Feasibility of using gene expression analysis to study canine soft tissue sarcomas

Comparative whole transcriptome analysis of gene expression in three canine soft tissue sarcoma types

Soft tissue sarcomas are pleiotropic tumors of mesenchymal cell origin. These tumors are rare in humans but common in veterinary practice, where they comprise up to 15% of canine skin and subcutaneous cancers. Because they present similar morphologies, primary sites, and growth characteristics, they are treated similarly, generally by surgical resection followed by radiation therapy. Previous studies have examined a variety of genetic changes as potential drivers of tumorigenesis and progression in soft tissue sarcomas as well as their use as markers for soft tissue sarcoma subtypes. However, few studies employing next generation sequencing approaches have been published. Here, we have examined gene expression patterns in canine soft tissue sarcomas using RNA-seq analysis of samples obtained from archived formalin-fixed and paraffin-embedded tumors. We provide a computational framework for using resulting data to categorize tumors, perform cross species comparisons and identify genetic changes associated with tumorigenesis. Functional overrepresentation analysis of differentially expressed genes further implicate both common and tumor-type specific transcription factors as potential mediators of tumorigenesis and aggression. Implications for tumor-type specific therapies are discussed. Our results illustrate the potential utility of this approach for the discovery of new therapeutic approaches to the management of canine soft tissue sarcomas and support the view that both common and tumor-type specific mechanisms drive the development of these tumors.

Metabolic Profiling of Urinary Chiral Amino-Containing Biomarkers for Gastric Cancer Using a Sensitive Chiral Chlorine-Labeled Probe by HPLC-MS/MS

Screening of characteristic biomarkers from chiral amino-containing metabolites in biological samples is difficult and important for the noninvasive diagnosis of gastric cancer (GC). Here, an enantiomeric pair of chlorine-labeled probes d-BPCl and l-BPCl was synthesized to selectively label d- and l-amino-containing metabolites in biological samples, respectively. Incorrect structural annotations were excluded according to the characteristic 3:1 abundance ratio of natural chlorine isotopes (³⁵Cl and ³⁷Cl) derived from the probes. A sensitive C18 HPLC-QQQ-MS/MS method in combination with the probes was then developed and applied in metabolomic analysis of amino-containing metabolites in urine samples. A total of 161 amino-containing metabolites were rapidly separated and determined, and 28 chiral amino acids and achiral glycine were quantified with good precision and accuracy. A total of 18 differential variables were discriminated by analyzing chiral amino-containing metabolites in urine samples of the GC patient and healthy person using the probe-based HPLC-MS/MS-MRM method combined with the orthogonal partial least squares discriminant analysis and Mann-Whitney U test with false discovery rate correction for multiple hypotheses. A diagnostic regression model including d-isoleucine, d-serine, and β-(pyrazol-1-yl)-l-alanine and age was then constructed with an average prediction correctness of 88.9% in the validation set. This work established a close connection between gastric cancer and chiral amino-containing metabolites. The mass spectrometry data analyzed in the study are publicly available via Mendeley Data (DOI: 10.17632/4bd93j9yrr.1).

Genomics and transcriptomics in veterinary oncology

The sequencing of the canine genome, combined with additional genomic technologies, has created opportunities for research linking veterinary genomics with naturally occurring cancer in dogs. Also, as numerous canine cancers have features in common with human cancers, comparative studies can be performed to evaluate the use of cancers in dogs as models for human cancer. There have been several reviews of veterinary genomics but, to the best of our knowledge, there has been no comprehensive review of the literature of canine cancer genomics. PubMed and CAB Abstracts databases were searched to retrieve relevant literature using the search terms ‘veterinary’, ‘cancer’ or ‘oncology’, and ‘genomics’ or ‘transcriptomics’. Results were manually assessed and grouped based on the techniques used, the cancer type investigated and genomic lesions targeted. The search resulted in the retrieval of 44 genomic and transcriptomic studies, with the most common technique employed being comparative genomic hybridization. Across both fields, the most commonly studied cancer type was canine osteosarcoma. Genomic and transcriptomic aberrations in canine cancer often reflected those reported in the corresponding human cancers. Analysis of the literature indicated that employing genomic and transcriptomic technologies has been instrumental in developing the understanding of the origin, development and pathogenesis of several canine cancers. However, their use in canine oncology is at an early phase, and there appears to be comparatively little understanding of certain canine cancer types in contrast to their human forms. Aberrations detected in all tumors were tabulated, and the results for osteosarcoma, lymphoma and leukemia, mast cell tumor, transmissible venereal tumor and urothelial carcinoma discussed in detail.

Sarcomas-A barren immunological wasteland or field of opportunity for immunotherapy?

Key advances in our understanding of immunobiology and the immunosuppressive mechanisms of the tumour microenvironment have led to significant breakthroughs in manipulating the immune system to successfully treat cancer. Remarkable therapeutic responses have occurred with tumours that carry a high mutational burden. In these cases, pre-existing tumour-specific T cells can be rejuvenated via checkpoint inhibition to eliminate tumours. Furthermore, durable remissions have been achieved in haematological malignancies following adoptive transfer of T cells that specifically target cell surface proteins where expression is restricted to the malignancy's cell of origin. Soft tissue sarcomas and bone sarcomas have a paucity of non-synonymous somatic mutations and do not commonly express known, targetable, tumour-specific antigens. Historically, soft tissue sarcomas have been considered immunologically 'cold' and as such, unlikely candidates for immune therapy. Here, we review the immune landscape of canine and feline sarcomas and the immunotherapeutic strategies that have been employed in veterinary clinical trials to improve patient outcome. We also provide insight into immunotherapeutic approaches being used to treat human sarcomas. Together, current data indicates that, rather than a barren immunological wasteland, sarcomas represent a field of opportunities for immunotherapies. Furthermore, we and others would suggest that strategic combinations of immunotherapeutic approaches may hold promise for more effective treatments for high grade soft tissue sarcomas and bone sarcomas.

Canine Soft Tissue Sarcomas: Can Being a Dog's Best Friend Help a Child?

Soft tissue sarcomas (STSs) remain a therapeutic challenge for pediatric and adolescent and young adult (AYA) patients. Still today, surgery, radiation therapy, and chemotherapy remain the mainstay of treatment. Obstacles in developing new treatment approaches to improve the outcome are: few patients to enroll in clinical trials, and the diversity of tumor biology between histologic subtypes. Pet dogs may offer an additional strategy to discover and test new therapeutic avenues. The number of dogs diagnosed with a STS each year in the United States is estimated to be around 27,000 to 95,000. In comparison, approximately 900 children less than 20 years old and 1,500 AYAs between 15 and 29 years old are diagnosed with a STS each year in the United States. The mainstay for treatment of STSs in dogs is also surgery, with radiation therapy and chemotherapy when necessary. Similar to what is seen in humans, grade and stage are prognostic in dogs. In one comparative study of the histology and immunohistochemistry of canine STSs, most tumors were diagnosed as the human equivalent of undifferentiated sarcoma, spindle cell sarcoma, or unclassified spindle cell sarcoma. But much work remains to be done to fully assess the validity of canine STSs as a model. Gene expression analysis has been done in a limited number of canine STSs. Tissue banking, development of cell lines, and the ability to mobilize large-scale clinical trials will become essential in veterinary medicine to benefit both dogs and humans.

Proteases as prognostic markers in human and canine cancers

The extracellular matrix (ECM) is composed of several types of proteins, which interact and form dynamic networks. These components can modulate cell behaviour and actively influence the growth and differentiation of tissues. ECM is also important in several pathological processes, such as cancer invasion and metastasis, by creating favourable microenvironments. Proteolysis in neoplastic tissues is mediated by proteinases, whose regulation involves complex interactions between neoplastic cells and non-neoplastic stromal cells. In this review, we discuss aspects of proteinase expression and tumor behaviour in humans and dogs. Different classes of proteases are summarized, with special emphasis being placed on molecules that have been shown to correlate with prognosis, reinforcing the need for a better understanding of the regulation of this microenvironment and its influences in tumor progression and metastasis, which should significantly aid the development of improved prognosis and treatment.

Gene expression profiling of histiocytic sarcomas in a canine model: the predisposed flatcoated retriever dog

BACKGROUND

The determination of altered expression of genes in specific tumor types and their effect upon cellular processes may create insight in tumorigenesis and help to design better treatments. The Flatcoated retriever is a dog breed with an exceptionally high incidence of histiocytic sarcomas. The breed develops two distinct entities of histiocytic neoplasia, a soft tissue form and a visceral form. Gene expression studies of these tumors have value for comparable human diseases such as histiocytic/dendritic cell sarcoma for which knowledge is difficult to accrue due to their rare occurrence. In addition, such studies may help in the search for genetic aberrations underlying the genetic predisposition in this dog breed.

METHODS

Microarray analysis and pathway analyses were performed on fresh-frozen tissues obtained from Flatcoated retrievers with localized, soft tissue histiocytic sarcomas (STHS) and disseminated, visceral histiocytic sarcomas (VHS) and on normal canine spleens from various breeds. Expression differences of nine genes were validated with quantitative real-time PCR (qPCR) analyses.

RESULTS

QPCR analyses identified the significantly altered expression of nine genes; PPBP, SpiC, VCAM1, ENPEP, ITGAD (down-regulated), and GTSF1, Col3a1, CD90 and LUM (up-regulated) in the comparison of both the soft tissue and the visceral form with healthy spleen. DAVID pathway analyses revealed 24 pathways that were significantly involved in the development of HS in general, most of which were involved in the DNA repair and replication process.

CONCLUSIONS

This study identified altered expression of nine genes not yet implicated in histiocytic sarcoma manifestations in the dog nor in comparable human histiocytic/dendritic sarcomas. Exploration of the downside effect of canine inbreeding strategies for the study of similar sarcomas in humans might also lead to the identification of genes related to these rare malignancies in the human.

A novel imaging system permits real-time in vivo tumor bed assessment after resection of naturally occurring sarcomas in dogs

BACKGROUND

Treatment of soft tissue sarcoma (STS) includes complete tumor excision. However, in some patients, residual sarcoma cells remain in the tumor bed. We previously described a novel hand-held imaging device prototype that uses molecular imaging to detect microscopic residual cancer in mice during surgery.

QUESTIONS/PURPOSES

To test this device in a clinical trial of dogs with naturally occurring sarcomas, we asked: (1) Are any adverse clinical or laboratory effects observed after intravenous administration of the fluorescent probes? (2) Do canine sarcomas exhibit fluorescence after administration of the cathepsin-activated probe? (3) Is the tumor-to-background ratio sufficient to distinguish tumor from tumor bed? And (4) can residual fluorescence be detected in the tumor bed during surgery and does this correlate with a positive margin?

METHODS

We studied nine dogs undergoing treatment for 10 STS or mast cell tumors. Dogs received an intravenous injection of VM249, a fluorescent probe that becomes optically active in the presence of cathepsin proteases. After injection, tumors were removed by wide resection. The tumor bed was imaged using the novel imaging device to search for residual fluorescence. We determined correlations between tissue fluorescence and histopathology, cathepsin protease expression, and development of recurrent disease. Minimum followup was 9 months (mean, 12 months; range, 9-15 months).

RESULTS

Fluorescence was apparent from all 10 tumors and ranged from 3 × 10(7) to 1 × 10(9) counts/millisecond/cm(2). During intraoperative imaging, normal skeletal muscle showed no residual fluorescence. Histopathologic assessment of surgical margins correlated with intraoperative imaging in nine of 10 cases; in the other case, there was no residual fluorescence, but tumor was found at the margin on histologic examination. No animals had recurrent disease at 9 to 15 months.

CONCLUSIONS

These initial findings suggest this imaging system might be useful to intraoperatively detect residual tumor after wide resections.

CLINICAL RELEVANCE

The ability to assess the tumor bed intraoperatively for residual disease has the potential to improve local control.

DCE-MRI: a review and applications in veterinary oncology

Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is a functional imaging technique that assesses the physiology of tumour tissue by exploiting abnormal tumour microvasculature. Advances made through DCE-MRI include improvement in the diagnosis of cancer, optimization of treatment choices, assessment of treatment efficacy and non-invasive identification of prognostic information. DCE-MRI enables quantitative assessment of tissue vessel density, integrity, and permeability, and this information can be applied to study of angiogenesis, hypoxia and the evaluation of various biomarkers. Reproducibility of DCE-MRI results is important in determining the significance of observed changes in the parameters. As improvements are made towards the utility of DCE-MRI and interpreting biologic associations, the technique will be applied more frequently in the study of cancer in animals. Given the importance of tumour perfusion with respect to tumour oxygenation and drug delivery, the use of DCE-MRI is a convenient and powerful way to gain basic information about a tumour.