Biology subjects

Porter, D. L.

Publications and source records attributed to Porter, D. L..

3 recordsLinked to original sources

bioRxiv2026

A Donor T-Cell Receptor Structural Signature Determines Alloreactive Potential and Predicts Acute Graft-Versus-Host Disease

Acute graft-versus-host disease (GVHD) remains a lethal barrier to successful allogeneic hematopoietic cell transplantation, yet pre-transplant donor selection entirely ignores hypervariable T-cell receptor (TCR) architecture. Here, by characterizing over 64,000 alloreactive clonotypes, we demonstrate that human alloreactivity is dictated by a constrained, predictable baseline structural signature. Pathogenic, tissue-infiltrating alloreactive T cells exhibit significantly shortened CDR3{beta} regions, altered antigen-facing biophysical features, biased VJ gene usage and extensive inter-donor sharing originating from public anti-pathogen memory reservoirs. These potent clones natively cluster within the high-frequency fraction of the unstimulated baseline donor repertoire. We introduce R50, an assay-independent metric quantifying this clonal dominance, which independently predicted a six-fold increased risk of acute GVHD in a cross-institutional cohort. This scalable in silico platform shifts pre-transplant risk stratification from HLA typing and demographic surrogates to precision immune-receptor modeling.

immunology↗

bioRxiv2026

Signal, noise, and sampling: How pool size and replication shape metabolomic inference

Metabolomics provides a direct readout of physiological state and is increasingly used in evolutionary and systems biology. In small organisms such as Drosophila melanogaster, metabolomic analyses typically require pooling individuals to obtain sufficient material, yet pool sizes vary widely across studies with little justification. How pooling and biological replication influence metabolome characterization and the detection of biological signal remains poorly understood. Here, we evaluate the effects of pool size and biological replication on metabolomic profiles and signal detection using two complementary experimental designs. In the first, we assess how pooling (5, 50, or 100 individuals) influences metabolomic structure and reproducibility in inbred and outbred populations. In the second, we test how pool size interacts with systematic variation in replicate number to affect detection of diet-associated metabolite changes under a high-sugar perturbation. Pool size strongly influenced metabolomic profiles, with samples pooled at five individuals consistently differing from larger pools, while profiles from 50 and 100 individuals were more similar. Larger pools improved reproducibility in a dataset-dependent manner. In the dietary experiment, smaller pool sizes substantially reduced sensitivity, leading to loss of true diet-associated metabolites without increasing false discoveries. Replicate downsampling further revealed that both pool size and biological replication jointly determine signal retention, with smaller pools accelerating the loss of detectable metabolites under reduced replication. Across all analyses, the ability to detect metabolite signals was strongly dependent on effect size and variability. Metabolites with larger and more stable effect estimates were consistently retained, whereas those with smaller or more variable effects were rapidly lost under reduced sampling. Linear mixed-effects modeling confirmed that detection probability is governed by a balance between biological signal strength and measurement variability, with pool size and replication jointly modulating this relationship. More broadly, our results demonstrate that metabolomic inference is governed by the interplay of signal, noise, and sampling design, with pool size and replication jointly shaping the detectability, stability, and interpretation of biological signals.

molecular biology↗

bioRxiv2024

TET2 regulates early and late transitions in exhausted CD8+ T-cell differentiation and limits CAR T-cell function

CD8+ T-cell exhaustion hampers disease control in cancer and chronic infections and limits efficacy of T-cell-based therapies, such as CAR T-cells. Epigenetic reprogramming of CAR T-cells by targeting TET2, a methylcytosine dioxygenase that mediates active DNA demethylation, has shown therapeutic potential; however, the role of TET2 in exhausted T-cell (TEX) development is unclear. In CAR T-cell exhaustion models and chronic LCMV infection, TET2 drove the conversion from stem cell-like, self-renewing TEX progenitors towards terminally differentiated and effector (TEFF)-like TEX. In mouse T-cells, TET2-deficient terminally differentiated TEX retained aspects of TEX progenitor biology, alongside decreased expression of the transcription factor TOX, suggesting that TET2 potentiates terminal exhaustion. TET2 also enforced a TEFF-like terminally differentiated CD8+ T-cell state in the early bifurcation between TEFF and TEX, indicating a broad role for TET2 in mediating the acquisition of an effector biology program that could be exploited therapeutically. Finally, we developed a clinically actionable strategy for TET2- targeted CAR T-cells, using CRISPR/Cas9 editing and site-specific adeno-associated virus transduction to simultaneously knock-in a CAR at the TRAC locus and a functional safety switch within TET2. Disruption of TET2 with this safety switch in CAR T-cells restrained terminal TEX differentiation in vitro and enhanced anti-tumor responses in vivo. Thus, TET2 regulates pivotal fate transitions in TEX differentiation and can be targeted with a safety mechanism in CAR T-cells for improved tumor control and risk mitigation. One Sentence SummaryModulation of exhausted CD8+ T-cell differentiation by targeting TET2 improves therapeutic potential of CAR T-cells in cancer.

immunology↗