Biology subjects

Watt, J.

Publications and source records attributed to Watt, J..

6 recordsLinked to original sources

bioRxiv2026

In-Depth Immune Profiling Reveals Cell-Type, Sex and Infection-Stage Dependent Differences for Tuberculosis Control

Tuberculosis (TB) disease consistently causes the highest number of annual deaths from infectious disease and is responsible for over 100 million disability-adjusted-life-years annually. Despite the dramatic impact on human health, TB treatments are intensive and moderately effective, while Bacille Calmette-Guerin (BCG), the primary TB vaccine strategy and the oldest vaccine in circulation, needs updating. One gap in knowledge is that the vaccine primed lung immune environment has not been systematically profiled following TB challenge, making it challenging to interpret how various vaccine strategies provide protection. Here we profiled the male and female mouse lung immune environment using Mass Cytometry by Time of Flight (CyTOF) and bacterial burden (colony forming units, CFU), to systematically identify immune cells contributing to Mycobacterium tuberculosis (Mtb) infection or vaccine-induced protection. We investigated the mouse immune system after various infection outcomes including primary Mtb infection, Mtb reinfection, Mtb challenge after BCG vaccination and Mtb challenge after vaccination with a live attenuated Mtb vaccine. Across all conditions we identified Thy1.2 expression on NK cells as a new candidate for a sex-specific correlate of protection. Our results further replicate and support known immune responses for vaccine-induced protection, such as T-cell activation and infiltration. These findings highlight the pan-immune response to vaccine-induced protection, showcase the importance of sex in rodent models of TB, and identify novel host immune candidates to protect the lung against TB disease.

immunology↗

bioRxiv2026

Mycobacterium tuberculosis Δlsr2 Vaccine Enhances Protection Against Tuberculosis

Tuberculosis (TB) has been a leading cause of death from a single infectious agent for decades. Bacille Calmette-Guerin (BCG) remains both the primary TB vaccine strategy and the oldest vaccine in circulation, with severe limitations in adult populations. Recently, live attenuated vaccine strategies, or generating safe strains of Mycobacterium tuberculosis (Mtb) through genetic engineering, have shown considerable promise. We previously developed an attenuated strain of Mtb lacking the nucleoid-associated protein Lsr2 ({Delta}lsr2) which is also phthiocerol dimycocerosates (PDIM) deficient and induces an immune response that represents an intermediate stage between the parental Mtb strain and BCG. In this study we examined the immune response of {Delta}lsr2 vaccinated mice in comparison to BCG and found a substantially stronger CD4 and CD8 T cell responses from {Delta}lsr2 vaccinated mice. Complementary, we conducted Mtb protection studies in {Delta}lsr2 and BCG vaccinated mice and guinea pigs, where we found that {Delta}lsr2 provided superior protection in both animals. This improved protection is shown with reduced bacterial burden and improved organ pathology in the lungs and spleen. Taken together, our work shows {Delta}lsr2 serves as a promising vaccine candidate for continued preclinical development.

immunology↗

bioRxiv2026

High Dimensional Immune Profiling Reveals CD39 as a Correlate of Tuberculosis Disease Severity

Immune biomarkers of tuberculosis (TB) disease severity present a challenging area of research that remains poorly understood. New technologies are able to perform larger, unbiased studies that can unravel the complex host-pathogen dynamics occurring during a Mycobacterium tuberculosis infection, the causative agent of TB. In this study, we designed a high dimensional approach combining viable bacterial burden (CFU, colony forming units) with time-of-flight mass cytometry (CyTOF) analysis to profile differences in cell-type abundance and cell-type specific protein expression during states of low, intermediate and high TB disease burden. Broadly, we segregated cell-type specific immune responses into those driven by bacterial burden and/or the mycobacterial infection strain. Interrogating these immune signatures allowed us to identify ATP-catabolizing protein CD39 as a correlate of disease severity. Treatment of mice with a small molecule inhibitor of CD39 promoted effector T cell functions and CD4 T cell expansion during Mtb infection. Collectively, our data defines the differential lung immune environment between various mycobacterial disease severity states and uncovers a potential immune biomarker of infection and therapeutic immunomodulating target to aid in the treatment of TB.

immunology↗

bioRxiv2025

AI-Assisted Cryo-ET Workflow for 3D Visualization of Chromatin during Cellular Differentiation

Understanding how chromatin architecture changes during cellular differentiation requires structural methods that can resolve native genomic organization at high resolution. Here, we present an AI-assisted cryo-electron tomography (cryo-ET) and segmentation workflow to quantify chromatin compaction across various stages of motor neuron differentiation from induced pluripotent stem cells (iPSC). By directly imaging extracted and vitrified chromatin, we preserve native structure and avoid artifacts from heavy metal staining and resin embedding. Using three-dimensional (3D) density analysis, we measure chromatin density and capture the progressive increase in chromatin compaction with lineage commitment. This is then correlated with population-averaged Hi-C experiments, observing consistency between the microscale higher order structure of chromatin and global contact patterns. Our approach enables direct visualization of chromatin organization under near-physiological conditions, bridging the gap between structural imaging and genome-wide contact mapping. This platform therefore establishes an AI-assisted experimental framework for linking chromatin architecture to regulatory mechanisms during differentiation.

genomics↗

bioRxiv2025

The SHR/Akr Y chromosome reveals repeated turnover of the rat pseudoautosomal region

Crossing-over between Chr X and Chr Y was first observed 90 years ago, in the brown rat, Rattus norvegicus. However, the sequence of the rat pseudoautosomal region (PAR) has remained a mystery. We produced a near-complete sequence of Chr Y from the SHR strain, along with nearly a megabase of sequence from both telomeres of Chr X. Both telomeric ends of Chr Y display extensive homology to Chr X, but no homology to the ancestral PAR of placental mammals. Using rat Y BACs probes for FISH on meiotic cells, we show that pairing almost always occurs between the tips of Yq and Xp, which are virtually identical in nucleotide sequence, but contain no protein-coding genes. Homology at the other ends of Chr X and Chr Y is likely the result of a recent transposition of five genes from Xq to Yp. These sequences are only 99.5% identical and pair infrequently, but show signs that it may have been pseudoautosomal in the ancestor of the rat genus. The rat Chr Y sequence presents opportunities for experimental studies of meiotic phenomena in a tractable model organism. The short PAR, with a correspondingly high recombination rate, represents a unique substrate for molecular studies of crossing-over. Likewise, the absence of extensively co-amplified testis gene families on the rat X and Y suggests they might serve as control for the intense competition between selfish elements that completely remodeled the mouse sex chromosomes.

genomics↗

bioRxiv2021

Intranasal HD-Ad Vaccine Protects the Upper and Lower Respiratory Tracts of hACE2 Mice against SARS-CoV-2

The COVID-19 pandemic has affected more than 120 million people and resulted in over 2.8 million deaths worldwide. Several COVID-19 vaccines have been approved for emergency use in humans and are being used in many countries. However, all of the approved vaccines are administered by intramuscular injection and this may not prevent upper airway infection or viral transmission. Here, we describe intranasal immunization of a COVID-19 vaccine delivered by a novel platform, the helper-dependent adenoviral (HD-Ad) vector. Since HD-Ad vectors are devoid of adenoviral coding sequences, they have a superior safety profile and a large cloning capacity for transgenes. The vaccine (HD-Ad_RBD) codes for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein and intranasal immunization induced robust mucosal and systemic immunity. Moreover, intranasal immunization of K18-hACE2 mice with HD-Ad_RBD using a prime-boost regimen, resulted in complete protection of the upper respiratory tract against SARS-CoV-2 infection. As such, intranasal immunization based on the HD-Ad vector promises to provide a powerful platform for constructing highly effective vaccines targeting SARS-CoV-2 and its emerging variants.

microbiology↗