Biology subjects

Jones, C. A.

Publications and source records attributed to Jones, C. A..

6 recordsLinked to original sources

bioRxiv2026

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

Modeling cellular behavior requires measurements that capture how cells evolve across time, environments, and interventions. Microscopy is uniquely suited to this goal: it is non-destructive and can be applied to living cells in their native context. Yet its phenotypic resolving power remains incompletely characterized relative to molecular assays. Here, we present a multimodal perturbation atlas of 1,000 pooled CRISPR knockouts in A549 cells, profiled by fluorescence microscopy (42 live, 13 fixed markers), label-free quantitative phase imaging of the same live cells (at single timepoints), and single-cell RNA sequencing (scRNA-seq). We develop deep learning frameworks to interpret the rich cell-biological signatures in these ~65M single-cell profiles. At matched reagent cost, phase imaging exceeds the phenotypic resolution of both fluorescence imaging and scRNA-seq, and more reliably recovers higher-order pathway organization. These results establish intrinsic morphology as a high-precision readout of cellular state, and lay a foundation for live-cell profiling of phenotypic trajectories.

systems biology↗

bioRxiv2025

Hypoxia/HIF Signaling Negatively Regulates Bone Marrow Adiposity after Radiation Exposure

Radiation therapy is an essential cancer treatment, yet collateral damage to normal tissues remains a major clinical challenge. In bone, radiation-induced toxicity is characterized by loss of hematopoietic function, reduced bone volume, and increased marrow adipose tissue (MAT). Importantly, cancer patients who undergo radiotherapy exhibit significantly higher fracture risk compared to those receiving similar treatments without radiation exposure, underscoring the clinical consequences of bone microenvironment (BME) injury. The BME is inherently hypoxic resulting in the activation of by hypoxia-inducible factor (HIF) signaling. Here, we demonstrate that radiation induces a rapid and persistent accumulation of MAT, with adipocytes localizing preferentially to hypoxic regions of the marrow. To investigate the role of hypoxia/HIF signaling in this process, we generated aP2Cre;Hif-1 fl/fl;Hif-2fl/fl conditional knockout mice. Surprisingly, these mice exhibited increased MAT expansion following radiation compared to controls, suggesting that HIF deletion in aP2-expressing cells exacerbates radiation-induced adipogenesis. Analysis aP2CreRosa26tdTomato/+ mice revealed that most aP2-expressing cells did not give rise to mature adipocytes, macrophages, or endothelial cells, pointing instead to an uncharacterized stromal population that influences MAT formation. In contrast, conditional ablation of HIF transcription factors in LepRCre-expressing skeletal stem cells, which contain a subpopulation of skeletal progenitors which directly contribute to marrow adipocytes, had no effect on radiation-induced MAT expansion. Collectively, these findings identify a previously unrecognized population of adipocyte-regulatory cells whose HIF-dependent activity constrains stress-induced marrow adiposity. This work provides new mechanistic insight into how radiation disrupts the marrow microenvironment and expands MAT, advancing our understanding of the cellular and molecular drivers of radiation-induced bone fragility. One Sentence SummaryLoss of HIF signaling in aP2Cre expressing cells enhances radiation induced marrow adiposity.

developmental biology↗

bioRxiv2025

Disease-causing mutations in the G protein β5 β-propeller disrupt its chaperonin-mediated folding trajectory

The Chaperonin Containing Tailless polypeptide 1 (CCT or TRiC) is an essential cytosolic chaperone that folds multiple protein substrates, including many with {beta}-propeller folds. One {beta}-propeller substrate is the G protein {beta}5 subunit (G{beta}5) of Regulator of G protein Signaling (RGS) complexes that determine the duration of G protein signals in neurons. In recent work, we used cryo-electron microscopy (cryo-EM) to visualize the complete CCT-mediated folding trajectory for G{beta}5, from an initiating electrostatic interaction of a single {beta}-strand in G{beta}5 with the CCT5 subunit to a completely folded {beta}-propeller structure. Here, we employed biochemistry and cryo-EM to determine key interactions with CCT that initiate G{beta}5 folding and how missense mutations in G{beta}5 that cause severe neurological diseases alter the G{beta}5 folding trajectory and lead to incompletely folded, trapped intermediates. These findings highlight how CCT recognizes folding substrates, how defects in chaperonin-mediated folding contribute to disease, and how strategies might be designed to stabilize misfolded proteins to restore function. SignificanceElectrostatic interactions between the CCT chaperonin and its protein substrates initiate the folding process. Using cryo-EM structure determinations, we found a striking specificity for these interactions that allow CCT-mediated G{beta}5 folding. Moreover, certain missense mutations in G{beta}5 lead to misfolding and are associated with neurological disorders. We tracked how these mutations disrupt the normal folding of G{beta}5 by CCT. Although mutant G{beta}5 still binds the complex, folding stalls mid-process, leaving the protein trapped in partially folded, non-functional states. These defects arise from disrupted packing of the G{beta}5 core that interferes with formation of the native structure. Our findings reveal a molecular basis for G{beta}5 misfolding in disease and suggest pharmacological chaperones that stabilize the folded state might restore proper function.

biochemistry↗

bioRxiv2022

4-Fluorouridine mitigates lethal infection with pandemic human and highly pathogenic avian influenza viruses

Influenza outbreaks are associated with substantial morbidity, mortality and economic burden. Next generation antivirals are needed to treat seasonal infections and prepare against zoonotic spillover of avian influenza viruses with pandemic potential. Having previously identified oral efficacy of the nucleoside analog 4-Fluorouridine (4-FlU, EIDD-2749) against SARS-CoV-2 and respiratory syncytial virus, we explored activity of the compound against seasonal and highly pathogenic influenza (HPAI) viruses in cell culture, human airway epithelium organoids, and/or two animal models, ferrets and mice, that assess IAV transmission and lethal viral pneumonia, respectively. 4-FlU inhibited a panel of relevant influenza A and B viruses with nanomolar potency in organoids. In vitro polymerase assays revealed immediate chain termination of IAV polymerase after 4-FlU incorporation, in contrast to delayed chain termination of SARS-CoV-2 and RSV polymerase. Once-daily oral treatment of ferrets with 2 mg/kg 4-FlU initiated 12 hours after infection rapidly stopped virus shedding and prevented direct-contact transmission to untreated sentinels. Treatment of mice infected with a lethal inoculum of pandemic A/CA/07/2009 (H1N1)pdm09 (Ca09) with 2 mg/kg 4-FlU alleviated pneumonia. Three doses mediated complete survival when treatment was initiated up to 60 hours after infection, indicating an unusually broad window for effective intervention. Therapeutic oral 4-FlU ensured survival of animals infected with HPAI A/VN/12/2003 (H5N1) and of immunocompromised mice infected with pandemic Ca09. Recoverees were fully protected against homologous reinfection. This study defines the mechanistic foundation for high sensitivity of influenza viruses to 4-FlU and supports 4-FlU as developmental candidate for the treatment of seasonal and pandemic influenza. Author SummaryNext-generation antiviral therapeutics are needed to better mitigate seasonal influenza and prepare against zoonotic virus spillover from animal reservoirs. At greatest risk are the immunocompromised and patients infected with highly pathogenic influenza viruses. In this study, we have demonstrated efficacy of a broad-spectrum nucleoside analog, 4-fluorouridine, against a representative panel of influenza viruses in cell culture, human organoids, and two animal models, ferrets and mice. Acting as an immediate chain terminator of the influenza virus polymerase, once-daily oral treatment protected against lethal infection with seasonal and highly pathogenic avian influenza viruses, prevented direct-contact transmission to untreated sentinels, and mitigated lethal infection of immunocompromised hosts. These results support the developmental potential of 4-fluorouridine for treatment of vulnerable patient groups and mitigation of pandemic influenza, providing a much-needed additional therapeutic option for improved disease management.

microbiology↗

bioRxiv2022

M2e-specific monoclonal antibody cocktails against influenza A virus are superior to individual monoclonal antibody treatments, universally effective, and viral escape mutant resistant

Influenza, a negative sense single-strand RNA virus of the genus Orthomyxoviridae, causes respiratory illness in humans and animals and significant morbidity and mortality worldwide. While exposure to a specific influenza A strain causes homologous protection, two immune-dominant influenza A virus (IAV)-encoded epitopes - Hemagglutinin (HA) and Neuraminidase (NA) - undergo antigenic shift and drift, resulting in IAVs to which humans lack pre-existing immunity. Without a universal vaccine or therapeutic agent, influenza virus infections will significantly threaten human health. The extracellular domain of the Matrix protein 2-ion channel (M2e) is an ideal antigenic target for a universal influenza therapy: it is highly conserved across influenza A serotypes, has a low mutation rate, and is essential for viral entry and replication. However, less than 20% of humans generate M2e-specific antibodies in response to IAV exposure, thus lacking the benefits of M2e-MAb-mediated immunity. To therapeutically address this deficit, we generated several non-neutralizing M2e-specific monoclonal antibodies (M2e-MAbs) with strong universal IAV treatment potential. Using three MAbs that bind to M2e differentially and competitively, we developed a low-dose M2e-MAb triple cocktail as an effective universal prophylactic and therapeutic agent. We identified the low-dose M2e-MAb triple cocktails optimal antibody-clone combination, isotype, minimum effective dosage, and administration time points in mouse models challenged with human and zoonotic BSL-2 and BSL-3 IAV strains, demonstrating its universal potential. Using the IgG2a isotype, which had proven most effective, we established Fc{gamma}RI, Fc{gamma}RIII, and Fc{gamma}RIV as required for M2e-MAb-mediated protection of IAV-challenged mice. Importantly, we established individual M2e-MAbs and the resulting triple cocktail as effective and viral escape mutant-resistant treatments in immunocompetent and immunodeficient mice. These unique qualities provide precedence for prioritizing our M2e-MAbs for therapeutic development. CONFLICT OF INTEREST STATEMENTSP serves on the scientific advisory board for Shoreline Biosciences, Qihan Biotechnology and is a Scientific Consultant for Qihan Biotechnology and the Genomics Institute of the Novartis Research Foundation. The remaining authors declare no competing interests.

immunology↗

bioRxiv2021

Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metagenomic next-generation sequencing

Encephalitis is most often caused by a variety of infectious agents, the identity of which is commonly determined through diagnostic tests utilising cerebrospinal fluid (CSF). Immune-mediated disorders are also a differential in encephalitis cases. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic next-generation sequencing of residual clinical samples of multiple tissue types and independent clinical review. A total of 43 specimens, from both sterile and non-sterile sites, were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. Samples were subjected to total RNA sequencing to determine the presence and abundance of potential pathogens, to reveal mixed infections, pathogen genotypes, and epidemiological origins, and to describe the possible aetiologies of unexplained encephalitis. From this, we identified five RNA and two DNA viruses associated with human infection from both non-sterile (nasopharyngeal aspirates, nose/throat swabs, urine, stool rectal swab) and sterile (cerebrospinal fluid, blood) sites. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. With the exception of picobirnavirus all have been previously associated with respiratory disease. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases reported here. Immune-mediated encephalitis was considered clinically likely in six cases and RNA sequencing did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasises the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that the routine inclusion of non-CNS sampling in encephalitis clinical guidelines/protocols could improve the diagnostic yield. Author SummaryEncephalitis is caused by both infectious agents and auto-immune disorders. However, the aetiological agents, including viruses, remain unknown in around half the cases of encephalitis in many cohorts. Importantly, diagnostic tests are usually based on the analysis of cerebrospinal fluid which may limit their utility. We used a combination of meta-transcriptomic sequencing and independent clinical review to identify the potential causative pathogens in cases of unexplained childhood encephalitis. Accordingly, we identified seven viruses associated with both sterile and non-sterile sampling sites. Human rhinovirus and seasonal coronaviruses were considered as most likely responsible for five of the 18 encephalitis cases studied, while immune-mediated encephalitis was considered the cause in six cases, and we were unable to determine the aetiology in nine cases. Overall, we demonstrate the role of respiratory viruses as a cause of unexplained encephalitis and that sampling sites other than cerebrospinal fluid is of diagnostic value.

microbiology↗