Biology subjects

Hart, C.

Publications and source records attributed to Hart, C..

12 recordsLinked to original sources

bioRxiv2026

Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics

Pooled CRISPR screens coupled with single-cell RNA sequencing enable high-throughput functional interrogation of gene regulatory networks, yet systematic comparisons of CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) remain limited. We established a single-cell CRISPRko workflow and benchmarked it against CRISPRi using 87 sgRNAs targeting 29 unfolded protein response genes. CRISPRko generated transcriptional phenotypes are highly concordant with CRISPRi, and induced comparable pathway-level responses. While CRISPRi allows direct assessment of target gene repression, CRISPRko provides an effective complementary approach for complete loss-of-function studies, expanding the toolkit for single-cell functional genomics.

genomics↗

bioRxiv2026

Scarless conditional sgRNAs via endogenous mascRNA processing enable rapid and temporally controlled genome editing

Precise temporal control of gene editing is essential for studying dynamic biological processes, interrogating essential gene function, and improving the interpretability of pooled perturbation screens. Cre-dependent single guide RNA (sgRNA) switches provide temporal regulation by coupling guide activation to site-specific recombination, but existing designs retain a loxP-derived 5' sequence (scar) on the mature sgRNA that can impair guide function. We developed a scarless conditional sgRNA platform that combines Cre-loxP recombination with endogenous RNA processing to restore the native sgRNA architecture following induction. A MALAT1-associated small cytoplasmic RNA (mascRNA) module was positioned upstream of the guide sequence such that, after Cre-mediated recombination, cellular RNase P and RNase Z remove the residual loxP-derived overhang, generating a mature sgRNA with an authentic 5' terminus. Using guides targeting endogenous cell-surface marker genes, the scarless design maintained stringent OFF-state control while improving ON-state editing performance compared with a conventional Cre-activated sgRNA switch, resulting in faster editing kinetics, greater perturbation penetrance, and more consistent editing efficiency. This modular strategy provides a simple approach for conditional CRISPR genome editing that preserves guide integrity and should be readily adaptable to time-resolved functional genomics and pooled screening applications.

cell biology↗

bioRxiv2026

DRP1 inhibition confers cardioprotection against doxorubicin while preserving anticancer efficacy

BackgroundAnthracyclines such as doxorubicin are effective chemotherapeutics but are limited by cardiotoxicity driven in part by mitochondrial dysfunction. Dysregulated mitochondrial dynamics, particularly excessive dynamin-related protein-1 (Drp1)-mediated fission, contribute to doxorubicin-induced cardiac injury and support selective survival of cancer cells. ObjectivesTo determine whether DRP1i2, a novel small molecule Drp1 inhibitor targeting a conserved domain shared between human and mouse, can function as a cardio-oncology therapeutic by reducing doxorubicin-induced cardiotoxicity while maintaining or enhancing anti-cancer efficacy. MethodsCardioprotective effects of DRP1i2 were evaluated in a murine model of chronic doxorubicin cardiotoxicity and in human induced pluripotent stem cell-derived cardiac microtissues exposed to acute doxorubicin injury. Anticancer activity was assessed across multiple cancer cell lines using 2D monolayers and 3D microtissues. ResultsIn vivo, DRP1i2 preserved left ventricular ejection fraction, reduced interstitial fibrosis and cardiomyocyte atrophy, and attenuated doxorubicin-induced myocardial proteomic remodelling. In human cardiac microtissues, DRP1i2 improved viability and restored contractile function despite persistent mitochondrial oxidative stress. DRP1i2 showed modest anticancer activity in MG63 osteosarcoma cells in both 2D and 3D systems and did not diminish doxorubicin efficacy in other cancer models (MDA-MB-231 breast, OVCAR3 ovarian, and A549 lung adenocarcinoma). Combined treatment further enhanced cytotoxicity selectively in MG63 cells. ConclusionsDRP1i2 exerts complementary cardioprotective and anticancer actions through modulation of shared mitochondrial pathways, identifying Drp1 as a druggable target in cardio-oncology. These findings support DRP1i2 as a first-in-class Drp1 inhibitor and highlight mitochondrial dynamics as a promising therapeutic axis to preserve anthracycline efficacy while reducing cardiotoxicity. Clinical PerspectivesExcessive Drp1-mediated mitochondrial fission links anthracycline cardiotoxicity with cancer cell survival. Inhibition with DRP1i2 preserved cardiac structure and function in a chronic doxorubicin cardiotoxicity model without compromising anti-cancer activity, representing mechanism-based cardioprotection, where the heart is protected by directly targeting the molecular processes driving injury. Translation will require pharmacologic profiling and testing in tumour-bearing and comorbid models, followed by early-phase trials to confirm safety and efficacy.

pharmacology and toxicology↗

bioRxiv2025

Localized immunomodulation with cytokine-producing cells to mitigate host immune rejection responses in rodents and a non-human primate

The efficacy of cell-based therapeutics is often compromised by host immune recognition of implanted cells and biomaterials, resulting in fibrotic encapsulation and loss of function. Here, we address this challenge with an immunomodulatory cell-based therapy, in which alginate-encapsulated retinal pigment epithelial cells continuously secrete cytokines to locally modulate the implant microenvironment. In a healthy rodent model, the localized production of interleukin-10 (IL-10) or IL-12 from encapsulated cytokine-producing cells prevented host immune rejection and fibrosis of alginate capsules. Mechanistically, treatment was associated with reduced expression of pro-fibrotic genes and immune shifts consistent with macrophage and T-cell regulation, supporting a cytokine-mediated mitigation of foreign body response. In a diabetic murine model (streptozotocin-induced C57BL/6J), co-implantation of human islets with IL-10-producing cells attenuated pericapsular fibrosis, preserved islet viability, and restored normoglycemia for up to 100 days (4.76 times longer than islets alone). Significantly, IL-10-producing cells were also effective in enabling the durability and function of encapsulated cells in a healthy non-human primate, showing translational feasibility. Collectively, these findings suggest that localized cytokine delivery can reduce fibrotic encapsulation and support durable graft function, offering a path to lessen reliance on systemic immunosuppression in islets transplantation and other implantable biomaterial therapies. TeaserEncapsulated IL-10-producing cells locally suppress fibrosis and extend graft function in rodent models and a non-human primate.

bioengineering↗

bioRxiv2024

Targeting LxCxE cleft pocket of retinoblastoma protein in M2 macrophages inhibits ovarian cancer progression

AbstractOvarian cancer remains a major health threat with limited treatment options available. It is characterized by immunosuppressive tumor microenvironment (TME) maintained by tumor- associated macrophages (TAMs) hindering anti-tumor responses and immunotherapy efficacy. Here we show that targeting retinoblastoma protein (Rb) by disruption of its LxCxE cleft pocket, causes cell death in TAMs by induction of ER stress, p53 and mitochondria-related cell death pathways. A reduction of pro-tumor Rbhigh M2-type macrophages from TME in vivo enhanced T cell infiltration and inhibited cancer progression. We demonstrate an increased Rb expression in TAMs in women with ovarian cancer is associated with poorer prognosis. Ex vivo, we show analogous cell death induction by therapeutic Rb targeting in TAMs in post-surgery ascites from ovarian cancer patients. Overall, our data elucidates therapeutic targeting of the Rb LxCxE cleft pocket as a novel promising approach for ovarian cancer treatment through depletion of TAMs and re-shaping TME immune landscape. Statement of significanceCurrently, targeting immunosuppressive myeloid cells in ovarian cancer microenvironment is the first priority need to enable successful immunotherapy, but no effective solutions are clinically available. We show that targeting LxCxE cleft pocket of Retinoblastoma protein unexpectedly induces preferential cell death in M2 tumor-associated macrophages. Depletion of immunosuppressive M2 tumor-associated macrophages reshapes tumor microenvironment, enhances anti-tumor T cell responses, and inhibits ovarian cancer. Thus, we identify a novel paradoxical function of Retinoblastoma protein in regulating macrophage viability as well as a promising target to enhance immunotherapy efficacy in ovarian cancer.

immunology↗

bioRxiv2023

Comparative pathogenesis of two lineages of Powassan virus reveals differing routes of neuroinvasion leading to distinct clinical outcome, neuropathology and inflammation

Tick-borne flaviviruses (TBFV) can cause severe neuroinvasive disease which may result in death or long-term neurological deficit in over 50% of survivors. Multiple mechanisms for invasion of the central nervous system (CNS) by flaviviruses have been proposed including axonal transport, transcytosis, endothelial infection, and Trojan horse routes. Flaviviruses may utilize different or multiple mechanisms of neuroinvasion depending on the specific virus, infection site, and host variability. In this work we have shown that infection of BALB/cJ mice with either Powassan virus lineage I (Powassan virus) or lineage II (deer tick virus) results in distinct spatial tropism of infection in the CNS which correlated with unique clinical presentation for each lineage. Comparative transcriptomics of infected brains demonstrates activation of different immune pathways and downstream host responses. Ultimately the comparative pathology and transcriptomics are congruent with different clinical signs in a murine model. These results suggest that different disease presentations would be occur in clinical cases due to the innate differences in the two lineages of Powassan virus. Author SummaryPowassan virus causes a nationally notifiable disease which can cause severe neurological disease in humans and has no approved vaccines or therapeutics. Although two distinct lineages circulate in North America, clinical differentiation is not typically performed, and pathology has been assumed to be similar between lineages. In this work, a direct comparison of lineage I (Powassan virus) and lineage II (deer tick virus) demonstrated distinct differences in the clinical presentation, pathology of the central nervous system, and immune response in immunocompetent mice. These differences suggest that deer tick virus and Powassan virus do not utilize the same mechanisms for neuroinvasion and dissemination within the CNS. This is clinically relevant as the development of treatment plans and therapeutics need to be evaluated for these virus lineages.

microbiology↗

bioRxiv2023

Human Rhinoviruses: a novel class of oncolytic virus

While continuing to develop new and improved OVs, researchers have been vigilant in optimizing their ability to safely infect, replicate, and induce an immune response within tumors. There are currently two crucial limitations in OV development, however: modification of viruses often negatively impact their ability to infect, and induction of strong immune responses also promotes rapid viral clearance. In this study, we investigate wild-type HRVs as a novel class of OV. Multiple HRV serotypes were propagated in human melanoma cell lines to produce highly oncolytic populations of virus. A large panel of cancer types were infected, with cytotoxicity evaluated using flow cytometry and real time live imaging. Pro-inflammatory signaling was assessed by cytokine multiplexing. Tumor responses to HRV were assessed in human xenograft and in syngeneic, immune-competent mouse tumor models. We find that HRVs are capable of infecting and killing a wide variety of human cancer cell lines in vitro and in vivo, inducing pro-inflammatory responses and, ultimately, tumor regression. We propose that the natural safety profile of these viruses, coupled with their anti-tumor efficacy and multivalent potential seen in our preclinical model systems, make HRVs ideal candidates for development as oncolytic viruses for clinical testing. Simple SummaryThe idea of utilizing viruses to combat cancer has been around for over a century, yet in practice has seen relatively modest therapeutic success following decades of strategic design to improve safety, efficacy, and tumor selectivity. Engagement of an immune response is critical to have lasting tumor regression upon treatment, but many patients are unable to mount a sufficient response to standard-of-care immunotherapy alone. Oncolytic viruses (OVs) have been shown to synergize with such therapies to accomplish this goal to varying degrees. The purpose of this study is to investigate human rhinoviruses (HRVs) to establish their efficacy as a novel class of anti-cancer agents. We aim to use HRVs to promote longer lasting and more effective immune responses to tumors by fostering viral persistence and immune evasion, in addition to developing multivalent treatment strategies that enhance tumor regression by preventing tumor escape from viral infection.

immunology↗

bioRxiv2023

Surveillance of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine (two novel) complete genomes across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk is unknown and warrants closer surveillance.

genomics↗

bioRxiv2022

IRF7 impacts on prostate cancer cell survival in response to radiation

Understanding the impact of radiotherapy on the evolution of treatment resistant prostate cancer is critical for selecting effective treatment combinations. Whilst activation of Type 1 interferon signalling is a hallmark of how cells respond to viral infection, in cancer cells, multiple stresses are known to activate this same response. In this study we have evaluated for the first time the changes in the interferon response induced by culturing prostate cancer cells under sphere- forming conditions and following irradiation. We report a conserved upregulated transcript profile for both conditions that is strongly associated with therapeutic resistance and cell survival in vitro and in vivo. The profile includes and is regulated by the Type 1 interferon master regulator IRF7 which, when depleted, delays tumour re-growth following irradiation. We immuno-stained two independent prostate cohorts for IRF7 and found that increased expression, particularly in cases with low PTEN expression, correlated with poor prognosis. To more comprehensively characterise the impact of IRF7 and radiation on cells, RNA-Seq was performed on IRF7 knockdown cells at different radiation doses. We identified a number of biological processes that were IRF7-dependent, including the formation of stem-like cell populations and also therapeutic vulnerabilities. For example, irradiation sensitised surviving cells to either a combination of an IKK{varepsilon}/TBK1 and a MEK inhibitor or treatment with an inhibitor of IDO1, an IRF7- dependent gene. Translationally our work suggests that IRF7 expression can be used to stratify patients who may not benefit from receiving radiotherapy alone but rather may benefit from treatment combinations. In two cohorts treated with radical intent, strong IRF7 staining was associated with disease-specific death implicating this pathway as a convergence point for therapeutic resistance in prostate and potentially other cancer types.

cancer biology↗

bioRxiv2022

Human Galectin-9 Promotes the Expansion of HIV Reservoirs in vivo in Humanized Mice

ObjectiveThe human endogenous {beta}-galactoside-binding protein Galectin-9 (Gal-9) reactivates latently HIV-infected cells, which may allow for immune-mediated clearance of these cells. However, Gal-9 also activates T cell Receptor (TCR) signaling pathways, which could negatively affect HIV persistence by promoting T cell expansion and chronic activation/exhaustion. This potential "double-edged sword" effect of Gal-9 during HIV infection raises the question of the overall beneficial versus detrimental impact of Gal-9 on HIV persistence in vivo. DesignWe used the BLT (bone marrow, liver, thymus) humanized mouse model to evaluate the overall impact of Gal-9 on HIV persistence in vivo during antiretroviral therapy (ART). MethodsTwo independent cohorts of BLT mice with high human immune reconstitution were infected with HIV, placed on ART, and then treated with either recombinant human Gal-9 or PBS during ART suppression. Plasma viral loads and levels of tissue-associated HIV DNA and RNA were measured by qPCR. Markers of T cell activation/exhaustion were measured by flow cytometry, and plasma markers of inflammation were measured by multiplex cytokine arrays. ResultsGal-9 treatment was tolerable in ART-suppressed humanized mice and did not significantly induce plasma markers of inflammation or T cell markers of activation/exhaustion. However, Gal-9 treatment during ART significantly increased levels of tissue-associated HIV DNA and RNA compared to controls (P=0.0007 and P=0.011, respectively, for cohort I and P=0.002 and P=0.005, respectively, for cohort II). ConclusionsOur study highlights the overall adverse effects of Gal-9 on HIV persistence and the potential need to block Gal-9 interactions during ART-suppressed HIV infection.

microbiology↗

bioRxiv2021

Active Rheumatoid Arthritis in a Mouse Model is not an Independent Risk Factor for Periprosthetic Joint Infection

IntroductionPeriprosthetic joint infection (PJI) represents a devastating complication of total joint arthroplasty associated with significant morbidity and mortality. Literature suggests a possible higher incidence of periprosthetic joint infection (PJI) in patients with rheumatoid arthritis (RA). There is, however, no consensus on this relative risk nor a well-defined mechanism of this purported risk. This study investigates how collagen-induced arthritis (CIA), a validated animal model of RA, impacts infectious burden in a well-established model of PJI. MethodsControl mice were compared against CIA mice. Whole blood samples were collected to quantify systemic IgG levels via ELISA. Ex vivo respiratory burst function was measured via dihydrorhodamine assay. Ex vivo Staphylococcus aureus Xen36 burden was measured directly via colony forming unit (CFU) counts and crystal violet assay to assess biofilm formation. In vivo, surgical placement of a titanium implant through the knee joint and inoculation with S. aureus Xen36 was performed. Bacterial burden was then quantified by longitudinal bioluminescent imaging. ResultsMice with CIA demonstrated significantly higher levels of systemic IgG compared with control mice (p = 0.003). Ex vivo, there was no significant difference in respiratory burst function (p=0.89) or S. aureus bacterial burden as measured by CFU counts (p=0.91) and crystal violet assay (p=0.96). In vivo, no significant difference in bacterial bioluminescence between groups was found at all postoperative time points. CFU counts of both the implant and the peri-implant tissue were not significantly different between groups (p=0.82 and 0.80, respectively). ConclusionThis study demonstrated no significant difference in S. aureus infectious burden between mice with CIA and control mice. These results suggest that untreated, active RA may not represent a significant intrinsic risk factor for PJI. Further mechanistic translational and clinical studies are, however, warranted to thoroughly investigate the infectious risk of RA.

immunology↗

bioRxiv2018

Functional Improbable Antibody Mutations Critical for HIV Broadly Neutralizing Antibody Development

HIV-1 broadly neutralizing antibodies (bnAbs) require high levels of activation-induced cytidine deaminase (AID) catalyzed somatic mutations for optimal neutralization potency. Probable mutations occur at sites of frequent AID activity, while improbable mutations occur where AID activity is infrequent. One bottleneck for induction of bnAbs is the evolution of viral envelopes (Envs) that can select bnAb B cell receptors (BCR) with improbable mutations. Here we define the probability of bnAb mutations and demonstrate the functional significance of key improbable mutations in three bnAb B cell lineages. We show that bnAbs are enriched for improbable mutations, implying their elicitation will be critical for successful vaccine induction of potent bnAb B cell lineages. We outline a mutation-guided vaccine strategy for identification of Envs that can select B cells with BCRs with key improbable mutations required for bnAb development. Our analysis suggests that through generations of viral escape, Env trimers evolved to hide in low probability regions of antibody sequence space.

immunology↗