Proteomic Analysis of Urine from California Sea Lions (Zalophus californianus): a Resource for Urinary Biomarker Discovery

Abstract

Urinary markers for the assessment of kidney diseases in wild animals are limited, in part, due to the lack of urinary proteome data, especially for marine mammals. One of the most prevalent kidney diseases in marine mammals is caused by Leptospira interrogans, which is the second most common etiology linked to stranding of California sea lions (Zalophus californianus). Urine proteins from eleven sea lions with leptospirosis kidney disease and eight sea lions without leptospirosis or kidney disease were analyzed using shotgun proteomics. In total, 2694 protein groups were identified and 316 were differentially abundant between groups. Major urine proteins in sea lions were similar to major urine proteins in dogs and humans except for the preponderance of resistin, lysozyme C, and PDZ domain containing 1, which appear to be over-represented.Previously reported urine protein markers of kidney injury in humans and animals were also identified. Notably, neutrophil gelatinase-associated lipocalin, osteopontin, and epidermal fatty acid binding protein were elevated over 20-fold in the leptospirosis-infected sea lions. Consistent with leptospirosis infection in rodents, urinary proteins associated with the renin-angiotensin system were depressed, including neprilysin. This study represents a foundation from which to explore the clinical use of urinary protein markers in California sea lions.

Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

“…First, we present two annotated, chromosome‐level genome assemblies of the California sea lion, Zalophus californianus (for taxonomic considerations see Lopes et al, 2021; Wolf et al, 2007). The California sea lion is a carnivoran species that is attracting increasing interest as a wild animal model to understand the genetic and environmental interactions involved in carcinogenesis (Browning et al, 2015; Buckles et al, 2007) and other diseases (Neely et al, ,2015, 2018). The lack of a high‐quality genome assembly has impeded progress in this area.…”

Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments

“…Broader efforts such as the ongoing proteomic data analysis pipeline comparison led by the ELIXR Proteomics Community 41 will help clarify pipeline performance. For the discussion herein, a previously published study 42 with a follow-up analysis 43 of label-free data-dependent acquisition shotgun proteomic data from mammalian urine was chosen. For this example, the data was analyzed using AWS Elastic Compute Cloud (EC2) instances with an arbitrarily chosen OpenMS-based Comet-Percolator workflow constructed with KNIME (Figure 2).…”

Serum proteomics identifies immune pathways and candidate biomarkers of coronavirus infection in wild vampire bats

“…Using only 2 μL sera from these small (25– 40 gram) bats, we identified 361 proteins across five orders of magnitude, including antiviral and antibacterial components, 20S proteasome complex, and redox activity proteins. Mass spectrometry–based proteomics can thus facilitate the relative quantification of classical immunological proteins while also providing insight into proteins yet to be fully recognized for their importance in resolving viral infection (Neely et al, 2014, 2018; Geyer et al, 2017).…”