In Parkinson's disease (PD), gastrointestinal features are common and often precede the motor signs. Braak and colleagues proposed that PD may start in the gut, triggered by a pathogen, and spread to the brain. Numerous studies have examined the gut microbiome in PD; all found it to be altered, but found inconsistent results on associated microorganisms. Studies to date have been small (N = 20 to 306) and are difficult to compare or combine due to varied methodology. We conducted a microbiome-wide association study (MWAS) with two large datasets for internal replication (N = 333 and 507). We used uniform methodology when possible, interrogated confounders, and applied two statistical tests for concordance, followed by correlation network analysis to infer interactions. Fifteen genera were associated with PD at a microbiome-wide significance level, in both datasets, with both methods, with or without covariate adjustment. The associations were not independent, rather they represented three clusters of co-occurring microorganisms. Cluster 1 was composed of opportunistic pathogens and all were elevated in PD. Cluster 2 was shortchain fatty acid (SCFA)-producing bacteria and all were reduced in PD. Cluster 3 was carbohydrate-metabolizing probiotics and were elevated in PD. Depletion of anti-inflammatory SCFA-producing bacteria and elevated levels of probiotics are confirmatory. Overabundance of opportunistic pathogens is an original finding and their identity provides a lead to experimentally test their role in PD.

In Parkinson's disease (PD), gastrointestinal features are common and often precede the motor signs. Braak and colleagues proposed that PD may start in the gut, triggered by a pathogen, and spread to the brain. Numerous studies have examined the gut microbiome in PD, all found it to be altered, but found inconsistent results on associated microorganisms. Studies to date have been small (N=20 to 306) and are difficult to compare or combine due to varied methodology. We conducted a microbiome-wide association study (MWAS) with two large datasets for internal replication (N=333 and 507). We used uniform methodology when possible, interrogated confounders, and applied two statistical tests for concordance, followed by correlation network analysis to infer interactions. Fifteen genera were associated with PD at a microbiome-wide significance level, in both datasets, with both methods, with or without covariate adjustment. The associations were not independent, rather represented 3 clusters of co-occurring microorganisms. Cluster 1 was composed of opportunistic pathogens; all were elevated in PD. Cluster 2 were short-chain-fatty-acid producing bacteria; all were reduced in PD.Cluster 3 were carbohydrate-metabolizing probiotics; elevated in PD. Depletion of antiinflammatory short-chain-fatty-acid producing bacteria and elevated levels of probiotics are confirmatory. Overabundance of opportunistic pathogens is a novel finding and their identity provides a lead to experimentally test their role in PD. animal models. [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] Every study that has compared the global composition of the gut microbiome in PD vs. controls found it to be significantly altered; in contrast, attempts to identify PD-associated microorganisms have produced inconsistent results. 31,32 Low reproducibility has been attributed to small sample sizes (missing true associations due to low power), relaxed statistical thresholds (inflating false positive results), and publishing without a replication dataset (required for genomic studies). Differences in methods of DNA extraction, sequencing, bioinformatics and statistics can all contribute to inter-study variations. The choice of taxonomic resolution for analysis (PD has been tested at all levels from phylum to species) and the inconsistent taxonomic assignments and nomenclature used in various reference databases add to the confusion when comparing results. Last but not least, is confounding by heterogeneity in the populations that were studied: PD is heterogenous and so is the microbiome. PD subtypes cannot be readily identified thus patient populations are inevitably varied. A myriad of factors can affect the microbiome ranging from diet, health and medication to cultural habits, life-styles, race and geography. 33,34 Identifying microorganisms involved in the dysbiosis of the microbiome is essential for understanding their role in disease. We conducted a hypothesis-free microbiome-wide association study (MWAS) modeled after and usi...

Osteoblasts support hematopoietic cell development, including B lymphopoiesis. We have previously shown that the nuclear factor of activated T cells (NFAT) negatively regulates osteoblast differentiation and bone formation. Interestingly, in smooth muscle, NFAT has been shown to regulate the expression of vascular cellular adhesion molecule-1 (VCAM-1), a mediator of cell adhesion and signaling during leukocyte development. To examine whether NFAT signaling in osteoblasts regulates hematopoietic development in vivo, we generated a mouse model expressing dominant-negative NFAT driven by the 2.3 kb fragment of the collagen-αI promoter to disrupt NFAT activity in osteoblasts (dnNFATOB). Bone histomorphometry showed that dnNFATOB mice have significant increases in bone volume (44%) and mineral apposition rate (131%) and decreased trabecular thickness (18%). In the bone microenvironment, dnNFATOB mice displayed a significant increase (87%) in Lineage−cKit+Sca-1+ (LSK) cells and significant decreases in B220+CD19−IgM− pre-pro-B cells (41%) and B220+CD19+IgM+ immature B cells (40%). Concurrent with these findings, LSK cell differentiation into B220+ cells was inhibited when cocultured on differentiated primary osteoblasts harvested from dnNFATOB mice. Gene expression and protein levels of VCAM-1 in osteoblasts decreased in dnNFATOB mice compared to controls. These data suggest that osteoblast-specific NFAT activity mediates early B lymphopoiesis, possibly by regulating VCAM-1 expression on osteoblasts.

Improved diagnostics are needed for children with musculoskeletal infections (MSKIs). We assessed the performance of target-enriched multiplex polymerase chain reaction (TEM-PCR) in children with MSKI. TEM-PCR was concordant with culture in pathogen identification and antibiotic susceptibility testing, while increasing the overall yield of pathogen detection. This technology has the potential to inform judicious antimicrobial use early in the disease course.

Background Multivariate index assays (MIAs) to evaluate disease status and/or therapeutic efficacy are increasingly being used in clinical laboratories as laboratory-developed tests (LDTs). Before clinical use, diagnostic and analytical performance specifications of LDTs must be established. Several regulatory guidelines have been published that address specific components of validation procedures, but the interpretation for the analytical validation of MIAs is ambiguous and creates confusion when implementing a novel MIA in the clinical laboratory. Content CLSI guidelines and published methods were evaluated to develop a validation strategy to establish analytical sensitivity, precision, specificity, and stability for qPCR-based MIAs. Limitations and challenges identified while evaluating guidelines and literature and implementing this strategy are discussed in this review, including sample sourcing and integrity, laboratory contamination, and sample throughput. Due to the diversity of qPCR-based MIAs, we discuss additional considerations for researchers intending to transfer MIAs to a clinical laboratory. Summary A practical strategy to assess the analytical performance characteristics for validation of qPCR-based MIAs was developed and tested before diagnostic clinical use. Several important limitations, challenges, and considerations were identified during development of the analytical validation procedures that are not addressed in regulatory guidelines or published literature. The described strategy can provide insight for future developers of MIAs and clinical laboratories implementing MIAs as LDTs.