Genetic characterization of a captive marmoset (Callithrix jacchus) colony using genotype-by-sequencing.

The marmoset is a fundamental nonhuman primate model for the study of aging, neurobiology, and many other topics. Genetic management of captive marmoset colonies is complicated by frequent chimerism in the blood and other tissues, a lack of tools to enable cost-effective, genome-wide interrogation of variation, and historic mergers and migrations of animals between colonies. We implemented genotype-by-sequencing (GBS) of hair follicle derived DNA (a minimally chimeric DNA source) of 82 marmosets housed at the Southwest National Primate Research Center (SNPRC). Our primary goals were the genetic characterization of our marmoset population for pedigree verification and colony management and to inform the scientific community of the functional genetic makeup of this valuable resource. We used the GBS data to reconstruct the genetic legacy of recent mergers between colonies, to identify genetically related animals whose relationships were previously unknown due to incomplete pedigree information, and to show that animals in the SNPRC colony appear to exhibit low levels of inbreeding. Of the >99,000 single-nucleotide variants (SNVs) that we characterized, >9800 are located within gene regions known to harbor pathogenic variants of clinical significance in humans. Overall, we show the combination of low-resolution (sparse) genotyping using hair follicle DNA is a powerful strategy for the genetic management of captive marmoset colonies and for identifying potential SNVs for the development of biomedical research models.

Cell-type deconvolution of bulk RNA-Seq from kidney using opensource bioinformatic tools.

Traditional bulk RNA-Seq pipelines do not assess cell-type composition within heterogeneous tissues. Therefore, it is difficult to determine whether conflicting findings among samples or datasets are the result of biological differences or technical differences due to variation in sample collections. This report provides a user-friendly, open source method to assess cell-type composition in bulk RNA-Seq datasets for heterogeneous tissues using published single cell (sc)RNA-Seq data as a reference. As an example, we apply the method to analysis of kidney cortex bulk RNA-Seq data from female (N=8) and male (N=9) baboons to assess whether observed transcriptome sex differences are biological or technical, i.e., variation due to ultrasound guided biopsy collections. We found cell-type composition was not statistically different in female versus male transcriptomes based on expression of 274 kidney cell-type specific transcripts, indicating differences in gene expression are not due to sampling differences. This method of cell-type composition analysis is recommended for providing rigor in analysis of bulk RNA-Seq datasets from complex tissues. It is clear that with reduced costs, more analyses will be done using scRNA-Seq; however, the approach described here is relevant for data mining and meta analyses of the thousands of bulk RNA-Seq data archived in the NCBI GEO public database.

Blood pressure and the kidney cortex transcriptome response to high-sodium diet challenge in female nonhuman primates.

Blood pressure (BP) is influenced by genetic variation and sodium intake with sex-specific differences; however, studies to identify renal molecular mechanisms underlying the influence of sodium intake on BP in nonhuman primates (NHP) have focused on males. To address the gap in our understanding of molecular mechanisms regulating BP in female primates, we studied sodium-naïve female baboons (n = 7) fed a high-sodium (HS) diet for 6 wk. We hypothesized that in female baboons variation in renal transcriptional networks correlates with variation in BP response to a high-sodium diet. BP was continuously measured for 64-h periods throughout the study by implantable telemetry devices. Sodium intake, blood samples for clinical chemistries, and ultrasound-guided kidney biopsies were collected before and after the HS diet for RNA-Seq and bioinformatic analyses. We found that on the LS diet but not the HS diet, sodium intake and serum 17 ß-estradiol concentration correlated with BP. Furthermore, kidney transcriptomes differed by diet-unbiased weighted gene coexpression network analysis revealed modules of genes correlated with BP on the HS diet but not the LS diet. Our results showed variation in BP on the HS diet correlated with variation in novel kidney gene networks regulated by ESR1 and MYC; i.e., these regulators have not been associated with BP regulation in male humans or rodents. Validation of the mechanisms underlying regulation of BP-associated gene networks in female NHP will inform better therapies toward greater precision medicine for women.

A need for reevaluation of sports participation recommendations for children with a solitary kidney.

PURPOSE: We sought to evaluate the incidence and outcome of blunt renal injury in children by mechanism of injury. These data could then be used to provide the basis for more rational recommendations to parents and physicians regarding participation in sporting activities. MATERIALS AND METHODS: We analyzed data on 49,651 pediatric trauma cases collected by 92 trauma centers as part of the National Pediatric Trauma Registry from 1995 to 2001. Cases involving renal injury were isolated and the data were stratified according to age, sex and injury, as well as procedures required for treatment and outcomes. RESULTS: Of 49,651 pediatric trauma patients 813 incurred renal injury. There were 516 males and 291 females, and sex was not documented in 6 children. Average age was 10.6 years. There were no reports of a solitary kidney. In the sports group there were 4 nephrectomies, which were associated with sledding (2), skiing (1) and rollerblading (1), and 2 deaths related to skiing (1) and jet skiing (1). All 3 nephrectomies in the nonsports/other group were associated with equestrian activities, and 1 death occurred in this population. The nonsports/other group includes minor sports that are outlined by the American Academy of Pediatrics Committee on Sports Medicine and Fitness. CONCLUSIONS: The majority of renal injuries in children associated with kidney loss (21 of 28) occurred as a result of motor vehicle accidents, pedestrians being struck by a vehicle or other object, and falls. There were no kidneys lost in any contact sport. Sledding, skiing and rollerblading resulted in kidney loss. Current recommendations of the American Academy of Pediatrics Committee on Sports Medicine and Fitness prohibiting children with a solitary kidney from participating in contact sports appear to be overly protective and need to be reevaluated. In some instances activities listed as limited contact sports resulted in renal loss, showing that the risk associated with these activities has been underestimated.