Clinical veterinary proteomics: Techniques and approaches to decipher the animal plasma proteome

Proteomic analysis of uterine lavage fluid of dairy cows at different time after delivery by mass spectrometry

Endometritis is a common disease in the reproductive system, which is the infection and inflammation of the endometrium. In severe cases, it can affect the myometrium and adversely affect the subsequent fertility of dairy cows. We used a mass spectrometry-based technique to compare proteomics of uterine lavage fluid between healthy cows and cows with cytological endometritis classified according to 100-day postpartum pregnancy results and diagnosis result. The uterine lavage fluid of dairy cows collected at 15 and 30 days after delivery was analyzed. 15 days postpartum, we identified a total of 1129 proteins in the control and cytological endometritis (CEM) groups. Among them, 160 proteins were accurately screened out. 30 days postpartum, we identified a total of 846 proteins in the control and cytological endometritis (CEM) groups. Among them, 186 proteins were accurately cytological endometritis (CEM). Endometritis is a costly reproductive disease in lactating cows, which needs to be diagnosed in time. Using proteomics method based on gel mass spectrometry, we compared the proteome of uterine lavage fluid of dairy cows with and without cytological endometritis to characterize the changes of proteomic characteristics associated with postpartum uterine disease. To provide reference for clinical application and basic research.

Acute phase proteins in cats: Diagnostic and prognostic role, future directions, and analytical challenges

While clinical studies on acute phase proteins (APPs) have significantly increased in the last decade, and most commercial labs are now offering major APPs in their biochemical profiles, APP testing has not been widely adopted by veterinary clinical pathologists and veterinarians. Measurement of APP concentration is a useful marker for detecting the presence or absence of inflammation in cats with various diseases. APPs can also be reliably measured in different biological fluids (eg, effusions and urine) to improve their diagnostic utility. Measurement of APPs can be extremely beneficial in cats with feline infectious peritonitis (FIP) to discriminate between FIP and non-FIP cats with similar clinical presentations. Additional benefits come from multiple and sequential measurements of APPs, particularly in the assessment of therapeutic efficacy. APPs are more sensitive than WBC counts for early detection of inflammation and to demonstrate an early remission or recurrence of the diseases. Given the potential utility of APPs, more studies are warranted, with a particular focus on the applications of APPs to guide the length of antimicrobial therapies, as suggested by the antimicrobial stewardship policy. New inflammatory markers have been discovered in human medicine, with a higher specificity for distinguishing between septic versus nonseptic inflammatory diseases. It is desirable that these new markers be investigated in veterinary medicine, to further test the power of APPs in diagnostic setting.

Curcuminoid supplementation in canine diabetic mellitus and its complications using proteomic analysis

Introduction

Inflammation and oxidative stress contribute to diabetes pathogenesis and consequences. Therapeutic approaches for canine diabetes remain a challenge. Curcumin has anti-inflammatory and anti-oxidative effects and is beneficial for humans with diabetes mellitus (DM); however, data on its impact on canine diabetes is limited. This study aimed to evaluate the potential for causing adverse effects, anti-inflammatory effects, anti-oxidative effects and proteomic patterns of curcuminoid supplementation on canine DM.

Methods

Altogether, 18 dogs were divided into two groups: DM (n = 6) and healthy (n = 12). Curcuminoid 250 mg was given to the DM group orally daily for 180 days. Blood and urine sample collection for hematological parameters, blood biochemistry, urinalysis, oxidative stress parameters, inflammatory markers and proteomics were performed every 6 weeks.

Results and discussion

Curcuminoid supplementation with standard therapy significantly decreased oxidative stress with the increased glutathione/oxidized glutathione ratio, but cytokine levels were unaffected. According to the proteomic analysis, curcuminoid altered the expression of alpha-2-HS-glycoprotein, transthyretin, apolipoprotein A-I and apolipoprotein A-IV, suggesting that curcuminoid improves insulin sensitivity and reduces cardiovascular complications. No negative impact on clinical symptoms, kidneys or liver markers was identified. This study proposed that curcuminoids might be used as a targeted antioxidant strategy as an adjunctive treatment to minimize diabetes complications in dogs.

Plasma proteomic changes in response to surgical trauma and a novel transdermal analgesic treatment in dogs

Assessment of pain responses and inflammation during animal surgery is difficult because traditional methods, such as visual analogue scores, are not applicable while under anaesthesia. Acute phase proteins (APPs), such as C-reactive protein and haptoglobin, that are typically monitored in veterinary research, do not show a significant change until at least 2 h post-surgery and therefore, immediate pathophysiological changes are uncertain. The current study used sequential window acquisition of all theoretical mass spectra (SWATH-MS) to investigate plasma proteome changes that occur immediately following surgery in dogs and also to assess the efficacy of a novel transdermal ketoprofen (TK) formulation. Castration was chosen as surgical model in this study. The procedure was performed on twelve dogs (n = 6 in two groups) and blood samples were collected at 0 h, 1 and 2 h after surgery for proteomic analysis. Following surgery, there was a general downregulation of proteins, including complement C- 3, complement factor B, complement factor D, transthyretin, and proteins associated with lipid, cholesterol, and glucose metabolisms, reflecting the systemic response to surgical trauma. Many of these changes were diminished in the transdermal group (TD) since ketoprofen, a non-steroidal anti-inflammatory drug (NSAID), inhibits prostanoids and the associated chemotactic neutrophil migration to site of tissue injury. SIGNIFICANCE: SWATH-MS Proteomic analysis revealed significant changes in plasma proteins, predominantly involved in early acute phase and inflammatory response at 1 & 2 h after surgery in castrated dogs. Pre-operative application of transdermal ketoprofen formulation had reduced the systemic immune response, which was confirmed by negligible alteration of proteins in transdermal treated group. A key outcome of this experiment was studying the efficacy of a novel transdermal NSAID formulation in dogs.

Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma

Mass spectrometry-based plasma proteomics offers a major advance for biomarker discovery in the veterinary field, which has traditionally been limited to quantification of a small number of proteins using biochemical assays. The development of foundational data and tools related to sequential window acquisition of all theoretical mass spectra (SWATH)-mass spectrometry has allowed for quantitative profiling of a significant number of plasma proteins in humans and several animal species. Enabling SWATH in dogs enhances human biomedical research as a model species, and significantly improves diagnostic and disease monitoring capability. In this study, a comprehensive peptide spectral library specific to canine plasma proteome was developed and evaluated using SWATH for protein quantification in non-depleted dog plasma. Specifically, plasma samples were subjected to various orthogonal fractionation and digestion techniques, and peptide fragmentation data corresponding to over 420 proteins was collected. Subsequently, a SWATH-based assay was introduced that leveraged the developed resource and that enabled reproducible quantification of 400 proteins in non-depleted plasma samples corresponding to various disease conditions. The ability to profile the abundance of such a significant number of plasma proteins using a single method in dogs has the potential to accelerate biomarker discovery studies in this species.

Leveraging homologies for cross-species plasma proteomics in ungulates using data-independent acquisition

The collection of blood plasma is minimally invasive, and the fluid is a rich source of proteins for biomarker studies in both humans and animals. Plasma protein analysis by mass spectrometry (MS) can be challenging, though modern data acquisition strategies, such as sequential window acquisition of all theoretical fragment ion spectra (SWATH), enable reproducible quantitation of hundreds of proteins in non-depleted plasma from humans and laboratory model animals. Although there is strong potential to enhance veterinary and translational research, SWATH-based plasma proteomics in non-laboratory animals is virtually non-existent. One limitation to date is the lack of comprehensively annotated genomes to aid protein identification. The current study established plasma peptide spectral repositories for sheep and cattle that enabled quantification of over 200 proteins in non-depleted plasma using SWATH approach. Moreover, bioinformatics pipeline was developed to leverage inter-species homologies to enhance the depth of baseline libraries and plasma protein quantification in bovids. Finally, the practical utility of using bovid libraries for SWATH data extraction in taxonomically related non-domestic ungulate species (giraffe) has been demonstrated. SIGNIFICANCE: Ability to quickly generate comprehensive spectral libraries is limiting the applicability of data-independent acquisition, such as SWATH, to study proteomes of non-laboratory animals. We describe an approach to obtain relatively shallow foundational plasma repositories from domestic ruminants and employ homology searches to increase the depth of data, which we subsequently extend to unsequenced ungulates using SWATH method. When applied to cross-species proteomics, the number of proteins quantified by our approach far exceeds what is traditionally used in plasma protein tests.

Faecal proteome in clinically healthy dogs and cats: Findings in pooled faeces from 10 cats and 10 dogs

BACKGROUND

In the scientific literature, there are only a few manuscripts available on small animal faecal proteomics.

METHODS

In the present pilot study, this evaluation was performed using pooled faecal samples from 10 clinically healthy dogs and, for the first time, in 10 clinically healthy cats by mean of two-dimensional electrophoresis followed by liquid chromatography-tandem mass spectrometry.

RESULTS

Our results showed the presence of nine (albumin, alkaline phosphatase, chymotrypsin-C-like, cytosol aminopeptidase, elastase-3B/proteinase E, immunoglobulins and nuclear pore membrane glycoprotein 210) and 14 (albumin, caspase recruitment domain-containing protein, chymotrypsin-like, deleted in malignant brain tumours 1 protein-like, hypothetical protein LOC107375, immunoglobulin, kallikrein-1, superoxide dismutase, transthyretin precursor, interstitial collagenase-like) different proteins in canine and feline faeces, respectively.

CONCLUSION

These preliminary findings document the presence of a range of proteins in the faeces of apparently healthy dogs and cats and may serve as a basis for larger, prospective studies to establish reference proteomic data against which diseased populations can be compared.

A search for predictive biomarkers of ovine pre-partum vaginal prolapse

Ovine pre-partum vaginal prolapse (known as bearings in sheep) occurs within a few weeks prior to lambing and unless treated both ewes and unborn lambs will die. It is a worldwide problem with no clear aetiology. Rates of prolapse in New Zealand typically vary from 0.1 to 2% per annum, varying between seasons and farms. In order to determine preclinical changes leading to prolapse, blood samples were collected prior to prolapse occurring and analysed for changes in both protein and specific hormone and vitamin levels. 650 ewes were ear tagged and blood samples were taken one month prior to the beginning of lambing; 28 of these ewes subsequently prolapsed. Using an improved proteomic method plasma samples were subjected to 2D DIGE (two dimensional differential in gel electrophoresis) to determine if there were differences between the pre-prolapse and non-prolapsing ewes. Acidic isoforms of haptoglobin, a major acute phase protein in ruminants, increased approximately 3-fold in ewes prior to prolapse occurring. Total haptoglobin quantitation was confirmed with an independent assay. Although another plasma protein, α-1B-glycoprotein, was down regulated close to prolapse, the biological significance of this is unknown. While vitamin D levels were not associated with subsequent prolapse there was, however, a negative correlation between cortisol and days to prolapse from sampling (r² = 0.36); i.e. ewes sampled closest to prolapse had higher plasma cortisol concentrations than controls. This raises the possibility that the ewes which prolapsed may have been suffering from chronic stress. Further research is needed.

Exosomal Cargo May Hold the Key to Improving Reproductive Outcomes in Dairy Cows

The reproductive status of dairy cows remains a challenge for dairy farmers worldwide, with impaired fertility linked to a significant reduction in herd profitability, due in part to impaired immunity, increased metabolic pressure, and longer postpartum anestrous interval (PPAI). Exosomes are nanovesicles released from a variety of cell types and end up in circulation, and carry proteins, bioactive peptides, lipids, and nucleic acids specific to the place of origin. As such, their role in health and disease has been investigated in humans and animals. This review discusses research into exosomes in the context of reproduction in dairy herds and introduces recent advances in mass-spectrometry (MS) based proteomics that have a potential to advance quantitative profiling of exosomal protein cargo in a search for early biomarkers of cattle fertility.

Good management practices of venomous snakes in captivity to produce biological venom-based medicines: achieving replicability and contributing to pharmaceutical industry

One of the factors responsible for lack of reproducible findings may be attributed to the raw material used. To date, there are no apparent studies examining reproducibility using venoms for the development of new toxin-based drugs with respect to regulatory agencies' policies. For this reason, protocols were implemented to produce animal toxins with quality, traceability, and strict compliance with Good Manufacturing Practices. This required validation of the production chain from the arrival of the animal to the vivarium, followed by handling, housing, as well as compliance with respect to extraction, freeze-drying, and, finally, storage protocols, aimed at generating compounds to serve as candidate molecules applicable in clinical trials. Currently, to produce quality snake venoms to support reproductive studies, the Center for the Study of Venoms and Venomous Animals (CEVAP) from São Paulo State University (UNESP), São Paulo, Brazil has 449 microchipped snakes through rigid and standardized operating procedures for safety, health, and welfare of animals. Snakes were frequently subjected to vet clinical examination, anthelmintic, and antiparasitic treatment. Venom milk used to destroy prey was collected from each animal in individual plastic microtubes to avoid contamination and for traceability. In addition, venoms were submitted to microbiological, and biochemical toxicological analyses. It is noteworthy that investigators are responsible for caring, maintaining, and manipulating snakes and ensuring their health in captivity. This review aimed to contribute to the pharmaceutical industry the experimental experience and entire snake venom production chain required to generate quality products for therapeutic human consumption.

Applications of mass spectrometry imaging in virus research

Mass spectrometry imaging (MSI) is a label-free molecular imaging technique allowing an untargeted detection of a broad range of biomolecules and xenobiotics. MSI enables imaging of the spatial distribution of proteins, peptides, lipids and metabolites from a wide range of samples. To date, this technique is commonly applied to tissue sections in cancer diagnostics and biomarker development, but also molecular histology in general. Advances in the methodology and bioinformatics improved the resolution of MS images below the single cell level and increased the flexibility of the workflow. However, MSI-based research in virology is just starting to gain momentum and its full potential has not been exploited yet. In this review, we discuss the main applications of MSI in virology. We review important aspects of matrix-assisted laser desorption/ionization (MALDI) MSI, the most widely used MSI technique in virology. In addition, we summarize relevant literature on MSI studies that aim to unravel virus-host interactions and virus pathogenesis, to elucidate antiviral drug kinetics and to improve current viral disease diagnostics. Collectively, these studies strongly improve our general understanding of virus-induced changes in the proteome, metabolome and metabolite distribution in host tissues of humans, animals and plants upon infection. Furthermore, latest MSI research provided important insights into the drug distribution and distribution kinetics, especially in antiretroviral research. Finally, MSI-based investigations of oncogenic viruses greatly increased our knowledge on tumor mass signatures and facilitated the identification of cancer biomarkers.

Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology

Data-independent acquisition mass spectrometry (DIA-MS) is a next generation proteomic methodology that generates permanent digital proteome maps offering highly reproducible retrospective analysis of cellular and tissue specimens. The adoption of this technology has ushered a new wave of oncology studies across a wide range of applications including its use in molecular classification, oncogenic pathway analysis, drug and biomarker discovery and unravelling mechanisms of therapy response and resistance. In this review, we provide an overview of the experimental workflows commonly used in DIA-MS, including its current strengths and limitations versus conventional data-dependent acquisition mass spectrometry (DDA-MS). We further summarise a number of key studies to illustrate the power of this technology when applied to different facets of oncology. Finally we offer a perspective of the latest innovations in DIA-MS technology and machine learning-based algorithms necessary for driving the development of high-throughput, in-depth and reproducible proteomic assays that are compatible with clinical diagnostic workflows, which will ultimately enable the delivery of precision cancer medicine to achieve optimal patient outcomes.

Plasma proteomic profiles differ between European and North American myotid bats colonized by Pseudogymnoascus destructans

Emerging fungal diseases have become challenges for wildlife health and conservation. North American hibernating bat species are threatened by the psychrophilic fungus Pseudogymnoascus destructans (Pd) causing the disease called white-nose syndrome (WNS) with unprecedented mortality rates. The fungus is widespread in North America and Europe, however, disease is not manifested in European bats. Differences in epidemiology and pathology indicate an evolution of resistance or tolerance mechanisms towards Pd in European bats. We compared the proteomic profile of blood plasma in healthy and Pd-colonized European Myotis myotis and North American Myotis lucifugus in order to identify pathophysiological changes associated with Pd colonization, which might also explain the differences in bat survival. Expression analyses of plasma proteins revealed differences in healthy and Pd-colonized M. lucifugus, but not in M. myotis. We identified differentially expressed proteins for acute phase response, constitutive and adaptive immunity, oxidative stress defence, metabolism and structural proteins of exosomes and desmosomes, suggesting a systemic response against Pd in North American M. lucifugus but not European M. myotis. The differences in plasma proteomic profiles between European and North American bat species colonized by Pd suggest European bats have evolved tolerance mechanisms towards Pd infection.

Bioinformatics approaches for improving seminal plasma proteome analysis

Reproduction efficiency of male animals is one of the key factors influencing the sustainability of livestock. Mass spectrometry (MS) based proteomics has become an important tool for studying seminal plasma proteomes. In this review, we summarize bioinformatics analysis strategies for current proteomics approaches, for identifying novel biomarkers of reproductive robustness.