Biology subjects

Ford, C.

Publications and source records attributed to Ford, C..

8 recordsLinked to original sources

bioRxiv2026

Distinct forms of dopamine transmission control locomotion and learning

The neuromodulator dopamine is essential for voluntary movement and learning from experience. While these behaviors often occur simultaneously and rely on overlapping nigrostriatal dopamine circuits, they are also separable and can manifest independently. How a single neuromodulatory system controls such disparate aspects of behavior in parallel remains poorly understood. Here we show that striatal dopamine is released through two spatially and functionally distinct modes that are independently regulated and serve distinct behavioral roles. Eliminating dopamine release underlying bulk extracellular accumulation reveals a spatially restricted mode of transmission that maintains phasic dopamine receptor activation on striatal projection neurons. We find that selective loss of diffuse dopamine impairs striatal circuit excitability and reduces locomotion, while point-to-point transmission is sufficient to maintain striatal spine density and support motor and associative learning. We propose that the geometry of dopamine release determines its behavioral output, a principle that explains the breadth of dopamines functions and more broadly elucidates how neurons multiplex different forms of information.

neuroscience↗

bioRxiv2025

Acute Administration of Oxytocin in the Functional Recovery of Neurocognitive and Social Deficits Following Juvenile Frontal Traumatic Brain Injury

IntroductionJuvenile traumatic brain injury (jTBI) is one of the leading causes of death and disability in children. The prefrontal cortex (PFC) is most susceptible to injury which leads to deficits in executive function, social behaviors, and cognitive flexibility. Prior research has shown a significant role of the oxytocin (OXT) system in the modulation of social behaviors, and that intranasal OXT (IN-OXT) is potentially neuroprotective. Therefore, we believe IN-OXT could improve functional recovery from a PFC injury. MethodsAnimals received a single midline cortical contusion bilaterally damaging the medial PFC (mPFC) and immediately given a single dose of IN-OXT, placebo, or no treatment. Animals were assessed using behavioral and histological measures. ResultsThe results indicated that jTBI significantly impacted the normal development of the OXT system, likely due to deficits in OXT synthesis in the SON. While IN-OXT alleviated these deficits, it had no impact on neuroinflammation. Similarly, behavioral effects of IN-OXT were not consistent. Mild improvements were observed in spatial learning but there were no improvements in spatial memory or social dominance. DiscussionThese results show that IN-OXT increases OXT levels in the brain via pathways originating in the SON and improved spatial learning.

neuroscience↗

bioRxiv2025

Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway

During tumor progression, it has been assumed that individual cells that have acquired advantageous mutations overtake the population. Cancers driven by extrachromosomal DNA (ecDNA) do not follow this paradigm. Instead, these tumors have a spectrum of oncogene copy numbers across cells, and graded ecDNA variation may function as a form of bet-hedging that equips tumors with a broad range of phenotypes. Using imaging, single-cell multiomics, and multiplexed proteomics, we systematically characterized ecDNA levels across thousands of single cells. Higher ecDNA dosage produces proportional changes in transcript abundance, chromatin accessibility, protein levels, cell-cycle progression, and proliferation. Genes amplified on ecDNA exhibit distinct transcriptional scaling regimes that shift when the same genes are reintegrated into chromosomal homogeneous staining regions. When we experimentally disrupted the continuum of ecDNA dosage by sorting cells into low- and high-copy number states, the population rapidly recovered its original, continuous distribution. Our time-course data, live-cell imaging, and stochastic models collectively show that restoring this spectrum is an active, deterministic process rather than the passive outcome of random segregation. Together, these findings position ecDNA-mediated expression as a distinct evolutionary mechanism that endows tumors with rapid, population-level adaptability. These findings offer insight into why ecDNA-driven cancers are among the most aggressive and treatment-resistant.

genomics↗

bioRxiv2025

Postsynaptic adaptations in direct pathway muscarinic M4-receptor signaling follow the temporal and regional pattern of dopaminergic degeneration

In Parkinson’s disease (PD), imbalances in dorsal striatum (DSt) output pathways leading to motor dysfunction are thought to be driven by the loss of dopamine (DA) itself and the disruption of its coordinated modulation with acetylcholine (ACh). While the gradual decline of DA across striatal regions over time is a defining characteristic of PD, less is known about the adaptive and/or pathological alterations in cholinergic signaling that develop throughout disease progression in response to DA loss. Here, we examined changes in cholinergic modulation of striatal direct pathway medium spiny neurons (dMSNs) in mice that were partially or completely depleted of DA, in order to model early and advanced stages of PD. We found a reduction in muscarinic M4 receptor signaling that began in the dorsolateral striatum (DLS) following a partial loss of DA, yet was not evident in the dorsomedial region (DMS) until the dopaminergic lesion was nearly complete. Combining electrophysiological, pharmacological and 2-photon imaging approaches, we determined that this decrease was the result of reduced postsynaptic M4 receptor function, and was not accounted for by changes in ACh release or clearance. Replacing the partial loss of endogenous DA with levodopa could not rescue the dysfunctional M4 receptors. Together, these findings reveal how changes in cholinergic modulation closely follow the temporal and regional pattern of dopaminergic degeneration, which is critical for understanding their shared role in PD progression, and for developing alternative therapeutic interventions.

neuroscience↗

bioRxiv2023

CytoCellDB: A Resource Database For Classification and Analysis of Extrachromosomal DNA in Cancer

Extrachromosomal DNA (ecDNA), or double minute chromosomes, are established cytogenetic markers for malignancy and genome instability. More recently, the cancer community has gained a heightened awareness of the roles of ecDNA in cancer proliferation, drug resistance and epigenetic remodeling. A current hindrance to understanding the biological roles of ecDNA is the lack of available cell line model systems with experimental cytogenetic data that confirm ecDNA status. Although several recent landmark studies have identified common cell lines and tumor models with ecDNA, the current sample size limits our ability to detect ecDNA-driven molecular differences due to limitations in power. Increasing the number of model systems known to express ecDNA would provide new avenues for understanding the fundamental underpinnings of ecDNA biology and would unlock a wealth of potential targeting strategies for ecDNA-driven cancers. To bridge this gap, we created CytoCellDB, a resource that provides karyotype annotations and leverages publicly available global cell line data from the Cancer Dependency Map (DepMap) and the Cancer Cell Line Encyclopedia (CCLE). Here, we identify 139 cell lines that express ecDNA, which is a 200% increase from the current sample size. We expanded the total number of cancer cell lines with ecDNA annotations to 577, which is a 400% increase or 31% of cell lines in CCLE/ DepMap. We demonstrate that a strength of CytoCellDB is the ability to interrogate ecDNA, and a compendium of other chromosomal aberrations, in the context of cancer-specific vulnerabilities, drug sensitivities, and molecular data (genomics, transcriptomics, methylation, proteomics). We anticipate that CytoCellDB will advance cytogenomics research and population-scale discoveries related to ecDNA as well as provide insights into strategies and best practices for determining novel therapeutics that overcome ecDNA-driven drug resistance.

genomics↗

bioRxiv2021

Pan-tissue and -cancer analysis of ROR1 and ROR2 transcript variants identify novel functional significance for an alternative splice variant of ROR1

BackgroundROR1/2 are putative druggable targets increasing in significance in translational oncology. Expression of ROR1/2 mRNA and transcript variants has not been systematically examined thus far. MethodsROR1/2 transcript variant sequences, signal peptides for cell surface localisation, and mRNA and transcript variant expression were examined in 34 transcriptomic datasets including 33 cancer types and 54 non-diseased human tissues. ResultsROR1/2 have four and eight transcript variants respectively. ROR1/2 mRNA and transcript variant expression was detected in various non-diseased tissues. Our analysis identifies predominant expression of ROR1 transcript variant ENST00000545203, which lacks a signal peptide for cell surface localisation, rather than the predicted principal variant ENST00000371079. ENST00000375708 is the predominantly expressed transcript variant of ROR2. ConclusionROR1/2 expression in healthy human tissues should be carefully considered for safety assessment of targeted therapy. Studies exploring the function and significance of the predominantly expressed ROR1 transcript variant ENST00000545203 are warranted.

cancer biology↗

bioRxiv2021

Contemporary clinical isolates of Staphylococcus aureus from pediatric osteomyelitis patients display unique characteristics in a mouse model of hematogenous osteomyelitis

Osteomyelitis can result from the direct inoculation of pathogens into bone during injury or surgery, or from spread via the bloodstream, a condition called hematogenous osteomyelitis (HOM). HOM disproportionally affects children, and more than half of cases are caused by Staphylococcus (S.) aureus. Laboratory models of osteomyelitis mostly utilize direct injection of bacteria into the bone or the implantation of foreign material, and therefore do not directly interrogate the pathogenesis of pediatric hematogenous osteomyelitis. In this study, we inoculated mice intravenously and characterized resultant musculoskeletal infections using two strains isolated from adults (USA300-LAC and NRS384) and five new methicillin-resistant S. aureus isolates from pediatric osteomyelitis patients. All strains were capable of creating stable infections over five weeks, although the incidence varied. Micro-computed tomography (microCT) analysis demonstrated decreases in trabecular bone volume fraction but little effect on bone cortices. Histologic assessment revealed differences in the precise focus of musculoskeletal infection, with varying mixtures of bone-centered osteomyelitis and joint-centered septic arthritis. Whole genome sequencing of three new isolates demonstrated distinct strains, two within the USA300 lineage and one USA100 isolate. Interestingly, the USA100 strain showed a distinct predilection for septic arthritis, compared to the USA300 strains, including NRS384 and LAC, which more frequently led to osteomyelitis or mixed bone and joint infections. Collectively, these data outline the feasibility of using pediatric osteomyelitis clinical isolates to study the pathogenesis of HOM in murine models and lay the groundwork for future studies investigating strain-dependent differences in musculoskeletal infection. ImportanceThe inflammation of bone tissue is called osteomyelitis, and more than half of cases are caused by an infection with the bacterium Staphylococcus aureus. In children, the most common route of infection is hematogenous, wherein bacteria seed the bone from the bloodstream without another known site of infection. Although these infections pose a significant health problem, they are understudied in the laboratory because of a dearth of robust animal models. In this study, we utilized several previously uncharacterized clinical isolates of S. aureus derived from children with bone infections to generate reproducible and stable musculoskeletal infection in mice with many features seen in human osteomyelitis, making them a valuable resource for future mechanistic and therapeutic studies.

pathology↗

bioRxiv2020

Whole Genome Sequencing of Plasmodium vivax Isolates Reveals Frequent Sequence and Structural Polymorphisms in Erythrocyte Binding Genes

Plasmodium vivax malaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. Recently, there has been a dramatic increase in the reporting of P. vivax cases in Africa, with a high number of them being in Duffy negative individuals, potentially indicating P. vivax has evolved an alternative invasion mechanism that can overcome Duffy negativity. Here, we analyzed single nucleotide polymorphism (SNP) and copy number variation (CNV) in Whole Genome Sequence (WGS) data from 44 P. vivax samples isolated from symptomatic malaria patients in southwestern Ethiopia, where both Duffy positive and Duffy negative individuals are found. A total of 236,351 SNPs were detected, of which 21.9% was nonsynonymous and 78.1% was synonymous mutations. The largest number of SNPs were detected on chromosomes 9 (33,478 SNPs; 14% of total) and 10 (28,133 SNPs; 11.9%). There were particularly high levels of polymorphism in erythrocyte binding gene candidates including reticulocyte binding protein 2c (RBP2c), merozoite surface protein 1 (MSP1), and merozoite surface protein 3 (MSP3.5, MSP3.85 and MSP3.9). Thirteen genes related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. Variation in gene copy number was also concentrated in genes involved in host-parasite interactions, including the expansion of the Duffy binding protein gene (PvDBP) on chromosome 6 and several PIR genes. Based on the phylogeny constructed from the whole genome sequences, the expansion of these genes was an independent process among the P. vivax lineages in Ethiopia. We further inferred transmission patterns of P. vivax infections among study sites and showed various levels of gene flow at a small geographical scale. The genomic features of P. vivax provided baseline data for future comparison with those in Duffy-negative individuals, and allowed us to develop a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale.

genomics↗