Biology subjects

Chandler, J.

Publications and source records attributed to Chandler, J..

8 recordsLinked to original sources

bioRxiv2026

IL-2- and IL-4-dependent signaling play separate and sequential roles in the differentiation of GATA3-hi TH2 cells in vivo

Naive CD4+ T cells differentiation into T-helper type 2 (TH2) cells requires Interleukin 2 (IL-2) and IL-4-dependent signaling as well as presentation of allergens by dendritic cells (DCs). The role of IL-2 and IL-4 in TH2 differentiation has been mostly studied in vitro, however, these models do not account for the heterogeneity of TH responses and bypass the DC-derived signals that are necessary in vivo. We used cytokine-blocking antibodies and IL-4RKO/IL-4RWT mixed bone marrow chimeras to show that IL-4 signaling was not required for initial upregulation of GATA3 by CD4+ T cells after intradermal immunization, but was necessary for later TH2 cell expansion and further GATA3 upregulation. Single-cell transcriptomics and computational analyses confirmed that IL-4 signaling was not necessary for TH2 identity but promoted TH2 proliferation and expression of a pathogenic signature. Early IL-2 blockade prevented GATA3 upregulation without affecting TH2 proliferation or the differentiation of TH1 and TFH subsets after immunization. Adoptive transfer experiments showed that reduced competition for IL-4 in vivo drove extensive T cell proliferation and preferential expansion of the GATA3hi population. Overall, our results suggest temporally and functionally distinct roles of IL-2 and IL-4 during TH2 differentiation: IL-2 is necessary for GATA3 upregulation, while IL-4 drives subsequent TH2 proliferation and licensing to effector activity. Therefore, IL-2 and IL-4 act in a co-ordinated manner to respectively promote TH2 differentiation, expansion, and effector commitment in the LN.

immunology↗

bioRxiv2026

Hormone signaling and immune programs define differential endocrine responsiveness in high-risk breast tissue

Hormone therapies are frequently used to reduce breast cancer risk in individuals at increased risk for primary or subsequent disease; however, tissue-level responses to these therapies are heterogeneous and incompletely understood. Background parenchymal enhancement (BPE) on breast magnetic resonance imaging (MRI) provides a non-invasive radiologic readout of breast tissue features associated with endocrine responsiveness and cancer risk. Although BPE is associated with hormonal exposure, a subset of patients with BPE do not show a response to preventive endocrine therapy and therefore may remain at increased breast cancer risk. In this study, we integrated single-nucleus RNA sequencing and spatial transcriptomics to define the determinants of endocrine responsiveness in the setting of BPE. We identify hormone-driven epithelial cells with high levels of estrogen signaling and endocrine responsiveness, together with immune-associated epithelial programs characterized by diminished luminal identity and increased expression of immune-modulatory pathways, including major histocompatibility complex (MHC) class II and CD74. Functional organoid assays validate that these epithelial states exhibit differential sensitivity to tamoxifen and demonstrate that inflammatory signals can induce immune-modulatory epithelial programs. Together, our findings identify hormone signaling and immune programs as key determinants of endocrine responsiveness in breast tissue and provide a biological basis for interpreting radiologic markers relevant to cancer prevention.

cancer biology↗

bioRxiv2025

High Dimensional Proteomic Multiplex Imaging of the Central Nervous System Using the COMET(TM) System

Sequential multiplex methodologies such as Akoya CODEX, Miltenyi MACSima, Rarecyte Orion, and others require modification of the antibodies by conjugation to an oligo or a specific fluorophore which means the use of off-the-shelf reagents is not possible. Modifications of these antibodies are typically performed via reduction chemistry and thus require verification and validation post-modification. Fixed panels are therefore developed due to various limitations including spectral overlap that creates spectral unmixing issues, steric hindrance, harsh antibody removal, and tissue degradation throughout the labeling. As such, a complex interrogation evaluating multiple study hypotheses and/or endpoints requires the development of sequential panels, reconstruction, and realignment of the tissue that necessitate a z-stack strategy. Standardized antibody panels are typically fixed and require substantial validation efforts to modify a single target and thus do not evolve with the pace of research interests. To increase the throughput of profiling cells within the human central nervous system (CNS), we developed and validated a CNS-specific library with an associated analysis platform using the newly developed Lunaphore COMETTM platform. The COMETTM is an automated staining/imaging instrument integrating a reagent deck for staining buffers and off-the-shelf label-free primary antibodies and fluorophore-labeled secondary antibodies, which feed into a circular plate holding up to 4 slides that are automatically imaged in microscope-operated control software. For this study, standard formalin fixed paraffin embedded histology slides are used. However, the COMET is capable of imaging fresh-frozen samples using specialized settings. Our methodologies address an unmet need in the neuroscience field while leveraging prior developmental efforts in the domain of immunology spatial profiling. Cataloging and validating a large series of antibodies on the COMET along with developing CNS autofluorescence management strategies while optimizing standard operating procedures have allowed for the visualization at the subcellular level. Forty analytes can be used to analyze one specimen which has clinical utility in cases in which the CNS can only be sampled by biopsy. CNS biopsies, depending on the anatomical location, can have limited available volume to a degree that requires prioritization and restriction to select analysis. In-depth bioinformatic imaging analysis can be done using standard bioinformatic tools and software such as Visiopharm(R). These results establish a general framework for imaging and quantifying cell populations and networks within the CNS while providing the scientific community with standard operating procedures.

bioinformatics↗

bioRxiv2024

Tissue resident memory CD4+ T cells are sustained by site-specific levels of self-renewal and replacement from precursors

Tissue-resident memory T cells (TRM) protect from repeat infections within organs and barrier sites. The breadth and duration of such protection is defined at minimum by three quantities; the rate at which new TRM are generated from precursors, their rate of self-renewal, and their rate of loss through death, egress, or differentiation. Quanti-fying these processes individually is challenging. Here we combine genetic fate mapping tools and mathematical models to untangle these basic homeostatic properties of CD4+ TRM in the skin and gut lamina propria (LP) of healthy adult mice. We show that CD69+CD4+ TRM in skin reside for [~]24 days and self-renew more slowly, such that clones halve in size approximately every 5 weeks; and approximately 2% of cells are replaced daily from precursors. CD69+CD4+ TRM in LP have shorter residencies ([~]14 days) and are maintained largely by immigration (4-6% per day). We also find evidence that the continuous replacement of CD69+CD4+ TRM at both sites derives from circulating effector-memory CD4+ T cells, in skin possibly via a local CD69- intermediate. Our approach maps the ontogeny of CD4+ TRM in skin and LP and exposes their dynamic and distinct behaviours, with continuous seeding and erosion potentially impacting the duration of immunity at these sites.

immunology↗

bioRxiv2021

Inactivation of SARS Coronavirus 2 and COVID-19 patient samples for contemporary immunology and metabolomics studies

In late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged from Wuhan, China spurring the Coronavirus Disease-19 (COVID-19) pandemic that has resulted in over 219 million confirmed cases and nearly 4.6 million deaths worldwide. Intensive research efforts ensued to constrain SARS-CoV-2 and reduce COVID-19 disease burden. Due to the severity of this disease, the US Centers for Disease Control and Prevention (CDC) and World Health Organization (WHO) recommend that manipulation of active viral cultures of SARS-CoV-2 and respiratory secretions from COVID-19 patients be performed in biosafety level 3 (BSL3) containment laboratories. Therefore, it is imperative to develop viral inactivation procedures that permit samples to be transferred and manipulated at lower containment levels (i.e., BSL2), and maintain the fidelity of downstream assays to expedite the development of medical countermeasures (MCMs). We demonstrate optimal conditions for complete viral inactivation following fixation of infected cells with paraformaldehyde solution or other commonly-used branded reagents for flow cytometry, UVC inactivation in sera and respiratory secretions for protein and antibody detection assays, heat inactivation following cDNA amplification of single-cell emulsions for droplet-based single-cell mRNA sequencing applications, and extraction with an organic solvent for metabolomic studies. Thus, we provide a suite of protocols for viral inactivation of SARS-CoV-2 and COVID-19 patient samples for downstream contemporary immunology assays that facilitate sample transfer to BSL2, providing a conceptual framework for rapid initiation of high-fidelity research as the COVID-19 pandemic continues.

microbiology↗

bioRxiv2021

An anti-ACVR1 antibody exacerbates heterotopic ossification by fibro/adipogenic progenitors in fibrodysplasia ossificans progressiva mice

Fibrodysplasia ossificans progressiva (FOP) is a rare genetic disease characterized by progressive and catastrophic heterotopic ossification (HO) of skeletal muscle and associated soft tissues. FOP is caused by dominantly acting mutations in the bone morphogenetic protein (BMP) type I receptor, ACVR1 (also known as ALK2), the most prevalent of which is an arginine to histidine substitution [ACVR1(R206H)] in the glycine-serine rich intracellular domain of the receptor. A fundamental pathological consequence of FOP-causing ACVR1 receptor mutations is to enable activin A to initiate canonical BMP signaling in responsive progenitors, which drives skeletogenic commitment and HO. With the clear targets of activin A and ACVR1 identified, development of antibody therapeutics to prevent ligand-receptor interactions is an interventional approach currently being explored. Here, we developed a monoclonal blocking antibody (JAB0505) to the extracellular domain of ACVR1 and tested its ability to inhibit HO in established FOP mouse models. JAB0505 inhibited BMP-dependent gene expression in wild-type and ACVR1(R206H)-overexpressing cell lines. Strikingly, however, JAB0505 treatment markedly exacerbated injury-induced HO in two independent FOP mouse models in which ACVR1(R206H) was either broadly expressed, or more selectively expressed in fibro/adipogenic progenitors (FAPs). JAB0505 drove HO even under conditions of activin A inhibition, indicating that JAB0505 has receptor agonist activity. JAB0505-treated mice exhibited multiple, distinct foci of heterotopic lesions, suggesting an atypically broad anatomical domain of FAP recruitment to endochondral ossification. In addition, skeletogenic differentiation was both delayed and prolonged, and this was accompanied by dysregulation of FAP population growth. Collectively, alterations in the growth and differentiative properties of FAPs and FAP-derived skeletal cells are implicated in the aggravated HO phenotype. These data raise serious safety and efficacy concerns for the use of anti-ACVR1 antibodies to treat FOP patients.

developmental biology↗

bioRxiv2020

Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function

In eukaryotic cells, chromatin structure is linked to transcription processes through the regulation of genome organization. Extending across multiple length-scales - from the nucleosome to higher-order three-dimensional structures - chromatin is a dynamic system which evolves throughout the lifetime of a cell. However, no individual technique can fully elucidate the behavior of chromatin organization and its relation to molecular function at all length- and timescales at both a single-cell and a cell population level. Herein, we present a multi-technique nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform that bridges electron tomography and optical superresolution imaging of chromatin conformation and transcriptional processes, with resolution down to the level of individual nucleosomes, with high-throughput, label-free analysis of chromatin packing and its dynamics in live cells. Utilizing nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nm, sub-Mb genomic size, and an internal fractal structure. The chromatin packing behavior of these domains is directly influenced by active gene transcription. Furthermore, we demonstrated that the chromatin packing domain structure is correlated among progenitor cells and all their progeny, indicating that the organization of chromatin into fractal packing domains is heritable across cell division. Further studies employing the nano-ChIA platform have the potential to provide a more coherent picture of chromatin structure and its relation to molecular function.

genomics↗

bioRxiv2017

De novo long-read assembly of a complex animal genome

Eukaryotic genome assembly remains a challenge in part because of the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing methods. At the same time, many nematodes are parasites and some represent a serious threat to human health. There is a pressing need for better molecular characterization of animal and plant parasitic nematodes. The advent of long-read DNA sequencing methods offers the promise of resolving complex genomes. Using Nippostrongylus brasiliensis as a test case, applying improved base-calling algorithms and assembly methods, we demonstrate the feasibility of de novo genome assembly matching current community standards using only MinION long reads. In doing so, we uncovered an unexpected diversity of very long and complex DNA repeat sequences, including massive tandem repeats of tRNA genes. The method has the added advantage of preserving haplotypic variants and so has the potential to be used in population analyses.

genomics↗