Biology subjects

Carter, J. A.

Publications and source records attributed to Carter, J. A..

8 recordsLinked to original sources

bioRxiv2026

The DNAJB1-PRKACA Oncogenic Fusion Drives Stepwise Biliary and Pancreatic Carcinogenesis from Intraductal Precursor Lesions

Intraductal oncocytic papillary neoplasms (IOPNs) are rare tumors that develop from biliary and pancreatic ductal epithelium and progress to lethal cancers. Human IOPNs and IOPN-associated carcinomas are known to harbor the DNAJB1-PRKACA gene fusion, however the role of the oncogenic fusion in carcinogenesis is poorly understood. We developed a Cre-inducible mouse model of human DNAJB1-PRKACA expression and substantiated that the DNAJB1-PRKACA fusion gene is a bona fide driver of IOPN-associated biliary and pancreatic carcinoma. By analyzing the unique histopathologic and transcriptional changes that occur at each stage of tumor development, we found that these murine tumors closely mimic human DNAJB1-PRKACA driven tumors. Furthermore, we identified that many of the salient features of invasive carcinoma are established at the pre-invasive stage, including evidence of tumor cell metabolic dysregulation, immunosuppressive tumor stroma and expression of genes strongly associated with invasive DNAJB1-PRKACA driven cancer in humans. Finally, we found that Slc16a14, a characteristic DNAJB1-PRKACA regulated super-enhancer associated gene, serves as a robust biomarker of malignant transformation from IOPN to invasive carcinoma.

cancer biology↗

bioRxiv2023

Characterization of the Entner-Douderoff Pathway in Pseudomonas aeruginosa Catheter-associated Urinary Tract Infections

Pseudomonas aeruginosa is an opportunistic nosocomial pathogen responsible for catheter-associated urinary tract infections (CAUTI). In a murine model of P. aeruginosa CAUTI, we previously demonstrated that urea within urine suppresses quorum sensing and induces the Entner-Douderoff (E-D) pathway. The E-D pathway consists of the genes zwf, pgl, edd, and eda. Zwf and Pgl convert glucose-6-phosphate into 6-phosphogluconate. Edd hydrolyzes 6-phosphogluconate to 2-keto-3-deoxy-6-phosphogluconate (KDPG). Finally, Eda cleaves KDPG to glyceraldehyde-3-phosphate and pyruvate, which enters the citric acid cycle. Here, we generated in-frame E-D mutants in strain PA14 and assessed their growth phenotypes on chemically defined media. These E-D mutants have a growth defect when grown on glucose or gluconate as sole carbon source which are similar to results previously reported for PAO1 mutants lacking E-D genes. RNA-sequencing following short exposure to urine revealed minimal gene regulation differences compared to the wild type. In a murine CAUTI model, virulence testing of E-D mutants revealed that two mutants lacking zwf and pgl showed minor fitness defects. Infection with the {Delta}pgl strain exhibited a 20% increase in host survival, and the {Delta}zwf strain displayed decreased colonization of the catheter and kidneys. Consequently, our findings suggest that the E-D pathway in P. aeruginosa is dispensable in this model of CAUTI. ImportancePrior studies have shown that the Entner-Douderoff pathway is up-regulated when Pseudomonas aeruginosa is grown in urine. Pseudomonads use the Entner-Douderoff pathway to metabolize glucose instead of glycolysis which led us to ask whether this pathway is required for urinary tract infection. Here, single-deletion mutants of each gene in the pathway were tested for growth on chemically defined media with single-carbon sources as well as complex media. The effect of each mutant on global gene expression in laboratory media and urine was characterized. The virulence of these mutants in a murine model of catheter-associated urinary tract infection revealed that these mutants had similar levels of colonization indicating that glucose is not the primary carbon source utilized in the urinary tract.

microbiology↗

bioRxiv2023

Identification of pan-cancer/testis genes and validation of therapeutic targeting in triple-negative breast cancer: Lin28a- and Siglece-based vaccination induces anti-tumor immunity and inhibits metastasis

BackgroundCancer-testis (CT) genes are targets for tumor antigen-specific immunotherapy given that their expression is normally restricted to the immune-privileged testis in healthy individuals with aberrant expression in tumor tissues. While they represent targetable germ-tissue antigens and play important functional roles in tumorigenesis, there is currently no standardized approach for identifying clinically relevant CT genes. Optimized algorithms and validated methods for accurate prediction of reliable CT antigens with high immunogenicity are also lacking. MethodsSequencing data from the Genotype-Tissue Expression (GTEx) and The Genomic Data Commons (GDC) databases was utilized for the development of a bioinformatic pipeline to identify CT exclusive genes. A CT germness score was calculated based on the number of CT genes expressed within a tumor type and their degree of expression. The impact of tumor germness with clinical outcome was evaluated using healthy GTEx and GDC tumor samples. We then used a triple-negative breast cancer mouse model to develop and test an algorithm that predicts epitope immunogenicity based on the identification of germline sequences with strong MHCI and MHCII binding affinities. Germline sequences for CT genes were synthesized as long synthetic peptide vaccines and tested in the 4T1 triple-negative model of invasive breast cancer with Poly(I:C) adjuvant. Vaccine immunogenicity was determined by flow cytometric analysis of in vitro and in vivo T cell responses. Primary tumor growth and lung metastasis was evaluated by histopathology, flow cytometry and colony formation assay. ResultsWe developed a new bioinformatic pipeline to reliably identify CT exclusive genes as immunogenic targets for immunotherapy. We identified CT genes that are exclusively expressed within the testis, lack detectable thymic expression, and are significantly expressed in multiple tumor types. High tumor germness correlated with tumor progression but not with tumor mutation burden, supporting CT antigens as appealing targets in low mutation burden tumors. Importantly, tumor germness also correlated with markers of anti-tumor immunity. Vaccination of 4T1 tumor bearing mice with Siglece and Lin28a antigens resulted in increased T cell anti-tumor immunity and reduced primary tumor growth and lung metastases. ConclusionOur results present a novel strategy for the identification of highly immunogenic CT antigens for the development of targeted vaccines that induce anti-tumor immunity and inhibit metastasis.

bioinformatics↗

bioRxiv2022

Perceptual warping exposes categorical representations for speech in human brainstem responses

The brain transforms continuous acoustic events into discrete category representations to downsample the speech signal for our perceptual-cognitive systems. Such phonetic categories are highly malleable and heir percepts can change depending on surrounding stimulus context. Previous work suggests these acoustic-phonetic mapping and perceptual warping of speech emerge in the brain no earlier than auditory cortex. Here, we examined whether these auditory-category phenomena inherent to speech perception occur even earlier in the human brain, at the level of auditory brainstem. We recorded speech-evoked frequency following responses (FFRs) during a task designed to induce more/less warping of listeners perceptual categories depending on stimulus presentation order of a speech continuum (random, forward, backward directions). We used a novel clustered stimulus paradigm to rapidly record the high trial counts needed for FFRs concurrent with active behavioral tasks. We found serial stimulus order caused perceptual shifts (hysteresis) near listeners category boundary confirming identical speech tokens are perceived differentially depending on stimulus context. Critically, we further show neural FFRs during active (but not passive) listening are enhanced for prototypical vs. category-ambiguous tokens and are biased in the direction of listeners phonetic label even for acoustically-identical speech stimuli. Our data expose FFRs carry category-level information and suggest top-down processing actively shapes the neural encoding and categorization of speech at subcortical levels. These findings suggest the acoustic-phonetic mapping and perceptual warping in speech perception occur surprisingly early along the auditory neuroaxis, which might aid understanding by reducing ambiguity inherent to the speech signal.

neuroscience↗

bioRxiv2021

Nonlinear dynamics in auditory cortical activity reveal the neural basis of perceptual warping in speech categorization

Surrounding context influences speech listening, resulting in dynamic shifts to category percepts. To examine its neural basis, event-related potentials (ERPs) were recorded during vowel identification with continua presented in random, forward, and backward orders to induce perceptual nonlinearities. Behaviorally, sequential order shifted listeners categorical boundary vs. random delivery revealing perceptual warping (biasing) of the heard phonetic category dependent on recent stimulus history. ERPs revealed later ([~]300 ms) activity localized to superior temporal and middle/inferior frontal gyri that predicted listeners hysteresis magnitudes. Findings demonstrate that top-down, stimulus history effects on speech categorization are governed by interactions between frontotemporal brain regions.

neuroscience↗

bioRxiv2020

Auditory cortex is susceptible to lexical influence as revealed by informational vs. energetic masking of speech categorization

Speech perception requires the grouping of acoustic information into meaningful phonetic units via the process of categorical perception (CP). Environmental masking influences speech perception and CP. However, it remains unclear at which stage of processing (encoding, decision, or both) masking affects listeners categorization of speech signals. The purpose of this study was to determine whether linguistic interference influences the early acoustic-phonetic conversion process inherent to CP. To this end, we measured source level, event related brain potentials (ERPs) from auditory cortex (AC) and inferior frontal gyrus (IFG) as listeners rapidly categorized speech sounds along a /da/ to /ga/ continuum presented in three listening conditions: quiet, and in the presence of forward (informational masker) and time-reversed (energetic masker) 2-talker babble noise. Maskers were matched in overall SNR and spectral content and thus varied only in their degree of linguistic interference (i.e., informational masking). We hypothesized a differential effect of informational versus energetic masking on behavioral and neural categorization responses, where we predicted increased activation of frontal regions when disambiguating speech from noise, especially during lexical-informational maskers. We found (1) informational masking weakens behavioral speech phoneme identification above and beyond energetic masking; (2) low-level AC activity not only codes speech categories but is susceptible to higher-order lexical interference; (3) identifying speech amidst noise recruits a cross hemispheric circuit (ACleft [->] IFGright) whose engagement varies according to task difficulty. These findings provide corroborating evidence for top-down influences on the early acoustic-phonetic analysis of speech through a coordinated interplay between frontotemporal brain areas.

neuroscience↗

bioRxiv2018

T-cell receptor αβ chain pairing is associated with CD4+ and CD8+ lineage specification

While a highly diverse T-cell receptor (TCR) repertoire is the hallmark of a healthy adaptive immune system, relatively little is understood about how the CD4+ and CD8+ TCR repertoires differ from one another. We here utilize high-throughput single T-cell sequencing to obtain approximately 100,000 TCR {beta} chain pairs from human subjects, stratified into CD4+ and CD8+ lineages. We reveal that substantial information about T-cell lineage is encoded by V{beta} gene pairs and, to a lesser extent, by several other TCR features such as CDR3 length and charge. We further find that the strength of association between the {beta} chain and T-cell lineage is surprisingly weak, similar in strength to that of the chain. Using machine learning classifiers to predict T-cell lineage from TCR features, we demon-strate that {beta} chain pairs are significantly more informative than individual chains alone. These findings provide unprecedented insight into the CD4+ and CD8+ TCR repertoires and highlight the importance of {beta} chain pairing in TCR function and specificity.

immunology↗

bioRxiv2017

Single-cell sequencing reveals αβ chain pairing shapes the T cell repertoire

A diverse T cell repertoire is a critical component of the adaptive immune system, providing protection against invading pathogens and neoplastic changes, relying on the recognition of foreign antigens and neoantigen peptides by T cell receptors (TCRs). However, the statistical properties and function of the T cell pool in an individual, under normal physiological conditions, are poorly understood. In this study, we report a comprehensive, quantitative characterization of the T cell repertoire from over 1.9 million cells, yielding over 200,000 high quality paired {beta} sequences in 5 healthy human subjects. The dataset was obtained by leveraging recent biotechnology developments in deep RNA sequencing of lymphocytes via single-cell barcoding in emulsion. We report non-random associations and non-monogamous pairing between the and {beta} chains, lowering the theoretical diversity of the T cell repertoire, and increasing the frequency of public clones shared among individuals. T cell clone size distributions closely followed a power law, with markedly longer tails for CD8+ cytotoxic T cells than CD4+ helper T cells. Furthermore, clonality estimates based on paired chains from single T cells were lower than that from single chain data. Taken together, these results highlight the importance of sequencing {beta} pairs to accurately quantify lymphocyte receptor diversity.

immunology↗