Research & Development

Exosomes

Background:

Exosomes, microparticles and apoptotic bodies, collectively referred to extracellular vesicles (EVs), have become a great point of interest in the last few years as potential biomarkers in conditions ranging from cancer to Alzheimer’s Disease. Although these three subgroups of particles have distinctive mechanisms of formation, all three are biologically active particles containing biological material which have been shown to play an important role in certain pathologies.

Relevance:

In the central nervous system (CNS), extracellular vesicles can mediate neuronal and glia communication, promote neuronal repair and growth and contribute to the progression of glioblastoma and neurodegenerative diseases. Growing evidence indicates that exosomes are potentially important biomarkers of neurodegenerative diseases such as Alzheimer’s and Parkinson’s Diseases.

In-house objectives and outcomes:

The EV field suffers from the lack of an easy, fast, and reliable method for quantification and characterization of these nanosized vesicles on a single particle level. Currently, characterization of EV is mainly based on the level of total amount of proteins and/or lipids in bulk isolates from biological samples. However, the methods used for bulk isolates, such as mass spectrometry or western blotting, are rigid because they cannot discern whether the observed difference in protein/lipid abundance reflects the change in the number of EVs or their composition, mostly due to the absence of invariant ‘‘household’’ EV markers.

Flow cytometry is a powerful technology for the rapid counting and characterization of cells (10,000 – 50,000 nm diameter) however current technology is still lacking in its capability to differentiate and characterize these particles. At Synexa, we are investigating a variety of platforms and in-house stabilization techniques in order to study the biomarker potential of these particles.

LymphoSure™

Background:

Whole blood quality control (QC) standards used for flow cytometric analysis have been continuously developed and improved over the last decade. Whole blood QCs have the advantage of mimicking properties of patient samples with no need for pre-analytical preparation. LymphoSure™ is a preparation of stabilized human peripheral blood developed using Synexa’s proprietary cell stabilization technology. LymphoSure™ overcomes the shortcomings of existing EQA standards, providing consistent scatter properties and a long shelf-life of up to 69 days. LymphoSure™ can be used as an internal- (IQA) or external quality assurance (EQA) standard and is currently distributed to almost 500 laboratories globally. LymphoSure™ is a research and IVD accredited medical device compatible with a wide range of flow cytometry platforms and bench-top analysers. It is the ideal QA standard for flow cytometric analysis of lymphocyte subsets, displaying clear and consistent scatter properties and enabling high-quality gating.

Relevance:

LymphoSure™ is used for TBNK lymphocyte subset analysis and is mainly relevant in HIV related research and diagnostic centres. In HIV/AIDS diagnosis, the World Health Organization Quality Guidelines recommend that in addition to viral load testing, CD4 count is necessary for the initiation of antiretroviral treatment for HIV patients. Whole blood QC materials such as LymphoSure™ are relevant for internal and external quality assurance and monitoring of disease progression and response to therapy. LymphoSure™ can also be used for the comparison of results across medical sites and for monitoring staff competency.

In-house objectives and outcomes:

Synexa aims to support immunological laboratory processes by providing a QC material that covers a variety of markers relevant to various clinical trial studies. Our goal is to expand on the product range and immunological relevance by collaborating with other scientific companies to explore R&D of more medical materials relevant to current and growing medical niche.

Microbiome

Background:

The human body is home to a vast network of microbial life which is dominated by bacteria, and complemented by fungi, archaea, and viruses. The vast majority of the microbiota is found in the intestinal tract, but other sites, such as the skin, oral cavity, respiratory system, genitals, and other systems, all have their own unique populations. Over the last decade, our understanding of the composition and function of the intestinal microbiota has grown exponentially and the number of species described to date is in excess of 1000, with any individual harbouring 300-400 species of bacteria in their intestinal tracts.
In addition to well-known functions such as aiding in digestion, assisting in the elimination of pathogens and production of beneficial chemicals, and protecting the integrity of the intestinal mucosal barrier, these commensal organisms are critical to immune homeostasis.

Relevance:

Many factors can disturb the balance (eubiosis) of the intestinal population, leading to dysbiosis. Major contributors to dysbiosis are repeated use of antibiotics, certain chronic medications, poor diet, and sedentary lifestyle. A continuously expanding list of diseases have been associated with dysbiosis, however, the causal relationship is not clearly defined in all cases.

Synexa objectives and outcomes:

In the clinical trial setting, the static and dynamic properties of the intestinal microbiome have emerged as potential biomarkers for the clarification of individual variability in response to therapeutics. In order to gain an understanding of the role played by the microbiome in variations in drug metabolism and its use as a biomarker in clinical trials, Synexa utilizes sequencing, PCR and culture-based technologies to study the microbiome in combination with the latest bioinformatic and in-house developed reporting formats to aid interpretation.

Circulating Tumour Cells (CTCs)

Background:

Traditionally, tissue biopsies have been the source of genetic and epigenetic oncology biomarkers. The presence of a driver and/or actionable mutations can act as a prognostic factor or as a predictor of either response or non-response to therapy. Examples of biomarkers as predictors of response include HER2 expression and BRCA mutation in breast cancer, BRAF mutation in melanoma, EGFR mutations in non-small cell lung cancer (NSCLC), KRAS mutations in colorectal cancer, and the Philadelphia chromosomal translocation in chronic myelogenous leukaemia.
It is apparent that there is a significant amount of tumour spatial and temporal heterogeneity. Thus, a single biopsy is not necessarily representative of the whole tumour’s mutational burden raising concerns about basing a therapy on the sequencing data of a single biopsy. Moreover, most solid tumours have an intrinsic genetic instability and treatment courses can result in the selection of acquired resistance mutations. Since the acquired resistance mutation generally appears during the course of the therapy, it would not have been present at the initial biopsy. However, multiple sequential biopsies are not routinely undertaken due to their invasive nature. Consequently, there are limitations to the information one could gather from tumour biopsies.

Relevance:

There are several alternative sources of cancer biomarkers other than biopsies. These include serum, plasma, sputum, saliva, bronchoalveolar lavage (BAL), pleural effusion, volatile organic compounds (VOC), urine and cerebrospinal fluid. However, often these tests provide insufficient material for genetic testing and do not fully represent tumour heterogeneity. They are often invasive, discomforting for the patient, and cannot be repeated on a regular basis.
A more recent approach aims to overcome the spatial and temporal heterogeneity limitations of biopsies as well the decreased sensitivity of serum biomarkers.
Liquid biopsies encompass circulating tumour cells (CTCs), circulating tumour DNA (ctDNA/cfDNA), circulating miRNAs and exosomes. These are shed into the bloodstream from the primary tumour and the metastases. Thus, a non-invasive blood sample can provide information on prognostic and predictive biomarkers, as well as monitoring the cancer progression and the presence of acquired
resistance mutations.

In-house objectives and outcomes:

Synexa uses the Parsortix® system technology to capture all CTC subpopulations, including epithelial, mesenchymal, stem-cell-like and CTC clusters. By capturing CTCs based on their physical properties rather than their biological properties, we are not limiting ourselves to capturing epithelial cells but instead capture all CTCs that are likely to have important biological roles in drug resistance, self-renewal and seeding capabilities.
Analysis of these CTC populations is focused on identifying the molecular profile that accounts for tumour heterogeneity. Downstream applications include gene expression analysis of captured CTCs using the Nanostring PanCancer panels, Ion Torrent NGS for identification of commonly occurring cancer mutations and digital drop PCR for detection of particular mutations of interest.
In addition to use in clinical trials, Synexa is also investigating this technology for use as a companion diagnostic for precision medicine and the real-time monitoring of tumour evolution and
treatment response.

Organotypic Culture

Background:

Cell culture is a widely used in vitro tool for improving our understanding of cell biology, tissue morphology, mechanisms of diseases, drug action and the development of tissue engineering. Cell culture refers to the removal of cells from an animal or plant and their subsequent growth in a favourable artificial environment. The cells can be removed from the tissue directly and disaggregated before cultivation, or they may be derived from a cell line or cell strain that has already been established. Established cell lines offer characterised models of various cell morphologies and diseases, that can be commercially sourced and easily propagated. Cell culture systems are indispensable tools that are used in a wide range of basic and clinical in vitro research studies and are often used in the preclinical research of many drugs. The classically preferred model is a static dish culture system which mainly generates adherent two-dimensional (2D) cell monolayers. The advantages of 2D cultures are associated with simple and low-cost maintenance, as well as easy environmental control, cell observation, measurement, and manipulation.

Relevance:

Drug development can be a very long and expensive process. Part of this process usually involves compound screening and molecule-cell interactions in 2D cultures. However, there is compelling evidence that suggests that cells cultured in 2D (non-physiological conditions) are not truly representative of the in vivo micro-environment, which is thought to be a significant factor in the high failure rate during drug discovery. 3D cultures provide a more accurate simulation of in vivo conditions. The additional dimension of 3D cultures influences the spatial organisation of cell surface receptors and affects gene expression, cellular behaviour, and signal transduction. When cells are grown in 3D aggregates, cell-to-cell interactions are easier and an extracellular matrix (ECM) can be formed. A more accurate and biologically representative screening system may be the key to reducing the length and costs of drug-based clinical trials.

Synexa objectives and outcomes:

Synexa offers a range of cell-based biomarker assays which allow for physiologically relevant quantification of important molecules, as well as allow for the assessment of protein interactio