Changes in the serum proteome of canine lymphoma identified by electrophoresis and mass spectrometry

Characterization of biomarkers in blood serum for cancer diagnosis in dogs using Raman spectroscopy

Biomarkers of cancer in sera of domestic dogs were detected through Raman spectroscopy with 830 nm excitation. Raman spectra of sera from 61 dogs (31 healthy and 30 with cancer, resulting in 154 and 200 spectra, respectively) were submitted to principal component analysis (PCA) for feature extraction and partial least squares (PLS) regression for discrimination between Healthy and Cancer groups. In the PCA, the peaks at 1132, 1342, 1368, and 1453 cm-1 (albumin and phenylalanine) were higher for the Cancer group. The "redshift" of the peaks at 621, 1003, and 1032 cm-1 (conformational change in proteins and/or bonds at sites close to the aromatic ring of amino acids) occurred in the Cancer group, and the peaks at 451 cm-1 (tryptophan) and 1441 cm-1 (lipids) were higher for the Healthy group. The PLS-DA classified the serum spectra in Healthy and Cancer groups with high accuracy (78%).

Generating Detailed Spectral Libraries for Canine Proteomes Obtained from Serum and Urine

Domestic dogs (Canis lupus familiaris) are popular companion animals. Increase in medical expenses associated with them and demand for extending their lifespan in a healthy manner has created the need to develop new diagnostic technology. Companion dogs also serve as important animal models for non-clinical research as they can provide various biological phenotypes. Proteomics have been increasingly used on dogs and humans to identify novel biomarkers of various diseases. Despite the growing applications of proteomics in liquid biopsy in veterinary medicine, no publicly available spectral assay libraries have been created for the proteome of canine serum and urine. In this study, we generated spectral assay libraries for the two-representative liquid-biopsy samples using mid-pH fractionation that allows in-depth understanding of proteome coverage. The resultant canine serum and urine spectral assay libraries include 1,132 and 4,749 protein groups and 5,483 and 25,228 peptides, respectively. We built these complimentary accessible resources for proteomic biomarker discovery studies through ProteomeXchange with the identifier PXD034770.

Urinary Proteins of Female Domestic Dog (Canis familiaris) during Ovarian Cycle

The presence and identity of non-volatile chemical signals remain elusive in canines. In this study, we aim to evaluate the urinary proteins of female domestic dogs in the estrus and anestrus phases to evidence the presence of non-volatile chemical signals and to elucidate their identities. We collected urine samples from eight female dogs in the estrus and anestrus phases. A total of 240 proteins were identified in the urine samples using liquid chromatography-mass spectrometry (LC-MS analysis). The comparison of the proteins revealed a significant difference between the estrus and anestrus urine. We identified proteins belonging to the lipocalin family of canines (beta-lactoglobulin-1 and beta-lactoglobulin-2, P33685 and P33686, respectively), one of whose function was the transport of pheromones and which was present only in the estrus urine samples. Moreover, proteins such as Clusterin (CLU), Liver-expressed antimicrobial peptide 2 (LEAP2), and Proenkephalin (PENK) were more abundant in the estrus urine when compared to the anestrus urine. LEAP2 was recently described as a ghrelin receptor antagonist and implicated in regulating food intake and body weight in humans and mice. Proenkephalin, a polypeptide hormone cleaved into opioid peptides, was also recognized as a candidate to determine kidney function. As of yet, none of these have played a role in chemical communication. Clusterin, an extracellular chaperone protecting from protein aggregation implicated in stress-induced cell apoptosis, is a plausible candidate in chemical communication, which is a claim that needs to be ascertained further. Data are available via ProteomeXchange with the identifier PXD040418.

Investigation of proteomic profiles in canine lymphoma using tandem mass tag-based quantitative proteomics approach

Background and Aim:

Specific tumor biomarkers are useful for the early diagnosis of cancer or can predict the recurrence of neoplastic disease in humans and animals. Lymphoma in dogs could be classified into B-, T-, and NK-cell origins. T-cell lymphoma has the worst prognosis with a shorter survival time and disease-free interval. This study aimed to identify the differential serum protein expressions of canine B- and T-cell lymphomas compared with healthy dogs using a tandem mass tag (TMT)-based quantitative proteomics.

Materials and Methods:

Serum samples were collected from 20 untreated canine lymphomas (14 B-cells and 6 T-cells) and four healthy control dogs. Sera peptides from each sample were processed for TMT 10-plex tagging and analyzed using liquid chromatography-mass spectrometry (MS). Differential proteome profiling was then compared between lymphoma and control.

Results:

We discovered 20 elevated and 14 decreased serum proteins in the lymphoma group relative to the healthy group. Six candidate increased proteins in canine lymphomas were beta-actin cytoplasmic 1 (ACTB, p=0.04), haptoglobin (p=0.002), beta-2 microglobulin (aaaaaaaa2M, p=0.007), beta-2 glycoprotein 1 (APOH, p=0.03), metalloproteinase inhibitor 1 (TIMP-1, p=0.03), and CD44 antigen (p=0.02). When compared between B- and T-cell lymphomas, B-cell phenotypes had upregulated immunoglobulin (Ig) heavy chain V region GOM (p=0.02), clusterin (p=0.01), apolipoprotein C1 (APOC1, p=0.05), and plasminogen (p=0.02).

Conclusion:

These findings were investigated quantitative serum proteomes between B- and T-cell lymphomas using TMT-based MS. ACTB, aaaaaaaa2M, APOH, TIMP-1, CD44 antigen, Ig heavy chain V region GOM, and APOC1 are novel candidate proteins and might serve as a lymphoma biomarker in dogs. However, evaluation with an increased sample size is needed to confirm their diagnostic and prognostic ability.

Prospective evaluation of the lymph node proteome in dogs with multicentric lymphoma supplemented with sulforaphane

Background

Lymphoma (LSA) is a common malignancy in dogs. Epigenetic changes are linked to LSA pathogenesis and poor prognosis in humans, and LSA pathogenesis in dogs. Sulforaphane (SFN), an epigenetic‐targeting compound, has recently gained interest in relation to cancer prevention and therapy.

Objective

Examine the impact of oral supplementation with SFN on the lymph node proteome of dogs with multicentric LSA.

Animals

Seven client‐owned dogs with multicentric LSA.

Methods

Prospective, nonrandomized, noncontrolled study in treatment‐naïve dogs with intermediate or large cell multicentric LSA. Lymph node cell aspirates were obtained before and after 7 days of oral supplementation with SFN, and analyzed via label‐free mass spectrometry, immunoblots, and Gene Set Enrichment Analysis.

Results

There was no clinical response and no adverse events attributed to SFN. For individual dogs, the expression of up to 650 proteins changed by at least 2‐fold (range, 2‐100) after supplementation with SFN. When all dogs where analyzed together, 14 proteins were significantly downregulated, and 10 proteins were significantly upregulated after supplementation with SFN (P < .05). Proteins and gene sets impacted by SFN were commonly involved in immunity, response to oxidative stress, gene transcription, apoptosis, protein transport, maturation and ubiquitination.

Conclusions and Clinical Importance

Sulforaphane is associated with major changes in the proteome of neoplastic lymphocytes in dogs.

Preliminary assessment of serum clusterin as a potential biomarker for canine lymphoma

Clusterin (CLU), also known as apolipoprotein J, is a widely expressed, heterodimeric, glycoprotein, important in tumourigenesis, apoptosis and immunoregulation. In humans, CLU expression has been associated with anaplastic large cell and Hodgkin's lymphoma. In this study, serum CLU levels in dogs with multicentric lymphoma (MLSA) were compared with healthy control dogs, using both western blot and enzyme-linked immunosorbent assay (ELISA). Western blot confirmed the presence of CLU in dog sera at the predicted molecular weight and the relative levels detected correlated with the levels detected by ELISA. CLU level analysis by ELISA found treatment naïve dogs with MLSA had a significantly (P < .001) lower serum CLU level compared with healthy controls. However, there was no significant difference between MLSA dogs prior to treatment and in complete remission. The wide variation in serum CLU levels may limit its potential as a single candidate biomarker for MLSA, although any prognostic predictive value of serum CLU concentrations has yet to be assessed.

Protein characterization using electrophoresis and immunofixation; a case-based review of dogs and cats

Protein electrophoresis and immunotyping can be a useful adjunct to the standard biochemical techniques for characterizing serum and urine proteins. This paper reviews currently available and commonly used methods for diagnostic protein electrophoresis, including both agarose gel and capillary zone electrophoretic techniques and total protein assessments. Immunofixation and immunosubtraction methods for identification of immunoglobulin location and class are also presented. Practical application of quality assurance and quality control strategies in compliance with American Society of Veterinary Clinical Pathology (ASVCP) best practices are discussed. Commonly encountered serum and urine electrophoretic diagnostic patterns, including electrophoretically normal, acute-phase protein responses, polyclonal gammopathies, restricted polyclonal/oligoclonal gammopathies, paraproteinemias (monoclonal or biclonal gammopathies), and Bence-Jones proteinurias are also reviewed using relevant case material. Cases in which immunofixation electrophoresis are particularly useful are highlighted, and methodologies to more accurately quantify serum monoclonal proteins (M-proteins), monitoring tests commonly used in human medicine, are discussed.

Serum protein electrophoresis in healthy and injured southern white rhinoceros (Ceratotherium simum simum)

Investigation of globulin fractions by serum protein electrophoresis (SPE) is the first step towards evaluation of the proteome in the southern white rhinoceros (Ceratotherium simum simum). Furthermore, identification of changes in globulins in animals with poaching and other injuries can guide discovery of potentially useful biomarkers of inflammation. The aim of this study was to develop reference intervals for agarose gel SPE in healthy white rhinoceros and to compare these serum protein electrophoresis results to those from animals with tissue trauma. Reference intervals for total serum protein and agarose gel electrophoretic albumin and globulin fractions were generated using serum samples from 49 healthy free-ranging adult white rhinoceros. A standardised gating system together with identification of specific proteins by mass spectrometry aided in fraction identification. Six globulin fractions were identified: α1a, α1b, α2, β1, β2 and γ. Reference intervals were generated for total serum protein (76–111 g/L), albumin (10–27 g/L) and globulin fractions (α1a: 1.6–3.2 g/L; α1b: 1.7–3.6 g/L; α2: 16.1–26.6 g/L; β1: 6.6–18.2 g/L; β2: 11.8–30.4 g/L; γ: 10.4–23.1 g/L; albumin: globulin ratio: 0.12–0.39). Results were compared to those from 30 animals with various degrees and chronicities of tissue trauma. Wounded animals had lower concentrations of total serum protein, albumin, total globulin, α and β1 globulins, lower percentages of α2 and β1 globulins, and higher percentages of β2 and γ globulins. These protein changes are similar to those seen in human patients with wounds rather than classic acute phase or chronic inflammatory responses.

Proteomic analysis of canine oral tumor tissues using MALDI-TOF mass spectrometry and in-gel digestion coupled with mass spectrometry (GeLC MS/MS) approaches

Oral tumors, including highly invasive and metastatic oral melanoma (OM), non-tonsillar oral squamous cell carcinoma (OSCC) and benign tumors (BN), are common neoplasms in dogs. Although these tumors behave differently, limited data of their protein expression profiles have been exhibited, particularly at the proteome level. The present study aimed to i.) characterize peptide-mass fingerprints (PMFs) and identify potential protein candidates of OM, OSCC, BN and normal control subjects, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS), ii.) identify potential protein candidates associated with the diseases, using in-gel digestion coupled with mass spectrometric analysis (GeLC-MS/MS) and iii.) search for relationships between chemotherapy drugs and disease-perturbed proteins. A distinct cluster of each sample group and unique PMFs with identified protein candidates were revealed. The unique peptide fragment at 2,274 Da of sacsin molecular chaperone (SACS) was observed in early-stage OM whereas the fragment at 1,958 Da of sodium voltage-gated channel alpha subunit 10 (SCN10A) was presented in early- and late-stage OM. The peptide mass at 2,316 Da of Notch1 appeared in early-stage OM and benign oral tumors while the peptide mass at 2,505 Da of glutamate ionotropic receptor N-methyl-D-aspartate type subunit 3A (GRIN3A) was identified in all groups. Markedly expressed proteins from GeLC-MS/MS included Jumonji domain containing 1C (JMJD1C) in benign tumors, inversin (INVS) and rho guanine nucleotide exchange factor 28 (ARHGEF28) in OM, BTB domain-containing 16 (BTBD16) in OSCC, and protein tyrosine phosphatase non-receptor type 1 (PTPN1), BRCA2, DNA repair associated (BRCA2), WW domain binding protein 2 (WBP2), purinergic receptor P2Y1 and proteasome activator subunit 4 (PSME4) in all cancerous groups. The network connections between these proteins and chemotherapy drugs, cisplatin and doxorubicin, were also demonstrated. In conclusion, this study unveiled the unique PMFs and novel candidate protein markers of canine oral tumors.

Application of post-genomic techniques in dog cancer research

Omics techniques have been widely applied to veterinary science, although mostly on farm animal productions and infectious diseases. In canine oncology, on the contrary, the use of omics methodologies is still far behind. This review presents the most recent achievement in the application of postgenomic techniques, such as transcriptomics, proteomics, and metabolomics, to canine cancer research. The protocols to recover material suitable for omics analyses from formalin-fixed, paraffin-embedded tissues are presented, and omics applications for biomarker discovery and their potential for cancer diagnostics in veterinary medicine are highlighted.

Evaluation of the modified Glasgow Prognostic Score to predict outcome in dogs with newly diagnosed lymphoma

The modified Glasgow Prognostic Score (mGPS) assigns a numerical value (0-2) from pre-treatment serum concentrations of C-reactive protein (CRP) and albumin to predict patient outcome. CRP and albumin were evaluated in 77 untreated dogs with lymphoma to determine the relationship of mGPS to clinicopathological parameters and whether it could predict progression-free (PFS) and overall survival (OS) in treated dogs. mGPS distribution was significantly associated with clinical stage, substage b, weight loss, gastrointestinal disturbances and lethargy at presentation. On univariate analysis, mGPS was significantly associated with OS and PFS, with shorter median survival times for mGPS 2 compared to mGPS 0 and 1 combined. Hypoalbuminaemia significantly reduced OS and PFS, however increased CRP had no effect. Only clinical stage was significantly associated with OS and PFS on both univariate and multivariate analysis. mGPS has potential prognostic value for canine lymphoma , but further studies are needed.

Transgenic soybeans and soybean protein analysis: an overview

To meet the increasing global demand for soybeans for food and feed consumption, new high-yield varieties with improved quality traits are needed. To ensure the safety of the crop, it is important to determine the variation in seed proteins along with unintended changes that may occur in the crop as a result various stress stimuli, breeding, and genetic modification. Understanding the variation of seed proteins in the wild and cultivated soybean cultivars is useful for determining unintended protein expression in new varieties of soybeans. Proteomic technology is useful to analyze protein variation due to various stimuli. This short review discusses transgenic soybeans, different soybean proteins, and the approaches used for protein analysis. The characterization of soybean protein will be useful for researchers, nutrition professionals, and regulatory agencies dealing with soy-derived food products.