Biology subjects

Smith, B. S.

Publications and source records attributed to Smith, B. S..

3 recordsLinked to original sources

bioRxiv2026

The Paipu framework enables creation of a large-scale mammalian cancer transcriptomics atlas

A plethora of studies have identified shared molecular mechanisms involved in tumor development across humans and other mammalian species. While these two-species analyses advance understanding of human disease, extending them across many species would provide evolutionary insight into molecular mechanisms driving human cancers. However, this expansion requires knowledge transfer and harmonization across species. Genomic differences between species, including variation in genome annotation quality, have historically hindered multi-species large-scale atlas creation. To overcome these challenges, we present Paipu, a comprehensive pipeline designed to streamline querying, preprocessing, harmonization, and retrieval of large-scale RNA-seq data and associated metadata from the NCBI Sequence Read Archive (SRA). Paipu facilitates multi-species analysis by creating a harmonized atlas from user-defined search terms and species. It consists of three components: reference genome preparation, SRA metadata retrieval, and RNA-seq data processing. We apply Paipu to 188 cancer-related terms in 239 non-human mammalian species, creating a harmonized atlas of 3,484 RNA-seq samples spanning 17 species and 35 cancers. This pan-mammalian pan-cancer atlas enables myriad comparative genomics analyses that leverage genetic variation to better understand rare human cancers. As such, Paipu serves as a resource for cross-species cancer genomics and supports atlas creation for any set of species and search terms. Graphical Abstract

bioinformatics↗

bioRxiv2025

Promoter hijacking by primate LINC00473 disrupts an ancestral CREB-PDE10A feedback loop

Thousands of human long noncoding RNAs (lncRNAs) evolved in primates, although much remains unknown about how these lncRNAs shaped human gene regulatory networks. The primate-specific lncRNA gene LINC00473 has a CREB-inducible promoter that is conserved beyond primates and the gene is located upstream of PDE10A, which encodes an inhibitor of CREB. To gain insight into the regulatory consequences of LINC00473 acquisition, we tested the cellular function of the conserved mouse promoter. We found that the homologous mouse promoter is induced by CREB and regulates the downstream Pde10a gene in C2C12 myoblast-like cells and neurons. Activation of this promoter by CRISPRa increased Pde10a transcript and protein levels, and proteomics revealed that elevated Pde10a promoted C2C12 differentiation at the expense of proliferation. Activation of Pde10a by CRISPRa also impaired CREB-dependent gene expression, suggesting that the mouse homolog of the LINC00473 promoter drives a CREB-Pde10a feedback loop. In contrast to the mouse homolog, human LINC00473 promoter activation by CRISPRa increased LINC00473 expression with either no change in PDE10A or delayed induction compared to mice. Our findings suggest that the newly evolved LINC00473 gene hijacked an ancestral CREB-inducible Pde10a promoter, thereby disrupting a negative feedback loop that may otherwise constrain CREB-dependent gene expression. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/680088v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1862846org.highwire.dtl.DTLVardef@be3ca8org.highwire.dtl.DTLVardef@1806b36org.highwire.dtl.DTLVardef@1fedc56_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

An engineered culture vessel and flow system to improve the in vitro analysis of volatile organic compounds

Volatile organic compounds (VOCs) are a biologically important subset of an organisms metabolome, yet in vitro techniques for the analysis of these small molecules vary substantially in practice, restricting the interpretation and reproducibility of study findings. Here, we present an engineered culture tool, termed the "Biodome", designed to enhance analyte sensitivity by integrating dynamic headspace sampling methodology for the recovery of VOCs from viable biological cultures. We validate the functionality of the device for in vitro volatile metabolomics utilizing computational modeling and fluorescent imaging of mammalian cell culture. We then leverage comprehensive two-dimensional gas chromatography coupled with a time-of-flight mass spectrometer and the enhanced sampling capabilities afforded by our tool to identify seven VOCs not found in the media or exogenously derived from the sampling method (typical pitfalls with in vitro volatilome analysis). We further work to validate the endogenous production of these VOCs using two independent approaches: (i) glycolysis-mediated stable isotopic labeling techniques using 13C6-D-glucose and (ii) RNA interference (RNAi) to selectively knockdown {beta}-oxidation via silencing of CPT2. Isotope labeling reveals 2-Decen-1-ol as endogenously derived with glucose as a carbon source and, through RNAi, we find evidence supporting endogenous production of 2-ethyl-1-hexene, dodecyl acrylate, tridecanoic acid methyl ester and a low abundance alkene (C17) with molecular backbones likely derived from fatty acid degradation. To demonstrate applicability beyond mammalian cell culture, we assess the production of VOCs throughout the log and stationary phases of growth in ampicillin-resistant DH5 Escherichia coli. We identified nine compounds with results supporting endogenous production, six of which were not previously associated with E. coli. Our findings emphasize the improved capabilities of the Biodome for in vitro volatile metabolomics and provide a platform for the standardization of methodology.

bioengineering↗