Biology subjects

Song, H.

Publications and source records attributed to Song, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Cardiac stress leads to regulation of Filamin C dimerisation via an ancient phosphorylation-modulated interaction with HSPB7

The biomechanical properties and responses of tissues underpin a variety of physiological functions and pathologies. In striated muscle, the actin-binding protein filamin C (FLNC) is a key protein whose variants causative for a wide range of cardiomyopathies and musculoskeletal pathologies. Seemingly a multi-functional protein that interacts with a variety of partners, how FLNC is regulated at the molecular level is not well understood. Here we have investigated its interaction with HSPB7, a cardiac-specific molecular chaperone whose absence is embryonically lethal. We found that FLNC and HSPB7 interact in cardiac tissue under biomechanical stress, forming a strong hetero-dimer whose structure we have solved by means of X-ray crystallography. Our quantitative analyses show that the hetero-dimer out-competes the FLNC homo-dimer interface, potentially acting to abrogate the ability of the protein to cross-link the actin cytoskeleton, and to enhance its diffusive mobility. We show that phosphorylation of FLNC at threonine 2677, located at the dimer interface and associated with cardiac stress, acts to favour the homo-dimer. Conversely, phosphorylation at tyrosine 2683, also at the dimer interface, has the opposite effect and shifts the equilibrium towards the hetero-dimer. Evolutionary analysis and ancestral sequence reconstruction reveals this interaction and its mechanisms of regulation to date around the time primitive hearts evolved in chordates. Our work rationalises on the molecular level how FLNC might switch between stabilising functions in the cell, and reveals how HSPB7 acts as a specific molecular chaperone that regulates FLNC.

molecular biology↗

bioRxiv2023

Dispersal and evolution of the invasive snail Pomacea canaliculata, an intermediate host of Angiostrongylus cantonensis: A field study around its initial introduction site in China

Eosinophilic meningitis caused by Angiostrongylus cantonensis is an emerging infectious disease in mainland China. The invasive snail (Pomacea canaliculata) is one of the main intermediate host of the zoonotic nematode. To gain insights into the spatial distribution, phenotypic variation and dispersal pattern of the snail populations. A field survey was conducted using modified nested sampling and selecting ditches as the main habitats. Snail distribution and abundance were displayed with predictions based on an inverse distance-weighted model. Correlation and spatial autocorrelation were analyzed among the measured parameters. The findings of this study demonstrate the well-established and abundant presence of P. canaliculata in ditches. A total of 564 sampling sites were assessed, with measurements taken on 10,145 snails having shell heights greater than 1.5 cm. The average population density was determined to be 20.31 {+/-} 11.55 snails per square meter. Morphological analysis revealed an average snail body mass of 8.93 {+/-} 3.95 g, shell height of 3.38 {+/-} 0.66 cm, a sex ratio of 2.39 {+/-} 1.01 female to male, and a shell color ratio of 9.34 {+/-} 7.52 brown to yellow. Among these measurements, body mass was found to be significantly correlated with shell height (r = 0.88, p < 0.01) and shell color (r = 0.55, p < 0.05). Spatial-correlation analysis proved that shell height was the only factor significantly spatially autocorrelated (MI = 0.27, z = 2.20, p = 0.03), although weak autocorrelations appeared in body mass and shell color. The observed geographic variations of phenotypic traits indicated a human-mediated evolving process of the snail populations and a potential complexity of the parasite transmission system. These findings may enhance the assessment of the epidemiological health risk posed by angiostrongyliasis and inform strategies for controlling infectious snails.

ecology↗

bioRxiv2023

Vitamin D attenuates diabetic myocardial injury via the Erbb4/ferroptosis axis

BackgroundHyperglycemia and hyperlipidemia lead to the ferroptosis, well as the phosphorylation of Erbb4, and thereby increase the risk of cardiac hypertrophy. Thus, our investigation aims to explore whether vitamin D could mitigate diabetic cardiac injury through modulation of the Erbb4/ferroptosis axis. Methods and resultsKKAy mice fed on a high-fat diet were utilized to construct the prediabetic model, which showed an up-regulated phosphorylation of Erbb4, with concurrent ferroptosis in cardiac tissues. Following the intervention with vitamin D for 16 weeks, the activity of Erbb4/YAP signaling was suppressed and the severeness of ferroptosis was improved. Meanwhile disturbances in glucose-lipid metabolism and insulin secretion induced by high fat were alleviated, along with improvements in cardiac hypertrophy and myocardial function. Moreover, we established an in vitro damage model by introducing H9c2 myocardial cells to high glucose (HG, 33.3 mM) and palmitic acid (PA, 0.25 mM). Unsurprisingly, similar results have been acquired after vitamin D supplementation. Subsequently, selective inhibitors of Erbb4 (Dacomitinib) and ferroptosis (Ferrostatin-1) were applied to evaluate the efficiency of Erbb4 signaling on modulating ferroptosis in vitro, and conclusively confirming that inhibiting of Erbb4 indeed reduce ferroptosis under HG and PA stimulus. Additionally, treatment of vitamin D was found to reduce cardiomyocyte hypertrophy and prevent cell death by inhibiting Erbb4 activity. Interestingly, the combined intervention of Vitamin D and Dacomitinib exerted a synergistic effect on ameliorating the abnormal conditions. ConclusionsOur study unveils, the correlation between Erbb4 and ferroptosis in diabetic heart. Providing evidences that vitamin D supplementation can improve ferroptosis related diabetic cardiac injury through inactivation of Erbb4. Proposing that the combination treatment of vitamin D and Erbb4 inhibitors may emerge as a highly feasible clinical strategy for diabetic myocardial injury.

pharmacology and toxicology↗

bioRxiv2023

RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4

Microsatellite instability high (MSI-H) tumors are malignant tumors that, despite harboring a high mutational burden, often have intact TP53. One of the most frequent mutations in MSI-H tumors is a frameshift mutation in RPL22, a ribosomal protein. Here, we identified RPL22 as a modulator of MDM4 splicing through an alternative splicing switch in exon 6. RPL22 loss increases MDM4 exon 6 inclusion, cell proliferation, and augments resistance to the MDM inhibitor Nutlin-3a. RPL22 represses expression of its paralog, RPL22L1, by mediating the splicing of a cryptic exon corresponding to a truncated transcript. Therefore, damaging mutations in RPL22 drive oncogenic MDM4 induction and reveal a common splicing circuit in MSI-H tumors that may inform therapeutic targeting of the MDM4-p53 axis and oncogenic RPL22L1 induction.

cancer biology↗

bioRxiv2023

Predicting the dynamic interaction between intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) participate in various biological processes. Interactions involving IDPs are usually dynamic and affected by their inherent conformation fluctuations. Comprehensive characterization of these interactions based on current techniques is challenging. Here, we present GSALIDP, a GraphSAGE-LSTM Network to capture the dynamic nature of IDP-involved interactions and predict their behaviors. This framework models multiple conformations of IDP as a dynamic graph which can effectively describe the fluctuation of its flexible conformation. The dynamic interaction between IDPs is studied and the datasets of IDP conformations and their interactions are obtained through atomistic molecular dynamic (MD) simulations. Residues of IDP are encoded through a series of features, including their frustration. GSALIDP can effectively predict the interaction sites of IDP and the contact residue pairs between IDPs. Its performance in predicting IDP interaction is on par with or even better than the conventional models in predicting the interaction of structural proteins. To the best of our knowledge, this is the first model to extend the protein interaction prediction to IDP-involved interactions.

molecular biology↗

bioRxiv2023

Dynamic Functional Connectivity Encodes Generalizable Representations of Emotional Arousal But Not Valence

Human affective experience varies along the dimensions of valence (positivity or negativity) and arousal (high or low activation). It remains unclear how these dimensions are encoded in the brain and if the representations are shared across different individuals and diverse situational contexts. Here we utilized two publicly available functional MRI datasets of participants watching movies to build predictive models of moment-to-moment valence and arousal from dynamic functional brain connectivity. We tested the models both within and across datasets and identified a generalizable arousal representation characterized by the interaction between multiple large-scale functional networks. The arousal representation generalized to two additional movie-watching datasets. Predictions based on multivariate patterns of activation underperformed connectome-based predictions and did not generalize. In contrast, we found no evidence of a generalizable valence representation. Taken together, our findings reveal a generalizable representation of arousal encoded in patterns of dynamic functional connectivity, revealing an underlying similarity in how arousal is encoded across individuals and situational contexts.

neuroscience↗

bioRxiv2023

Single cell transcriptional profiling of benign prostatic hyperplasia reveals a progenitor-like luminal epithelial cell state within an inflammatory microenvironment

Benign prostatic hyperplasia (BPH) is characterized by excessive cell proliferation and inflammation and affects most aging men. The development of new therapies for BPH requires a deeper understanding of the underlying pathophysiology and cellular components of BPH. Here, we characterize at single cell resolution the cellular states of BPH and identify cell populations enriched in BPH that contribute to cell proliferation and inflammation. Single-cell RNA-sequencing was performed on prostate tissue from 15 patients undergoing holmium laser enucleation of the prostate for treatment of BPH. Clustering and differential expression analysis on aligned single cell RNA-seq data was performed to annotate all cell types. Pseudotime, gene set enrichment, gene ontology, and ligand-receptor analyses were performed. 16,234 cells were analyzed and specific stromal, epithelial, and immune subgroups were found to be strongly associated with inflammation. A rare luminal subgroup was identified and pseudotime analysis indicated this luminal subgroup was more closely related to club and basal cells. Using a gene set derived from epithelial stem cells, we found that this luminal subgroup had a significantly higher stem cell signature score than all other epithelial subgroups, suggesting this subgroup is a luminal precursor state. Ligand-receptor interactions between stromal, epithelial, and immune cells were explored with CellPhoneDB. Unique interactions highlighting MIF, a pro-inflammatory cytokine that promotes epithelial cell growth and inflammation in the prostate, were found between fibroblasts and the progenitor luminal subgroup. This luminal subgroup also interacted with neutrophils and macrophages through MIF. Our single-cell profiling of BPH provides a roadmap for inflammation-linked cell subgroups and highlights a novel luminal progenitor subgroup interacting with other cell groups via MIF that may contribute to the inflammation and cell proliferation phenotype associated with BPH.

genomics↗

bioRxiv2023

Kairos infers in situ horizontal gene transfer in longitudinally sampled microbiomes through microdiversity-aware sequence analysis

Horizontal gene transfer (HGT) occurring within microbiomes is linked to complex environmental and ecological dynamics that are challenging to replicate in controlled settings. Consequently, most extant studies of microbiome HGT are either simplistic experimental settings with tenuous relevance to real microbiomes or correlative studies that assume that HGT potential is a function of the relative abundance of mobile genetic elements (MGEs), the vehicles of HGT. Here we introduce Kairos as a bioinformatic tool deployed in nextflow for detecting HGT events "in situ," i.e., within a microbiome, through analysis of time-series metagenomic sequencing data. The in-situ framework proposed here leverages available metagenomic data from a longitudinally sampled microbiome to assess whether the chronological occurrence of potential donors, recipients, and putatively transferred regions could plausibly have arisen due to HGT over a range of defined time periods. The centerpiece of the Kairos workflow is a novel competitive read alignment method that enables discernment of even very similar genomic sequences, such as those produced by MGE-associated recombination. A key advantage of Kairos is its reliance on assemblies rather than metagenome assembled genomes (MAGs), which avoids systematic exclusion of accessory genes associated with the binning process. In an example test-case of real world data, use of assemblies directly produced a 264-fold increase in the number of antibiotic resistance genes included in the analysis of HGT compared to analysis of MAGs with MetaCHIP. Further, in silico evaluation of contig taxonomy was performed to assess the accuracy of classification for both chromosomally- and MGE-derived sequences, indicating a high degree of accuracy even for conjugative plasmids up to the level of class or order. Thus, Kairos enables the analysis of very recent HGT events, making it suitable for studying rapid prokaryotic adaptation in environmental systems without disturbing the ornate ecological dynamics associated with microbiomes. Current versions of the Kairos workflow are available here: https://github.com/clb21565/kairos.

bioinformatics↗

bioRxiv2023

Expression of Filaments of the Geobacter Extracellular Cytochrome OmcS in Shewanella oneidensis

The physiological role of Geobacter sulfurreducens extracellular cytochrome filaments is a matter of debate and the development of proposed electronic device applications of cytochrome filaments awaits methods for large-scale cytochrome nanowire production. Functional studies in Geobacter sulfurreducens are stymied by the broad diversity of redox-active proteins on the outer cell surface and the redundancy and plasticity of extracellular electron transport routes. G. sulfurreducens is a poor chassis for producing cytochrome nanowires for electronics because of its slow, anaerobic growth. Here we report that filaments of the G. sulfurreducens cytochrome OmcS can be heterologously expressed in Shewanella oneidensis. Multiple lines of evidence demonstrated that a strain of S. oneidensis, expressing the G. sulfurreducens OmcS gene on a plasmid, localized OmcS on the outer cell surface. Atomic force microscopy revealed filaments with the unique morphology of OmcS filaments emanating from cells. Electron transfer to OmcS appeared to require a functional outer-membrane porin-cytochrome conduit. The results suggest that S. oneidensis, which grows rapidly to high culture densities under aerobic conditions, may be a suitable for development of a chassis for producing cytochrome nanowires for electronics applications and may also be good model microbe for elucidating cytochrome filament function in anaerobic extracellular electron transfer.

synthetic biology↗

bioRxiv2023

A compact, ultrahigh-density headstage with high-fidelity hybrid integration for large-scale deep-brain opto-electrophysiology

Recent neuroscientific research seeks to comprehend the sophisticated deep-brain networks of neural circuits consisting of large scale neuronal ensembles across multiple brain regions. An ideal way to unveil the complex connectome might be stimulating individual neurons with high spatial resolution in a broad range of brain, while seamlessly monitoring the correspondent neuronal activities. Optogenetics is known as a key technology to enable such a goal thanks to its high spatial and temporal selectivity in neuromodulation. Existing silicon probe technologies have been able to partially achieve such a goal by recording broad region of brain activities through multiple electrodes per shank, but those cannot complete perfect coverage due to the limited channel counts for the optogenetic stimulation. Here, we present an high-channel-count optogenetic system with simultaneous 256 recoding and 128 optogenetic stimulation sites, exhibiting the highest channel density ever reported, enabled by a flexible polyimide cable-based hybrid-integration of a low-stimulation-artifact micro-LED ({micro}LED) opto-electrode with a low-power and -noise, area-efficient CMOS interfacing integrated-circuit (IC). The presented optogenetic system provides 256-neuron-size electrodes (11 x 15 {micro}m2) with a 40 {micro}m inter-electrode pitch for high spatial oversampling in recording and 128-soma-size {micro}LEDs (8 x 11 {micro}m2) with a 20 {micro}m inter-LED pitch for single-cell resolution in stimulation, resulting in a vertical span of 640 {micro}m and a horizontal span of 2,100 {micro}m with a total 8 shanks. For versatility in optogenetics-based experiments from small rodents to primates with user-preferable settings, the system base that provides programmability of recording and stimulation parameters and rest of signal processing, such as filtering, digitization, and data transmission including serial peripheral interface (SPI) has also been designed within small area of 23.8 x 28.8 mm2 with only 3.5-gram weight, resulting in the highest channel density both in size (0.56 channels/mm2) and weight (109.71 channels/gram) among the state-of-the-art optogenetics-based neuromodulation systems. To verify the system operation in vivo, a compact optogenetics headstage has been also fabricated. Using the prepared optogenetic headstage, 169 isolated neurons have been observed with various stimulation intensities. The results offered in this article indicate that the presented hybrid integrated ultrahigh-density, high-channel-count headstage can be used to realize the massive-scale in-depth brain studies with optogenetics.

bioengineering↗

bioRxiv2023

Transmission of highly virulent CXCR4 tropic HIV-1 through the mucosal route in an individual with a wild-type CCR5 genotype

Nearly all transmitted/founder (T/F) HIV-1 are CCR5 (R5)-tropic. While previous evidence suggested that CXCR4 (X4)-tropic HIV-1 are transmissible, detection was not at the earliest stages of acute infection. Here, we identified an X4-tropic T/F HIV-1 in a participant in acute infection cohort. Coreceptor assays demonstrated that this T/F virus is strictly CXCR4 tropic. The participant experienced significantly faster CD4 depletion compared with R5 virus infected participants in the same cohort. Naive and central memory CD4 subsets declined faster than effector and transitional memory subsets. All CD4 subsets, including naive, were productively infected. Increased CD4+ T cell activation was observed over time. This X4-tropic T/F virus is resistant to broadly neutralizing antibodies (bNAbs) targeting V1/V2 and V3 regions. These findings demonstrate that X4-tropic HIV-1 is transmissible through the mucosal route in people with the wild-type CCR5 genotype and have implications for understanding the transmissibility and immunopathogenesis of X4-tropic HIV-1.

microbiology↗

bioRxiv2023

High-accuracy mapping of human and viral direct physical protein-protein interactions using the novel computational system AlphaFold-pairs

Protein-protein interactions are central, highly flexible components of regulatory mechanisms in all living cells. Over the years, diverse methods have been developed to map protein-protein interactions. These methods have revealed the organization of protein complexes and networks in numerous cells and conditions. However, these methods are also time consuming, costly and sensitive to various experimental artifacts. To avoid these caveats, we have taken advantage of the AlphaFold-Multimer software, which succeeded in predicting the structure of many protein complexes. We designed a relatively simple algorithm based on assessing the physical proximity of a test protein with other AlphaFold structures. Using this method, named AlphaFold-pairs, we have successfully defined the probability of a protein-protein interaction forming. AlphaFold-pairs was validated using well-defined protein-protein interactions found in the literature and specialized databases. All pairwise interactions forming within the 12-subunit transcription machinery RNA Polymerase II, according to available structures, have been identified. Out of 66 possible interactions (excluding homodimers), 19 specific interactions have been found, and an additional previously unknown interaction has been unveiled. The SARS-CoV-2 surface glycoprotein Spike (or S) was confirmed to interact with high preference with the human ACE2 receptor when compared to other human receptors. Notably, two additional receptors, INSR and FLT4, were found to interact with S. For the first time, we have successfully identified protein-protein interactions that are likely to form within the reassortant Eurasian avian-like (EA) H1N1 swine G4 genotype Influenza A virus, which poses a potential zoonotic threat. Testing G4 proteins against human transcription factors and molecular chaperones (a total of 100 proteins) revealed strong specific interactions between the G4 HA and HSP90B1, the G4 NS and the PAQosome subunit RPAP3, as well as the G4 PA and the POLR2A subunit. We predict that AlphaFold-pairs will revolutionize the study of protein-protein interactions in a large number of healthy and diseased systems in the years to come.

bioinformatics↗

bioRxiv2023

Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data

BackgroundOncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to a large number of metabolites in a cell and the presence of multiple genes associated with cancer development. ResultsHere we report the development of a computational workflow that predicts metabolite-gene-pathway sets (MGPs). MGPs present metabolites and metabolic pathways significantly associated with specific somatic mutations in cancers. The computational workflow uses both cancer patient-specific genome-scale metabolic models (GEMs) and mutation data to generate MGPs. A GEM is a computational model that predicts reaction fluxes at a genome scale, and can be constructed in a cell-specific manner by using omics data (e.g., RNA-seq). The computational workflow is first validated by comparing the resulting metabolite-gene (MG) pairs with multi-omics data (i.e., mutation data, RNA-seq data, and metabolome data) from 17 acute myeloid leukemia samples and 21 renal cell carcinoma samples collected in this study. The computational workflow is further validated by evaluating the MGPs predicted for 18 cancer types, by using RNA-seq data publicly available, in comparison with the reported studies. Therapeutic potential of the resulting MGPs is also discussed. ConclusionsValidation of the MGP-predicting computational workflow indicates that a decent number of metabolites and metabolic pathways appear to be significantly associated with specific somatic mutations. The computational workflow and the resulting MGPs will help identify novel oncometabolites, and also suggest cancer treatment strategies.

systems biology↗

bioRxiv2023

Crk/Crkl regulates early angiogenesis in mouse embryos by accelerating endothelial cell maturation

RationaleUbiquitously expressed cytoplasmic adaptors CRK and CRKL mediate multiple signaling pathways in mammalian embryogenesis. They are also associated with cardiovascular defects occurring in Miller-Dieker syndrome and 22q11.2 deletion syndrome, respectively. The embryonic mesoderm contributes to the formation of the cardiovascular system, yet the roles that Crk and Crkl play there are not understood on a single cell level. ObjectivesTo determine functions of Crk and Crkl in the embryonic mesoderm during early mouse vascular development. Secondly, we will examine the molecular mechanisms responsible for early embryonic endothelial cell (EC) defects by performing single cell RNA-sequencing (scRNA-seq) and in vivo validation experiments. Methods and ResultsInactivation of both Crk and Crkl together using Mesp1Cre resulted embryonic lethality with severe vascular defects. Although vasculogenesis appeared normal, angiogenesis was disrupted both in the yolk sac and embryo proper, leading to disorganized vascular networks. We performed scRNA-seq of the Mesp1Cre mesodermal lineage and found that there was upregulation of a great number of angiogenesis and cell migration related genes in ECs in the mutants, including NOTCH signaling genes such as Dll4 and Hey1. Further bioinformatic analysis of EC subpopulations identified a relative increase in the number of more differentiated angiogenic ECs and decrease in EC progenitors. Consistent with this, we identified an expansion of Dll4 expressing cells within abnormal arteries, in vivo. Also, our bioinformatic data indicates that there is dysregulated expression of lineage genes that promote EC differentiation causing accelerated cell fate progression during EC differentiation. ConclusionsOur results show that Crk and Crkl are crucial for regulating early embryonic angiogenesis. Combined inactivation of Crk/Crkl caused precocious EC maturation with an increase of atypical differentiated angiogenic ECs and failed vascular remodeling. This is in part due to increased NOTCH signaling and altered expression of cell migration genes.

developmental biology↗

bioRxiv2023

Phase-Amplitude Coupling Detection and Analysis of Human 2-Dimensional Neural Cultures in Multi-well Microelectrode Array in Vitro

Human induced pluripotent stem cell (hiPSC)- derived neurons offer the possibility of studying human-specific neuronal behaviors in physiologic and pathologic states in vitro. However, it is unclear whether these cultured neurons can achieve the fundamental network behaviors that are required to process information in the human brain. Investigating neuronal oscillations and their interactions, as occurs in cross-frequency coupling (CFC), is potentially a relevant approach. Microelectrode array culture plates provide a controlled framework to study populations of hiPSC-derived cortical neurons (hiPSC-CNs) and their electrical activity. Here, we examined whether networks of two-dimensional cultured hiPSC-CNs recapitulate the CFC that is present in networks in vivo. We analyzed the electrical activity recorded from hiPSC-CNs grown in culture with hiPSC-derived astrocytes. We employed the modulation index method for detecting phase-amplitude coupling (PAC) and used an offline spike sorting method to analyze the contribution of a single neurons spiking activities to network behavior. Our analysis demonstrates that the degree of PAC is specific to network structure and is modulated by external stimulation, such as bicuculine administration. Additionally, the shift in PAC is not driven by a single neurons properties but by network-level interactions. CFC analysis in the form of PAC explores communication and integration between groups of nearby neurons and dynamical changes across the entire network. In vitro, it has the potential to capture the effects of chemical agents and electrical or ultrasound stimulation on these interactions and may provide valuable information for the modulation of neural networks to treat nervous system disorders in vivo. SignificancePhase amplitude coupling (PAC) analysis demonstrates that the complex interactions that occur between neurons and network oscillations in the human brain, in vivo, are present in 2-dimensional human cultures. This coupling is implicated in normal cognitive function as well as disease states. Its presence in vitro suggests that PAC is a fundamental property of neural networks. These findings offer the possibility of a model to understand the mechanisms and of PAC more completely and ultimately allow us to understand how it can be modulated in vivo to treat neurologic disease.

neuroscience↗

bioRxiv2023

Spatial profiling of neuro-immune interactions in gastroenteropancreatic NETs

Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are heterogeneous malignancies that arise from complex cellular interactions within the tissue microenvironment. Here, we sought to decipher tumor-derived signals from the surrounding microenvironment by applying Nanostring Digital Spatial Profiling (DSP) to hormone-secreting and non-functional GEP-NETs. DSP was used to evaluate the expression of 40 neural and immune-related proteins in surgically resected duodenal and pancreatic NETs (n=20) primarily comprised of gastrinomas (18/20). A total of 279 regions of interest were examined between tumors, adjacent normal and abnormal-appearing epithelium, and the surrounding stroma. The results were stratified by tissue type and Multiple Endocrine Neoplasia I (MEN1) status and protein expression was validated by immunohistochemical (IHC) staining. A tumor immune cell autonomous inflammatory signature was further evaluated by IHC and RNAscope, while functional pro-inflammatory signaling was confirmed using patient-derived duodenal organoids. Gastrin-secreting and non-functional pancreatic NETs showed a higher abundance of immune cell markers and immune infiltrate compared to duodenal gastrinomas. Tumors displayed strong intra-tissue variation in the expression of neural- and immune-related proteins. Compared to non-MEN1 tumors, MEN1 gastrinomas showed reduced expression of immune cell markers and upregulated expression of neuropathological proteins. Duodenal gastrinomas showed strong expression of the pro- inflammatory and pro-neural factor IL-17B. Treatment of human duodenal organoids with IL- 17B activated NF-kB and STAT3 signaling and induced the expression of neuroendocrine markers. In conclusion, multiplexed spatial protein analysis identified tissue-specific neuro- immune signatures in GEP-NETs. Moreover, duodenal gastrinomas cell autonomously express immune and pro-inflammatory factors, including tumor-derived IL-17B, that stimulate the neuroendocrine phenotype.

cancer biology↗

bioRxiv2023

Exploiting the therapeutic vulnerability of IDH-mutant gliomas with zotiraciclib

Isocitrate dehydrogenase (IDH)-mutant gliomas have distinctive metabolic and biological traits that may render them susceptible to targeted treatments. Here, by conducting a high-throughput drug screen, we pinpointed a specific susceptibility of IDH-mutant gliomas to zotiraciclib (ZTR). ZTR exhibited selective growth inhibition across multiple IDH-mutant glioma in vitro and in vivo models. Mechanistically, ZTR at low doses suppressed CDK9 and RNA Pol II phosphorylation in IDH-mutant cells, disrupting mitochondrial function and NAD+ production, causing oxidative stress. Integrated biochemical profiling of ZTR kinase targets and transcriptomics unveiled that ZTR-induced bioenergetic failure was linked to the suppression of PIM kinase activity. We posit that the combination of mitochondrial dysfunction and an inability to adapt to oxidative stress resulted in significant cell death upon ZTR treatment, ultimately increasing the therapeutic vulnerability of IDH-mutant gliomas. These findings prompted a clinical trial evaluating ZTR in IDH-mutant gliomas towards precision medicine (NCT05588141). HighlightsO_LIZotiraciclib (ZTR), a CDK9 inhibitor, hinders IDH-mutant glioma growth in vitro and in vivo. C_LIO_LIZTR halts cell cycle, disrupts respiration, and induces oxidative stress in IDH-mutant cells. C_LIO_LIZTR unexpectedly inhibits PIM kinases, impacting mitochondria and causing bioenergetic failure. C_LIO_LIThese findings led to the clinical trial NCT 05588141, evaluating ZTR for IDH-mutant gliomas. C_LI

cancer biology↗

bioRxiv2023

Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures

The epigenomic landscape of human immune cells is dynamically shaped by both genetic factors and environmental exposures. However, the relative contributions of these elements are still not fully understood. In this study, we employed single-nucleus methylation sequencing and ATAC-seq to systematically explore how pathogen and chemical exposures, along with genetic variation, influence the immune cell epigenome. We identified distinct exposure-associated differentially methylated regions (eDMRs) corresponding to each exposure, revealing how environmental factors remodel the methylome, alter immune cell states, and affect transcription factor binding. Furthermore, we observed a significant correlation between changes in DNA methylation and chromatin accessibility, underscoring the coordinated response of the epigenome. We also uncovered genotype-associated DMRs (gDMRs), demonstrating that while eDMRs are enriched in regulatory regions, gDMRs are preferentially located in gene body marks, suggesting that exposures and genetic factors exert differential regulatory control. Notably, disease-associated SNPs were frequently colocalized with meQTLs, providing new cell-type-specific insights into the genetic basis of disease. Our findings underscore the intricate interplay between genetic and environmental factors in sculpting the immune cell epigenome, offering a deeper understanding of how immune cell function is regulated in health and disease.

genomics↗