Biology subjects

Wood, O.

Publications and source records attributed to Wood, O..

8 recordsLinked to original sources

bioRxiv2025

Harmine Selectively Drives Human Beta Cell Differentiation and Function Via Protein Kinase A Pathways

Harmine and other small molecule inhibitors of the kinase DYRK1A induce human beta cells to replicate and regenerate in vitro and in vivo, and are effective at reversing diabetes in animal models. In addition to its beta cell proliferative and regenerative effects, harmine also induces expression of transcription factors and other genes involved in beta cell differentiation and function, exemplified by PDX1, MAFA, NKX6.1, GLP1R, PCSK1 and many others. Harmine also rapidly enhances glucose-stimulated insulin secretion in vitro and in vivo, reversing diabetes within days in diabetic mice transplanted with a marginal mass of human islets. We had assumed that this pro-differentiation or pro-function effect was a common feature of all DYRK1A inhibitors, and was mediated by DYRK1A inhibition. Thus, DYRK1A is a primary target (we refer to it as Target 1) for harmine. Here, to our surprise, we report that the pro-differentiation effect is not a generalized action for all small molecule DYRK1A inhibitors and does not result from DYRK1A interference or genetic silencing. Instead, the prodifferentiation effect is restricted to a small select subset of DYRK1A inhibitors (harmine, 2-2c and 5-IT). Remarkably, the pro-differentiation effect results from the unique ability of these drugs to activate protein kinase A (PKA), a dual mechanism that distinguishes this class from other DYRK1A inhibitors. The beneficial effects of harmine on PKA appear to be indirect, driven by an as yet unidentified, Target 2 in the PKA pathway. These findings make it clear that all DYRK1A inhibitors are not interchangeable, and that those that drive both proliferation and differentiation/function will likely be preferable in human clinical therapeutic settings. They also provide a novel target or roadmap for enhancing human beta cell differentiation in Type 1 and Type 2 diabetes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/692818v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@bd015corg.highwire.dtl.DTLVardef@a46f9borg.highwire.dtl.DTLVardef@19b4f65org.highwire.dtl.DTLVardef@179aa28_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Intra- and intercellular immune responses across diverse in vitro stimuli and inflammatory disease

In vitro stimulation of healthy human immune cells is commonly used to reproduce the immune states observed in disease, both to understand pathology and to test therapeutic approaches. However, experiments typically focus on individual cell types and stimuli and a comprehensive cellular comparison of common immunomodulators and their relevance to disease is lacking. To this end, we performed integrated single-cell transcriptomic profiling of human peripheral blood mononuclear cells treated with 11 different common in vitro stimuli, totalling over 150,000 cells from 21 immune cell subtypes. Comparative analysis of the immunomodulations revealed their shared and unique pathways, for instance stimulation via the T cell receptor (anti-CD3, CytoStimTM) and IFN- induced broad activation signatures including off-target effects across multiple cell types, whereas TNF- and LPS elicited more specific responses. Ligand-receptor interaction mapping also uncovered the common and distinct intercellular signalling pathways across stimuli. Comparing the stimuli to patient samples enabled identification of specific inflammatory disease features best replicated by each. For example, IFN- stimulation recapitulated signatures of SLE across cell types, whereas LPS induced SLE-like changes specifically within monocytes. Comparative cell-cell network analysis showed that in vitro stimuli were able to recreate some, but not all, aspects of intercellular interactions upregulated in SLE, highlighting the limitations of these model systems. This resource provides new insights into the similarities and differences of established immune stimuli at cellular resolution and facilitates appropriate use of in vitro systems to study pathways relevant to disease.

immunology↗

bioRxiv2024

Machine Learning Predictions Surpass Individual mRNAs as a Proxy of Single-cell Protein Expression

BackgroundExpansive repositories of single-cell RNA-seq data are now available. These data are often analysed assuming that mRNA abundance reflects the expression of their cognate proteins. However, post-transcriptional and translational regulation make mRNA an inadequate proxy for protein. High sparsity in low abundance mRNAs from single-cell transcriptomics data further complicates the extrapolation of protein expression levels. Although methods for single-cell surface protein quantification exist, they incur additional technical steps at greater expense and have yet to see wide-spread adoption. Computational approaches for protein imputation from scRNAseq data have been published, which learn transcriptome-wide patterns that predict protein expression. These models can then be applied to infer surface protein expression on RNA-seq only data, to increase the utility of existing data repositories. ResultsWe tested 8 such methods and compared the accuracy of predictions between approaches, and against cognate mRNAs as a direct proxy. Predictions from the trained models outperformed the use of mRNA expression as a proxy. We identify notable cases of cell surface proteins with very poor correlation with their mRNA that were predicted very successfully by imputation using the whole transcriptome. We find cell type signatures are a major determinant of predicted protein levels and, as such, prediction methods require representative training data. ConclusionsThese results reiterate that mRNA level is not a reliable predictor of cell surface protein expression, and that whole-transcriptome informed imputation can improve protein estimations given appropriately trained models.

bioinformatics↗

bioRxiv2024

Proteogenomics guided identification of functional neoantigens in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) has poor survival even with modern checkpoint inhibitor therapies. Personalised vaccines based on short peptide neoantigens containing tumour mutations are an attractive precision medicine strategy, but identifying therapeutically relevant neoantigens remains challenging, with existing methods yielding positive responses in only 6% of candidates tested. We developed an immunopeptidomics approach to improve neoantigen identification in 24 NSCLC patients (15 adenocarcinoma, 9 squamous cell carcinoma). We directly identified one neoantigen and using whole exome sequencing, transcriptomics and mass spectrometry-based immunopeptidomics, we filtered predicted neoantigens based on observed cohort HLA peptide presentation. This approach achieved positive functional responses in 5 of 6 patients tested (83% success rate) with 13% of putative neoantigens (9 out of 70) eliciting strong responses. Bayesian modelling of our initial rules-based neoantigen selection further revealed patient specific peptide presentation patterns and propensities. Our findings demonstrate that incorporating donor specific HLA peptide presentation data substantially improves neoantigen identification success rates and immune response specificity, advancing personalised cancer vaccine development.

immunology↗

bioRxiv2024

Select DYRK1A Inhibitors Enhance Both Proliferation and Differentiation in Human Pancreatic Beta Cells

The small molecule DYRK1A inhibitor, harmine, induces human beta cell proliferation, expands beta cell mass, enhances expression of beta cell phenotypic genes, and improves human beta cell function in vitro and in vivo. It is unknown whether the "pro-differentiation effect" is a DYRK1A inhibitor class-wide effect. Here we compare multiple commonly studied DYRK1A inhibitors. Harmine, 2-2c and 5-IT increase expression of PDX1, MAFA, NKX6.1, SLC2A2, PCSK1, MAFB, SIX2, SLC2A2, SLC30A8, ENTPD3 in normal and T2D human islets. Unexpectedly, GNF4877, CC-401, INDY, CC-401 and Leucettine fail to induce expression of these essential beta cell molecules. Remarkably, the pro-differentiation effect is independent of DYRK1A inhibition: although silencing DYRK1A induces human beta cell proliferation, it has no effect on differentiation; conversely, harmine treatment enhances beta cell differentiation in DYRK1A-silenced islets. A careful screen of multiple DYRK1A inhibitor kinase candidate targets was unable to identify pro-differentiation pathways. Overall, harmine, 2-2c and 5-IT are unique among DYRK1A inhibitors in their ability to enhance both beta cell proliferation and differentiation. While beta cell proliferation is mediated by DYRK1A inhibition, the pro-differentiation effects of harmine, 2-2c and 5-IT are distinct, and unexplained in mechanistic terms. These considerations have important implications for DYRK1A inhibitor pharmaceutical development.

molecular biology↗

bioRxiv2023

Single Cell RNA-Seq Analysis of Regenerative Drug-Treated Human Pancreatic Islets Identifies A Cycling Alpha Cell Population As Key Beta Cell Progenitors

Diabetes ultimately results from an inadequate number of functional, insulin-producing human beta cells. Although current attempts to replenish the remaining beta cell pool in people with diabetes are encouraging, scalability and cost limit access for the millions of people with diabetes. The small molecule DYRK1A inhibitor class of beta cell regenerative drugs, either alone or in combination with GLP1 receptor agonists or TGF{beta} superfamily inhibitors, are capable of inducing beta cell replication in vitro and increasing beta cell mass in vivo. Despite these advances, the precise mechanisms of action of DYRK1A inhibitors remain incompletely understood. To address the mechanisms more deeply, we performed single cell RNA sequencing on human pancreatic islets treated with a DYRK1A inhibitor, either alone, or in combination with a GLP1 receptor agonist or a TGF{beta} superfamily inhibitor. We identify a cluster of Cycling Alpha Cells as the cells most responsive to DYRK1A inhibition. Velocity and pseudotime lineage trajectory analyses suggest that Cycling Alpha Cells serve as the primary target cell type for of DYRK1A inhibitors, and may serve as precursor cells that transdifferentiate into functional human beta cells in response to the DYRK1A inhibition. In addition to providing a novel mechanism of action for DYRK1A inhibitors, our findings suggest that efforts to target regenerative drugs to human beta cells may be mis-directed: the proper target may be Cycling Alpha Cells.

cell biology↗

bioRxiv2022

Identification of neoantigens in esophageal adenocarcinoma

Esophageal adenocarcinoma (EAC) has a relatively poor long-term survival and limited treatment options. Promising targets for immunotherapy are short peptide neoantigens containing tumor mutations, presented to cytotoxic T-cells by human leukocyte antigen molecules (HLA). Despite an association between putative neoantigen abundance and therapeutic response across cancers, immunogenic neoantigens are challenging to identify. Here we characterized the mutational and immunopeptidomic landscapes of tumors from a cohort of seven patients with EAC. We directly identified one HLA-I presented neoantigen from one patient, and report functional T-cell responses from a predicted HLA-II neoantigen in a second patient. The predicted class II neoantigen contains both HLA I and II binding motifs. Our exploratory observations are consistent with previous neoantigen studies in finding that neoantigens are rarely directly observed, and an identification success rate following prediction in the order of 10%. However, our identified putative neoantigen is capable of eliciting strong T-cell responses, emphasizing the need for improved strategies for neoantigen identification.

cancer biology↗

bioRxiv2020

CD4+ follicular helper-like T cells are key players in anti-tumor immunity

To determine the nature of CD4+ T cells that provide help for generating robust anti-tumor CD8+ cytotoxic T cell (CTL) responses, we profiled the transcriptomes of patient-matched CD4+ and CD8+ T cells present in the tumor micro-environment (TME) and analyzed them jointly using integrated weighted gene correlation network analysis. We found the follicular helper T cell (TFH) program in CD4+ T cells was strongly associated with proliferation and tissue-residency in CD8+ CTLs. Single-cell analysis demonstrated the presence of TFH-like cells and features linked to cytotoxic function and their provision of CD8+ T cell help. Tumor-infiltrating TFH-like cells expressed PD-1 and were enriched in tumors following checkpoint blockade, suggesting that they may respond to anti-PD-1 therapy. Adoptive transfer or induction of TFH cells in mouse models resulted in augmented CD8+ CTL responses and impairment of tumor growth, indicating an important role of TFH-like CD4+ T cells in anti-tumor immunity.

immunology↗