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Chu, T.

Publications and source records attributed to Chu, T..

At least 19 recordsLinked to original sources

Evidence Accumulation in Synaptic Efficacy: Activity-Silent Decision-Making with Short-Term Plasticity

Decision-making requires accumulation of evidence over time, yet exactly how neural circuits implement this computation remains debated. Classical models posit that evidence accumulation is realized by ramping neural activity, whereas recent experimental findings suggest an alternative mechanism in which neural activity remains largely silent before abruptly transitioning into an active decision state. This mechanism leaves a fundamental question unanswered: how is evidence accumulated during the neural activity-silent period? To address this question, we trained excitatory-inhibitory recurrent neural networks (RNNs) with short-term synaptic plasticity (STP) on a reaction-time decision task. We found that after training, the networks learned to leverage STP to make decisions in an activity-silent manner. Choice-tuning analysis revealed a clear functional organization of the network, and connection-pruning analysis uncovered the coupling between choice-selective excitatory and inhibitory neural groups. Guided by the architecture of trained RNNs, we constructed a minimal neural circuit model, in which evidence accumulates in facilitated synaptic efficacy that progressively reshapes the circuit's phase portrait, eventually driving the network state across the stability boundary and triggering a rapid transition to a choice state. We further compared activity before a choice between the theoretical STP and Static models to examine the potential energy benefit of activity-silent decision-making. Together, our results suggest STP as a mechanism for evidence accumulation in activity-silent decision-making and offer insights into the design of energy-efficient artificial neural networks.

neuroscience↗

Cross-species analysis links cell-cell communication rewiring to NOTCH2 during serous endometrial carcinogenesis

Cell-cell interactions shape the fate of mutant cells during cancer initiation but how these interactions evolve during progression to pathologically recognizable lesions remain poorly understood. Here, we investigated cell-cell communication during serous endometrial carcinoma (SEC; also known as uterine serous carcinoma) development using a lineage-traceable mouse model and cross-species analyses of the mouse and human neoplastic endometrium. In mice, the early, pre-dysplastic stage was marked by a global decrease in inferred cell-cell interactions, followed by extensive communication network rewiring during neoplastic progression. Pathway-specific analysis revealed a similar pattern for NOTCH signaling, with NOTCH2 emerging as the dominant NOTCH receptor in Trp53/Rb1-mutant immature epithelial cells. Functionally, NOTCH2 promoted the outgrowth of more proliferative mutant organoids. Cross-species transcriptomic analysis identified conserved immature epithelial states in mouse and human neoplastic endometrial epithelium. In human tissues, NOTCH2 was overexpressed in serous endometrial intraepithelial carcinoma, a precursor of SEC, and in overt SEC. Furthermore, elevated NOTCH2 expression was associated with poor patient survival. These findings link cell-cell communication rewiring during experimental SEC development to conserved neoplastic epithelial states and identify NOTCH2 as an early marker and a potential target of disease interception.

cancer biology↗

VITAL-3D: Volumetric Single-Cell Quantification Reveals Microenvironment-Dependent Drug Responses in Breast Cancer

Preclinical drug evaluation relies heavily on two-dimensional (2D) monolayer assays, which fail to recapitulate the structural and functional complexity of the tumor microenvironment and may therefore misrepresent therapeutic efficacy. Here, we present VITAL (Volumetric Imaging-based Toxicity and Live Analysis), a high-throughput imaging platform that enables direct single-cell quantification of proliferation and cell death in both 2D and three-dimensional (3D) extracellular matrix (ECM) cultures using a 96-well format. By combining volumetric imaging with automated single-cell analysis, VITAL enables dynamic assessment of drug responses beyond conventional viability assays and EC measurements. Using breast cancer cell lines treated with anticancer agents, we systematically compared drug responses between 2D and 3D microenvironments. Although EC values were often comparable between culture formats, growth kinetics and concentrations required to induce complete growth arrest or net cell loss differed substantially in 3D cultures. In particular, drug concentrations required to induce net cell loss were consistently higher in 3D, revealing microenvironment-dependent survival responses that were not captured by EC alone. Furthermore, clinically expected subtype-specific responses, including tamoxifen sensitivity in ER-positive cells and olaparib sensitivity in BRCA1-mutant cells, were more accurately resolved under 3D culture conditions and extended treatment durations. Together, these findings demonstrate that growth-based, single-cell quantification provides a more comprehensive assessment of therapeutic efficacy than conventional endpoint measurements and establish VITAL as a scalable platform for physiologically relevant preclinical drug screening.

cancer biology↗

Spatial co-expression and cell-cell communication inference from spatially resolved transcriptomics with CONCISE

Cell-cell communication is fundamental to tissue organization, homeostasis, and disease progression. Recent advances in spatial transcriptomics provide unprecedented opportunities to systematically characterize ligand-receptor interactions directly within intact tissues. However, robust inference of spatial ligand-receptor interactions remains challenging because intrinsic features of spatial transcriptomics data, including spatial autocorrelation, variation in total molecular counts, and measurement errors, can induce spurious spatial co-expression and lead to inflated false-positive results. Most existing methods do not adequately account for these confounding factors, limiting the reliability of inferred cellular communication. Here, we present CONCISE, a statistical method for spatially constrained co-expression and ligand-receptor interaction inference that jointly models spatial autocorrelation, variation in total molecular counts, measurement errors, and spatial proximity constraints. CONCISE combines efficient moment-based parameter estimation with analytical hypothesis testing, enabling fast and statistically rigorous inference without restrictive distributional assumptions. Through extensive simulations, real-data permutation experiments, and biologically motivated negative-control analyses across different spatial transcriptomics platforms, we show that most existing methods presented inflated false-positive rates, whereas CONCISE achieved well-calibrated inference, robust false-positive control, and improved detection power. Application of CONCISE to high-resolution MERFISH and CosMx datasets from intestinal inflammation and non-small cell lung cancer further highlights its biological utility in disease contexts. CONCISE uncovered inflammation-associated fibroblast-specific interactions during intestinal inflammation and delineated complex tumor-immune and tumor-stromal signaling networks within the tumor microenvironment.

bioinformatics↗

Epithelial stem cells in the premenopausal human vagina

The vagina undergoes physiologic changes across the menstrual cycle, pregnancy, birth and menopause. Most women will experience vaginal dysfunction at some point during their lives and treatment options are limited. The cyclic regeneration of the vaginal epithelium during each menstrual cycle suggests it is a stem-cell based tissue; however, human vaginal epithelial stem cells (veSCs) have not been identified. We utilized in vitro colony forming and organoid assays to confirm that cells in the human vaginal epithelium have self-renewal and differentiation potential. Specifically, we determined that stem cell activity resides in the ITGA6+ and NGFR+ fractions of the basal epithelium. We performed single-cell RNA sequencing to identify the distinct cellular compartments of the full thickness human vagina, including spatially distinct populations comprising layers of the stratified vaginal epithelium. Markers of these cells within the vaginal epithelium were validated by immunohistochemistry. CD9+ITGA6+NGFR+ and CD9+ITGA6+NGFR- cells were capable of efficient colony formation but only the CD9+ITGA6+NGFR+ fraction produced organoids containing basal, intermediate and superficial layers of the vaginal epithelium. We characterized the premenopausal human vagina at single cell resolution, validated markers and assays to test veSC developmental potential, and identified putative stem cells that may open new avenues for treating vaginal dysfunction.

cell biology↗

Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally-Diverse Cohort

Endometrial cancer (EC) exhibits one of the most striking racial disparities in oncology with black women disproportionately affected by aggressive high-grade subtypes that have poorer outcomes. While social and environmental factors undoubtedly contribute, the molecular underpinnings of these disparities remain critically understudied. To bridge this knowledge gap, we performed matched tumor-normal whole-genome sequencing and tumor transcriptome sequencing on 71 predominantly high-grade EC patient samples from an ancestrally diverse cohort of women recruited at a large hospital system in the New York metropolitan area. Our analysis characterized the germline and somatic mutation landscape, identifying ancestry-associated molecular differences. Notably, focal amplification of the EVI1 transcription factor (encoded at the MECOM locus) was significantly more frequent in African ancestry patients and associated with poorer clinical outcomes in an external validation cohort. Additionally transcriptome analysis revealed decreased CD8+ T cell infiltration with increasing African ancestry, suggesting tumor immune microenvironment differences with potential therapeutic implications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/721962v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@12125b9org.highwire.dtl.DTLVardef@133c787org.highwire.dtl.DTLVardef@707af0org.highwire.dtl.DTLVardef@97615c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThis study represents the most ancestrally diverse whole-genome sequencing characterization of high-grade endometrial cancer, with 62% of patients of African ancestry. C_LIO_LIMECOM focal amplification preferentially targets the oncogenic short isoform (EVI1) and is more frequent in patients of African ancestry. C_LIO_LIAfrican ancestry is associated with reduced CD8+ T cell infiltration and differential activation of immune and metabolic pathways in copy-number high endometrial tumors. C_LI

cancer biology↗

Engineering Dual-Target Chimeric Lysins for Synergistic Eradication of Porphyromonas gingivalis

Periodontitis is a chronic inflammatory disease driven by complex subgingival multispecies biofilms, in which Porphyromonas gingivalis plays a central role in coordinating microbial interactions. Together with host-associated factors, these microbial communities create dual constraints that limit antimicrobial efficacy. In this study, we engineered a library of recombinant lysins by fusing membrane-destabilizing peptides to the periodontal pathogen-derived lysin LysPd078 and identified four optimized variants (PlyPd06, PlyPd19, PlyPd27, and PlyPd44) with enhanced salt tolerance, environmental stability, and bactericidal activity. In a clinically derived polymicrobial oral biofilm, PlyPd44 at only 25 g/mL eradicated 96.6% of P. gingivalis. In a humanized oral microbiota mouse model of periodontitis, selected PlyPds significantly reduced inflammation and inhibited alveolar bone loss compared with LysPd078 and minocycline. Collectively, these results establish membrane-destabilizing peptide-enabled lysins as a promising platform for developing microenvironment-adapted precision antimicrobials for periodontitis.

microbiology↗

Single-nucleus multiome sequencing identifies candidate regulators of mouse gastric epithelial homeostasis

Background & AimsGastric epithelial cells maintain homeostasis through dynamic self-renewal mechanisms involving stem and progenitor cells; however, identifying them has been challenging. This study aims to identify stem cells of healthy gastric epithelium and cell type-specific regulators defining gastric epithelial homeostasis via single-nucleus multiome analysis. MethodsTen unique gastric samples were collected from 8-12 week old wildtype mice. Isolated nuclei were subjected to simultaneous profiling of gene expression and chromatin accessibility. After quality control, 31,598 cells were analyzed with Seurat and Signac using weighted-nearest neighbors analysis for joint RNA and ATAC clustering. Furthermore, SCENIC+, MultiVelo, EpiCHAOS and Cell plasticity score were used to uncover gene regulatory networks, cell state dynamics and lineage trajectories. ResultsOur analyses were validated by the identification of known regulators of stem-cell differentiation into mature cell types. More importantly, it revealed previously uncharacterized regulatory networks comprising novel transcription factor combinations that define cell identities, including Ppara, Pparg, Arid5b and Sox5 as candidate regulators of parietal, foveolar, chief and neck cells, respectively. Further, our data support the identity of isthmus cells as stem-like cells of healthy gastric epithelium, as evidenced by epigenetic plasticity that simultaneously contains open chromatin states of all differentiated cell types in the absence of transcriptional reprogramming. ConclusionConsistent with Waddingtons epigenetic landscape hypothesis, gastric epithelial homeostasis is controlled by orchestrated epigenetic and transcriptional programs. Contrary to the prevailing hypothesis, stem cells can be defined not by a separate epigenetic state but by epigenetic superposition of differentiated cell states. Future work is needed to define the universality of these results.

genomics↗

A Single-Cell Atlas of Uterine Carcinosarcoma from Diverse Ancestries

Uterine carcinosarcoma (UCS) is an aggressive endometrial cancer defined by coexisting malignant epithelial and mesenchymal components, rapid metastatic dissemination, and poor therapeutic response. However, its cellular ecosystem remains poorly resolved, particularly in patients of African ancestry who are underrepresented in genomic datasets despite a disproportionate disease burden. Here, we generated a single-cell atlas of 15 primary and metastatic UCS specimens from a diverse cohort of 13 patients enriched for African ancestry, integrated with whole-genome sequencing. Malignant cells exhibited epithelial-like, mesenchymal-like, transitional, and stem/progenitor-like states within individual tumors that mapped to patient-specific copy number-defined subclones and RNA-velocity trajectories, supporting metaplastic state transitions. Compared to normal endometrium, primary tumors were enriched for epithelial-mesenchymal-transition (EMT), mTORC1, and glycolytic programs, whereas matched metastases show enhanced TNF-NF{kappa}B-associated invasive programs. The tumor microenvironment contained immunosuppressive myeloid states and diverse cancer-associated fibroblast (CAF) subsets, including pericyte-like and matrix-remodeling subsets that act as predicted communication hubs through chemokine and immune-checkpoint circuits. We found a CAF-centered CCL2-CXCL1/2-IL10 module linked to CD8 T-cell dysfunction and a TIGIT-CD96-PVR checkpoint module. These data define the UCS cellular ecosystem in which malignant plasticity is coupled to stromal-immune cell remodeling in a patient cohort of enriched ancestries and nominate stromal-immune axes for further therapeutic investigation.

cancer biology↗

A Patient-derived Organoid Platform for Uterine Carcinosarcoma that Emulates Disease Characteristics

Uterine carcinosarcoma (UCS) is a rare but extremely lethal endometrial cancer that metastasizes early and resists current treatment modalities. It is biphasic, built from malignant epithelial and mesenchymal cells. Genomic studies indicate that these tumors are clonal, and that the mesenchymal cells arise from the epithelial cells through cancer cell plasticity. This biology has been hard to study, because faithful patient-derived models are scarce. The gap is widened by inequity. Women of African ancestry carry the greatest burden of UCS, yet are underrepresented in existing models. To address this, we established patient-derived organoids (PDOs) from an ancestrally inclusive UCS cohort, alongside matched normal endometrial PDOs. The organoids reproduced the biphasic histology of the original tumors. Across four sequencing platforms, they retained the tumor mutation and copy-number landscape, remained stable across passages, and expanded for up to 28 months. At single-cell resolution, UCS PDOs captured both malignant compartments and traced continuous transcriptional trajectories along the epithelial-to-mesenchymal axis, capturing patient-specific cancer cell plasticity. The models also nominated candidate vulnerabilities in proof-of-concept therapeutic testing. UCS PDOs were enriched for CREB-family transcriptional programs, and CREB inhibition reduced their viability. Combined FGFR and YAP inhibition outperformed either agent alone. Together, this work delivers a histologically, genomically, and transcriptionally faithful, ancestrally inclusive, and lineage-resolved UCS organoid platform for studying cancer cell plasticity and its vulnerabilities in an aggressive and inequitably burdened cancer.

cancer biology↗

A Targeting Parameter Space for Personalized 4x1 HD-tES: Montage Description, Optimization and Application

BackgroundPersonalized optimization of 4x1 high-definition transcranial electrical stimulation (HD-tES) faces inherent trade-offs between montage flexibility, computational efficiency, and implementation accessibility. Conventional 10-10 electrode systems constrain placement to discrete landmark positions, while unconstrained optimization relies on stochastic algorithms that risk converging to local optima and requires neuronavigation equipment often unavailable in rehabilitation settings. Here we introduce a scalp geometry-based parameter space (SGP) that parameterizes 4x1 HD-tES montages using three intuitive scalp-defined parameters--position, radius, and orientation--and characterize parameter-performance regularities through exhaustive electric field simulations across 30 subjects and 624 cortical targets (>3.6 million configurations). ResultsPosition primarily determined proximity to optimal performance, radius governed the intensity-focality trade-off, and orientation served as fine-tuning. Exploiting these regularities, a minimal search space (SGP-MSS) was constructed that reduced computational complexity by over 90% while guaranteeing global optima identification. Compared with standard 10-10 montages, SGP-MSS achieved up to 99% higher targeting intensity and 126% higher focality (all p < 0.0001). Compared with lead-field-free optimization, SGP-MSS achieved comparable performance with greater cross-subject stability. ConclusionsThe SGP framework enables efficient individualized HD-tES optimization without neuronavigation. Its scalp-based parameterization supports electrode positioning via standard cranial landmark measurements, facilitating translation to routine clinical and home-based rehabilitation settings.

biophysics↗

The Epigenetic Factor PHF13 Governs Trophoblast Stemness and Differentiation

Differentiation of trophoblast stem (TS) cells or progenitor cytotrophoblasts (CTBs) into multinucleated syncytiotrophoblasts (STBs) is essential for placental development. Disruption of this process contributes to major obstetrical syndromes, including fetal growth restriction and preeclampsia, and Trisomy 21. However, the chromatin mechanisms governing trophoblast stemness and differentiation remain inadequately defined. Here we identify the chromatin-associated factor PHF13, uncovered through a high-throughput microRNA target screen, as a key regulator of trophoblast cell fate. PHF13 knockout TS cells exhibited defects that ultimately resulted in loss of cell viability, whereas PHF13 knockdown promoted expression of fusion-associated genes, including ERVFRD-1 and human chorionic gonadotropin (hCG). Consistently, PHF13 depletion in BeWo trophoblast cells increased hCG expression and secretion while reducing expression of canonical stemness-associated transcription factors ELF5 and TEAD4. Integrated genomic analyses further revealed that PHF13 target genes comprise a gene regulatory network that maintains trophoblast stemness and restrains differentiation. Notably, the pluripotency-associated transcription factor THAP11 partially co-occupies genomic sites with PHF13. Together, these findings establish PHF13 as a previously unrecognized chromatin regulator of trophoblast stemness and differentiation, providing mechanistic insight into pathways critical for placental development and function. HighlightsO_LIPHF13 preserves trophoblast stem cell identity C_LIO_LIPHF13 restrains syncytiotrophoblast differentiation C_LIO_LIPHF13 controls trophoblast chromatin programs with THAP11 C_LI

molecular biology↗

Tex11 Mutant Mouse Models of Human Azoospermia

Non-obstructive azoospermia (NOA) is the absence of sperm in the ejaculate due to spermatogenic failure. Fifty percent of NOA cases are unexplained but may arise from unidentified genetic mutations. Variants in TEX11 have been identified in men with NOA; and Tex11 knockout in mice causes NOA. Here we attempt to validate three TEX11 variants discovered in NOA patients by knocking them into the orthologous region of the mouse genome using CRISPR/Cas9 gene editing. Compared to wild type (144.2 {+/-} 9.87 mg; 1.7 {+/-} 0.5 million sperm/cauda epididymis 4.8 {+/-} 1.3 pups/breeding), Tex11D mice (frameshift mutation) had reduced testis weight (28.33 {+/-} 1.16 mg); no sperm in the epididymis; and were infertile with a maturation arrest testicular phenotype. We did not observe any spermatogenesis or fertility defects Tex11A mice (missense mutation). Tex11L mice had reduced testis weight (87.5 {+/-} 14.79 mg) and epididymal sperm counts (0.33{+/-}0.13 million/cauda epididymis) but an incompletely penetrant infertility phenotype (5.4 {+/-} 1.13 pups/breeding) with one third of mice being infertile. Infertile Tex11L mice also had a distinct epididymal phenotype with reduced sperm density in the caput and no sperm in the cauda, which was filled with amorphous material.

genetics↗

Re-evaluating the Need for Double Centrifugation in Plasma Cell-Free DNA Analysis

Plasma cell-free DNA (cfDNA) is a central analyte in liquid biopsy applications spanning prenatal testing, oncology, and epigenomic profiling. To minimize contamination by high-molecular-weight genomic DNA (gDNA) released from nucleated blood cells, standard pre-analytical workflows typically mandate a double-centrifugation protocol prior to cfDNA extraction. This requirement has limited the use of many existing plasma biorepositories that were prepared using only a single low-speed centrifugation step. In this study, we evaluated whether single-spun plasma is sufficient for accurate cfDNA analysis when samples are processed under controlled conditions. Using paired single- and double-spun plasma aliquots derived from the same early-pregnancy maternal blood samples collected in EDTA tubes, we performed whole-genome DNA methylation sequencing and assessed cfDNA integrity across multiple orthogonal dimensions. These included cell-type proportion deconvolution using large and small DNA methylation reference signatures, CpG-level methylation rate estimation with explicit variance modeling, beta-binomial-corrected correlation analyses across libraries, cfDNA fragment length profiling, and genotype-based fetal fraction estimation. Across all analyses, we found no evidence that a second high-speed centrifugation step improved accuracy, reduced technical variability, or enhanced analytical fidelity. Cell-type proportion estimates and CpG-level methylation rates were statistically indistinguishable between single- and double-spun plasma, fragment length distributions were nearly identical, and fetal fraction estimates showed near-perfect concordance. Together, these results demonstrate that a single low-speed centrifugation step is sufficient for high-fidelity cfDNA methylation, fragmentomic, and genotyping analyses. Our findings support the expanded use of legacy single-spun plasma collections for liquid biopsy research and assay development and motivate a re-evaluation of rigid double-centrifugation requirements in cfDNA workflows.

genomics↗

Wavelet Based Whole Genome Doubling Aware Single Cell Copy Number Calling

Advances in single cell whole genome sequencing enable profiling of the copy number state of thousands of cells with minimal sequencing bias across the genome. The Direct Library Preparation + technique is an whole genome amplification-free single cell whole genome sequencing method that achieves high throughput by fragmenting each cells genome and ligating sequencing adapters using a modified Tn5 transposase, and sequencing to less than 0.1x coverage. Despite recent advances in experimental approaches, data analysis of single cell whole genome sequencing lags behind and the existing methods are not optimized for the analysis of frozen samples with variable DNA preservation. Furthermore, existing tools predominantly rely on read depth ratio in predefined genomic bins to call copy number, making whole genome duplication unidentifiable. To address this, we introduce Songbird, a single cell whole genome sequencing copy number caller that is whole genome duplication sensitive, and outperforms existing tools both in breakpoints identification and true copy number detection. We demonstrate that Songbird is robust down to extremely low coverage, adaptable to a variety of genome versions (hg19, hg38, hs.1), and is extensible to other single cell whole genome sequencing methods that rely on Tn5 tagmentation to fragment the genome.

bioinformatics↗

Inhibitory potential of autologous neutralizing antibodies sets quantitative limits on the rebound-competent HIV-1 reservoir

HIV-1 cure requires preventing viral rebound after treatment interruption, but quantitative criteria defining the rebound-competent reservoir are lacking. We studied individuals undergoing observational treatment interruption without confounding interventions to identify virologic and immunologic determinants of rebound. In 9 of 13 participants, rebound viruses were genetically identical or similar to proviruses in circulating resting CD4+ T-cells. We found no evidence of recombination among rebound sequences. Instead, resistance to autologous neutralizing antibodies (aNAbs) was a critical determinant of viral rebound. Increased suppression of viral outgrowth by contemporaneous IgG isolated from plasma was correlated with longer time to rebound. Using inhibitory potential (IP), the log reduction in single-round infection at physiologic IgG concentrations, we defined quantitative limits governing rebound-competency with respect to contemporaneous aNAbs. Contemporaneous IgG antibodies inhibited different reservoir variants with a wide range of IP values (0.4-8.2 logs), whereas rebound viruses were minimally inhibited (0.5-2.8 logs), indicating that inhibition by even up to 2.8 logs (631-fold) cannot prevent rebound. Longitudinal analyses revealed that waning aNAb potency over time on ART allows previously neutralized variants to gain rebound potential, consistent with the finding that rebound can come from variants deposited in the reservoir at different pre-ART time points. Thus, rebound competency is a dynamic, immune-governed property defined by quantitative immunologic constraints, including those exerted by aNAbs. SIGNIFICANCE STATEMENTPreventing viral rebound after treatment interruption is the goal of HIV-1 cure research, but the latent proviruses responsible remain undefined. Although rebound is initiated in lymphoid tissues, we found rebound viruses are genetically similar to proviruses in circulating resting CD4+ T-cells. Rebound is not explained by recombination and is not solely from proviruses seeded at treatment initiation. Instead, rebound potential is governed by autologous neutralizing antibodies (aNAbs). We define a quantitative threshold of aNAb-mediated inhibition identifying reservoir variants with rebound potential. During treatment, waning aNAb levels allow previously neutralized variants to become rebound-competent. Thus rebound-competency is not a static property, but a dynamic immune-governed feature. Durable aNAb responses against all rebound-competent reservoir variants may be required for functional HIV-1 cure.

immunology↗

MSC-delivered High-Affinity Variants of soluble PD1 lead to tumour regression

Immune checkpoint therapies aim to restore anti-tumour immunity by blocking inhibitory signals that suppress T-cell activation. The most effective current strategies use humanised antibodies targeting PD1 or its ligand PDL1. However, due to their large size, antibodies often exhibit limited tissue diffusion, resulting in poor penetration into solid tumours. To address this challenge, we developed a novel checkpoint inhibitor approach that uses mesenchymal stromal cells (MSCs) to deliver a high-affinity, soluble PD1 receptor (sPD1HAC). We found that sPD1HAC produced as an IgG1-Fc fusion protein provided functional expression in MSCs. The sPD1HAC-IgG1-Fc fusion protein showed strong and specific binding to PDL1 and could outcompete recombinant PD1 and anti-PDL1 antibodies, including the clinically approved durvalumab. Although the sPD1HAC variant was designed to block human PD1-PDL1 signalling, it also bound murine PDL1 and blocked the binding of mouse-specific PD1 antibodies as well as recombinant murine PD1 protein. Accordingly, we found significant anti-tumour activity of intravenously administered MSCs.PD1HAC in an aggressive B16-F10 cancer model. This cell-based immune checkpoint approach offers a potential therapeutic option for targeting stroma-rich, treatment-resistant tumours.

cancer biology↗

Dynamic Causal Modelling for Functional Near-Infrared Spectroscopy Using Spatial Priors Derived from Diffuse Optical Tomography

Functional near-infrared spectroscopy (fNIRS) is an optical neuroimaging technique that measures brain activity by detecting changes in oxygenated and deoxygenated hemoglobin concentrations. Although methods exist for estimating causal interactions among brain regions using fNIRS data, current approaches typically rely on node locations defined at the sensor measurement level near the cortical surface. To address this limitation, this study extends dynamic causal modeling (DCM) for fNIRS by incorporating source-level locations derived from diffuse optical tomography (DOT). The proposed method was applied to an experimental dataset comprising 104 participants recorded during a Go/No-Go response inhibition task. Bayesian model selection confirmed that DCM models using DOT-informed neuronal source locations outperformed models using sensor-level locations. Furthermore, posterior means of effective connectivity parameters validated the inhibitory influence of the right inferior frontal gyrus on regions within the motor network during response inhibition. By providing precise neuronal source localization informed by statistical parametric mapping of DOT-reconstructed data, the proposed DCM approach enables more accurate inference of directed connectivity at the neuronal level from optical density measurements. Given the compact and portable nature of fNIRS systems, this method can readily be applied in realistic, naturalistic environments to investigate network-level modulation of brain responses.

neuroscience↗