Unique Enrichment Research Articles

Breeding-induced changes in the rhizosphere microbial communities in Lima bean (Phaseolus lunatus)

Lima bean (Phaseolus lunatus L.) breeding aims to select more productive and uniform plant varieties, impacting various plant traits, including root characters. Changes in root traits have repercussions on the rhizosphere, thereby influencing the composition of rhizospheric microbial communities. In this study, we assessed the structure and composition of the microbial community through 16S rRNA sequencing to compare the rhizosphere of different genotypes during lima bean breeding. Specifically, we compared the rhizospheric microbial communities of two parents (P1 - UFPI 628 and P2 – G25276, from Brazil and Argentina, respectively) and their segregation generations (F2 and F7). The microbial richness and diversity remained consistent across all genotypes, while the structure of the microbial community differed between parents (P1 and P2) and the advanced lineage (F7). We observed genotype-specific enrichment of bacterial groups, indicating a nuanced interaction between lima bean genotypes and microbial communities. Moreover, segregating generations exhibited unique enrichment of bacterial families associated with plant growth promotion, such as Pedosphaeraceae (F2) and Xanthobacteraceae (F7). Analysis of microbial interactions revealed an alteration in network complexity, with advanced lineages, particularly F7, displaying a higher number of interactions. Despite taxonomic differences across generations, functional traits remained consistent between parents and advanced lineages. These findings offer valuable insights into optimizing plant-microbe interactions to enhance lima bean yield in breeding programs. By understanding the dynamics of rhizospheric microbial communities in response to breeding efforts, we can harness beneficial interactions to improve plant performance and sustainability in agricultural systems.

Exosomal miR-27a-5p attenuates inflammation through Toll-like receptor 7 in foodborne Salmonella infections.

Salmonella is a common food-borne pathogen that is highly pathogenic and infectious, causing serious harm to livestock breeding and food safety. Uncovering the mechanisms of Salmonella infection and immune evasion can effectively prevent Salmonella contamination of livestock and poultry food. Here, small RNA sequencing results showed that exosomes produced by naïve murine macrophages RAW 264.7 cells contained a unique enrichment of a set of microRNAs (miRNAs) after Salmonella infection. Quantitative real-time polymerase chain reaction (qPCR) analysis verified that the tested miRNA (i.e. miR-27a-5p, miR-92a-1-5p and miR-1249-5p) showed similar expression patterns, consistent with small RNA sequencing data. TargetScan database predicted that the most promising targets for the differentially expressed miRNAs were abundant in the immune system, infectious diseases, and signal transduction pathways. Dual-luciferase reporter assays confirmed that Toll-like receptor 7 (TLR7) was the target of miR-27a-5p. Western blotting and enzyme-linked immunosorbent assay (ELISA) results revealed that overexpression of miR-27a-5p suppressed inflammation by targeting TLR7/nuclear factor kappa-B (NF-κB) signaling pathway and leading interleukin-6 (IL-6) and IL-1β cytokines slightly reduction in recipient macrophages, suggesting that exosomal miR-27a-5p uptake by naïve macrophages may inhibit pro-inflammatory macrophage differentiation. Therefore, these results contribute to our systematic understanding of the mechanism of exosomal miRNA in Salmonella infection, providing a potential target for preventing immune escape from Salmonella.

Unraveling the genetic mysteries of sarcopenia: A bioinformatics approach

Objective To study the genetic expression of sarcopenia using bioinformatics methods. Methods A Weighted Gene Coexpression Network Analysis (WGCNA) was conducted to construct coexpression networks, along with protein-protein interaction networks. Diagnostic biomarker potential was evaluated using receiver operating characteristic curves. An analysis of Single-Sample Gene Set Enrichment Analysis (ssGSEA) was performed in order to determine the amount of immune cell infiltration. We analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) enrichment using the KEGG. Results WGCNA identified modules linked to bone metabolism, ssGSEA showed unique gene enrichment patterns, and 268 genes were found to be differentially expressed in sarcopenia. Fourteen co-expression modules related to bone metabolism were identified, with one showing a strong positive correlation. KEGG pathway analysis indicated downregulation of the renin-angiotensin system and Alzheimer's disease pathways. The differentially expressed genes were primarily involved in adipocyte differentiation. Conclusion This study analyzes genetic changes and immune cell patterns in sarcopenia, providing insights into its causes and potential diagnostic markers for future research on treatments.

Abstract B036: Pathway repression in progression on osimertinib therapy in NSCLC via a comprehensive genomic and epigenomic circulating tumor DNA (ctDNA) assay

Abstract Background: Osimertinib is currently the most common precision therapy for patients with non- small cell lung cancer (NSCLC) with EGFR mutations. While it prolongs progression-free survival, resistance eventually develops in many, leading to disease progression. Somatic NGS has identified resistance mutations in the EGFR pathway and other oncogenes, but these account for only 40-45% of cases, suggesting non-genetic factors, such as epigenetic changes, may be involved. This study investigates the epigenetic landscape at diagnosis and progression on first- line osimertinib, focusing on cases with and without canonical resistance mutations. Methods: We defined two cohorts from GuardantINFORM, a clinico-genomics database, restricting to only patients with a test on the Guardant Infinity platform, a comprehensive blood-based NGS assay, that analyzes DNA sequence variants and performs extensive methylation profiling (∼15Mb) in >20,000 differentially methylated regions (DMRs) assessed for sample-specific methylation patterns. (A) Diagnosis Cohort: Comprised of 34 NSCLC patients with blood samples collected within six days prior to the initiation of first-line osimertinib therapy. (B) Progression Cohort: Comprised of 36 patients who were on first-line osimertinib therapy, with blood samples collected within 60 days of discontinuation. The progression cohort was further stratified based on the presence or absence of known resistance mutations identified through somatic variant analysis by Guardant360. Gene set enrichment analysis was conducted on these methylation profiles using the Reactome database to define pathway-level differences between the cohorts. Results: Pathway enrichment analysis in the diagnosis and progression cohorts found expected biological processes in NSCLC such as extracellular matrix organization, G- protein coupled receptor (GPCR) signaling, and FGFR pathways. Additionally, the progression cohort lacking canonical resistance mutations (n=23) exhibited unique enrichment in two specific pathways: Glucose-dependent Insulinotropic Polypeptide and Physiological Factors. These pathways include genes such as GATA4, which has been implicated in the epithelial- mesenchymal transition (EMT)—a process associated with transforming to a small cell phenotype, a known mechanism of resistance to EGFR inhibition, including osimertinib. Conclusion: This study demonstrates the utility of epigenetic profiling via liquid biopsies in uncovering non-genetic mechanisms underlying osimertinib resistance in advanced NSCLC. Identification of unique epigenetic pathways in progressing patients without canonical resistance mutations highlights the potential for discovering novel biomarkers of resistance. Further investigation into these findings may advance our understanding of resistance mechanisms across various cancer therapies, particularly for patients without identified genomic resistance, and inform clinical decision-making and trial design. Citation Format: Aaron Hardin, Leslie Bucheit, Amar Das, Craig Eagel, Helmy Eltoukhy. Pathway repression in progression on osimertinib therapy in NSCLC via a comprehensive genomic and epigenomic circulating tumor DNA (ctDNA) assay [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B036.

Distribution Characteristics of Trace Elements in Carboniferous–Permian Coal from the Western Margin of Ordos Basin: Emphasis on Their Complex Geological Genesis

The Carboniferous–Permian coal deposits in the western margin of the Ordos Basin are known for their unique geological characteristics and potential enrichment of trace elements; however, there have been limited studies on the complex geological genesis of these elements, hindering the development of effective strategies for mineral resource exploration in this region. This study aims to investigate the distribution characteristics of trace elements in Carboniferous–Permian coal from the western margin of Ordos Basin, focusing on their complex geological genesis using techniques such as optical microscopy, X-ray fluorescence spectrometry, and inductively coupled plasma mass spectrometry. The results show that the average maximum vitrinite reflectance values in the Helanshan coalfield, Zhuozishan coalfield, and Ningdong coalfield are 1.25%, 0.83%, and 0.69%, respectively. Compared with the world’s hard coals, Li and Ga in Carboniferous–Permian coal from the western margin of the Ordos Basin are mildly enriched (CC, concentration coefficients; 2 < CC < 5) or enriched (5 < CC < 10). On the basis of revealing the response of the geochemical characteristics of coal to the geological development of the basin, the composite genetic model of terrigenous clastic supply, fault structure, low-temperature hydrothermal fluid and coal metamorphism have been established in Carboniferous–Permian coal in the western margin of the Ordos Basin. In this complex genetic model, folds and faults are very well developed. Although the provenance may have provided sufficient detrital sources for the study area, frequent tectonic changes, denudation, or scour led to the loss of detrital supply, and the provenance did not ultimately cause the enrichment of elements in the study area. However, the widely developed fault structure provided channels for sulfur-containing hydrothermal fluids, and the increase in coal metamorphism resulted in the enrichment of trace elements in the Carboniferous–Permian coal in the western margin of the Ordos Basin.

The plastisphere ecology: Assessing the impact of different pollution sources on microbial community composition, function and assembly in aquatic ecosystems

In aquatic ecosystems microplastics (MPs) provide new habitat for microbes, forming the plastisphere. While, the effect of different pollution sources on microbiome compositions, functions and assembly processes remains largely cryptic, and hence requires further investigation. Thus, in this study microplastic and surrounding water samples were collected from four different locations and performed meta-analysis to evaluate the impact of different pollution sources on microbial community composition, function and assembly in plastisphere and surrounding environment. Results demonstrated that pollution source had a significant effect on microbial diversity (p = 0.0012) and composition (PERMANOVA F = 16.386; R2 = 0.15, p < 0.001) in surface water and plastisphere. Specifically, plastisphere harboured distinct microbial community and recruited unique taxa compared to surface water, suggesting that microplastics serve as new ecological habitats. We observed a clear shift in microbial community composition, with Bacteroidetes being significantly higher in surface water significantly, whereas α- and β-Proteobacteria dominated the plastic surface (p < 0.05). These change in microbial communities were more likely due to unique chemical properties and substrates enrichment on plastic surfaces and different pollution sources. Genes involved in metabolism, signaling, cell motility, vesicular transport energy production and defence were significantly enriched in plastisphere (p = 0.001). The environmental factors such as DO and salinity drive the microbial communities in plastisphere. Niche-based selection process govern assembly in plastisphere microbiome, while as stochastic processes dominated the assembly process in aquatic microbial communities. These finding suggest that trajectory, continued microplastic emission and transport in aquatic ecosystems could pose serious planetary and health issues.

Brain Morphometric Alterations in Focal to Bilateral Tonic-Clonic Seizures in Epilepsy Associated With Excitatory/Inhibitory Imbalance.

Focal to bilateral tonic-clonic seizures (FBTCS) represent the most severe seizure type in temporal lobe epilepsy (TLE), associated with extensive network abnormalities. Nevertheless, the genetic and cellular factors predispose specific TLE patients to FBTCS remain poorly understood. This study aimed to elucidate the relationship between brain morphometric alterations and transcriptional profiles in TLE patients with FBTCS (FBTCS+) compared to those without FBTCS (FBTCS-). We enrolled 126 unilateral TLE patients (89 FBTCS+ and 37 FBTCS-) along with 60 age- and gender-matched healthy controls (HC). We assessed gray matter volume to identify morphometric differences between patients and HC. Partial least squares regression was employed to investigate the association between the morphometric disparities and human brain transcriptomic data obtained from the Allen Human Brain Atlas. Compared with HC, FBTCS+ patients exhibited morphometric alterations in bilateral cortical and subcortical regions. Conversely, FBTCS- patients exhibited more localized alterations. Imaging transcriptomic analysis revealed both FBTCS- and FBTCS+ groups harbored genes that spatially correlated with morphometric alterations. Additionally, pathway enrichment analysis identified common pathways involved in neural development and synaptic function in both groups. The FBTCS- group displayed unique pathway enrichment in catabolic processes. Furthermore, mapping these genes to specific cell types indicated enrichment in excitatory and inhibitory neurons in the FBTCS- group, while FBTCS+ group only enriched in excitatory neurons. The distinct cellular expression differences between FBTCS- and FBTCS+ groups are consistent with the distribution patterns of GABAergic expression. We applied imaging transcriptomic analysis linking the morphometric changes and neurobiology in TLE patients with and without FBTCS, including gene expression, biological pathways, cell types, and neurotransmitter receptors. Our findings revealed abnormalities in inhibitory neurons and altered distribution patterns of GABAergic receptors in FBTCS+, suggesting that an excitatory/inhibitory imbalance may contribute to the increased susceptibility of certain individuals to FBTCS.

Machine Learning Uncovers Vascular Endothelial Cell Identity Genes by Expression Regulation Features in Single Cells.

Deciphering cell identity genes is pivotal to understanding cell differentiation, development, and many diseases involving cell identity dysregulation. Here, we introduce SCIG, a machine-learning method to uncover cell identity genes in single cells. In alignment with recent reports that cell identity genes are regulated with unique epigenetic signatures, we found cell identity genes exhibit distinctive genetic sequence signatures, e.g., unique enrichment patterns of cis-regulatory elements. Using these genetic sequence signatures, along with gene expression information from single-cell RNA-seq data, enables SCIG to uncover the identity genes of a cell without a need for comparison to other cells. Cell identity gene score defined by SCIG surpassed expression value in network analysis to uncover master transcription factors regulating cell identity. Applying SCIG to the human endothelial cell atlas revealed that the tissue microenvironment is a critical supplement to master transcription factors for cell identity refinement. SCIG is publicly available at https://github.com/kaifuchenlab/SCIG , offering a valuable tool for advancing cell differentiation, development, and regenerative medicine research.

M2 macrophage-derived extracellular vesicles ameliorate Benzalkonium Chloride-induced dry eye

Dry eye disease (DED) is a common ocular condition affecting a significant portion of the global population, yet effective treatment options remain elusive. This study investigates the therapeutic potential of M2 macrophage-derived extracellular vesicles (M2-EVs) in a mouse model of DED. The DED model was established using 0.2% benzalkonium chloride (BAC) eye drops, applied twice daily for a week. Post induction, the mice were categorized into 5 groups: PBS, Sodium Hyaluronate (HA, 0.1%), Fluoromethalone (FM, 0.1%), M0-EVs, and M2-EVs. The efficacy of M2-EVs was assessed through tear production, corneal fluorescein staining and HE staining. RNA sequencing (RNA-seq) was employed to investigate the mechanisms underlying the therapeutic effects of M2-EVs in DED. Notably, the M2-EVs treated group exhibited the highest tear secretion, indicating improved tear film stability and reduced corneal surface damage. Histological analysis revealed better corneal structure organization in the M2-EVs group, suggesting enhanced ocular surface repair and corneal preservation. Furthermore, M2-EVs treatment significantly decreased pro-inflammatory cytokine levels and showed unique enrichment of genes related to retinal development. These findings suggest that M2-EVs could serve as a promising noninvasive therapeutic approach for human DED, targeting ocular surface inflammation.

Synthesis of spiroindoline derivatives and biphenyl compounds in green solvent via a “capture–release” mechanism using modified polyacrylonitrile fiber as a catalyst

Green synthesis of critical bioactive molecules and fine chemicals is attracting increasing interest. This study investigates the use of two distinct functionalized polyacrylonitrile (PAN) fibers (PANEDBPF and PANEDBP-Pd0F) as effective catalysts in a green solvent comprising ethanol and water. Firstly, a PAN fiber was modified using 2-(diphenylphosphino) ethylamine, a strongly nucleophilic phosphine compound, to obtain PANEDBPF. Spiroindoline derivatives were obtained in 98 % yields when the reaction was conducted using 5 mol% of PANEDBPF as the catalyst at 70 °C for 30 min. Next, we loaded PdNPs onto PANEDBPF to obtain PANEDBP-Pd0F. When the Suzuki coupling reaction was conducted at room temperature (25 °C) using 0.5 mol% of PANEDBP-Pd0F, the products were obtained in an extremely high yield of 99 %. Additionally, the unique enrichment of the substrate by the functionalized fibers during the reaction and the subsequent release of the product from the microenvironment conform to the “capture–release” reaction mode of catalysis. Both PANEDBPF and PANEDBP-Pd0F demonstrated good gram-scale amplification, repeatability, catalytic activity, and stability. Hence, they are highly promising candidates for green chemistry applications.

Dynamic stress- and inflammatory-based regulation of psychiatric risk loci in human neurons.

The prenatal environment can alter neurodevelopmental and clinical trajectories, markedly increasing risk for psychiatric disorders in childhood and adolescence. To understand if and how fetal exposures to stress and inflammation exacerbate manifestation of genetic risk for complex brain disorders, we report a large-scale context-dependent massively parallel reporter assay (MPRA) in human neurons designed to catalogue genotype x environment (GxE) interactions. Across 240 genome-wide association study (GWAS) loci linked to ten brain traits/disorders, the impact of hydrocortisone, interleukin 6, and interferon alpha on transcriptional activity is empirically evaluated in human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons. Of ~3,500 candidate regulatory risk elements (CREs), 11% of variants are active at baseline, whereas cue-specific CRE regulatory activity range from a high of 23% (hydrocortisone) to a low of 6% (IL-6). Cue-specific regulatory activity is driven, at least in part, by differences in transcription factor binding activity, the gene targets of which show unique enrichments for brain disorders as well as co-morbid metabolic and immune syndromes. The dynamic nature of genetic regulation informs the influence of environmental factors, reveals a mechanism underlying pleiotropy and variable penetrance, and identifies specific risk variants that confer greater disorder susceptibility after exposure to stress or inflammation. Understanding neurodevelopmental GxE interactions will inform mental health trajectories and uncover novel targets for therapeutic intervention.

Unveiling Spatial Immune Cell Profile in Kidney Allograft Rejections Using 36-plex Immunofluorescence Imaging.

Kidney allograft rejections are orchestrated by a variety of immune cells. Because of the complex histopathologic features, accurate pathological diagnosis poses challenges even for expert pathologists. The objective of this study was to unveil novel spatial indices associated with transplant rejection by using a spatial bioinformatic approach using 36-plex immunofluorescence image data. The image obtained from 11 T cell-mediated rejection (TCMR) and 12 antibody-mediated rejection (AMR) samples were segmented into 753 737 single cells using DeepCell's Mesmer algorithm. These cells were categorized into 13 distinct cell types through unsupervised clustering based on their biomarker expression profiles. Cell neighborhood analysis allowed us to stratify kidney tissue into 8 distinct neighborhood components consisting of unique cell type enrichment profiles. In contrast to TCMR samples, AMR samples exhibited a higher frequency of neighborhood components that were characterized by an enrichment of CD31+ endothelial cells. Although the overall frequency of CD68+ macrophages in AMR samples was not significantly high, CD68+ macrophages within endothelial cell-rich lesions exhibited a significantly higher frequency in AMR samples than TCMR samples. Furthermore, the frequency of interactions between CD31+ cells and CD68+ cells was significantly increased in AMR samples, implying the pivotal role of macrophages in AMR pathogenesis. Importantly, patients demonstrating a high frequency of CD31:CD68 interactions experienced significantly poorer outcomes in terms of chronic AMR progression. Collectively, these data indicate the potential of spatial bioinformatic as a valuable tool for aiding in pathological diagnosis and for uncovering new insights into the mechanisms underlying transplant rejection.

Differential enrichment mechanism of helium in the Jinqiu gas field of Sichuan Basin, China

Helium is extensively utilized in aerospace, healthcare, electronics, semiconductors, advanced science, and renewable energy sectors, playing a pivotal role in the advancement of human technology. Presently, helium is primarily extracted from natural gas as an associated resource. The cost of extraction decreases with an increase in the helium concentration within the gases. Therefore, understanding the mechanisms involved in helium generation, migration, and accumulation underground is vital. This article delves into the differential enrichment mechanism of helium in the Jinqiu gas field, situated in the Sichuan Basin of China, by analyzing the molecular and isotopic composition characteristics of the major gases and noble gases, employing gas dissolution and diffusion models. Compared with other Jurassic gas reservoirs in the Sichuan Basin, the Jinqiu gas field contains a significantly higher helium concentration, displaying unique enrichment patterns within its area. The majority of hydrocarbon gases originate from the local underlying Triassic Xujiahe Formation source rocks. Specifically, the western section of the Jinqiu field is primarily supplied by the higher maturity Xujiahe Formation source rocks located in the western Sichuan Basin. Notably, there is no significant contribution of mantle-derived volatile components in the Jinqiu field. Helium and argon are primarily radiogenic, whereas neon primarily originates from atmosphere. The good linear correlation between 4He and 20Ne suggests that their transfer is primarily facilitated through groundwater. The solubility calculation reveals that the helium exsolved from the in-situ pore water of the reservoir, due to stratigraphic uplift during the Himalayan movement, comprises only 0.04%–0.11% of the existing reserves. This suggests that gas desolvation plays a relatively minor role in helium enrichment in the Jinqiu field. Additionally, the calculation results of gas diffusion indicate that diffusion's contribution to helium enrichment in the Jinqiu gas field remains minimal. Finally, our analysis of methane reserve changes suggests that the combined effect of differential loss and dilution of hydrocarbon gases is the primary mechanism for helium's differential enrichment in the Jinqiu field. Notably, methane and carbon dioxide depletion may be a significant factor in helium enrichment within the crustal natural gas system.

Differential isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 mutation-related landscape in intrahepatic cholangiocarcinoma.

Patients with intrahepatic cholangiocarcinoma (ICC) are prone to recurrence and poor survival. Targeted therapy related to isocitrate dehydrogenase (IDH) is an extremely important treatment. IDH1 and IDH2 mutations are generally thought to have similar effects on the tumor landscape. However, it is doubtful whether these 2 mutations have exactly the same effects on tumor cells and the tumor microenvironment. All collected tumor samples were subjected to simultaneous whole-exon sequencing and proteome sequencing. IDH1 mutations accounted for 12.2%, and IDH2 mutations accounted for 5.5%, all missense mutations. Tumors with IDH mutations had lower proportions of KRAS and TP53 mutations. Mutated genes were obviously enriched in the kinase pathway in the tumors with IDH2 mutations. The signaling pathways were mainly enriched in the activation of cellular metabolic activities and an increase of inhibitory immune cells in the tumors with IDH mutations. Moreover, tumors had unique enrichment in DNA repair in IDH1 mutants and secretion of biological molecules in IDH2 mutants. Inhibitory immune cells might be more prominent in IDH2 mutants, and the expression of immune checkpoints PVR and HLA-DQB1 was more prominent in IDH1 mutants. IDH mutants were more related to metabolism-related and inflammation-immune response clusters, and some belonged to the DNA replication and repair cluster. These results revealed the differential IDH1 and IDH2 mutation-related landscapes, and we have provided an important reference database to guide ICC treatment.

Differential IDH1 and IDH2 mutation-related landscape in intrahepatic cholangiocarcinoma.

e16224 Background: Patients with intrahepatic cholangiocarcinoma (ICC) are prone to recurrence and poor survival. Targeted therapy related to isocitrate dehydrogenase (IDH) is an extremely important treatment. IDH1 and IDH2 mutations are generally thought to have similar effects on the tumor landscape. However, it is doubtful whether these two mutations have exactly the same effects on tumor cells and the tumor microenvironment. Methods: All collected tumor samples were subjected to simultaneous whole-exon sequencing and proteome sequencing. Results: IDH1 mutations accounted for 12.2%, and IDH2 mutations accounted for 5.5%, all missense mutations. Tumors with IDH mutations had lower proportions of KRAS and TP53 mutations. Mutated genes were obviously enriched in the kinase pathway in the tumors with IDH2 mutations. The signaling pathways were mainly enriched in the activation of cellular metabolic activities and an increase of inhibitory immune cells in the tumors with IDH mutations. Moreover, tumors had unique enrichment in DNA repair in IDH1 mutants and secretion of biological molecules in IDH2 mutants. Inhibitory immune cells might be more prominent in IDH2 mutants, and the expression of immune checkpoints PVR and HLA-DQB1 were more prominent in IDH1 mutants. IDH mutations were more related to metabolism-related and inflammation-immune response clusters, and some belonged to the DNA replication cluster. Conclusions: These results revealed the differential IDH1 and IDH2 mutation-related landscapes, and we have provided an important reference database to guide ICC treatment.

Domain-based analysis of RUNX1somatic mutations in myeloid neoplasms.

6542 Background: RUNX1is a master regulator of hematopoiesis. ELN2022 risk stratification categorizes RUNX1 as an AML/MDS gene associated with poor prognosis. Functional domains in RUNX1are the Runt homology domain (RHD) and a transactivation domain (TAD), with DNA binding and co-activator recruitment functions, respectively. Domain-based analysis can elucidate the functional and biological impact of somatic RUNX1mutations, which have not yet been reported in the literature. Methods: Sequencing data from Karmanos Cancer Institute and a publicly available meta-analytic cohort [Awada et al., Blood 2021, Kewan et al., Nature Communications 2023, cBioPortal (Cerami et al., 2012) and AACR GENIE (v 13.1)] were used to construct a larger dataset of 16,565 patients with myeloid neoplasms. Baseline clinical and molecular characteristics were noted. The chi-square test was used to study various parameters described, and Kaplan-Meier curves were used to estimate survival. Results: RUNX1was mutated in 10.8% (1804/16,565) of patients. Median OS (mOS) for RUNX1MT vs. RUNX1WT was significantly worse at 16.4 vs 23.4 mos. (p &lt; 0.0001). 990 patients with somatic mutations were studied; germline variants were screened and excluded if VAF was between 40-60%. Among somatic RUNX1MT patients, primary AML was the most frequent at 52.8%, followed by secondary AML-35.7% and MDS-9%. Most patients had mutations in the RHD (53.8%), followed by TAD (22%), and the remaining in non-RHD, non-TAD zones (NRNT). There was no statistically significant difference in OS by domain stratification; TAD had the numerically least mOS at 13.6 mos, RHD at 16.1 mos, and NRNT at 20.4 mos. The median age of patients was 70.9 (62-76) years, similar across domains. TAD patients were less likely to be male when compared to RHD (47% vs. 56%, p=0.04). No specific enrichment of disease type or abnormal karyotype was observed across domains. Co-mutational profiles across RHD and TAD domains among all diseases showed spliceosome co-signature enriched in RHD vs. TAD (59% vs. 46%, p=0.01). NPM1was noted to be inversely correlated with RUNX1 in general, with 1% and 3.5% in RHD and TAD. ASXL1was the most frequently distributed co-mutation in both groups, but not statistically different (41% vs. 33%, p=0.11). TAD patients with spliceosome co-mutation had worse mOS (11.4 mos) than those without spliceosome mutation (16.2 mos, p=0.02) or RHD patients with spliceosome co-mutation (16 mos, p=0.001). Missense mutations were strongly associated with RHD (55.3% vs. 7.9%); p &lt;0.00001, while frameshift mutations were enriched in TAD (24.1% vs. 69.8%); p&lt;0.0001. Conclusions: Domain-based analysis of somatic RUNX1MT myeloid neoplasms reveals TAD mutation to be common in females, frequently a frameshift mutation, and numerically has the worst survival. There appears to be a unique spliceosome signature enrichment in RHD compared to TAD, with worse OS in TAD patients with spliceosome co-mutations overall.

Functional implications of NHR-210 enrichment in C. elegans cephalic sheath glia: insights into metabolic and mitochondrial disruptions in Parkinson's disease models.

Glial cells constitute nearly half of the mammalian nervous system's cellular composition. The glia in C. elegans perform majority of tasks comparable to those conducted by their mammalian equivalents. The cephalic sheath (CEPsh)glia, which are known to be the counterparts of mammalian astrocytes, are enriched with two nuclear hormone receptors (NHRs)-NHR-210 and NHR-231. This unique enrichment makes the CEPsh glia and these NHRs intriguing subjects of study concerning neuronal health. We endeavored to assess the role of these NHRs in neurodegenerative diseases and related functional processes, using transgenic C. elegans expressing human alpha-synuclein. We employed RNAi-mediated silencing, followed by behavioural, functional, and metabolic profiling in relation to suppression of NHR-210 and 231. Our findings revealed that depleting nhr-210 changes dopamine-associated behaviour and mitochondrial function in human alpha synuclein-expressing strains NL5901 and UA44, through a putative target, pgp-9, a transmembrane transporter. Considering the alteration in mitochondrial function and the involvement of a transmembrane transporter, we performed metabolomics study via HR-MAS NMR spectroscopy. Remarkably, substantial modifications in ATP, betaine, lactate, and glycine levels were seen upon the absence of nhr-210. We also detected considerable changes in metabolic pathways such as phenylalanine, tyrosine, and tryptophan biosynthesis metabolism; glycine, serine, and threonine metabolism; as well as glyoxalate and dicarboxylate metabolism. In conclusion, the deficiency of the nuclear hormone receptor nhr-210 in alpha-synucleinexpressing strain of C. elegans, results in altered mitochondrial function, coupled with alterations in vital metabolite levels. These findings underline the functional and physiological importance of nhr-210 enrichment in CEPsh glia.

Colostrum Supplementation to Rescue Antibiotic-Induced Dysbiosis and Reduce Long-Term Obesity Risk

The prevalence of metabolic disease in the United States has increased from 30.4% to 41.9% in the past decades, with rising rates among children. Emerging evidence implicates intestinal microbiome function as contributing to metabolic disease risk, with dysbiosis being associated with overweight and obese status. While sometimes lifesaving, antibioticssuch as azithromycin cause microbiota ecological instability and are significantly associated with a greater risk ofmetabolic disease and obesity in children. Since antibiotics are often necessary, the identification of nutritional interventions to restore microbial membership and function has a high potential value for millions of patients. Colostrum is the first milk produced by mammals immediately after birth and shapes intestinal colonization patterns, specifically enriching Bifidobacterium, Lactobacillus, and limiting the colonization of Proteobacteria. Bovine colostrum containsimmunomodulators, lactoferrin, oligosaccharides, bioactive compounds, and macronutrients. The compounds are similar across mammalian species. Considering the impact of colostrum in the sterile early-life gut, we hypothesized that bovine colostrum provided as a supplemental nutraceutical therapy would augment gut microbial recolonization following antibiotic exposures and mitigate long-term metabolic consequences. Specific pathogen-free (SPF) C57BL/6 mice (male, three weeks old, Jackson Laboratory) were housed under standard laboratory conditions with a 45% high-fat diet. Tylosintartrate antibiotic (ABX) was administered to some mice in drinking water 3 days/week over three weeks, with four days washout/week. To examine colostrum, some animals were provided colostrum gavage during or immediately following ABX exposures. After intervention, body composition and metabolic phenotypes were monitored for 16 weeks.Compared with ABX alone, colostrum following ABX maintained similar body composition and glucose tolerance as controls, while colostrum during ABX appeared similar to ABX alone. Examination of the gut microbiome showed unique enrichment of Akkermansia and Sutterella with decreased Enterobacteriaceae in mice treated with ABX followed by colostrum. Analysis of the gut mucosa demonstrated ABX decreased goblet cell numbers per villi (7.2/villus) compared with control (9.8/villus), and colostrum following ABX elevated goblet cells (8.6/villus). These data suggest colostrum may stimulate epithelial responses that foster host-microbial symbiosis at the mucosal surface and play a role in intestinal recolonization to benefit long-term homeostasis. Dairy Innovation Hub, UW-Madison. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Liquid Biopsy for Detection of Pancreaticobiliary Cancers by Functional Enrichment and Immunofluorescent Profiling of Circulating Tumor Cells and Their Clusters.

Circulating tumor cells (CTCs) have historically been used for prognostication in oncology. We evaluate the performance of liquid biopsy CTC assay as a diagnostic tool in suspected pancreaticobiliary cancers (PBC). The assay utilizes functional enrichment of CTCs followed by immunofluorescent profiling of organ-specific markers. The performance of the assay was first evaluated in a multicentric case-control study of blood samples from 360 participants, including 188 PBC cases (pre-biopsy samples) and 172 healthy individuals. A subsequent prospective observational study included pre-biopsy blood samples from 88 individuals with suspicion of PBC and no prior diagnosis of cancer. CTCs were harvested using a unique functional enrichment method and used for immunofluorescent profiling for CA19.9, Maspin, EpCAM, CK, and CD45, blinded to the tissue histopathological diagnosis. TruBlood® malignant or non-malignant predictions were compared with tissue diagnoses to establish sensitivity and specificity. The test had 95.9% overall sensitivity (95% CI: 86.0-99.5%) and 92.3% specificity (95% CI: 79.13% to 98.38%) to differentiate PBC (n = 49) from benign conditions (n = 39). The high accuracy of the CTC-based TruBlood test demonstrates its potential clinical application as a diagnostic tool to assist the effective detection of PBC when tissue sampling is unviable or inconclusive.

Tissue-specific reprogramming leads to angiogenic neutrophil specialization and tumor vascularization in colorectal cancer.

Neutrophil (PMN) tissue accumulation is an established feature of ulcerative colitis (UC) lesions and colorectal cancer (CRC). To assess the PMN phenotypic and functional diversification during the transition from inflammatory ulceration to CRC we analyzed the transcriptomic landscape of blood and tissue PMNs. Transcriptional programs effectively separated PMNs based on their proximity to peripheral blood, inflamed colon, and tumors. In silico pathway overrepresentation analysis, protein-network mapping, gene signature identification, and gene-ontology scoring revealed unique enrichment of angiogenic and vasculature development pathways in tumor-associated neutrophils (TANs). Functional studies utilizing ex vivo cultures, colitis-induced murine CRC, and patient-derived xenograft models demonstrated a critical role for TANs in promoting tumor vascularization. Spp1 (OPN) and Mmp14 (MT1-MMP) were identified by unbiased -omics and mechanistic studies to be highly induced in TANs, acting to critically regulate endothelial cell chemotaxis and branching. TCGA data set and clinical specimens confirmed enrichment of SPP1 and MMP14 in high-grade CRC but not in patients with UC. Pharmacological inhibition of TAN trafficking or MMP14 activity effectively reduced tumor vascular density, leading to CRC regression. Our findings demonstrate a niche-directed PMN functional specialization and identify TAN contributions to tumor vascularization, delineating what we believe to be a new therapeutic framework for CRC treatment focused on TAN angiogenic properties.