Abundance Profiles Research Articles

Four sides to the story: A proteomic comparison of liquid-phase and matrix-bound extracellular vesicles in 2D and 3D cell cultures.

Multipotent mesenchymal stromal cells (MSCs)-derived extracellular vesicles (EVs) play important roles in cellular communication and are extensively studied as promising therapeutic agents. While there is a substantial pool of studies on liquid-phase EVs, data on EVs bound to the extracellular matrix (ECM) is lacking. There is also an emerging trend of accumulating and comparing data on characteristics of EVs obtained in different culturing conditions. Aiming to reveal proteomic signatures of EVs obtained from conditioned media and ECM of MSCs cultured in 2D and 3D conditions, we performed liquid chromatography with tandem mass spectrometry. Bioinformatic analysis revealed common patterns in proteomic composition of liquid-phase EVs and matrix-bound vesicles (MBVs), namely extracellular environment organization, immune, and transport pathways enrichment. However, extracellular environmental organization pathways are more enriched in liquid-phase EVs than in MBVs, while MBVs proteins noticeably enrich enzymatic pathways. Furthermore, each type of EVs from 2D and 3D cultures has a unique differential abundance profile. We have also performed comparative functional assays, namely scratch assay to assess EVs effect on cell migration and tubulogenesis assay to evaluate EVs angiogenic potential. We found that both liquid-phase EVs and MBVs enhance cell migration, while angiogenic potential is higher in MBVs. Results of the present study suggest that while both liquid-phase EVs and MBVs have therapeutic potential, some unique features of each subgroup may determine optimal areas of their application.

High-throughput qPCR and Amplicon Sequencing as Complementary Methods for Profiling Antibiotic Resistance Genes in Urban Wetland Parks

Urban wetland parks are an important practice for urban wetland protection and utilization due to the vast ecosystem service value. As emerging contaminants, antibiotic resistance genes (ARGs) are great attractions for environmental research and public concerns. Based on high-throughput qPCR and high-throughput amplicon sequencing techniques, we investigated the occurrence, abundance, and distribution profiles of antibiotic resistance genes in the aquatic environment of Xiamen urban wetland parks (five sites). The influencing factors and driving mechanisms of antibiotic resistance genes were deciphered on the basis of microbial community structure and water quality. Diverse and abundant ARGs were observed and coexisted in urban wet parks. A total of 217 ARGs were detected in the water body of urban wetland parks, with an abundance up to 6.48×109 copies·L-1. Urban wetland parks were important hotspots and repositories of the antibiotic resistome. A total of nine bacterial genera, including Marivivens, NS5_marine_group, and Planktomarina, were identified as the potential carriers of diverse resistance genes (41 ARGs). The microbial communities could alone explain 51% of alterations in the antibiotic resistome in the aquatic environment of the urban wetland parks. Therefore, the microbial community was the key driving force for the occurrence and evolution of ARGs in urban wetland parks. Based on the results, with the presence of ARGs and antibiotic resistance bacteria, it is suggested that the water environments of urban wetland parks have potential risks of water ecological security and human health, and it is necessary to further enhance the research and control of microbial contaminants in the aquatic environment of urban wetland parks.

SpatialHeatmap: visualizing spatial bulk and single-cell assays in anatomical images.

Visualizing spatial assay data in anatomical images is vital for understanding biological processes in cell, tissue, and organ organizations. Technologies requiring this functionality include traditional one-at-a-time assays, and bulk and single-cell omics experiments, including RNA-seq and proteomics. The spatialHeatmap software provides a series of powerful new methods for these needs, and allows users to work with adequately formatted anatomical images from public collections or custom images. It colors the spatial features (e.g. tissues) annotated in the images according to the measured or predicted abundance levels of biomolecules (e.g. mRNAs) using a color key. This core functionality of the package is called a spatial heatmap plot. Single-cell data can be co-visualized in composite plots that combine spatial heatmaps with embedding plots of high-dimensional data. The resulting spatial context information is essential for gaining insights into the tissue-level organization of single-cell data, or vice versa. Additional core functionalities include the automated identification of biomolecules with spatially selective abundance patterns and clusters of biomolecules sharing similar abundance profiles. To appeal to both non-expert and computational users, spatialHeatmap provides a graphical and a command-line interface, respectively. It is distributed as a free, open-source Bioconductor package (https://bioconductor.org/packages/spatialHeatmap) that users can install on personal computers, shared servers, or cloud systems.

Impact of propiconazole fungicide on soil microbiome (bacterial and fungal) diversity, functional profile, and associated dehydrogenase activity.

Pesticides, protect crops but can harm the environment and human health when used without caution. This study evaluated the impact of propiconazole, a fungicide that acts on fungal cell membranes, on soil microbiome abundance, diversity, and functional profile, as well as soil dehydrogenase activity (DHA). The study conducted microcosm experiments using soil samples treated with propiconazole and employed next-generation sequencing (MiSeq) and chromatographic approaches (GC-MS/MS) to analyze the shift in microbial communities and propiconazole level, respectively. The results showed that propiconazole significantly altered the distribution of microbial communities, with notable changes in the abundance of various bacterial and fungal taxa. Among soil bacterial communities, the relative abundance of Proteobacteria and Planctomycetota increased, while that of Acidobacteria decreased after propiconazole treatment. In the fungal communities, propiconazole increased the abundance of Ascomycota and Basidiomycota in the treated soil, while that of Mortierellomycota was reduced. Fungicide application further triggered a significant decrease in DHA over time. Analysis of the functional profile of bacterial communities showed that propiconazole significantly affected bacterial cellular and metabolic pathways. The carbon degradation pathway was upregulated, indicating the microbial detoxification of the contaminant in the treated soil. Our findings suggest that propiconazole application has a discernible impact on soil microbial communities, which could have long-term consequences for soil health, quality, and function.

ATOMIUM: Molecular inventory of 17 oxygen-rich evolved stars observed with ALMA

Context. The dusty winds of cool evolved stars are a major contributor of the newly synthesised material enriching the Galaxy and future generations of stars. However, the details of the physics and chemistry behind dust formation and wind launching have yet to be pinpointed. Recent spatially resolved observations show the importance of gaining a more comprehensive view of the circumstellar chemistry, but a comparative study of the intricate interplay between chemistry and physics is still difficult because observational details such as frequencies and angular resolutions are rarely comparable. Aims. Aiming to overcome these deficiencies, ATOMIUM is an ALMA Large Programme to study the physics and chemistry of the circumstellar envelopes of a diverse set of oxygen-rich evolved stars under homogeneous observing conditions at three angular resolutions between ~0.02″−1.4″. Here we summarize the molecular inventory of these sources, and the correlations between stellar parameters and molecular content. Methods. Seventeen oxygen-rich or S-type asymptotic giant branch (AGB) and red supergiant (RSG) stars have been observed in several tunings with ALMA Band 6, targeting a range of molecules to probe the circumstellar envelope and especially the chemistry of dust formation close to the star. We systematically assigned the molecular carriers of the spectral lines and measured their spectroscopic parameters and the angular extent of the emission of each line from integrated intensity maps. Results. Across the ATOMIUM sample, we detect 291 transitions of 24 different molecules and their isotopologues. This includes several first detections in oxygen-rich AGB/RSG stars: PO v = 1, SO2 v1 = 1 and v2 = 2, and several high energy H2O transitions. We also find several first detections in S-type AGB stars: vibrationally excited HCN v2 = 2,3 and SiS v = 4,5,6, as well as first detections of the molecules SiC, AlCl, and AlF in W Aql. Overall, we find strong correlations between the following molecular pairs: CS and SiS, CS and AlF, NaCl and KCl, AlO and SO, SO2 and SO, and SO2 and H2O; meaning both molecules tend to have more detected emission lines in the same sources. The measured isotopic ratios of Si and S are found to be consistent with previous measurements, except for an anomalously high 29Si/30Si ratio of 4 ± 1 in the RSG VX Sgr. Conclusions. This paper presents the overall molecular inventory and an initial analysis of the large ATOMIUM dataset, laying the groundwork for future work deriving molecular abundances and abundance profiles using radiative transfer modeling which will provide more rigorous tests for chemical models.

Effect of Nutmeg Meal on Microbial Abundance of Biohydrogenation Process, and Fatty Acid Profile of Goat Rumen Fluid In Vitro

This study aimed to evaluate the effect of nutmeg meal as a source of phenol on the abundance of dominant microbes in the biohydrogenation process and the fatty acid profile of goat rumen fluid in vitro. This study used a randomized complete block design with four treatments and three replicates of in vitro batches, each replicate in duplicate. The dietary treatments consisted of elephant grass (40%), soybean meal (10%), with varying proportion of wheat pollard, canola oil and nutmeg meal hence, treatment P0 (40:10:45:5:0); P1 (40:10:40:5:5); P2 (40:10:35:5:15); P3 (40:10:30:5:10). Fermentation using the in vitro gas production method described by Menke and Steinggas with an incubation period of 48 hours. Parameters observed included microbial abundance and fatty acid profile of goat rumen fluid. The statistical analysis showed that adding nutmeg meal starting at the 5% level decreased the abundance of the main biohydrogenation process bacteria anaerovibrio, butyrivibrio fibrisolvens, and pseudobutyrivibrio. Total saturated fatty acid and stearate fatty acid concentrations decreased (P<0.05), while total unsaturated fatty acid, linoleic and oleic acid concentrations increased (P<0.05).

Increased blood CSF3R+ myeloid-derived suppressor cell is a predictor for breast cancer recurrence.

Early detection of cancer recurrence using specific biomarkers remains a clinically unmet need, although methodologies for monitoring tumor markers, cell-free DNA, and circulating tumor cells have been established for decades. Tumor recurrence develops in metastatic or dormant cancer cells under continuous immune surveillance. Alterations in the population and function of immune cells may contribute to cancer recurrence. Here, we utilized an animal model to imitate breast tumor recurrence after surgical resection and investigated the abundance and gene expression profiles of immune cells using NanoString analysis. Bioinformatic analysis of a published single-cell RNA sequencing database of myeloid-derived suppressor cells (MDSCs) was performed to identify common targets between the two studies. Identified biomarkers were validated using human peripheral blood mononuclear cell (PBMC) datasets. The inhibitory effect of MDSCs on T-cell proliferation was assessed in vitro. Our data demonstrated that the number of MDSCs significantly increased during recurrence. Comparison of our NanoString data with a single-cell RNA sequencing dataset of MDSCs in another spontaneous breast cancer model identified colony-stimulating factor 3 receptor (Csf3r)-positive MDSCs as a potential marker for predicting tumor relapse. We validated our findings using two previously published PBMC databases of patients with breast cancer with or without recurrence and confirmed the elevated MDSC gene signature and CSF3R expression in patients with tumor recurrence. 35 patients with breast cancer were also included in our study, that patients with higher levels of CSF3R had worse survival. In vitro experiments demonstrated that Csf3r + MDSCs exhibited enhanced reactive oxygen species (ROS) levels and robust T-cell suppression ability. We conclude that an increase in CSF3R + MDSCs is a potential biomarker for early detection of tumor recurrence in patients with breast cancer.

Formulation of Ascorbic Acid and Skim Milk in Feed for Salinity Stress in Artemia sp.

Artemia sp. is recognized for its abundant and comprehensive nutritional profile, yet it lacks the inherent ability to produce vital elements such as vitamins, Eicosapentaenoic Acid (EPA), and Docosahexaenoic Acid (DHA), necessitating their acquisition from external sources. To augment the nutritional quality of Artemia sp., enrichment becomes imperative. This research aimed to evaluate the toxicity of ascorbic acid when used as a feed for Artemia sp. and investigate the influence of ascorbic acid enrichment and the addition of skim milk to the feed on Artemia sp.'s response to salinity stress. The study employed a Completely Randomized Design (CRD). The toxicity assessment of ascorbic acid utilized the Brine Shrimp Lethality Test (BSLT) method, yielding an LC50 value of 200.84 (> 1000 ppm), indicating toxicity to Artemia sp. Salinity stress resistance exhibited variability across treatments, with the longest survival times observed sequentially in Artemia sp. subjected to AS treatment 3 (20 hours), AS 2, and the control (16 hours), SM, AS 3, and C 1 (12 hours), and C 2 (8 hours). The enrichment of Artemia sp. feed with ascorbic acid and skim milk significantly influenced (sig. = 0.002) its resistance to salinity stress, with the optimal formulation identified at 200 ppm of ascorbic acid.

Endosymbion microbials low abundance of Nilaparvata lugens (Stal) (Hemiptera: Delphacidae) from Indonesia rice production center based on metagenomic study using 16Sr RNA

Insects have a long history of association with endosymbiont microbes. There are several indications that endosymbiont microbes are associated with insects and participate in the degradation of organic and inorganic molecules. This research aims to identify the profile of abundance and diversity of endosymbiont microbes associated with Nilaparvata lugens in Konawe (Southeast Sulawesi), Pasuruan (East Java), Klaten (Central Java), and Karawang (West Java) using a metagenomic study approach. We analyzed 15 pairs samples of N. lugens obtained from several regions in Indonesia. Endosymbionts were identified using a full-length primer 27F and 1492R targeting the 16S rRNA gene. The results showed that the proteobacteria phylum dominated all samples. Arsenophonus nasoniae (Morganellaceae; Enterobacterales) contributed the highest abundance (50-62%) based on total NumRead nucleotide base sequences from each sample. The bacterial diversity in these four samples was classified as moderate. This research showed that there were similarities in the communities and profiles of endosymbiont microbial constituents in each region, and this study becomes the basis for further research regarding the role of endosymbiont microbes on their hosts.

A temporal record of microplastic accumulation in sediment cores of the Great Lakes, North America, reflects macroeconomic and regional influences

Documented plastic pollution throughout the Laurentian Great Lakes system prompted investigation of microplastics (MPs) in sediment cores. We examined offshore sediment cores from Lake Huron (LH43) and Lake Ontario (403A) to understand temporal trends and changes in microplastic (MP) pollution in the size range 53 µm to 2 mm. MP abundances varied from 18.1 to 280.1 particles per g of dry weight sediment ( N g−1 dw) in LH43, and 8.2–488.4 g−1 dw in core 403A. The 15 cm cores are equivalent to 56 years of accumulation in Lake Huron and 72 years of accumulation in Lake Ontario. Analysis of the two cores shows an increasing trend in MP accumulation from 1964 to 1989, which mirrors the global plastic production rate. Subsequent peaks and troughs in the MP abundance profiles reflect macroeconomic changes and regional controls. These results show how changing abundances of MPs in lake sediment cores can act as proxies for global perturbations in oil supply as well as national economic shifts.

Network impact of a single-time-point microbial sample.

The human microbiome plays a crucial role in determining our well-being and can significantly influence human health. The individualized nature of the microbiome may reveal host-specific information about the health state of the subject. In particular, the microbiome is an ecosystem shaped by a tangled network of species-species and host-species interactions. Thus, analysis of the ecological balance of microbial communities can provide insights into these underlying interrelations. However, traditional methods for network analysis require many samples, while in practice only a single-time-point microbial sample is available in clinical screening. Recently, a method for the analysis of a single-time-point sample, which evaluates its 'network impact' with respect to a reference cohort, has been applied to analyze microbial samples from women with Gestational Diabetes Mellitus. Here, we introduce different variations of the network impact approach and systematically study their performance using simulated 'samples' fabricated via the Generalized Lotka-Volttera model of ecological dynamics. We show that the network impact of a single sample captures the effect of the interactions between the species, and thus can be applied to anomaly detection of shuffled samples, which are 'normal' in terms of species abundance but 'abnormal' in terms of species-species interrelations. In addition, we demonstrate the use of the network impact in binary and multiclass classifications, where the reference cohorts have similar abundance profiles but different species-species interactions. Individualized analysis of the human microbiome has the potential to improve diagnosis and personalized treatments.

High-throughput single-cell mass spectrometry enables metabolic network analysis by resolving phospholipid C[double bond, length as m-dash]C isomers.

Single-cell mass spectrometry (MS) is an essential technology for sensitive and multiplexed analysis of metabolites and lipids for cell phenotyping and pathway studies. However, the structural elucidation of lipids from single cells remains a challenge, especially in the high-throughput scenario. Technically, there is a contradiction between the inadequate sample amount (i.e. a single cell, 0.5-20 pL) for replicate or multiple analysis, on the one hand, and the high metabolite coverage and multidimensional structure analysis that needs to be performed for each single cell, on the other hand. Here, we have developed a high-throughput single-cell MS platform that can perform both lipid profiling and lipid carbon-carbon double bond (C[double bond, length as m-dash]C) location isomer resolution analysis, aided by C[double bond, length as m-dash]C activation in unsaturated lipids by the Paternò-Büchi (PB) reaction and tandem MS, termed single-cell structural lipidomics analysis. The method can achieve a single-cell analysis throughput of 51 cells per minute. A total of 145 lipids were structurally characterized at the subclass level, of which the relative abundance of 17 isomeric lipids differing in the location of C[double bond, length as m-dash]C from 5 lipid precursors was determined. While cell-to-cell variations in MS1-based lipid profiling can be large, an advantage of quantifying lipid C[double bond, length as m-dash]C location isomers is the significantly improved quantitation accuracy. For example, the relative standard deviations (RSDs) of the relative amounts of PC 34:1 C[double bond, length as m-dash]C position isomers in MDA-MB-468 cells are half smaller than those measured for PC 34:1 as a whole by MS1 abundance profiling. Taken together, the developed method can be effectively used for in-depth structural lipid metabolism network analysis by high-throughput analysis of 142 MDA-MB-468 human breast cancer cells.

Long-slit spectral study of the unusual post-interacting galaxy Arp 263

ABSTRACT Arp 263 is a single irregularly shaped galaxy with intense star formation. Its short tidal features of low brightness visible in both optics and the H i line, as well as the strong non-circular motion of atomic gas in the outskirts, give pieces of evidence of a recent merging with some intruder, non-observed directly. We carried out spectral observations of this galaxy at the 6 m telescope of the Special Astrophysical Observatory. The spectra for three positions of the spectral slit were obtained: two of them cross the central region of the galaxy and the third one runs along the nearly straight narrow chain of clumps of emission gas with a length of 4–5 kpc. We derived the profiles of velocity, fluxes, and oxygen abundances (O/H) along the slits. We confirm that within the radius of several kpc the galaxy rotates regularly. The maximal value of the rotational velocity allows us to conclude that the dark mass of the galaxy prevails over the mass of its visible components. The observed velocity profile along the peripheral star-forming chain gives pieces of evidence that it is located outside of the plane of the disc, and the gas that formed the chain is probably falling back on to the disc after being ejected from the galaxy. We discuss that the observed chain of clumps is the result of gravitational instability of the gaseous filament.

Functional and evolutionary significance of unknown genes from uncultivated taxa

Many of the Earth’s microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in most metagenomic studies1. Here we analysed 149,842 environmental genomes from multiple habitats2–6 and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date. The FESNov catalogue is enriched in clade-specific traits, including 1,034 novel families that can distinguish entire uncultivated phyla, classes and orders, probably representing synapomorphies that facilitated their evolutionary divergence. Using genomic context analysis and structural alignments we predicted functional associations for 32.4% of FESNov families, including 4,349 high-confidence associations with important biological processes. These predictions provide a valuable hypothesis-driven framework that we used for experimental validatation of a new gene family involved in cell motility and a novel set of antimicrobial peptides. We also demonstrate that the relative abundance profiles of novel families can discriminate between environments and clinical conditions, leading to the discovery of potentially new biomarkers associated with colorectal cancer. We expect this work to enhance future metagenomics studies and expand our knowledge of the genetic repertory of uncultivated organisms.

Cell pleomorphism and changes in the enzymatic profile of selected Candida albicans strains in interaction with Escherichia coli – pilot study

Interactions between C. albicans and the microbiota play an important role in maintaining the balance between commensal and pathogenic organisms. Although the exact role of bacteria in reducing the pathogenicity of yeast remains poorly understood, a few examples have been documented so far: probiotics administration effectively reduces the formation of biofilm and bacterial metabolites inhibit the formation of hyphae.The aim of the study was to analyze C. albicans virulence levels based on the changes in the morphological structure and enzymatic profile in experimental cultures mixed with Escherichia coli. Viable cell abundance, cell pleomorphism and enzymatic profile were analyzed in single and mixed cultures (C. albicans + E. coli).The microscope analysis showed a large decrease in the number of viable C. albicans cells in mixed cultures with E. coli from 485.3±132.1 immediately after the establishment of the culture to 238.1±71.2 after an hour of incubation and 24.4±5.4 after 24 h. The length of C. albicans cells differed significantly between the single-species cultures and the mixed cultures for 24 h. Our present findings indicate a significant reduction in the secretion of several enzymes by fungi following contact with E. coli, including acid phosphatase, N-acetyl-β-glucosaminidase, naphthol-AS-BI-phosphohydrolase and leucine arylamidase.The interactions between fungi and bacteria appear to be extremely complex. On the one hand, during C. albicans with E. coli co-incubation, the bacteria stimulated the elongation of yeast cells, leading to the formation of a filamentous form; however, the number of yeast cells and their enzymatic activity decreased significantly. Therefore, it can be concluded that while E. coli stimulates some pathogenic properties, e.g. cell elongation, it also inhibits other virulence features, e.g. enzymatic activity of C. albicans.

Glycation-induced enhancement of yeast cell protein for improved stability and curcumin delivery in Pickering high internal phase emulsions

Pickering high internal phase emulsions (HIPEs) have gained significant attention for various applications within the food industry. Yeast cell protein (YCP), derived from spent brewer's yeast, stands out as a preferred stabilizing agent due to its cost-effectiveness, abundance, and safety profile. However, challenges persist in utilizing YCP, notably its instability under high salt concentration, thermal processing, and proximity to its isoelectric point. This study aimed to enhance YCP's emulsifying properties through glycation with glucose and evaluate its efficacy as a stabilizer for curcumin (CUR)-loaded HIPEs. The results revealed that glycation increased YCP's surface hydrophobicity, exposing hydrophobic groups. This augmentation, along with steric hindrance from grafted glucose molecules, improved emulsifying properties, resulting in a thicker interfacial layer around oil droplets. This fortified interfacial layer, in synergy with steric hindrance, bolstered resistance to pH changes, salt ions, and thermal degradation. Moreover, HIPEs stabilized with glycated YCP exhibited reduced oxidation rates and improved CUR protection. In vitro digestion studies demonstrated enhanced CUR bioaccessibility, attributed to a faster release of fatty acids. This study underscores the efficacy of glycation as a strategic approach to augment the applicability of biomass proteins, exemplified by glycated YCP, in formulating stable and functional HIPEs for diverse food applications.

Effects of Ureaplasma parvum infection in the exosome biogenesis-related proteins in ectocervical epithelial cells.

Ureaplasma parvum is a mycoplasma commonly associated with female reproductive pathologies, such as preterm birth and infertility. It can survive intracellularly and utilize exosomes to propagate infection and its virulence factors. This study explored the differential protein composition of exosomes derived from normal and U. parvum-infected cells. We also investigated the impact of U. parvum on exosome biogenesis in ectocervical epithelial cells. Ectocervical epithelial (ECTO) cells were infected with U. parvum, and immunocytochemical staining was performed using U. parvum-specific marker multiple banded antigen (mba) and exosome marker CD9. NanoLC-MS/MS analysis was conducted to identify differentially expressed proteins in exosomes. Ingenuity Pathway Analysis (IPA) was performed to identify affected canonical pathways and biological functions associated with the protein cargo of exosomes. Western blot analysis of ECTO cells validated the proteomic findings in ECTO cells. U. parvum exhibited colonization of ECTO cells and colocalization with CD9-positive intraluminal vesicles. Proteomic analysis revealed decreased protein abundance and distinct protein profiles in exosomes derived from U. parvum-infected ECTO cells. Differentially expressed proteins were associated with clathrin-mediated endocytosis and various signaling pathways indicative of infection, inflammation, and cell death processes. Additionally, U. parvum infection altered proteins involved in exosome biogenesis. In ECTO cells, U. parvum infection significantly decreased clathrin, ALIX, CD9, and CD63 and significantly increased TSG101, Rab5, Rab35, and UGCG. These findings contribute to our understanding of the infection mechanism and shed light on the importance of exosome-mediated communication in the pathophysiology of diseases affecting the cervix, such as cervicitis and preterm birth.

Abstract PR001: Interpretation of patient-specific ex vivo immunotherapy response for ovarian cancer

Abstract Background: Immunotherapies have shown great benefits, including durable clinical responses. However, the overall response rate remains low and it is challenging to select sensitive patients upfront. Patient-derived ex vivo tumor tissues with preserved tumor microenvironment (TME) represent the ideal model for patient-specific testing of immunotherapy sensitivities. This study aims to confirm that patient-specific ex vivo immunotherapy responses are matched by the presence of relevant immune components. Material & Methods: Ascites of 84 patients with predominantly primary high grade ovarian carcinoma was collected between 2019 and 2023 in the Netherlands (IRB P18.032). Fresh tumor clusters with TME were seeded and exposed to six immunotherapies and the superantigen Staphylococcus aureus (SEA) as positive control. Tumor killing and immune cell proliferation were measured using 3D imaging. Ex vivo tumor sensitivity was classified on percentage and statistical significance of tumor killing. Immunohistochemical staining (IHC) for immune cell markers (CD3, CD68) (n=40) and proteomics analyses (n=26) were performed prior to drug exposure. Results: SEA response was observed in 52% (44/84). Differential patient response profiles were observed, with 30% of the patients tissues displaying highly significant sensitivity for at least one of the therapies tested. Clustering the patients based on pathology scores uncovered four distinct groups: 1) CD68-/CD3-, 2) CD3-/CD68+, 3) CD3+/CD68+ and 4) CD3++/CD68++. Clustering and regression analysis demonstrated a significant correlation of increased CD3 and CD68 expression to ex vivo SEA sensitivity (p-value < 0.05). Protein biomarker analysis supported these results, reporting significantly higher levels of chemokines and interleukins in SEA responders. Finally, different immune checkpoint inhibitors demonstrated distinct protein abundance profiles consistent with their mode of action. Conclusion: This study reports classification and characterization of patient-specific sensitivity to 6 immunotherapies in 84 ovarian cancer patients enabled by a robust image-based ex vivo 3D tumor testing platform. The results demonstrate a positive relationship between the ex vivo sensitivity to immune-stimulatory compounds and the presence of functional immune components in the patient's TME. This confirms the interpretability of 3D ex vivo tumor testing for classification of patient-specific immune responses. Discussion: We previously demonstrated the predictive value of the platform by correlation of ex vivo sensitivity to clinical chemotherapy responses of ovarian cancer patients. Assay feasibility was also established for NSCLC, mesothelioma and bladder cancer. The two-week timeline enables its application in clinical practice. Quantifying ex vivo immunotherapy sensitivity will facilitate improved patient stratification for standard of care and novel treatments. Clinical trials are currently ongoing to establish the correlation of the assay with patients' response to immunotherapy. Citation Format: Lieke Ceton, Esmee Koedoot, Timothy Sijsenaar, Marta Montero Garcia, Fanny Grillet, Jurrian van der Valk, Klaus Weber, Roman Schoenauer, Katrin Hufnagel, Ronny Schmidt, Nadine Stroh, Henning Boekhoff, Cor de Kroon, Anne van Altena, Dieudonné van der Meer, Willemijn Vader, Nelleke Ottevanger, Judith Kroep. Interpretation of patient-specific ex vivo immunotherapy response for ovarian cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr PR001.

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India

BackgroundThe health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge. ResultsTo explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances. ConclusionBaner river’s metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.

People with obesity exhibit losses in muscle proteostasis that are partly improved by exercise training.

This pilot experiment examines if a loss in muscle proteostasis occurs in people with obesity and whether endurance exercise positively influences either the abundance profile or turnover rate of proteins in this population. Men with (n=3) or without (n=4) obesity were recruited and underwent a 14-d measurement protocol of daily deuterium oxide (D2O) consumption and serial biopsies of vastus lateralis muscle. Men with obesity then completed 10-weeks of high-intensity interval training (HIIT), encompassing 3 sessions per week of cycle ergometer exercise with 1min intervals at 100% maximum aerobic power interspersed by 1min recovery periods. The number of intervals per session progressed from 4 to 8, and during weeks 8-10 the 14-d measurement protocol was repeated. Proteomic analysis detected 352 differences (p<0.05, false discovery rate<5%) in protein abundance and 19 (p<0.05) differences in protein turnover, including components of the ubiquitin-proteasome system. HIIT altered the abundance of 53 proteins and increased the turnover rate of 22 proteins (p<0.05) and tended to benefit proteostasis by increasing muscle protein turnover rates. Obesity and insulin resistance are associated with compromised muscle proteostasis, which may be partially restored by endurance exercise.