The relationship between genomic sequence composition and transcriptomic output remains an area of active investigation. The systematic enumeration of short nucleotide sequences of fixed length, or k-mers, offers a powerful framework for characterizing sequence structure at a resolution more specific than the entire genome but more broad than gene-level examination, retaining information about the compositional and structural patterns of the sequences themselves. Here, we apply k-mer frequency profiling across multiple lengths to compare the genomic and transcriptomic sequence landscapes of two mammalian species, mice and humans. We find strong Pearson correlations between genome-derived and transcriptome-derived k-mer frequency distributions, suggesting that the overall compositional structure of the genome is largely reflected in transcribed sequences. Despite this broad concordance, a distinct subset of k-mers deviates markedly from the expected correlation, pointing to non-random patterns that warrant further investigation. These findings raise questions about the mechanisms governing sequence composition in transcribed regions and the potential functional or structural significance of such patterns across mammalian genomes.

This abstract has been withheld from publication.

Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality, emphasizing the critical need for selective therapeutic strategies. Cytosolic HSP90 inhibitors have shown limited clinical success, often resulting in toxicity and resistance due to activation of the pro-survival heat shock response. The mitochondrial chaperone HSP75 (TRAP1) has emerged as a promising alternative target of inhibition. In particular, Gamitrinib (GAM), a mitochondrial-targeted HSP75 inhibitor, circumvents the compensatory heat shock response and systemic toxicities associated with HSP90 inhibition, offering a more potent and selective therapeutic window for the treatment of NSCLC. In this study, the efficacy and mechanism of action of GAM were investigated across a panel of NSCLC cell lines. Trypan Blue Assays assessed cell viability in various NSCLC cell lines, in which different responses to GAM were observed. The H2170 and PC9 cell lines were particularly sensitive to HSP75 inhibition. Caspase Glo Assays measured apoptosis in CRISPR knockouts of HSP75 and related apoptotic machinery, including Voltage-Dependent Anion Channel (VDAC), BCL2-associated protein X (BAX), and BCL2 homologous antagonist killer (BAK). Upon GAM treatment, both PC9 and H2170 NSCLC cell lines underwent apoptosis in a VDAC- and BAX/BAK-dependent manner. These findings support the role of mitochondrial HSP75 as a critical regulator of NSCLC cell survival and highlight the potential of GAM as a selective therapeutic agent in NSCLC.

The eye’s outermost layer, corneal epithelium, is continuously exposed to the external environment and depends on limbal epithelial stem cells (LESCs) for regeneration. The regenerative capacity of corneal epithelium is compromised in diabetes mellitus (DM). A significant proportion of patients develop epithelial pathologies due to DM (diabetic keratopathy), and because current treatments are mainly symptomatic, targeted noninvasive regenerative therapies are needed. Our study is focused on diabetic corneal stem cell dysfunction and the identification of novel targets that might be relevant for future treatment. We compared global gene expression changes across limbal epithelial cell (LEC) subpopulations isolated from DM and non-diabetic (N) human corneas using single-cell RNA sequencing (scRNA-seq). We identified 13 unique subpopulations of cells in the corneal epithelium with significant alterations in LEC subpopulations by DM. Of these, POSTN (encodes periostin) was downregulated by DM. Exogenous periostin significantly improved wound healing in DM-LEC but not N-LEC by scratch wound assay. Moreover, silencing of POSTN by siRNA in N-LEC impaired wound healing. These data demonstrate that periostin is a new diabetic marker that plays a role in corneal wound healing and may have potential as a new therapeutic target for the treatment of diabetic keratopathy.

CRISPR has recently taken the world by storm. However, the quantity of template DNA remains a problem. Without sufficient template, the DNA can repair itself unedited or with errors. Therefore, we turn to retrons, a RNA hairpin primary structure that can be reverse transcribed to form an RNA and DNA complex. After reverse transcription, the retron RNA is degraded and the reverse transcribed DNA can be used as a template. Previous experiments using yeast that predominantly utilize HDR and a repair template that induces an accumulation of a red purine intermediate, produced conflicting results. Within the same colony, only half would express the knockout, producing simultaneously red and white dots. One possible explanation for this discrepancy is that there is simply not enough retron, i.e. repair template. Therefore, current research focuses on a possible element of this discrepancy, the promoter. Three different strains will be used. In the constitutive strain, retrons are always made, leading to an increase of the repair template and therefore fully red cells. In the retron without a promoter, some repair template should still be made, theoretically decreasing the amount of red cells compared to the constitutive strain. Finally, as a negative control, in the experiment with solely the repair template, fully white cells are expected. If the cells with constitutive retrons show a significant increase in repair efficacy in comparison to the controls, it could mark a major enhancement to the efficiency of Cas9 gene editing.