Biology subjects

Schwartz, K.

Publications and source records attributed to Schwartz, K..

10 recordsLinked to original sources

bioRxiv2026

Immune activation during broadly neutralizing antibody-mediated HIV suppression prior to post-intervention control

Broadly neutralizing antibodies (bNAbs) have been associated with enhancement of HIV-specific T or B cell responses and sustained partial control of HIV replication in some people with HIV (PWH). The mechanisms through which bNAbs may potentiate host immunity in this context are not known. We previously reported the outcomes of a clinical trial in which ten PWH on antiretroviral therapy (ART) received a combination of immunotherapies including two bNAbs administered immediately preceding an analytic treatment interruption (ATI). After bNAb levels waned, seven participants exhibited varying degrees of post-intervention control of HIV linked to a robust expansion of activated CD8+ T cells in response to rebounding virus. To investigate the role of the bNAbs in enhancing endogenous immune responses, we looked for evidence of HIV-specific or broader immune activation during the period after ART was paused and prior to rebound when bNAbs were controlling HIV replication. At a timepoint early post-ART interruption and at least one month before virus emerged in plasma, we detected an increase in levels of plasma inflammatory proteins as well as phenotypic and transcriptional activation of innate and adaptive immune cells. Compared to non-controllers, post-intervention controllers demonstrated unique transcriptional activation patterns as well as differential longitudinal plasma inflammatory protein trends. No enhancement of HIV-specific T cell or antibody responses was observed in this window. This study identifies activated cell types and inflammatory pathways that are recruited early during bNAb-mediated HIV suppression and that may play a role in potentiating long-lasting HIV immune control after bNAb therapy. One Sentence SummaryIn a combination immunotherapy trial with high rates of post-intervention control, bNAb-mediated HIV suppression was associated with increased immune activation compared to HIV suppression by ART.

immunology↗

bioRxiv2026

Bivalent bispecific CD28 antibodies reinforce T-cell responsiveness and revert anergy/quiescence in patients treated with bispecific CD3 antibodies

Bispecific T-cell engagers stimulating CD3 (TCEs) rapidly gain momentum in oncological therapy. We report that single-agent TCE-treatment of cancer patients induces T cell hyporesponsiveness including abolished proliferative and lytic capacity. Single-cell RNA-sequencing identified transcriptional features of anergy/quiescence like upregulation of CBLB and BACH2, and suppression of AP 1-dependent activation programs due to isolated provision of T cell signal-1. To restore T cell functionality, we engineered bispecific costimulators (BiCos) which deliver signal-2 via highly efficient bivalent CD28-binding yet maintain strictly target-restricted activity after binding antigens expressed not only by tumor cells but also the extracellular matrix. Preclinical analyses documented that BiCos potentiate efficacy of single-agent TCE treatment with activity exceeding that of univalent Knob-into-Hole CD28-costimulators and revert T cell hyporesponsiveness. In humanized mice, BiCos induced elimination of established tumors in combination with very low doses of TCE. Finally, BiCos reversed molecular hallmark features of quiescence such as high expression of BACH2 and KLF2 in T cells of TCE-treated patients resulting in complete restoration of cellular function, thereby reinstating durable antitumor immunity.

immunology↗

bioRxiv2026

β-hydroxybutyrate modulates enteric pathogen susceptibility through regulation of commensal bacteria and intestinal Th17 responses

T helper 17 (Th17) cells are a critical T lymphocyte subset involved in mucosal immunity and host defense against enteric pathogens. Although ketogenic diets (KD) and the major ketone body {beta}-hydroxybutyrate (BHB) reshape gut microbiota and suppress Th17 responses under defined diet conditions, it remains unclear whether elevation of BHB alone, independent of dietary macronutrient composition and systematic metabolic shift, is sufficient to remodel Th17-inducing commensals and alter host susceptibility to enteric infection. Here, we used 1,3-butanediol (BD), a precursor metabolized to BHB independently of KD, to elevate systemic BHB levels in mice. BD treatment significantly reduced the frequency of ileal Th17 cells, as assessed by flow cytometry for Th17 markers IL-17A and ROR{gamma}t. 16S rRNA gene sequencing revealed that BD altered gut microbial community structure, as indicated by beta-diversity analysis based on Bray-Curtis dissimilarity, and reduced Shannon diversity and evenness. Linear discriminant analysis effect size identified segmented filamentous bacteria (SFB) as significantly decreased in the ileum following BD treatment, and SFB abundance positively correlated with Th17 markers. Microbiota transplantation demonstrated that BD-shaped microbiota was sufficient to suppress Th17 responses in recipient mice, accompanied by reduced SFB abundance. In a Citrobacter rodentium infection model, BD treatment was associated with increased pathogen burden, and fecal C. rodentium levels were negatively correlated with SFB abundance. Together, these results indicate that BD-induced elevation of BHB reshapes commensal microbiota, including decreasing SFB levels, resulting in dampened Th17 responses and increased susceptibility to enteric infection. IMPORTANCEDiet is a key determinant of gut microbial composition and mucosal immune function, yet the microbial mechanisms linking how diet-mediated changes to metabolism regulate immune responses remain incompletely understood. Th17 cells play central roles in both protective mucosal immunity and inflammatory pathology, making them a critical target of immunometabolic regulation. In this study, we show that {beta}-hydroxybutyrate (BHB), generated independently of diet, suppresses intestinal Th17 responses by reshaping the gut microbiota, reducing SFB levels, a potent Th17-inducing murine commensal. We further demonstrate that BHB-associated microbiota changes are linked to increased susceptibility to enteric infection. This work provides a mechanistic framework illustrating how metabolic state can influence host immunity through selective effects on commensal microbes. These findings inform future studies of microbiota-mediated immune regulation.

microbiology↗

bioRxiv2026

Loss of neuronal population organization links pathology to behavior in a model of Alzheimer's disease

Alzheimers disease (AD) and related dementias (ADRD) are defined by molecular and cellular pathology and cognitive decline, but linking these levels requires understanding how pathology alters large-scale neuronal activity. We longitudinally tracked behavior, multi-area neuronal population activity, and fluid and histological biomarkers in a macaque model of early-stage ADRD. As pathology progressed, visually guided behavior became increasingly disorganized, reflected in less structured exploration despite preserved task performance. Guided by systems neuroscience principles linking neuronal population activity with organized goal-directed behavior, we found progressive reductions in coordinated neuronal population activity within and between visual and parietal cortices, even as single-neuron tuning and basic feature encoding remained stable. These changes emerged when tau pathology was largely confined to regions providing feedback to visual cortex. This disorganized state appears modifiable: proof-of-concept methylphenidate administration was associated with transient improvement in behavioral organization. Together, these findings identify disruption of neuronal population organization as a defining feature of early-stage ADRD and frame early dysfunction as a disorder of coordinated population activity.

neuroscience↗

bioRxiv2024

Etomidate as an Effective Alternative Method of Euthanizing Adult Zebrafish (Danio Rerio)

We assessed the efficacy of etomidate in euthanizing adult zebrafish. The aims of this study were to investigate: 1) the efficacy of 2 concentrations and 2) the effects at 2 densities. Aim 1-Fish (n=10 fish/group) were immersed in either 6 mg/L (Eto-6) or 10 mg/L (Eto-10) etomidate. Aim 2- either 5 or 10 fish were immersed in Eto-6. Tanks were video recorded and scored by two blinded observers. The parameters monitored included: 1) loss of righting reflex (LORR); 2) undulation cessation; 3) cessation of operculation (COO); and 4) loss of startle reflex. After the 30 minute immersion, fish were transferred to recovery tanks and monitored once every 5 minutes for 60 minutes. Results - Aim 1, the time to undulation cessation, COO, and loss of startle reflex was significantly shorter in the Eto-10 group and there was no difference in LORR. Aim 2, the time to LORR and undulation cessation was significantly shorter in the 5 fish/L group and there was no significant difference in time to COO or loss of startle reflex. No aversive behaviors were noted and fish in all groups were effectively euthanized by 30 minutes. This study indicates that Eto-6 or Eto-10 effectively euthanizes adult zebrafish.

animal behavior and cognition↗

bioRxiv2022

Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by transposons and microhomology-mediated recombination

There are many mechanisms that give rise to genomic change: while point mutations are often emphasized in genomic analyses, evolution acts upon many other types of genetic changes that can result in less subtle perturbations. Changes in chromosome structure, DNA copy number, and novel transposon insertions all create large genomic changes, which can have correspondingly large impacts on phenotypes and fitness. In this study we investigate the spectrum of adaptive mutations that arise in a population under consistently fluctuating nitrogen conditions. We specifically contrast these adaptive alleles and the mutational mechanisms that create them, with mechanisms of adaptation under batch glucose limitation and constant selection in low, non-fluctuating nitrogen conditions. We observe that retrotransposon activity accounts for a substantial number of adaptive events, along with microhomology-mediated mechanisms of insertion, deletion, and gene conversion. In addition to loss of function alleles, which are often exploited in genetic screens, we identify adaptive gain of function alleles and alleles acting through as-of-yet unclear mechanisms. Taken together, our findings emphasize that how selection (fluctuating vs. non-fluctuating) is applied also shapes adaptation, just as the selective pressure (nitrogen vs. glucose) does itself. Fluctuating environments can activate different mutational mechanisms, shaping adaptive events accordingly. Experimental evolution, which allows a wider array of adaptive events to be assessed, is thus a complementary approach to both classical genetic screens and natural variation studies to characterize the genotype-to-phenotype-to-fitness map.

evolutionary biology↗

bioRxiv2019

Genetic characterization of Streptococcus equi subspecies zooepidemicus associated with high swine mortality in United States

High mortality events due to Streptococcus equi subspecies zooepidemicus (S. zooepidemicus) in swine have not previously been reported in the United States. In September and October 2019, outbreaks with swine mortality up to 50% due to S. zooepidemicus septicemia were reported in Ohio and Tennessee. Genomic epidemiological analysis revealed that the eight outbreak isolates were clustered together with ATCC 36246, a Chinese strain caused outbreaks with high mortality, also closely related to three isolates from human cases from Virginia, but significantly different from an outbreak-unrelated swine isolate from Arizona and most isolates from other animal species. Comparative genomic analysis on two outbreak isolates and another outbreak-unrelated isolate identified several genomic islands and virulence genes specifically in the outbreak isolates only, which are likely associated with the high mortality observed in the swine population. These findings have implications for understanding, tracking, and possibly preventing diseases caused by S. zooepidemicus in swine.

microbiology↗

bioRxiv2019

Evolutionary dynamics of de novo mutations and mutant lineages arising in a simple, constant environment

A large, asexual population founded by a single clone evolves into a population teeming with many, whether or not its environment is structured, and whether or not resource levels are constant or fluctuating. The maintenance of genetic complexity in such populations has been attributed to balancing selection, or to either clonal interference or clonal reinforcement, arising from antagonistic or synergistic interactions, respectively. To distinguish among these possibilities, to identify targets of selection and establish when and how often they are hit, as well as to gain insight into how de novo mutations interact, we carried out 300-500 generation glucose-limited chemostat experiments founded by an E. coli mutator. To discover all de novo mutations reaching [≥]1% frequency, we performed whole-genome, whole-population sequencing at [~]1000X-coverage every 50 generations. To establish linkage relationships among these mutations and depict the dynamics of evolving lineages we sequenced the genomes of 96 clones from each population when allelic diversity was greatest. Operon-specific mutations that enhance glucose uptake arose to high frequency first, followed by global regulatory mutations. Late-arising mutations were related to energy conservation as well as to mitigating pleiotropic effects wrought by earlier regulatory changes. We discovered extensive polymorphism at relatively few loci, with identical mutations arising independently in different lineages, both between and within replicate populations. Out of more than 3,000 SNPs detected in nearly 1,800 genes or intergenic regions, only 17 reached a frequency [≥] 98%, indicating that the evolutionary dynamics of adaptive lineages was dominated by clonal interference. Finally, our data show that even when mutational input is increased by an ancestral defect in DNA repair, the spectrum of beneficial mutations that reach high frequency in a simple, constant resource-limited environment is narrow, resulting in extreme parallelism where many adaptive mutations arise but few ever go to fixation. Author SummaryMicrobial evolution experiments open a window on the tempo and dynamics of evolutionary change in asexual populations. High-throughput sequencing can be used to catalog de novo mutations, determine in which lineages they arise, and assess allelic interactions by tracking the fate of those lineages. This adaptive genetics approach makes it possible to discover whether clonal interactions are antagonistic or synergistic, and complements genetic screens of induced deleterious/loss-of-function mutants. We carried out glucose-limited chemostat experiments founded by an E. coli mutator and performed whole-genome, whole-population sequencing on 300-500 generation evolutions, cataloging 3,346 de novo mutations that reached [≥]1% frequency. Mutations enhancing glucose uptake rose to high frequency first, followed by global regulatory changes that modulate growth rate and limiting resource assimilation, then by mutations that favor energy conservation or mitigate pleiotropic effects of earlier regulatory changes. We discovered that a few loci were highly polymorphic, with identical mutations arising independently in different lineages, both between and within replicate populations. Thus, when mutational input is increased by an ancestral defect in DNA repair, the spectrum of beneficial mutations that arises under constant resource-limitation is narrow, resulting in extreme parallelism where many adaptive mutations arise but few ever become fixed.

evolutionary biology↗

bioRxiv2018

Identification and characterization of a phase-variable element that regulates the autotransporter UpaE in uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) are the most common etiological agent of uncomplicated urinary tract infection (UTI). An important mechanism of gene regulation in UPEC is phase variation that involves inversion of a promoter-containing DNA element via enzymatic activity of tyrosine recombinases, resulting in biphasic, ON or OFF expression of target genes. The UPEC reference strain CFT073 has five tyrosine site-specific recombinases that function at two previously characterized promoter inversion systems, fimS and hyxS. Three of the five recombinases are located proximally to their cognate target elements, which is typical of promoter inversion systems. The genes for the other two recombinases, IpuA and IpuB are located distal from these sites. Here, we identified and characterized a third phase variable invertible element in CFT073, ipuS located proximal to ipuA and ipuB. The inversion of ipuS is catalyzed by four of the five CFT073 recombinases. Orientation of the element drives transcription of a two-gene operon containing ipuR, a predicted LuxR-type regulator, and upaE, a predicted autotransporter. We show that the predicted autotransporter UpaE is surface-located and facilitates biofilm formation as well as adhesion to extracellular matrix proteins in a K-12 recombinant background. Consistent with this phenotype, the ipuS ON condition in CFT073 results in defective swimming motility, increased adherence to human kidney epithelial cells, and a positive competitive kidney colonization advantage in experimental mouse UTI infections. Overall, the identification of a third phase-switch in UPEC that is regulated by a shared set of recombinases describes a complex phase-variable virulence network in UPEC.\n\nImportanceUropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). ON versus OFF phase-switching by inversion of small DNA elements at two chromosome sites in UPEC regulates the expression of important virulence factors, including the type 1 fimbriae adhesion organelle. In this report, we describe a third invertible element, ipuS, in the UPEC reference strain CFT073. The inversion of ipuS controls the phase variable expression of upaE, an autotransporter gene that encodes a surface protein involved in adherence to extracellular matrix proteins and colonization of the kidneys in a murine model of UTI.

microbiology↗

bioRxiv2017

The dynamics of adaptive genetic diversity during the early stages of clonal evolution

The dynamics of genetic diversity in large clonally-evolving cell populations are poorly understood, despite having implications for the treatment of cancer and microbial infections. Here, we combine barcode lineage tracking, sequencing of adaptive clones, and mathematical modelling of mutational dynamics to understand diversity changes during experimental evolution. We find that, despite differences in beneficial mutational mechanisms and fitness effects between two environments, early adaptive genetic diversity increases predictably, driven by the expansion of many single-mutant lineages. However, a crash in diversity follows, caused by highly-fit double-mutants fed from exponentially growing single-mutants, a process closely related to the classic Luria-Delbruck experiment. The diversity crash is likely to be a general feature of clonal evolution, however its timing and magnitude is stochastic and depends on the population size, the distribution of beneficial fitness effects, and patterns of epistasis.

evolutionary biology↗