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Objectives: The aim of the retrospective study was to describe the brain biopsy procedure using a new frameless optical neuronavigation system and to report diagnostic yield and complications associated with the procedure. Materials and Methods: The medical records for all dogs with forebrain lesions that underwent brain biopsy with a frameless optical neuronavigation system in a single referral hospital between 2013 and 2020 were retrospectively analysed. Following data were collected: signalment, neurological signs, diagnostic findings, number of brain biopsy samples, sampled region, complications, duration of hospitalisation, whether the samples were diagnostic and histopathological diagnoses. The device consists of a computer workstation with navigation software, an infrared camera, patient tracker and reflective instruments. The biopsy needle was equipped with reflective spheres, so the surgeon could see the position of the needle during sampling the intracranial lesion free handed through a mini-burr hole. Results: Ten dogs were included. Absolute diagnostic yield based on specific histopathological diagnosis was 73.9%. Three dogs had immune-mediated necrotizing encephalitis, two dogs showed a necrotizing leukoencephalitis and two dogs a meningoencephalitis of unknown origin. In two dogs, the brain specimen showed unspecific changes. In one dog, the samples were non-diagnostic. Seven dogs showed no neurological deterioration, one dog mild temporary ataxia and two dogs died within 36 hours post brain biopsy. Clinical Significance: In these 10 dogs, the frameless optical neuronavigation system employed was useful to gain diagnostic brain biopsy samples. Considering the mortality rate observed, further studies are needed to confirm the safety of this procedure and prove its actual clinical effectiveness.

<p>The annual incidence rate of tumours in the brain and central nervous system (CNS) was 19.89 per 100,000 persons between 2004 and 2008 in the United States. Surgery is a common treatment option for brain and CNS tumours. Typically, biopsy followed by histological analysis is used to confirm tumour types and margin during neurosurgery as an intraoperative diagnostic tool. However, this biopsy method is invasive, sampling number limited and not in real-time. To overcome these problems, many minimally invasive optical techniques, called optical biopsies, have been developed towards intraoperative diagnosis.</p> <p>The research work carried out in this dissertation focuses on combining the time-resolved fluorescence (TRF) and diffuse reflectance (DR) spectroscopy towards intraoperative tumour margin detection in neurosurgery. Combining these two modalities allows us to obtain additional contrast features, thus potentially improving the diagnostic accuracy. To achieve this goal, first, a clinically compatible integrated TRF-DR spectroscopy instrument was developed for <em>in vivo</em> brain tumour study. An acousto-optical-tunable-filter-based spectrometer was designed to acquire the time-resolved fluorescence signal. A dual-modality fibre optic probe was used to collect the TRF and DR signals in a small volume. The system’s capabilities of resolving fluorescence spectrum and lifetime, and optical properties were characterized and validated using tissue phantoms. Second, in order to retrieve the fluorescence impulse response function accurately from measured fluorescence signals, a robust Laguerre-based deconvolution method was optimized by using the constrained linear least squares fitting and high order Laguerre function basis. This optimized Laguerre-based deconvolution method overcomes the over-fitting problem introduced by low signal-to-noise ratio and complex fitting model. Third, an <em>ex vivo</em> clinical study of brain tumours was carried out using the TRF and DR spectroscopy. Fluorescence spectra and lifetime features were selected to classify various tumour types. The sensitivity and specificity of meningioma grade I differentiated from meningioma grade II are both 100%. Finally, in order to increase the measurement tissue volume and obtain imaging contrast features, a scanning-based hyperspectral fluorescence lifetime imaging system was developed. This setup can provide time-, space-, spectrum- resolved multi-dimensional images for tumour margin detection.</p> / Doctor of Philosophy (PhD)

The endangered St. Lawrence beluga (Delphinapterus leucas) population is not recovering from severe depletion despite its protected status over the past 20 years. DNA fingerprinting analysis of St. Lawrence beluga whales with three minisatellite probes (Jeffreys 33.6, 33.15 and Ml3) indicate a reduced level of genetic variability compared to Mackenzie Delta animals. The average band-sharing between individuals of the St. Lawrence beluga population for the three probes (0.534, 0.573, 0.478) was significantly higher than the average band-sharing of the Mackenzie Delta beluga population for the same probes (0.343, 0.424, 0.314). Higher levels of mean homozygosity in the isolated St. Lawrence belugas (0.33 vs 0.21) as well as a high degree of relatedness suggest that this population is inbred and that inbreeding depression is a factor in the lack of recovery of the St. Lawrence beluga population. Because sampling of some beluga populations may be biased, there is the need of alternative sampling procedures such as biopsy darting. To evaluate the impact of biopsy darting on beluga whales, different combinations of dart and stop sizes were tested on fresh beluga carcasses and the effect of different factors on the success of retrieval and the extent of wounding were evaluated. Tips with smaller diameters were more likely to retrieve a sample than those with larger diameters (p <0.05) and longer tips were also more likely to retrieve a sample than shorter tips (p < 0.10). The force of impact, a function of draw weight and distance, had a significant effect on the severity of wounding (p<0.05). The samples obtained from all biopsy darts tested yielded sufficient amounts of DNA for genetic analysis. / Thesis / Master of Science (MS)

Extracellular vesicles (EVs) are small membrane-surrounded structures containing transmembrane proteins and enclosing cytosolic proteins and nucleic acids. They are released in the extracellular space by both normal and neoplastic cells and play an important role in cell-cell communication in numerous physiological processes and pathological conditions, through the transfer of their functional cargo to recipient cells. EVs are highly abundant in biological fluids, and even more represented in cancer patients’ biofluids, therefore many studies suggested that they can be instrumental in liquid biopsies as prognostic markers or for early detection of tumors. Moreover, being secreted by potentially all the cells, they can serve in oncology to represent the tumor heterogeneity, which is underestimated by the current diagnostic tools. Given their small size, EVs are difficult to isolate in a high-throughput way and, therefore, one of the main obstacles to their clinical application, is that the existing isolation methods are impractical. During these years, I worked at the development and optimization of a novel technique that allows purification of heterogeneous EVs from biological fluids in an efficient, fast and reproducible way. This technique, named Nickel-Based Isolation (NBI), is a biochemical assay that allows obtaining polydisperse EVs in a physiological pH solution, therefore, preserving their morphology, heterogeneity, and stability. We tested and optimized this assay in protein-enriched systems and comparing it to the techniques currently used to characterize and measure EVs, such as flow cytometry and Tunable Resistive Pulse Sensing. We challenged the reproducibility of this method by isolating EVs from different biological fluids. Interestingly, the EVs purified with NBI result more intact and stable compared to the ones obtained with other methods, and can be studied in a clinical setting and used as an innovative tool for detection of molecules associated with diseases. We demonstrated the specificity of the procedure by using individual isolated vesicles in biochemical and molecular assay, optimized to characterize the biological content of EVs. We were able to detect picomolar concentration of PSMA on 105 EVs isolated from plasma of prostate cancer patients and BRAF-V600E transcript in just 103 EVs from the plasma of colon cancer patients, reaching unprecedented matching with tissue biopsy results. We also investigated the transcriptome of EVs isolated from glioblastoma cancer stem cells, in order to exploit the potential of EVs as diagnostic markers.

Biopsy is a standard practice in the diagnosis and treatment of many cancers. Despite its integral role in cancer diagnosis, in some instances, the biopsy tool facilitates metastasis by transferring cancerous cells attached to its exterior into the healthy tissue or the blood circulation during its retraction from the tumor. These few cancer cells can then serve as seeds for the malignant tumor to grow in the healthy tissue. Cauterization using extreme heat or cold can destroy cells in the region and minimize the chance of seeding but this can be an inexact process that increases damage to otherwise healthy tissue and prolongs healing time following a biopsy procedure. In our laboratory, we have developed the concept of a new smart biopsy tool that can reduce the chance of cancer cell dissemination during a biopsy. This tool improves on the conventional biopsy needle by introducing an impedance sensor on the biopsy tool which is housed in a sliding sheath. Due to the significant difference in the electrical conductivity of the tumor and the healthy tissue, the sensor is able to distinguish between the two and locate the exact tumor interface. The protective sheath placed around the instrumented biopsy tool and above the interface isolates the healthy tissue and prevents or at least minimizes the transfer of tumor cells. Delivering an RF dose through the sheath can kill any malignant cells that might be lurking around the interface. This thesis, in particular, will concentrate on the development of the design, fabrication and calibration of the impedance sensor and its integration with the biopsy tool. The impedance sensor essentially consists of conductive electrodes sandwiched between insulating layers. They are built on thin-film polymer, Polyimide, using conventional microfabrication techniques. These sensors are further calibrated to estimate the cell constant. Once calibrated, these probes are used to measure the conductivity of porcine tissues, and in-house prepared agar phantoms. / Master of Science

Early detection of breast cancer is critical for increasing survival rates. However, currently available screening strategies provide ambiguous results, leaving invasive tissue biopsy procedures necessary for definitive diagnosis. Considerable efforts have investigated using nipple aspirate fluid (NAF), a liquid biopsy rich in proteins representative of the breast microenvironment, as a non-invasive source of early detection biomarkers. However, by using traditional two-dimensional discovery proteomic approaches, many technical challenges of using NAF have limited analysis of large sample sizing: such as low expressed volume (<10µL) or insufficient analytical material (<200µg protein). Following non-invasive collection by manual massage, we developed a one-dimensional sample preparation workflow that reduced sample handling steps, minimised sample losses and increased sample throughput to 96-samples by using a PVDF-membrane based system, which was ideally suited to the NAF proteome. Samples were prepared within a single working day, and results correlated significantly with conventional in-solution protocols. ​Proteins typically associated with the dysregulation of innate immune response and haemostatic pathways had a significantly altered proteome profile in response to breast cancer. Overall, our new workflow will allow future studies to take a more high-throughput approach, revealing biomarkers for breast cancer early detection, and providing a real impact.

Lymphoma is a common hematopoietic malignancy in canines. Current diagnostic techniques to diagnose lymphoma are often invasive and expensive. Additionally, tumor heterogeneity complicates the accurate classification and diagnosis of specific subtypes, hindering the development of targeted therapy and prognostic assessments. We propose a minimally invasive liquid biopsy technique involving blood collection to detect cell-free DNA from tumors using Next-generation sequencing. We hypothesize that identical tumor aberrations can be found in matching plasma and tumor DNA. Five dogs diagnosed with B-cell lymphoma through flow cytometry or PAAR were enrolled in the study. Samples collected included: (1) blood for plasma (cfDNA), (2) tumor tissue fine-needle aspirates (tumor DNA), and (3) buccal swabs (genomic DNA, germline control). Whole Genome Sequencing was performed using Illumina NovaSeq 6000, and the sequenced output was analyzed with bioinformatics tools to detect somatic variants in plasma and tumor samples. Our results revealed many shared somatic variants between matched cfDNA and tumor DNA samples, with 1.7-49% of tumor variants also found in corresponding plasma samples. Shared variants constituted only 0.5-9% of all plasma somatic variants. Specific B-cell lymphoma mutations were identified in cfDNA, including MYC, POT1, and TRAF3, alongside other cancer-related genes. Tumor samples showed mutations in genes associated with canine and human B-cell lymphoma. This study suggests that tumor-specific genomic mutations can be detected in plasma, supporting the potential of liquid biopsy as a less invasive diagnostic tool. However, cfDNA may not capture the full genetic heterogeneity of tumors due to low tumor-derived DNA content in limited plasma volumes. / Master of Science / Lymphoma is a type of blood cancer affecting white blood cells. Canine lymphoma is a common neoplasia, with an incidence rate of 20 to 100 cases per 100,000 dogs, making it a significant research focus. Current diagnostic methods are invasive and costly. Additionally, the wide variety of tumor types in lymphoma makes it challenging to determine the exact subtypes, which is crucial for selecting the best treatment approach. To overcome these challenges, we proposed a less invasive method known as "liquid biopsy". This technique involves taking a blood sample of a dog to find cell-free DNA from tumor cells using Next-Generation Sequencing technologies. We aimed to see if blood DNA could provide the same information as tumor DNA. In our study, we worked with five dogs diagnosed with B-cell lymphoma through traditional methods. We collected blood, tissue from needle biopsies, and buccal swabs from each dog. We then performed DNA extraction and sequencing on these samples. Our findings showed that 1.7-50% of the mutations in tumor DNA were also detected in matched blood DNA, though these represented only a small fraction of all changes found in blood samples. Additionally, the blood samples also revealed mutations related to canine B-cell lymphoma in genes like MYC, POT1, and TRAF3. In conclusion, our study supports the use of liquid biopsy as a feasible and less invasive method to diagnose lymphoma in dogs. However, they might not show all genetic variations of the tumor due to limited tumor DNA content.

Yes / Background Buruli ulcer (BU) is an infectious disease caused by Mycobacterium ulcerans and considered the third most prevalent mycobacterial disease in humans. Secondary bacterial infections in open BU lesions are the main cause of pain, delayed healing and systemic illness, resulting in prolonged hospital stay. Thus, understanding the diversity of bacteria, termed the microbiome, in these open lesions is important for proper treatment. However, adequately studying the human microbiome in a clinical setting can prove difficult when investigating a neglected tropical skin disease due to its rarity and the setting. Methodology/Principal findings Using 16S rRNA sequencing, we determined the microbial composition of 5 BU lesions, 3 non-BU lesions and 3 healthy skin samples. Although no significant differences in diversity were found between BU and non-BU lesions, the former were characterized by an increase of Bacteroidetes compared to the non-BU wounds and the BU lesions also contained significantly more obligate anaerobes. With this molecular-based study, we were also able to detect bacteria that were missed by culture-based methods in previous BU studies. Conclusions/Significance Our study suggests that BU may lead to changes in the skin bacterial community within the lesions. However, in order to determine if such changes hold true across all BU cases and are either a cause or consequence of a specific wound environment, further microbiome studies are necessary. Such skin microbiome analysis requires large sample sizes and lesions from the same body site in many patients, both of which can be difficult for a rare disease. Our study proposes a pipeline for such studies and highlights several drawbacks that must be considered if microbiome analysis is to be utilized for neglected tropical diseases.

No / Improving the patient's experience of a bone marrow biopsy ¿ an RCT Aims. To compare nitrous oxide 50%/oxygen 50% (N2O/O2 ¿ entonox) plus local anaesthetic (LA) with placebo (oxygen) plus LA in the management of pain experienced by patients undergoing a bone marrow biopsy. . Bone marrow biopsies are a common procedure for many haematological conditions. Despite the use of a LA, pain during the procedure has frequently been reported by patients. Previous research in pain management of other invasive diagnostic procedures (e.g. sigmoidoscopy) has reported N2O/O2 as an effective alternative to LA. Design. Double-blind randomized controlled trial. Methods. Forty-eight patients requiring a bone marrow biopsy were randomized to receive either N2O/O2 or oxygen in addition to their LA. Participants were asked to complete a pain score and comment on their experience of the procedure. Results. Although the overall pain scores were moderate, there was a wide range of scores. N2O/O2 resulted in significantly less pain for men, but not for women. All patients who had had previous biopsies reported significantly more pain, regardless of the gas used. There were no significant adverse effects in either group. Conclusion. N2O/O2 is a safe, effective, easy-to-use analgesic which merits further investigation in potentially painful diagnostic (and other) interventions.