Biology subjects

Carpenter, E.

Publications and source records attributed to Carpenter, E..

10 recordsLinked to original sources

bioRxiv2026

Fatty acids in the tumor microenvironment reprogram neutrophils to induce immunosuppression via adenosine

As solid tumors progress, the tumor microenvironment (TME) becomes increasingly immunosuppressive, impairing cytotoxic T-cell activity and limiting the efficacy of the immune checkpoint blockade. However, the mechanistic drivers of this immunosuppression remain poorly understood. Here, we identify a tumor-derived lipid-neutrophil-adenosine axis as a critical regulator of immune suppression in advanced colorectal cancer (CRC). We show that fatty acids enriched in tumor interstitial fluid reprogram neutrophils to generate adenosine via PPAR activation, leading to T-cell suppression. Using AB928, a dual A2aR/A2bR adenosine receptor antagonist currently in clinical trials, we restored T-cell proliferation, effector function, and tumor-killing capacity in vitro and in vivo. Importantly, AB928 synergized with anti-PD-1 therapy to enhance survival in an autochthonous model of metastatic CRC. Our findings define a metabolic immune evasion mechanism in the TME and provide a rationale for targeting neutrophil-derived adenosine signaling to improve immunotherapy responses in CRC and other solid tumors.

cancer biology↗

bioRxiv2025

Data-driven Cognitive Clusters in Persistent Developmental Dyslexia

Developmental dyslexia is a neurodevelopmental condition characterized by persistent reading difficulties despite adequate intelligence and educational opportunities. The cognitive underpinnings of dyslexia remain incompletely understood. Although multiple causal pathways have been proposed, there is a gap in studies that can reliably identify dyslexia subtypes based on comprehensive evaluations that go beyond measures of reading and phonology. We employed one of the largest detailed samples of children with developmental dyslexia resistant to intervention, consisting of 147 extensively phenotyped school-age children aged 7-14 years who were recruited from specialized schools for students with learning differences. We implemented data-driven analyses leveraging a comprehensive neuropsychological assessment to delineate cognitive subdomains and characterize the heterogeneity in the sample. Hierarchical clustering of 24 cognitive measures aided in constructing a framework to subsequently interpret emerging clusters. Four clusters emerged, predominantly associated with: Processing Speed & Executive Function, Visuospatial & Mathematical Reasoning, Phonological Manipulation, and Verbal Short-term Memory & Word Retrieval. Subsequent latent profile analysis identified two distinct dyslexia profiles: one characterized by marked difficulties in executive functioning and processing speed, and another displaying impairments primarily in verbal short-term memory and word retrieval relative to the other profile. Importantly, both profiles exhibited comparable severity of persistent reading difficulties despite their divergent cognitive profiles. These findings show that phenotypically similar reading impairments can arise from distinct underlying cognitive factors, emphasizing the role of comprehensive neuropsychological evaluation in developing tailored interventions for affected children.

neuroscience↗

bioRxiv2024

Inclusivity in fNIRS Studies: Quantifying the Impact of Hair and Skin Characteristics on Signal Quality with Practical Recommendations for Improvement

Functional Near-Infrared Spectroscopy (fNIRS) holds transformative potential for research and clinical applications in neuroscience due to its non-invasive nature and adaptability to real-world settings. However, despite its promise, fNIRS signal quality is sensitive to individual differences in biophysical factors such as hair and skin characteristics, which can significantly impact the absorption and scattering of near-infrared light. If not properly addressed, these factors risk biasing fNIRS research by disproportionately affecting signal quality across diverse populations. Our results quantify the impact of various hair properties, skin pigmentation as well as head size, sex and age on signal quality, providing quantitative guidance for future hardware advances and methodological standards to help overcome these critical barriers to inclusivity in fNIRS studies. We provide actionable guidelines for fNIRS researchers, including a suggested metadata table and recommendations for cap and optode configurations, hair management techniques, and strategies to optimize data collection across varied participants. This research paves the way for the development of more inclusive fNIRS technologies, fostering broader applicability and improved interpretability of neuroimaging data in diverse populations.

neuroscience↗

bioRxiv2024

Plant G x Microbial E: Plant genotype interaction with soil bacterial community shapes rhizosphere composition during invasion

It is increasingly recognized that different genetic variants can uniquely shape their microbiomes. Invasive species often evolve in their introduced ranges, but little is known about the potential for microbial associations to evolve during invasion as a result. We investigated invader genotype (G) and microbial environment (E) interactions in C. solstitialis (yellow starthistle), a Eurasian plant that is known to have evolved novel genotypes, and to have altered microbial interactions, in its severe invasion of California, USA. We conducted an experiment in which native and invading genotypes were inoculated with native and invaded range soil microbial communities. We used amplicon sequencing to characterize rhizosphere bacteria in both the experiment and the field soils from which they were derived. We found that bacterial diversity is higher in invaded soils, but that invading genotypes accumulated a lower diversity of bacteria and unique microbial composition in experimental inoculations, relative to native genotypes. Associations with potentially beneficial Streptomycetaceae were particularly interesting, as these were more abundant in the invaded range and accumulated on invading genotypes. Thus variation in microbial associations of invaders was driven by the interaction of G and E, and microbial communities appear to change in composition along with host evolution during invasion.

evolutionary biology↗

bioRxiv2022

Arginase 1 is a key driver of immune suppression in pancreatic cancer

An extensive fibroinflammatory stroma rich in macrophages is a hallmark of pancreatic cancer. In this disease, it is well appreciated that macrophages are immunosuppressive and contribute to the poor response to immunotherapy; however, the mechanisms of immune suppression are complex and not fully understood. Immunosuppressive macrophages are classically defined by expression of the enzyme Arginase 1 (Arg1), which we demonstrated is potently expressed in pancreatic tumor associated macrophages from both human patients and mouse models. While routinely used as a polarization marker, Arg1 also catabolizes arginine, an amino acid required for T cell activation and proliferation. To investigate this metabolic function, we used a genetic and a pharmacologic approach to target Arg1 in pancreatic cancer. Genetic inactivation of Arg1 in macrophages, using a dual recombinase genetically engineered mouse model of pancreatic cancer, delayed formation of invasive disease, while increasing CD8+ T cell infiltration. Treatment of established tumors with the arginase inhibitor CB-1158 exhibited further increased CD8+ T cell infiltration, beyond that seen with the macrophage-specific knockout, and sensitized the tumors to anti-PD1 immune checkpoint blockade. Thus, our data demonstrate that Arg1 is more than simply a marker of macrophage function. Rather, Arg1 is also a driver of immune suppression and represents a promising immunotherapeutic target for pancreatic cancer.

cancer biology↗

bioRxiv2021

Cation and anion channelrhodopsins: Sequence motifs and taxonomic distribution

Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from three channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out electrophysiological analysis of 33 natural channelrhodopsin variants from different phylogenetic lineages and 10 metagenomic homologs in search of sequence determinants of ion selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins. Our results show that association of a reduced number of glutamates near the conductance path with anion selectivity depends on a wider protein context, because prasinophyte homologs with the identical glutamate pattern as in cryptophyte ACRs are cation-selective. Desensitization is also broadly context-dependent, as in one branch of stramenopile ACRs and their metagenomic homologs its extent roughly correlates with phylogenetic relationship of their sequences. Regarding spectral tuning, two prasinophyte CCRs exhibit red-shifted spectra to 585 nm, although their retinal-binding pockets do not match those of previously known similarly red-shifted channelrhodopsins. In cryptophyte ACRs we identified three specific residue positions in the retinal-binding pocket that define the wavelength of their spectral maxima. Lastly, we found that dinoflagellate rhodopsins with a TCP motif in the third transmembrane helix and a metagenomic homolog exhibit channel activity. IMPORTANCEChannelrhodopsins are widely used in neuroscience and cardiology as research tools and are considered as prospective therapeutics, but their natural diversity and mechanisms remain poorly characterized. Genomic and metagenomic sequencing projects are producing an ever-increasing wealth of data, whereas biophysical characterization of the encoded proteins lags behind. In this study we used manual and automated patch clamp recording of representative members of four channelrhodopsin families including a family that we report in this study in dinoflagellates. Our results contribute to a better understanding of molecular determinants of ionic selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins.

biochemistry↗

bioRxiv2021

MYC controls metastatic heterogeneity in pancreatic cancer

The degree of metastatic disease varies widely amongst cancer patients and impacts clinical outcomes. However, the biological and functional differences that drive the extent of metastasis are poorly understood. We analyzed primary tumors and paired metastases using a multi-fluorescent lineage-labeled mouse model of pancreatic ductal adenocarcinoma (PDAC) - a tumor type where most patients present with metastases. Genomic and transcriptomic analysis revealed an association between metastatic burden and gene amplification or transcriptional upregulation of MYC and its downstream targets. Functional experiments showed that MYC promotes metastasis by recruiting tumor associated macrophages (TAMs), leading to greater bloodstream intravasation. Consistent with these findings, metastatic progression in human PDAC was associated with activation of MYC signaling pathways and enrichment for MYC amplifications specifically in metastatic patients. Collectively, these results implicate MYC activity as a major determinant of metastatic burden in advanced PDAC.

cancer biology↗

bioRxiv2019

EGR1 transcriptional control of human cytomegalovirus latency

Sustained phosphotinositide3-kinase (PI3K) signaling is critical to the maintenance of herpesvirus latency. We have previously shown that the beta-herpesvirus, human cytomegalovirus (CMV), regulates epidermal growth factor receptor (EGFR), upstream of PI3K, to control states of latency and reactivation. Inhibition of EGFR signaling enhances CMV reactivation from latency and increases viral replication, but the mechanisms by which EGFR impacts replication and latency is not known. We demonstrate that HCMV downregulates MEK/ERK and AKT phosphorylation, but not STAT3 or PLC{gamma} for productive replication. Similarly, inhibition of either MEK/ERK or PI3K/AKT, but not STAT or PLC{gamma}, pathways increases viral reactivation from latently infected CD34+ hematopoietic progenitor cells (HPCs), defining a role for these pathways in latency. We hypothesized that CMV modulation of EGFR signaling might impact viral transcription. Indeed, EGF-stimulation increased expression of the UL138 latency gene, but not immediate early or early viral genes, suggesting that EGFR signaling promotes latent gene expression. The early growth response-1 (EGR1) transcription factor is induced downstream of EGFR signaling through both PI3K/AKT and MEK/ERK pathways. EGR1 expression is important for the maintenance of HPC stemness and its downregulation drives HPC differentiation and mobilization. We demonstrate that EGR1 binds upstream of UL138 and is sufficient to promote UL138 expression. Further, disruption of EGR1 binding upstream of UL138 prevented CMV from establishing a latent infection in CD34+ HPCs. Our results indicate a model whereby UL138 modulation of EGFR signaling feeds back to promote UL138 expression and suppression of replication to establish or maintain viral quiescence.\n\nAUTHOR SUMMARYCMV regulates EGFR signaling to balance states of viral latency and replication. CMV blocks downstream PI3K/AKT and MEK/ERK signaling pathways through down-regulation of EGFR at the plasma membrane. PI3K/AKT and MEK/ERK signaling increases expression of the EGR1 transcription factor that is necessary for the maintenance of stem cell stemness. A decrease in EGR1 expression promotes HPC mobilization to the periphery and differentiation, a known stimulus for CMV reactivation. We identified functional EGR1 binding sites upstream of the UL138 gene and EGR-1 binding stimulates UL138 expression. Additionally, down-regulation of EGR1 by CMV miR-US22 decreases UL138 expression emphasizing the importance of this transcription factor in expression of this latency gene. Lastly, we demonstrate that a CMV mutant virus lacking an upstream EGR1 binding site is unable to establish latency in CD34+ HPCs. This study defines one mechanism by which EGFR signaling impacts viral gene expression to promote CMV latency.

molecular biology↗

bioRxiv2018

Highly specific enrichment of rare nucleic acids using Thermus thermophilus Argonaute

Characterization of disease-associated, cell-free nucleic acids (liquid biopsy) provides a powerful, minimally-invasive means for early detection, genotyping, and personalized therapy; but is challenged by alleles of interest differing by single nucleotide from and residing among large abundance of wild-type alleles. We describe a new multiplexed enrichment assay, dubbed NAVIGATER, that utilizes short nucleic acid-guided endonucleases Argonaute (Ago), derived from the bacterium Thermus thermophilus (TtAgo), to specifically cleave complementary DNA and RNA while sparing alleles having single nucleotide mismatches with the guides. NAVIGATER greatly increases the fractions of rare alleles of interest in samples and enhances sensitivity of downstream procedures such ddPCR, sequencing, and clamped enzymatic amplification. We demonstrate 60-fold enrichment of KRAS G12D in blood samples from pancreatic cancer patients and detection of KRAS, EGFR, and BRAF mutants with XNA-PCR at 0.01% fraction.

molecular biology↗

bioRxiv2018

A Pentatricopeptide Repeat Protein in the Plasmodium apicoplast is essential and shows sequence-specific RNA binding

The malaria parasite Plasmodium and other apicomplexans such as Toxoplasma evolved from photosynthetic organisms and contain an essential, remnant plastid termed the apicoplast. Transcription of the apicoplast genome is polycistronic with extensive RNA processing. Little is known about the mechanism of post-transcriptional processing. In plant chloroplasts, post-transcriptional RNA processing is controlled by multiple pentatricopeptide repeat (PPR) proteins. Here, we present the biochemical characterisation of the single apicoplast-targeted PPR protein. Apicoplast PPR1 is essential, and binds specific RNA sequences corresponding with previously characterized RNA processing sites. We identify the specific binding motif of PPR1. In RNAse protection assays, PPR1 shields apicoplast transcripts from ribonuclease degradation. Our results show that apicoplast RNA processing is under the control of a single protein, thus presenting an Achilles heel for the development of new anti-malarial drugs.

microbiology↗