Biology subjects

Fitzpatrick, M.

Publications and source records attributed to Fitzpatrick, M..

9 recordsLinked to original sources

bioRxiv2026

Preclinical CRX augmentation therapies for CRX-associated autosomal dominant cone-rod dystrophies

Cone-rod dystrophies (CoRD) are inherited retinal diseases (IRDs) with variable ages of onset, characterized by the progressive loss of cones, followed by secondary degeneration of rods. Cone-rod homeobox (CRX) is a transcription factor that regulates gene expression essential for photoreceptor development and maintenance. Mutations in CRX gene, including CRXE168d2 and CRXE80A, are implicated in autosomal dominant CoRDs. Although these mutations show distinct pathogenic mechanisms, published studies in knock-in mouse models have suggested a common treatment strategy: increasing WT CRX expression to reduce the detrimental activities of mutant proteins. This study employs two independent strategies of CRX augmentation to evaluate their therapeutic potential in CrxE168d2/+ and CrxE80A/+ mouse models. The Tet-On-hCRX transgenic system, a platform of proof-of-principle gene therapy, induces consistent and pan-photoreceptor expression of CRX augmentation in diseased retinae, allowing for the faithful assessment of functional and behavioral recovery. AAV-mediated CRX augmentation confirms the biosafety, delivery efficiency and efficacy of viral transduction in diseased retinae. Both strategies have achieved significant treatment outcomes in cone photoreceptor survival and overall photoreceptor functions in young adulthood. Treated cones survive past the age point of complete cone loss in untreated controls of both models. Treated rods show functional improvement and long-term survival through later adulthood. This preclinical study establishes valuable treatment regimens and benchmarks for CRX augmentation in the treatment of CRX-associated IRDs, and offers new insights into the mechanisms for photoreceptor development and survival.

neuroscience↗

bioRxiv2025

Climate and hybridization shape stomatal trait evolution in Populus

O_LIStomata play a critical role in regulating plant responses to climate. Where sister species differ in stomatal traits, interspecific gene flow can influence the evolutionary trajectory of trait variation, with consequences to adaptation. C_LIO_LILeveraging six latitudinally-distributed transects spanning the natural hybrid zone between Populus trichocarpa-P. balsamifera, we used whole genome resequencing and replicate common garden experiments to test the role that interspecific gene flow and selection play to stomatal trait evolution. C_LIO_LIWhile species-specific differences in the distribution of stomata persist between P. balsamifera and P. trichocarpa, hybrids on average resembled P. trichocarpa. Admixture mapping identified several candidate genes associated with stomatal trait variation in hybrids including TWIST, a homolog of SPEECHLESS in Arabidopsis, that initiates stomatal development via asymmetric cell divisions. Geographic clines revealed candidate genes deviating from genome-wide average patterns of introgression, suggesting restricted gene flow and the maintenance of adaptive differences. Climate associations, particularly with precipitation, indicated selection shapes local ancestry at candidate genes across transects. C_LIO_LIThese results highlight the role of climate in shaping stomatal trait evolution in Populus and demonstrate how interspecific gene flow creates novel genetic combinations that may enhance adaptive potential in changing environments. C_LI

evolutionary biology↗

bioRxiv2025

The role of cytonuclear interactions to plant adaptation across a Populus hybrid zone

Co-adaptation of cytoplasmic and nuclear genomes are critical to physiological function for many species. Despite this understanding, hybridization can disrupt co-adaptation leading to a mismatch between maternally-inherited cytoplasmic genomes and biparentally inherited nuclear genomes. Few studies have examined the consequences of cytonuclear interactions to physiological function across environments. Here, we quantify the degree of co-introgression between chloroplast and nuclear-chloroplast (N-cp) genes across repeated hybrid zones and its consequences to physiological function across environments. We use whole-genome resequencing and common garden experiments with clonally replicated genotypes sampled across the natural hybrid zone between Populus trichocarpa and P. balsamifera. We use geographic clines to test for co-introgression of the chloroplast genome with N-cp and non-interacting nuclear genes. Co-introgression of chloroplast and N-cp genes was limited although contact zone-specific patterns suggest that local environments may influence co-introgression. Combining ancestry estimates with phenotypic data across common gardens revealed that mismatches between chloroplast and nuclear ancestry can influence physiological performance, but the strength and direction of these effects vary depending on the environment. Overall, this study highlights the importance of cytonuclear interactions to adaptation, and the role of environment in modifying the effect of those interactions.

evolutionary biology↗

bioRxiv2024

Protein-coding mutation in Adcy3 increases adiposity and alters emotional behaviors sex-dependently in rats

1ObjectiveAdenylate cyclase 3 (Adcy3) has been linked to both obesity and major depressive disorder (MDD). Our lab identified a protein-coding variant in the 2nd transmembrane (TM) helix of Adcy3 in rats, and similar obesity variants have been identified in humans. The current study investigates the role of a TM variant in adiposity and behavior. MethodsWe used CRISPR-SpCas9 to mutate the TM domain of Adcy3 in WKY rats (Adcy3mut/mut). We also created a heterozygous knockout rat in the same strain (Adcy3+/-). Wild-type (WT), Adcy3+/-, and Adcy3mut/mut rats were fed a high-fat diet for 12 weeks. We measured body weight, fat mass, glucose tolerance, food intake, metabolism, emotion-like behaviors, and memory. ResultsAdcy3+/- and Adcy3mut/mut rats weighed more than WT rats due to increased fat mass. There were key sex differences: adiposity was driven by increased food intake in males but by decreased energy expenditure in females. Adcy3mut/mut males displayed increased passive coping and decreased memory while Adcy3mut/mut females displayed increased anxiety-like behavior. ConclusionsThese studies show that the ADCY3 TM domain plays a role in protein function, that Adcy3 may contribute to the relationship between obesity and MDD, and that sex influences the relationships between Adcy3, metabolism, and behavior. Study Importance QuestionsO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIAdcy3 has been linked to both obesity and depression in humans, with protein-coding variants in the transmembrane domain leading to increased obesity. Yet the underlying mechanisms are unknown, and it is unknown if the same Adcy3 variants can cause both obesity and depression. C_LIO_LIRodent Adcy3 knockout models show increased adiposity and altered emotional behaviors, but no rodent models have assessed the role of protein-coding variants in Adcy3. Very few studies have assessed sex differences. C_LI What are the new findings in your manuscript?O_LIThis is the first study to assess the role of a protein-coding variant in the transmembrane domain of Adcy3, showing increases in both obesity and emotion-like behaviors in a rat model. C_LIO_LIWe observed striking sex differences, where male and female rats had different factors driving their adiposity and different patterns of altered behavior. C_LI How might your results change the direction of research or the focus of clinical practice?O_LIUnderstanding the role of Adcy3 in obesity and MDD may lead to improved treatments for both diseases. C_LIO_LIImproving our understanding of the sex differences caused by the same Adcy3 mutation emphasizes the importance of studying both sexes and paves the way for personalized medicine approaches. C_LI

genetics↗

bioRxiv2021

A multisensory circuit for gating intense aversive experiences

The ventral hippocampus (vHPC) is critical for both learned and innate fear, but how discrete projections control different types of fear is poorly understood. Here, we report a novel excitatory circuit from a subpopulation of the ventral hippocampus CA1 subfield (vCA1) to the inhibitory peri-paraventricular nucleus of the hypothalamus (pPVN) which then routes to the periaqueductal grey (PAG). We find that vCA1[->]pPVN projections modulate both learned and innate fear. Fiber photometric calcium recordings reveal that activity in vCA1[->]pPVN projections increases during the first moments of exposure to an unconditioned threat. Chemogenetic or optogenetic silencing of vCA1[->]pPVN cell bodies or vCA1[->]pPVN axon terminals in the pPVN enhances the initial magnitude of both active and passive unconditioned defensive responses, irrespective of the sensory modalities engaged by a particular innate threat. Moreover, silencing produces a dramatic impact on learned fear without affecting milder anxiety-like behaviors. We also show that vCA1[->]pPVN projections monosynaptically route to the PAG, a key brain region that orchestrates the fear response. Surprisingly, optogenetic silencing of vCA1 terminals in the pPVN titrates the level of c-Fos neural activity in the PAG differently for learned versus innate threats. Together, our results show how a novel vCA1[->]pPVN circuit modulates neuronal activity in the PAG to regulate both learned and innate fear. These findings have implications for how initial trauma processing may influence maladaptive defensive behaviors across fear and trauma-related disorders. One Sentence SummaryA multisensory gate for high intensity aversive experiences.

neuroscience↗

bioRxiv2020

Relationships between climate and phylogenetic community structure of fossil pollen assemblages are not constant during the last deglaciation

Disentangling the influence of environmental drivers on community assembly is important to understand how multiple processes influence biodiversity patterns and can inform understanding of ecological responses to climate change. Phylogenetic Community Structure (PCS) is increasingly used in community assembly studies to incorporate evolutionary perspectives and as a proxy for trait (dis)similarity within communities. Studies often assume a stationary relationship between PCS and climate, though few if any studies have tested this assumption over long time periods with concurrent community data. We estimated Nearest Taxon Index (NTI) and Net Relatedness index (NRI), two PCS metrics, of fossil pollen assemblages of angiosperms in eastern North America data over the last 21 ka BP at 1ka intervals. We analyzed spatiotemporal relationships between PCS and seven climate variables, evaluated the potential impact of deglaciation on PCS, and tested for the stability of climate-PCS relationships. The broad scale patterns of PCS, with overdispersion increasing towards the southern and eastern parts of the study area, remained largely stable across time. Most importantly, we found that significant relationships between climate variables and PCS (slope) were unstable as climate changed during the last deglaciation and new ice-free regions were colonized. We also found weak, but significant, relationships between both PCS metrics (i.e., NTI and NRI) and climate and time-since-deglaciation, which were stable even though the baselines (intercepts) changed through time. Overall, our results suggest that (1) PCS of fossil Angiosperm assemblages during the last 21ka BP have had predictable spatial patterns, but (2) the instability in the relationships between PCS and climate brings into question their usefulness in predictive modeling of community assembly.

ecology↗

bioRxiv2020

Multiplexed imaging of human tuberculosis granulomas uncovers immunoregulatory features conserved across tissue and blood

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that is distinctly characterized by granuloma formation within infected tissues. Granulomas are dynamic and organized immune cell aggregates that limit dissemination, but can also hinder bacterial clearance. Consequently, outcome in TB is influenced by how granuloma structure and composition shift the balance between these two functions. To date, our understanding of what factors drive granuloma function in humans is limited. With this in mind, we used Multiplexed Ion Beam Imaging by Time-of-Flight (MIBI-TOF) to profile 37 proteins in tissues from thirteen patients with active TB disease from the U.S. and South Africa. With this dataset, we constructed a comprehensive tissue atlas where the lineage, functional state, and spatial distribution of 19 unique cell subsets were mapped onto eight phenotypically-distinct granuloma microenvironments. This work revealed an immunosuppressed microenvironment specific to TB granulomas with spatially coordinated co-expression of IDO1 and PD-L1 by myeloid cells and proliferating regulatory T cells. Interestingly, this microenvironment lacked markers consistent with T-cell activation, supporting a myeloid-mediated mechanism of immune suppression. We observed similar trends in gene expression of immunoregulatory proteins in a confirmatory transcriptomic analysis of peripheral blood collected from over 1500 individuals with latent or active TB infection and healthy controls across 29 cohorts spanning 14 countries. Notably, PD-L1 gene expression was found to correlate with TB progression and treatment response, supporting its potential use as a blood-based biomarker. Taken together, this study serves as a framework for leveraging independent cohorts and complementary methodologies to understand how local and systemic immune responses are linked in human health and disease.

immunology↗

bioRxiv2020

The low complexity motif of cytoplasmic polyadenylation element binding protein 3 (CPEB3) is critical for the trafficking of its targets in neurons

Biomolecular condensates, membraneless organelles found throughout the cell, play critical roles in many aspects of cellular function. Ribonucleoprotein granules (RNPs), a type of biomolecular condensate found in neurons that are necessary for local protein synthesis and are involved in long-term potentiation (LTP). Several RNA-binding proteins present in RNPs are necessary for the synaptic plasticity involved in LTP and long-term memory. Most of these proteins possess low complexity motifs, allowing for increased promiscuity. We explore the role the low complexity motif plays for RNA binding protein cytoplasmic polyadenylation element binding protein 3 (CPEB3), a protein necessary for long-term memory persistence. We found that RNA binding and SUMOylation are necessary for CPEB3 localization to the P body, thereby having functional implications on translation. Here, we investigate the role of the low complexity motif of CPEB3 and find that it is necessary for P body localization and downstream targeting for local protein synthesis.

neuroscience↗

bioRxiv2017

A system-wide approach to monitor responses to synergistic BRAF and EGFR inhibition in colorectal cancer cells

Intrinsic and/or acquired resistance represents one of the great challenges in targeted cancer therapy. A deeper understanding of the molecular biology of cancer has resulted in more efficient strategies, where one or multiple drugs are adopted in novel therapies to tackle resistance. This beneficial effect of using combination treatments has also been observed in colorectal cancer patients harboring the BRAF(V600E) mutation, whereby dual inhibition of BRAF(V600E) and EGFR increases antitumor activity. Notwithstanding this success, it is not clear whether this combination treatment is the only or most effective treatment to block intrinsic resistance to BRAF inhibitors. Here, we investigate molecular responses upon single and multi-target treatments, over time, using BRAF(V600E) mutant colorectal cancer cells as a model system. Through integration of transcriptomic, proteomic and phosphoproteomics data we obtain a comprehensive overview, revealing both known and novel responses. We primarily observe widespread upregulation of receptors tyrosine kinases and metabolic pathways upon BRAF inhibition. These findings point to mechanisms by which the drug-treated cells switch energy sources and enter a quiescent-like state as a defensive response, while additionally reactivating the MAPK pathway.

cancer biology↗