding both the mechanisms underpinning spatial arrangement of bacterial compartments and the potential benefits of adopting different spatiotemporal patterns.

microbiology↗