Biology subjects

Haley, J. D.

Publications and source records attributed to Haley, J. D..

6 recordsLinked to original sources

bioRxiv2025

Mdig shapes 3D chromatin architecture of immune checkpoint genes and limits metastasis of triple negative breast cancer cells

Despite decades of progress in metastasis research, the identity of bona fide metastasis-driving genes remains elusive. By shifting the focus from individual genes to the three-dimensional (3D) architecture of the genome, we identify the mineral dust-induced gene (mdig) as a chromatin-topology regulator that suppresses immune-checkpoint activation and metastasis in triple-negative breast cancer (TNBC). Re-expression of mdig in mdig-knockout (KO) cells markedly reduced liver metastasis, whereas mdig loss activated epithelial-mesenchymal transition (EMT), T-cell exhaustion, and antigen-presentation pathways. Across multiple cancer types, high mdig expression predicted improved responses to immune checkpoint blockade (ICB). Mechanistically, mdig depletion derepressed inhibitory checkpoint genes, including PD-L1, PD-L2, LGALS9, and PLXNB1/2, accompanied by increased H3K9me3 and H3K36me3 at these loci. Hi-C profiling revealed that mdig maintains topologically associating domains (TADs) and long-range repressive loops at checkpoint loci; loss of mdig disrupted these structures, enabling coordinated activation of immune-evasion programs. Genome-wide analyses showed extensive TAD remodeling in mdig KO cells, with pronounced alterations on chromosome X. Collectively, these findings position mdig as a key chromatin-architectural regulator of immune evasion and metastatic behavior, underscoring its potential as a biomarker for ICB responsiveness in TNBC and beyond. Significance statementMetastasis remains the leading cause of cancer mortality, yet bona fide metastasis-driving genes remain difficult to define. By examining three-dimensional genome architecture rather than individual gene function, we identify mdig as a chromatin-topology regulator that restrains immune evasion and metastasis in triple-negative breast cancer. Loss of mdig disrupts TAD structures and long-range repressive loops at immune-checkpoint loci, enabling coordinated activation of EMT, antigen-presentation, and T-cell-exhaustion programs. Restoring mdig expression markedly reduces liver metastasis, and high mdig levels across cancers predict improved responses to immune-checkpoint blockade. These findings establish mdig as a key regulator of chromatin organization and a potential biomarker for immunotherapy responsiveness.

cancer biology↗

bioRxiv2025

Fosl2 regulates the transition from parietal epithelial cells to myofibroblasts in the kidney

Activation and proliferation of parietal epithelial cells (PECs), located along the inner rim of Bowmans capsule, drives disease progression in subtypes of glomerulonephritis and focal segmental glomerulosclerosis. In examining the mechanisms contributing to PEC activation two established mouse models were utilized in this study, nephrotoxic serum nephritis (transient model) and podocyte-specific Klf4 knockout (progressive model). A role for transcription factor FRA2 (Fosl2) was uncovered through single nuclear multiomic approaches relating to the regulation of PEC transcriptional/chromatin dynamics. Co-immunoprecipitation followed by mass spectrometry assessed the FRA2 protein interactome in cultured PECs, revealing a potential role for FRA2 in alternative splicing. Fosl2 expression was then blunted through CRISPR-Cas9 gene editing in cultured PECs, revealing reduced proliferative capacity and the downregulation of myofibroblast markers. In-vivo genetic lineage tracing of PECs after nephrotoxic serum revealed PEC-to-myofibroblast trans-differentiation events. Finally, immunostaining of human kidney biopsies with varied subtypes of glomerulonephritis confirmed Fosl2 expression in activated PECs within crescentic lesions, with single cell deconvolution strategies assigning PEC-skewed proportion ratios to bulk RNA-seq patient data from the NEPTUNE consortium. These results suggest that FRA2 (Fosl2) directs a conserved molecular program of PEC-specific responses in subtypes of glomerulonephritis and focal segmental glomerulosclerosis.

pathology↗

bioRxiv2025

Identifying Modulators of the Post-Antibiotic Effect

The post-antibiotic effect (PAE) is the delay in bacterial regrowth following antibiotic removal. It has important implications for dosing regimens since drugs that have extended activity following their elimination can be dosed less frequently, widening the therapeutic window. While the PAE has been associated with target vulnerability and the rate of target turnover, little is known about the genetic components that modulate the PAE. Here, we developed a high-throughput assay to screen the Escherichia coli Keio collection of [~]4000 deletion strains, identifying genes that enhance the PAE for CHIR-090, an inhibitor of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC). This screen revealed approximately 400 gene knockouts that enhanced the PAE of CHIR-090. The list of PAE enhancers was enriched for genes involved in transmembrane transport and outer membrane synthesis. Notably, deletion of the rfaE gene, which is involved in lipopolysaccharide (LPS) biosynthesis, increased the PAE of the LpxC inhibitors CHIR-090 and LPC-058 by 2 h and 3 h, respectively. Consistent with this phenotype, co-treatment of wild-type E. coli with an RfaE inhibitor increased the PAE of CHIR-090 or LPC-058 by 1 h. To probe the mechanism of this interaction, we measured the rate of LpxC turnover and found that knocking out rfaE reduced its half-life by 2-fold, suggesting that disrupting RfaE increases the stability of LpxC, increasing target vulnerability and enhancing the PAE of LpxC inhibitors. SIGNIFICANCEAntibiotics are generally dosed at very high levels leading to unwanted side effects and non-compliance, which in turn results in the emergence of drug-resistant bacterial infections. The goal of this work was to develop strategies that will enable antibiotics to be dosed at lower levels, thereby improving safety and compliance. In the present work, we have screened 4,000 strains of Escherichia coli to identify compounds that result in an increase in the post-antibiotic effect (PAE), which is the delay in bacterial regrowth following antibiotic exposure and removal. Drugs that cause a PAE are dosed less frequently, and the method we describe will provide a new approach to developing safer drugs.

microbiology↗

bioRxiv2022

Development of a 5-FU Modified miR-129 Mimic as a Therapeutic for Non-Small Cell Lung Cancer

Lung cancer is the leading cause of cancer-related deaths in the United States with non-small cell lung cancer (NSCLC) accounting for most cases. Despite advances in cancer therapeutics, the 5-year survival rate has remained poor due to several contributing factors, including its resistance to therapeutics. Therefore, there is a pressing need to develop therapeutics that can overcome resistance. Non-coding RNAs, including microRNAs (miRNAs), have been found to contribute to cancer resistance and therapeutics by modulating the expression of several targets involving multiple key mechanisms. In this study, we investigated the therapeutic potential of miR-129 modified with 5-fluorouracil (5-FU) in NSCLC. Our results show that 5-FU modified miR-129 (5-FU-miR-129) inhibits proliferation, induces apoptosis, and retains function as a miRNA in NSCLC cell lines A549 and Calu-1. Notably, we observed that 5-FU-miR-129 was able to overcome resistance to tyrosine kinase inhibitors and chemotherapy in cell lines resistant to erlotinib or 5-FU. Furthermore, we observed that the inhibitory effect of 5-FU-miR-129 can also be achieved in NSCLC cells under vehicle-free conditions. Finally, 5-FU-miR-129 inhibited NSCLC tumor growth and extended survival in vivo without toxic side effects. Altogether, our results demonstrate the potential of 5-FU-miR-129 as a highly potent cancer therapeutic in NSCLC.

cancer biology↗

bioRxiv2021

Integrative multi-omics profiling reveals cAMP-independent mechanisms regulating hyphal morphogenesis in Candida albicans

Microbial pathogens grow in a wide range of different morphologies that provide distinct advantages for virulence. In the fungal pathogen Candida albicans, adenylyl cyclase (Cyr1) is thought to be a master regulator of the switch to invasive hyphal morphogenesis and biofilm formation. However, faster growing cyr1{Delta}/{Delta} pseudorevertant (PR) mutants were identified that form hyphae in the absence of cAMP. Isolation of additional PR mutants revealed that their improved growth was due to loss of one copy of BCY1, the negative regulatory subunit of protein kinase (A) from the left arm of chromosome 2. Furthermore, hyphal morphogenesis was improved in some of PR mutants by multigenic haploinsufficiency resulting from loss of large regions of the left arm of chromosome 2, including global transcriptional regulators. Interestingly, hyphal-associated genes were also induced in a manner that was independent of cAMP. This indicates that basal protein kinase A activity is an important prerequisite to induce hyphae, but activation of the cAMP pathway is not needed. Instead, phosphoproteomic analysis indicated that the Cdc28 cyclin-dependent kinase and the casein kinase 1 family member Yck2 play key roles in promoting polarized growth. In addition, integrating transcriptomic and proteomic data reveals hyphal stimuli induce increased production of key transcription factors that contribute to polarized morphogenesis. AUTHOR SUMMARYThe human fungal pathogen Candida albicans switches between budding and filamentous hyphal morphologies to gain advantages for virulence and survival in the host. Although adenylyl cyclase has been thought to be a master regulator that controls this switch, we identified C. albicans pseudorevertant mutants that grow better and form hyphae in the absence of adenylyl cyclase and cAMP. The mutant cells were also able to induce hyphal-associated genes in the absence of cAMP that are needed for virulence. Integrating information from different omics approaches identified cAMP-independent mechanisms that promote hyphal growth. This includes phosphoproteomic studies that revealed key roles for the Cdc28 cyclin-dependent kinase and casein kinase 1 in promoting hyphal growth. In addition, integrating transcriptomic and proteomic data revealed that post-transcriptional mechanisms regulate the levels of a set of key transcription factors that are important for hyphal induction, suggesting a novel form of translational regulation. These studies better define the pathways that stimulate C. albicans to switch from budding to hyphal growth, which is important for invasion into tissues, escape from the immune system, and biofilm formation.

microbiology↗

bioRxiv2020

SREBP1 regulates mitochondrial metabolism in oncogenic KRAS expressing NSCLC

Cancer cells require extensive metabolic reprogramming in order to provide the bioenergetics and macromolecular precursors needed to sustain a malignant phenotype. Mutant KRAS is a driver oncogene that is well known for its ability to regulate the ERK and PI3K signaling pathways. However, it is now appreciated that KRAS can promote tumor growth via upregulation of anabolic metabolism. We recently showed that oncogenic KRAS promotes a gene expression program of de novo lipogenesis in non-small cell lung cancer (NSCLC). To define the mechanism(s) responsible, we focused on the lipogenic transcription factor SREBP1. We observed that KRAS increases SREBP1 expression and genetic knockdown of SREBP1 significantly inhibited cell proliferation of mutant KRAS-expressing cells. Unexpectedly, lipogenesis was not significantly altered in cells subject to SREBP1 knockdown. Carbon tracing metabolic studies showed a significant decrease in oxidative phosphorylation and RNA-seq data revealed a significant decrease in mitochondrial encoded subunits of the electron transport chain (ETC). Taken together, these data support a novel role, distinct from lipogenesis, of SREBP1 on mitochondrial function in mutant KRAS NSCLC.

cancer biology↗