Biology subjects

Kelly, P. J.

Publications and source records attributed to Kelly, P. J..

6 recordsLinked to original sources

bioRxiv2026

GROQ-seq Datasets Across Transcription Factors (LacI, RamR, VanR), T7 RNA Polymerase and TEV Protease

Predicting any proteins function from its sequence alone would be a significant breakthrough in molecular biology. Although machine learning approaches have sought to tackle this, their limited generalizability reflects the absence of sufficiently large, open, diverse, and unified datasets. To address this data gap, we developed a high-throughput experimental platform called GROQ-seq (Growth-based Quantitative Sequencing). In GROQ-seq, a proteins function can be linked to a sequencing-based readout that enables scalable characterization of large variant libraries in Escherichia coli. Here, we present pilot datasets demonstrating its performance across three distinct protein function classes: transcription factors, polymerases, and proteases. The objective of this report is to present the datasets and to provide users with a clear and transparent characterization of their properties, including both the strengths and limitations.

bioengineering↗

bioRxiv2026

GROQ-seq Enables Cross-site Reproducibility for High-Throughput Measurement of Protein Function

High-throughput functional assays are increasingly used to generate large-scale protein function datasets for protein engineering and machine learning applications. However, the utility of such datasets depends on the reproducibility of the underlying measurements. Here we report reproducible, quantitative measurements of protein sequence-to-function data at scale across two facilities. We analyze GROQ-seq (Growth-based Quantitative Sequencing) measurements of three bacterial transcription factors. Independent barcode measurements of the same sequence produce highly consistent functional estimates, demonstrating strong biological reproducibility (across all transcription factors the mean Root Mean Square Deviation [RMSD] {approx} 0.53 and mean Spearman {approx} 0.63). We also compared experiments performed at two facilities using a shared protocol, but with differing levels of automation and system integration. We observe strong agreement between measurements taken at the two sites (mean RMSD {approx} 0.41 and mean Spearman {approx} 0.730). Orthogonal tests further support this agreement: a classifier trained to distinguish data by site performs near random (AUC = 0.559), and top-ranking variants show strong statistical overlap between experiments. Together, these results demonstrate that GROQ-seq enables reproducible, scalable measurement of protein function suitable for large aggregated datasets.

bioengineering↗

bioRxiv2025

CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma

Mutations in KRAS are a dominant driver of pancreatic ductal adenocarcinoma (PDAC), with over 40% of PDAC patients presenting with KRASG12D mutations. The recent development of small molecule inhibitors targeting KRASG12D has enabled targeting of mutant KRAS signaling and suppression of PDAC; however, the contribution of the tumor microenvironment (TME) to the sustained therapeutic efficacy of KRASG12D inhibition and mechanism/s of resistance to KRASG12D suppression remain to be elucidated. Here, we employed spatial transcriptomics, single cell RNA sequencing, and CODEX-based spatial proteomics to evaluate cancer cell intrinsic and extrinsic responses to KRASG12D inhibition with MRTX1133. While KRASG12D inhibition initially increases CD11c+ cells with impactful T cell infiltration within proximity to cancer cells, long-term treatment with MRTX1133 resulted in reversal of the immune responses leading to KRASG12D therapy resistance promoted by CDK8, a multiprotein mediator complex associated kinase. CDK8 imparts resistance in part through induction of downstream CXCL2 chemokine secretion, inhibition of FAS expression, and remodeling of the TME to promote immune evasion. Targeting CDK8 by itself and in combination with CTLA-4 immunotherapy overcomes resistance to KRASG12D inhibition with prolonged survival with translational implications.

cancer biology↗

bioRxiv2024

Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design

The grand challenge of protein engineering is the development of computational models to characterize and generate protein sequences for arbitrary functions. Progress is limited by lack of 1) benchmarking opportunities, 2) large protein function datasets, and 3) access to experimental protein characterization. We introduce the Protein Engineering Tournament--a fully-remote competition designed to foster the development and evaluation of computational approaches in protein engineering. The tournament consists of an in silico round, predicting biophysical properties from protein sequences, followed by an in vitro round where novel protein sequences are designed, expressed and characterized using automated methods. Upon completion, all datasets, experimental protocols, and methods are made publicly available. We detail the structure and outcomes of a pilot Tournament involving seven protein design teams, powered by six multi-objective datasets, with experimental characterization by our partner, International Flavors and Fragrances. Forthcoming Protein Engineering Tournaments aim to mobilize the scientific community towards transparent evaluation of progress in the field. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/606135v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@8f9769org.highwire.dtl.DTLVardef@11da734org.highwire.dtl.DTLVardef@1cc51c0org.highwire.dtl.DTLVardef@10b3c27_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Oncogenic KrasG12D specific non-covalent small molecule inhibitor reprograms tumor microenvironment and reverses early precursor lesions and in combination with immunotherapy regresses advanced PDAC in a CD8+ T cells dependent manner

Pancreatic ductal adenocarcinoma (PDAC) is associated with mutations in Kras, a known oncogenic driver of PDAC; and the KRASG12D mutation is present in nearly half of PDAC patients. Recently, a non-covalent small molecule inhibitor (MRTX1133) was identified with specificity to the KrasG12D mutant protein. Here we explore the impact of KrasG12D inhibition by MRTX1133 on advanced PDAC and its influence on the tumor microenvironment. Employing different orthotopic xenograft and syngeneic tumor models, eight different PDXs, and two different autochthonous genetic models, we demonstrate that MRTX1133 reverses early PDAC growth, increases intratumoral CD8+ effector T cells, decreases myeloid infiltration, and reprograms cancer associated fibroblasts. Autochthonous genetic mouse models treated with MRTX1133 leads to regression of both established PanINs and advanced PDAC. Regression of advanced PDAC requires CD8+ T cells and immune checkpoint blockade therapy (iCBT) synergizes with MRTX1133 to eradicate PDAC and prolong overall survival. Mechanistically, inhibition of mutant Kras in advanced PDAC and human patient derived organoids (PDOs) induces Fas expression in cancer cells and facilitates CD8+T cell mediated death. These results demonstrate the efficacy of MRTX1133 in different mouse models of PDAC associated with reprogramming of stromal fibroblasts and a dependency on CD8+ T cell mediated tumor clearance. Collectively, this study provides a rationale for a synergistic combination of MRTX1133 with iCBT in clinical trials.

cancer biology↗

bioRxiv2020

Effects of seasonality and land use on the abundance and distribution of mosquitoes on St. Kitts, West Indies

BackgroundHigh quality mosquito surveys that collect fine resolution local data on mosquito species abundances provide baseline data to help us understand potential host-pathogen-mosquito relationships, accurately predict disease transmission, and target mosquito control efforts in areas at risk of mosquito borne diseases. MethodsAs part of an investigation into arboviral sylvatic cycles on the Caribbean island of St. Kitts, we carried out an island wide mosquito survey from November 2017 to March 2019. Using Biogents Sentinel 2 and miniature CDC light traps that were set monthly and run for 48 hour intervals, we collected mosquitoes from a total of 30 sites distributed across the five common land covers on the island (agricultural, mangrove, rainforest, scrub, and urban). We developed a mixed effects negative binomial regression model to predict the effects of land cover, seasonality, and precipitation on observed counts of the most abundant mosquito species we found. ResultsWe captured 10 of the 14 mosquito species reported on the island, the four most abundant being Aedes taeniorhynchus, Culex quinquefasciatus, Aedes aegpyti, and Deinocerites magnus. Sampling in the mangroves yielded the most mosquitoes, with Ae. taeniorhynchus, Cx. quinquefasciatus, and De. magnus predominating. Aedes aegypti was recovered primarily from urban and agricultural habitats, but also at lower frequency in other land covers. Psorophora pygmaea and Toxorhynchites guadeloupensis were only captured in scrub habitat. Capture rates in rainforests were low. Our models indicated the relative abundance of the four most common species varied seasonally and with land cover. They also suggested that the extent to which monthly average precipitation influenced counts varied according to species. ConclusionsThis study demonstrates there is high seasonality in mosquito abundances and that land cover influenced the distribution and abundance of mosquito species on St. Kitts. Further, human-adapted mosquito species (e.g. Ae. aegypti and Cx. quinquefasciatus) that are known vectors for many human relevant pathogens are the most wide-spread (across land covers) and the least responsive to seasonal variation in precipitation.

ecology↗