Biology subjects

Breheny, P.

Publications and source records attributed to Breheny, P..

12 recordsLinked to original sources

bioRxiv2026

Developmental Cerebellar Pathology in Mouse Models of SCN2A Premature Termination Codon Variants

Autism spectrum disorder is a neurodevelopmental disorder with both genetic and environmental contributors. SCN2A, the gene which encodes the alpha subunit of the voltage-gated sodium channel Nav1.2, is a known monogenetic risk factor for autism spectrum disorder. The cerebellum is frequently implicated in autism spectrum disorder and other neurodevelopmental disorders but has largely been unexplored in relation to SCN2A variants, especially from a developmental perspective. Nav1.2 is highly expressed within the cerebellum, specifically within cerebellar granule neurons, where it helps to drive action potential generation and propagation. Cerebellar granule neuron activity and maturation is crucial for shaping the development and morphology of the rest of the cerebellar cortex. Here we investigated early-postnatal cerebellar development in two mouse models carrying patient-derived SCN2A premature termination codon variants, Scn2a-p.Y84X and -p.R1627X. Overall, both Scn2a premature termination codon variant mouse lines displayed largely normal physical development and unaffected non-cerebellar developmental milestones. Scn2aY84X/+ mice, but not Scn2aR1627X/+ mice, demonstrated alterations in cerebellar-driven motor behaviors, specifically faster performance in the surface righting reflex and cliff avoidance compared to wildtype littermates. Coinciding with the behavioral findings, Scn2a variants had divergent and age-dependent effects on cerebellar glutamatergic presynaptic marker expression, indicating that some, but not all, Scn2a premature termination codons impair glutamatergic synapse development. Both Scn2a variants exhibited changes to cerebellar cytoarchitecture, such as reductions in Purkinje cell density and soma size, which was more prominent in Scn2aY84X/+ mice, and faster migration of cerebellar granule neurons from the external granule layer to the internal, indicating a possible shift in the timing of cerebellar maturation. Our results situate the cerebellum as an early site for SCN2A pathophysiology and establish that cerebellar consequences of SCN2A premature termination codon variants may be position- and age-dependent, suggesting that influences beyond simple heterozygous loss of Nav1.2 drive phenotypes. Our characterization of how Scn2a premature termination codon variants differentially impair cerebellar development may help explain the heterogeneity of clinical presentations of SCN2A loss of function variants and potentially inform upon the timing of therapeutic intervention.

neuroscience↗

bioRxiv2026

Post-daunorubicin treatment effects on cardiovascular function in the Ts65Dn mouse model of Down syndrome

Adults with Down syndrome (DS) are two times more likely to be diagnosed with chronic heart failure post-anthracycline chemotherapy compared to age and sex-matched adults without DS. They have an elevated lifetime risk of cardiovascular diseases, increasing their likelihood of anthracycline-induced chronic cardiovascular toxicity. We investigated the chronic effects of daunorubicin on the cardiovascular system of the adult Ts65Dn mouse model of DS compared to wild type euploid mice (WT). WT and Ts65Dn mice received two doses of 2mg/kg or 4mg/kg of daunorubicin or saline and were monitored for up to 117 days. Cardiac and vascular function were evaluated using left ventricular catheterization, histology, pulse wave velocity, and cardiac troponin tests. Survival significantly decreased in the Ts65Dn 4mg/kg group compared to saline controls (p<0.001). Further experiments were carried out with the saline and 2mg/kg groups, which exhibited lower mortality, more consistent with chronic toxicity. Body weight (p=0.001), end-diastolic pressure (p=0.016), and left ventricular mass (p=0.021) decreased in treated mice. The effect of treatment differed significantly between strains for ejection fraction (p=0.029). Pulse wave velocity increased over time (p<0.001). A significant interaction between treatment and strain was observed for collagen in both the left ventricles and thoracic aorta (p=0.002 and p<0.001, respectively). There was a strain difference for cardiac troponin I, indicating an increase in Ts65Dn mice (p=0.020). Daunorubicin treatment results in a distinct cardiovascular remodeling phenotype in Ts65Dn mice. More mechanistic studies are warranted to outline the pathophysiology of anthracycline cardiovascular toxicity in DS.

cancer biology↗

bioRxiv2026

Conservation of transcriptional regulatory networks in zebrafish and human periderm facilitates identification of GRHL1 as an orofacial cleft risk gene

Most heritable risk for orofacial clefts (OFC) remains unassigned to specific genes or loci. IRF6 and GRHL3, two established OFC risk genes, encode transcription factors (TFs) essential for the differentiation of the periderm, a transient embryonic tissue required for secondary palate fusion. To identify novel risk candidates, we modeled the zebrafish periderm transcriptional regulatory network (TRN). Using single-cell multiome sequencing (RNA-seq and ATAC-seq) from shield-stage embryos, we inferred TF-to-target gene connections by integrating correlated gene expression with TF binding site predictions within chromatin elements open in periderm cells. We generated sets of gold-standard edges by conducting RNA-seq on TF-depleted embryos and ChIP-seq/CUT&RUN on wild-type embryos and used them to benchmark model performance. Within the top-performing model, zebrafish periderm modules are strongly preserved in human embryonic periderm and orthologs of human OFC-associated genes have higher centrality and edge-sum scores than non-associated genes. Functional validation confirmed the networks predictive power: depleting high-centrality TFs, including grhl1, klf6a, tead3b, and klf17, disrupted periderm differentiation in sensitized embryos. Moreover, analysis of whole-genome sequencing data from 2,415 OFC trios identified 15 individuals with rare or de novo GRHL1 variants, four of which introduced premature stop codons. This study establishes GRHL1 as a novel OFC risk gene and highlights the power of cross-species gene regulatory network analysis to prioritize candidates for rare variants in complex structural birth defects.

developmental biology↗

bioRxiv2026

Intratumoral plasma cells are required for activation of CD8+ T cells and success of immune checkpoint blockade therapy in de novo MPNSTs

BackgroundThe role of intratumoral plasma cells in immune checkpoint blockade (ICB) therapy has never been tested although their presence is linked with improved patient response and survival. Malignant peripheral nerve sheath tumors (MPNSTs) are deadly sarcomas with minimal responsiveness to ICB therapies. Strikingly, drugs inhibiting cyclin-dependent kinases 4/6 (CDK4/6) and MEK sensitize de novo MPNSTs to immunotherapy targeting programmed death-ligand 1 (PD-L1), which correlates with increased intratumoral plasma cells. Here, we tested if plasma cells mediate the MPNST response to anti-PD-L1 therapy. MethodsAnti-tumor activity of PD-L1 inhibition, with or without CDK4/6-MEK inhibition, was measured in de novo MPNSTs within wild-type versus plasma cell-deficient mice. Plasma cell-dependent effects of CDK4/6-MEK inhibition on priming the MPNST immune environment were determined by single cell transcriptomics and immunostaining. FindingsMPNSTs lacking plasma cells failed to respond to anti-PD-L1 monotherapy and were no longer sensitized to immunotherapy by CDK4/6-MEK inhibition. Plasma cell-deficient MPNSTs exposed to CDK4/6-MEK inhibitors had impaired antigen presentation on major histocompatibility class I (MHC-I) and decreased CD8+ T cell infiltration and activation. Complementary analyses of human sarcomas showed increased intratumoral plasma cell signatures prognose better patient survival. InterpretationPlasma cells favorably remodel the tumor immune environment by increasing CD8+ T cell infiltration and are critical for successful ICB therapy in MPNSTs. This work may help inform ICB treatment strategies and cancer patient stratification for many different tumor types. FundingThis research was supported by University of Iowa Sarcoma Research Program awards and NIH grants T34-GM141143, T32-GM067795, F31-CA281312, P30-CA086862, and R01-NS119322. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSFor many types of cancer, intratumoral plasma cells have been correlated with better patient survival and improved response to immune checkpoint blockade (ICB) therapies. However, the biology underlying those associations is not understood and no study has examined the requirement of plasma cells in immunotherapy response. Compelling data in malignant peripheral nerve sheath tumors (MPNSTs) showed that dual kinase inhibition of oncogenic CDK4/6 and MEK induced intratumoral plasma cell accumulation and sensitized tumors to ICB therapy. While CDK4/6-MEK inhibition is known to enhance antitumor immunity in other tumor types by CD8+ T cells or natural killer (NK) cells, a role for plasma cells has never been explored. Added value of this studyStudies were performed in MPNSTs, an under-researched cancer that normally responds poorly to ICB monotherapies. This is the first investigation to show that intratumoral plasma cells are essential for successful ICB therapy and they support anti-tumor immunity by promoting a pro-inflammatory, CD8+ T cell state involving MHC-I antigen presentation. Findings provide new insight into immunomodulatory effects of CDK4/6-MEK inhibitor therapies, revealing plasma cells are needed for those drugs to activate CD8+ T cell mediated antitumor immunity. Implications of all the available evidenceThe fundamental advance in understanding how plasma cells promote successful ICB immunotherapy is likely applicable to other solid tumors and may guide novel therapeutic strategies in which plasma cell-inducing agents are combined with ICB antibodies. Moreover, an increased presence of intratumoral plasma cells in tumor specimens may streamline clinical decisions regarding which patients are most likely to benefit from ICB therapy.

cancer biology↗

bioRxiv2025

Spontaneous peripheral oxygen desaturation and apnea events in mice vary by strain and inspired oxygen level

Mouse models of chronic intermittent hypoxia are widely used in research to understand the role of sleep apnea in disease pathogenesis. Mice exposed to periodic reductions in FIO2 model arterial desaturations observed in humans and recapitulate many comorbidities of sleep apnea. Here, we perform a detailed characterization and confirm reports that mice in room air experience spontaneous, periodic desaturation events. We measured peripheral oxygen saturation in the four mouse strains most commonly used in intermittent hypoxia research (C57BL/6J, CD1, BALB/c, and 129S1) and subjected them to conscious barometric plethysmography to measure oxygen desaturations and apneas simultaneously and took measurements across a range of fractional inspired oxygen (FIO2). As expected, all strains experienced periodic apneas that were followed by desaturations and decreasing FIO2 resulted in a reduction of spontaneous apneic events (p = 0.001). Surprisingly, most oxygen desaturations were not preceded by apneas or hypopneas, and mice experienced more desaturations at lower FIO2 (p < 0.001), despite less frequent apneas. Furthermore, we found strain differences in ventilatory response consistent with prior findings and a novel strain difference in 129S1 mice. These data suggest that spontaneous desaturations are caused not only by apneas and hypopneas but also by other mechanisms, independent of respiration. Our findings provide important context for mouse models of sleep apnea and associated diseases, and future work should explore the extent to which these findings are relevant in humans.

physiology↗

bioRxiv2025

EHE cell cultures: a platform for mechanistic and therapeutic investigation

Epithelioid hemangioendothelioma (EHE) is a difficult to treat vascular sarcoma defined by TAZ- CAMTA1 or YAP-TFE3 fusion proteins. Human cell lines needed to further understand the pathogenesis of EHE have been lacking. Herein, we describe a method to generate EHE extended primary cell cultures. An integrated multi -omic and functional approach was used to characterize these cultures. The cell cultures, relatively homogenous by single cell RNA-Seq, demonstrated established characteristics of EHE including increased proliferation, anchorage independent growth, as well as the overall gene expression profile and secondary genetic alterations seen in EHE. Whole genome sequencing (WGS) identified links to epigenetic modifying complexes, metabolic processes, and pointed to the importance of the extracellular matrix (ECM) in these tumors. Bulk RNA-Seq demonstrated upregulation of pathways including PI3K-Akt signaling, ECM/ECM receptor interaction, and the Hippo signaling pathway. Development of these extended primary cell cultures allowed for single-cell profiling which demonstrated different cell compartments within the cultures. Furthermore, the cultures served as a therapeutic platform to test the efficacy of TEAD inhibitors in vitro. Overall, the development of EHE primary cell cultures will aid in the mechanistic understanding of this sarcoma and serve as a model system to test new therapeutic approaches.

cancer biology↗

bioRxiv2025

PI3K regulates TAZ/YAP and mTORC1 axes that can be synergistically targeted

Abstract/SummaryO_ST_ABSPurposeC_ST_ABSSarcomas are a heterogeneous group of cancers with few shared therapeutic targets. PI3K signaling is activated in various subsets of sarcomas, representing a shared oncogenic signaling pathway. Oncogenic PI3K signaling has been challenging to target therapeutically. An integrated view of PI3K and Hippo pathway signaling is examined to determine if this could be leveraged therapeutically. Experimental designA tissue microarray containing sarcomas of various histological types was evaluated for PTEN loss and correlated with levels of activated TAZ and YAP. PI3K and Hippo pathways were dissected in sarcoma cell lines. The role of TAZ and YAP were evaluated in a PI3K-driven mouse model. The efficacy of mTORC1 inhibition and TEAD inhibition were evaluated in sarcoma cell lines and in vivo. ResultsPI3K signaling is frequently activated in sarcomas due to PTEN loss (in 30-60%), representing a common therapeutic target. TAZ and YAP are transcriptional co-activators regulated by PI3K and drive a transcriptome necessary for tumor growth in a PI3K-driven sarcoma mouse model. Combination therapy using IK-930 (TEAD inhibitor) and everolimus (mTORC1 inhibitor) synergistically diminished proliferation and anchorage independent growth of PI3K-activated sarcoma cell lines at low, physiologically achievable doses. Furthermore, this combination therapy showed a synergistic effect in vivo, reducing tumor proliferation and size. ConclusionsTAZ and YAP are transcriptional co-activators downstream of PI3K signaling, a pathway that has lacked a well-defined oncogenic transcription factor. This PI3K-TAZ/YAP axis exists in parallel to the known PI3K-Akt-mTORC1 axis allowing for synergistic combination therapy targeting the TAZ/YAP-TEAD interaction and mTORC1 in sarcomas.

cancer biology↗

bioRxiv2021

RABL6A promotes pancreatic neuroendocrine tumor angiogenesis and progression in vivo

Pancreatic neuroendocrine tumors (pNETs) are difficult-to-treat neoplasms whose incidence is rising. Greater understanding of pNET pathogenesis is needed to identify new biomarkers and targets for improved therapy. RABL6A, a novel oncogenic GTPase, is highly expressed in patient pNETs and required for pNET cell proliferation and survival in vitro. Here, we investigated the role of RABL6A in pNET progression in vivo using a well-established model of the disease. RIP-Tag2 (RT2) mice develop functional pNETs (insulinomas) due to SV40 large T-antigen expression in pancreatic islet {beta} cells. RABL6A loss in RT2 mice significantly delayed pancreatic tumor formation, reduced tumor angiogenesis and mitoses, and extended survival. Those effects correlated with upregulation of anti-angiogenic p19ARF and downregulation of proangiogenic c-Myc in RABL6A-deficient islets and tumors. Our findings demonstrate that RABL6A is a bona fide oncogenic driver of pNET angiogenesis and development in vivo.

cancer biology↗

bioRxiv2020

Locally-invasive, castrate-resistant prostate cancer in a Pten/Trp53 double knockout mouse model of prostate cancer monitored with non-invasive bioluminescent imaging

Here we have improved an existing mouse model of prostate cancer based on prostate-specific deletion of Pten and Trp53 by incorporating a Cre-activatable luciferase reporter. By coupling the deletion of those genes to the activation of a luciferase reporter, we were able to monitor tumor burden non-invasively over time. We show that, consistent with previous reports, deletion of both Pten and Trp53 on a C57BL/6 background accelerates tumor growth and results in both the loss of androgen receptor expression and castrate resistant tumors as compared with loss of Pten alone. Loss of Trp53 results in the development of sarcomatoid histology and the expression of markers of epithelial-to-mesenchymal transition Zeb1 and vimentin, with kinetics and penetrance dependent on whether one or both alleles of Trp53 were deleted. Homozygous deletion of Trp53 and Pten resulted in uniformly lethal disease by 25 weeks. While we were able to detect locally invasive disease in the peritoneal cavity in aggressive tumors from the double knockout mice, we were unable to detect lymphatic or hematogenous metastatic disease in lymph nodes or at distant sites.

cancer biology↗

bioRxiv2020

Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18

Genome wide association studies for non-syndromic orofacial cleft (OFC) have identified single nucleotide polymorphisms (SNPs) at loci where the presumed risk-relevant gene is expressed in oral periderm. The functional subsets of such SNPs are difficult to predict because the sequence underpinnings of periderm enhancers are unknown. We applied ATAC-seq to models of human palate periderm, including zebrafish periderm, mouse embryonic palate epithelia, and a human oral epithelium cell line, and to complementary mesenchymal cell types. We identified sets of enhancers specific to the epithelial cells and trained gapped-kmer support-vector-machine classifiers on these sets. We used the classifiers to predict the effect of 14 OFC-associated SNPs at 12q13 near KRT18. All the classifiers picked the same SNP as having the strongest effect, but the significance was highest with the classifier trained on zebrafish periderm. Reporter and deletion analyses support this SNP as lying within a periderm enhancer regulating KRT18/KRT8 expression.

developmental biology↗

bioRxiv2019

Modulation of the combinatorial code of odorant receptor response patterns in odorant mixtures

The perception of odors relies on combinatorial codes consisting of odorant receptor (OR) response patterns to encode odor identity. The modulation of these patterns by odorant interactions at ORs potentially explains several olfactory phenomena: mixture suppression, unpredictable sensory outcomes, and the perception of odorant mixtures as unique objects. We determined OR response patterns to 4 odorants and 3 binary mixtures in vivo in mice, identifying 30 responsive ORs. These patterns typically had a few strongly responsive ORs and a greater number of weakly responsive ORs. The ORs responsive to an odorant were often unrelated sequences distributed across several OR subfamilies. Mixture responses predicted pharmacological interactions between odorants, which were tested in vitro by heterologous expression of ORs in cultured cells. These tests provided independent evidence confirming odorant agonists for 13 ORs and identified both suppressive and additive effects of mixing odorants. This included 11 instances of antagonism of ORs by an odorant, 1 instance of additive responses to a binary mixture, 1 instance of suppression of a strong agonist by a weak agonist, and the discovery of an inverse agonist for an OR. These findings demonstrate that interactions between odorants at ORs are common.

cell biology↗

bioRxiv2019

Cancer cells resist mechanical destruction in the circulation via RhoA-myosin II axis

During metastasis cancer cells are exposed to potentially destructive hemodynamic forces including fluid shear stress (FSS) while en route to distant sites. However, prior work indicates that cancer cells are more resistant to brief pulses of high-level fluid shear stress (FSS) in vitro relative to non-transformed epithelial cells. Herein we identify a mechanism of FSS resistance in cancer cells, and extend these findings to mouse models of circulating tumor cells (CTCs). We show that cancer cells acutely isolated from primary tumors are resistant to FSS. Our findings demonstrate that cancer cells activate the RhoA-myosin II axis in response to FSS, which protects them from FSS-induced plasma membrane damage. Moreover, we show that the myosin II activity is protective to CTCs in mouse models. Collectively our data indicate that viable CTCs actively resist destruction by hemodynamic forces and are likely to be more mechanically robust than is commonly thought.

cancer biology↗