The Spatial Extracellular Proteomic Tumor Microenvironment Distinguishes Molecular Subtypes of Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) mortality rates continue to increase faster than those of other cancer types due to high heterogeneity, which limits diagnosis and treatment. Pathological and molecular subtyping have identified that HCC tumors with poor outcomes are characterized by intratumoral collagenous accumulation. However, the translational and post-translational regulation of tumor collagen, which is critical to the outcome, remains largely unknown. Here, we investigate the spatial extracellular proteome to understand the differences associated with HCC tumors defined by Hoshida transcriptomic subtypes of poor outcome (Subtype 1; S1; n = 12) and better outcome (Subtype 3; S3; n = 24) that show differential stroma-regulated pathways. Collagen-targeted mass spectrometry imaging (MSI) with the same-tissue reference libraries, built from untargeted and targeted LC-MS/MS was used to spatially define the extracellular microenvironment from clinically-characterized, formalin-fixed, paraffin-embedded tissue sections. Collagen α-1(I) chain domains for discoidin-domain receptor and integrin binding showed distinctive spatial distribution within the tumor microenvironment. Hydroxylated proline (HYP)-containing peptides from the triple helical regions of fibrillar collagens distinguished S1 from S3 tumors. Exploratory machine learning on multiple peptides extracted from the tumor regions could distinguish S1 and S3 tumors (with an area under the receiver operating curve of ≥0.98; 95% confidence intervals between 0.976 and 1.00; and accuracies above 94%). An overall finding was that the extracellular microenvironment has a high potential to predict clinically relevant outcomes in HCC.

Impact of Prebiotic ß-glucan Treatment at Juvenile Age on the Gut Microbiota Composition and the Eventual Type 1 Diabetes Onset in Non-obese Diabetic Mice.

Complex dietary polysaccharides such as ß-glucans are widely used for their anti-inflammatory properties. We reported before that oral administration of Yeast ß-glucan (YBG) in adult mice can help delay type 1 diabetes (T1D) onset and suppress gut inflammation through modulation of the structure and function of gut microbiota. Since juvenile age is characterized by profoundly changing immature gut microbiota, we examined the impact of oral treatment with YBG in non-obese diabetic (NOD) mice at this age. Juvenile mice that received daily oral administration of YBG starting at 15 days of age for 7 or 30 days were examined for changes in gut microbiota, immune characteristics, and T1D incidence. Mice that received YBG for 30 days but not 7 days, showed considerable changes in the composition and diversity of fecal microbiota as compared to controls. Predictive functional analysis, based on 16S rDNA sequences, revealed overrepresentation of glycan biosynthesis and metabolism, energy metabolism, and fatty acid biosynthesis pathways in mice that received YBG for 30 days. Immune phenotype of the colon showed skewing toward immune regulatory and Th17 cytokines with increases in IL-10, IL-17, and IL-21 and a decrease in TNF-α, although increases in some pro-inflammatory cytokines (IL-1b, IFN-γ) were observed. Most importantly, mice that received YBG treatment for 30 days showed significantly suppressed insulitis and delayed onset of hyperglycemia compared to controls. Overall, this study suggests that oral consumption of YBG beginning at pre-diabetic juvenile ages could have positive maturational changes to gut microbiota and immune functions and could result in a delay in the disease onset in those who are pre-disposed to T1D.

Dynamics of Structural and Functional Changes in Gut Microbiota during Treatment with a Microalgal ß-Glucan, Paramylon and the Impact on Gut Inflammation.

Previously, we have shown that oral administration of yeast derived ß-1,3/1,6-d-glucan enhances immune regulation and alters the composition of the gut microbiota. However, it is not known if other structurally distinct ß-glucans have similar properties. Here, using C57BL/6 mice, we show the potential of a microalgae derived ß-1,3-d-glucan, paramylon (PM), in shaping the gut microbiota and modulating the susceptibility to colitis. The community structure within the gut microbiota showed progressive changes including selective enrichment of specific communities and lowered community richness and diversity during prolonged oral treatment with PM. Compared to control mice, the gut microbiota of PM-treated mice had significantly higher abundance of Verrucomicrobia and lower abundance of Firmicutes. Specific taxa that were significantly more abundant in PM-treated mice include Akkermansia muciniphila and several Bacteroides members. Predictive functional analysis revealed overrepresentation of carbohydrate metabolism function in the fecal microbiota of PM recipients compared to controls, and this function was linked to Bacteroides spp. Prolonged pretreatment with PM not only diminished susceptibility to dextran sulfate sodium induced colitis severity, but also caused enhanced immune regulation. Overall, this study demonstrates the prebiotic properties of PM and the potential benefits of its prolonged oral consumption to gut health.

Composition, diversity, and activity of aerobic ammonia-oxidizing Bacteria and Archaea in the intertidal sands of a grand strand South Carolina beach.

Aerobic ammonia oxidation to nitrite has been established as an important ecosystem process in regulating the level of nitrogen in marine ecosystems. This process is carried out by ammonia-oxidizing bacteria (AOB) within the classes Betaproteobacteria and Gammaproteobacteria and ammonia-oxidizing Archaea (AOA) from the phylum Thaumarchaeota, and the latter of which has been established as more prevalent in marine systems. This study investigated the presence, abundance, and activity of these groups of microbes at a beach near Springmaid Pier in Myrtle Beach, South Carolina, through the implementation of next generation sequencing, quantitative PCR (qPCR), and microcosm experiments to monitor activity. Sequencing analysis revealed a diverse community of ammonia-oxidizing microbes dominated by AOA classified within the family Nitrosopumilaceae, and qPCR revealed the abundance of AOA amoA genes over AOB by at least an order of magnitude in most samples. Microcosm studies indicate that the rates of potential ammonia oxidation in these communities satisfy Michaelis-Menten substrate kinetics and this process is more active at temperatures corresponding to summer months than winter. Potential rates in AOA medium were higher than that of AOB medium, indicating a potentially greater contribution of AOA to this process in this environment. In conclusion, this study provides further evidence of the dominance of AOA in these environments compared with AOB and highlights the overall efficiency of this process at turning over excess ammonium that may be present in these environments.

Microbial community structure shows differing levels of temporal stability in intertidal beach sands of the grand strand region of South Carolina.

Studies of microbial community structure in intertidal and supratidal beach sands along the California and Gulf of Mexico coasts have begun to reveal geographical patterns in microbial diversity through the use of next generation sequencing technology. Only a few studies have targeted communities along the Eastern seaboard, leaving a variety of microbial ecosystems uncharacterized. In this study, we examine the microbial community structure within three South Carolina beaches along the Grand Strand via sequencing of the V4 region of the 16S rRNA gene to discern relationships between diversity and temporal or regional factors. Gammaproteobacteria, Planctomycetes, Acidobacteria, and Actinobacteria dominated the composition of these beaches. Diversity analyses revealed that highly diverse communities were similar in overall composition and diversity but showed different levels of community structure stability over time. The community structure in Pawleys Island sands showed no significant change over time, while Garden City experienced significant shifts between each sampling date. Community structure also differed between beaches and, to a lesser degree, sampling date. These data provide evidence of the high microbial diversity within these beach sands and suggest that even though beaches of the same geographic region can show similarity in composition and diversity at a particular timepoint, the nature of their community structure and underlying diversity may differ comparatively and over time.