Ontario Genomics

Abstract Dominant variants in the retinoic acid receptor beta (RARB) gene cause a complex disorder known as RARB-related disorder (RARB-RD), characterized by multiple congenital anomalies, global developmental delay, and dystonia. RARB-RD variants have been classified as either gain-of-function (GOF) or dominant-negative (DN) based on their cell-based transcriptional responses to retinoids. To investigate the mechanisms underlying this disorder, we generated mouse models carrying either the p.R387C or p.L402P RARB-RD variant, previously categorized as GOF and DN, respectively. Homozygous mice for either RARB-RD variant died perinatally with colonic aganglionosis, while heterozygous mice survived and recapitulated several features of RARB-RD. In addition to microphthalmia, both Rarb R387C/+ and Rarb L402P/+ mice exhibited progressive coordination deficits, increased active-phase locomotor activity, and cognitive impairment in the novel object recognition test. In contrast, mice heterozygous for a null allele of Rarb ( Rarb +/- ) did not display these abnormalities. In the brain, Rarb is predominantly expressed in the two major populations of projection neurons of the striatum recognizable by the expression of dopamine receptors D1R/ Drd1 and D2R/ Drd2 . Marker analysis revealed a reduction in Drd2 -expressing neurons without changes in Drd1 -expressing neurons in both RARB-RD models. Furthermore, RARB-RD mice showed partial resistance to the cataleptic effects of haloperidol, a D2R-specific antagonist. These behavioral, cellular, and dopaminergic deficits—though not the cognitive impairments—have previously been observed in Rarb -/- mice. To determine whether the in vitro effects of RARB-RD variants correlate with distinct transcriptional signatures in vivo , we compared the striatal transcriptome of Rarb R387C/+ , Rarb L402P/+ , Rarb -/- and Rarb +/- mice with their littermate controls. We found that the heterozygous RARB-RD variants and the homozygous null allele affected a large subset of common genes, with putative direct RARB targets predominantly downregulated. Notably, the transcriptional impact of the RARB-RD variants was more profound than that of the null allele, regardless of zygosity. Additionally, transcriptional changes in RARB-RD mice extensively overlapped with those observed in mouse models of Huntington’s disease, suggesting shared mechanisms affecting neuronal survival in the striatum. We conclude that the p.R387C and p.L402P variants similarly compromise striatal integrity and function, likely through a DN mechanism. Progressive emergence of most neurologic deficits highlights a potential therapeutic window. Our results support the development of strategies aimed at silencing RARB-RD alleles.

The ongoing civil war in Myanmar (Burma) has severely disrupted the country's health care system, forcing widespread displacement and creating a critical shortage of medical care and prosthetic devices for refugees and migrants along the Thai border. Prohibitive costs, resource shortages, and movement constraints severely limit access to essential health care and functional prosthetics in this region. This article details a collaboration between Queen's University and the Burma Children Medical Fund (BCMF), a nongovernmental organization (NGO) that established a 3-D-printed prosthetic program in 2019 using open-source technology. Since 2023, this collaboration has facilitated a three-year student mobility program, sending researchers to Thailand to enhance BCMF's existing initiative by addressing technical limitations and improving design autonomy. Using the development of a short transradial (below-elbow) prosthetic as a case study for this collaborative framework, the team employed low-cost 3-D scanning and computer-aided design (CAD) to modify an open-source prosthetic model for better suspension and fit. Our approach prioritized local capacity building by training local staff in CAD to ensure design autonomy and implementing filament dryers to mitigate humidity-related printing errors. From 2019 to 2024, the program provided free prostheses to 76 individuals, including five recipients of the customized below-elbow design. Pilot evaluations using the Orthotics Prosthetics Users Survey (OPUS) indicated positive results, with recipients reporting high levels of functionality and satisfaction, and no reported adverse effects. Ultimately, this work demonstrates the feasibility of a framework for academic-NGO partnerships that leverages adaptable, open-source technology to deliver equitable prosthetic care in conflict-affected and resource-constrained settings.

Chromosomal microdeletions represent a complex class of genetic disorders. Recently, 16p13.3 microdeletions encompassing TBC1D24 and ATP6V0C have gained prominence as structural variants associated with neurodevelopmental disorders, but their occurrence mechanisms remain unexplored. We used a comprehensive range of sequencing technologies (mate pair genome sequencing, linked-pair genome sequencing, nanopore sequencing, targeted locus amplification (TLA), long range and nested PCR followed by Sanger sequencing), to map the exact 16p13.3 microdeletion breakpoints in eight previously reported individuals. Microdeletion breakpoints were successfully mapped in all patients using TLA, split read analysis, PCR/Sanger sequencing, or nanopore sequencing. Alu sequences and/or non-B DNA motifs were detected in all patients. Mechanistic analysis identified distinct pathways underlying these rearrangements. Noteworthy, two unrelated individuals carried identical microdeletions that might have been mediated by an atypical form of non-allelic homologous recombination, given the presence of a 639 bp sequence with 96.2% homology. Microhomology-mediated end-joining and non-homologous end-joining emerged as other mechanisms driving these 16p13.3 microdeletions, which differs from other studied contiguous gene deletion syndromes. This research contributes to a deeper understanding of microdeletion-associated disorder pathophysiology in medical genetics.

Various modeling efforts have been conducted to evaluate ecosystem services (ES) of agricultural conservation practices but typically these models are too complex for conservation stakeholders to use. This research developed a cloud-based WebGIS tool for communicating integrated ES modeling to conservation stakeholders. The integrated ES modeling was developed by linking farm economic, watershed hydrologic, and soil carbon modeling within a spatial optimization framework for identifying conservation practices to minimize economic costs subject to multiple ES targets including water quality and soil carbon improvement benefits. The WebGIS tool, named "Ecosystem Services Assessment Tool" (ESAT), has a suite of functions to visualize watershed characteristics, summarize the effectiveness of existing agricultural conservation practices, examine the cost, effectiveness, and cost-effectiveness of future agricultural conservation practices, and further, identify optimal sets of conservation practices for achieving cost-effectiveness. The study area for the integrated ES modeling and WebGIS tool development was the 4,820-km2 Modeste watershed in Alberta, Canada. The ESAT application demonstrated its functionalities to support decision making, particularly in identifying cost-effective conservation practices for achieving sediment, phosphorus or nitrogen reduction, or soil carbon increase target. In the research, conservation stakeholders including municipal and provincial governments, conservation management agencies, and NGOs were actively engaged in data collection, modeling development, WebGIS tool development, and training for the use of the WebGIS tool. Conservation stakeholders assessed that the ESAT is a very useful tool for supporting decision making in agri-environmental programs. However, the WebGIS tool can be further simplified and streamlined to improve the user-friendliness of the ESAT.

Increasing the productivity of planted forests may efficiently provide an important part of the world’s growing demand for wood while protecting natural forests. In this study, we developed an integrated modelling framework to evaluate the financial impacts of improving productivity of planted forests by tree breeding. Using this framework, we compared three genetic improvement scenarios of white spruce plantations, a key reforestation species in North America, and evaluated the differences in the derived wood product assortments in terms of quantity, quality, and revenues. Favouring the production of wood volume appears as the best way to enhance financial gains from white spruce plantations in the current market. The scenario that focused on increasing tree height produced a greater volume of wood products and larger lumber pieces, which resulted in the greatest revenues. In comparison, favouring wood stiffness over volume led to poorer results, as the increased product quality was not sufficient to surpass the financial gain associated with greater wood volumes. While we successfully provided an evaluation of the product assortments derived from genetically improved plantations, the proposed framework would benefit from more data input to help maximize financial gains from a range of tree breeding strategies.

Smoldering multiple myeloma (SMM) is a precursor stage that precedes multiple myeloma (MM). SMM is heterogenous with nearly 40% of patients progressing to MM in the first 5 years. The high rate of progression of SMM patients highlights the need for early intervention, which underscores the importance of identifying SMM patients with the highest risk of progression. Several risk stratification models showed utility in identifying high-risk SMM patients; however, these systems showed limited sensitivity. To date, identifying high-risk SMM patients remains an important clinical need. In this study, we present the 3-dimensional telomere profiling as a structural biomarker capable of stratifying SMM patients as a function of genomic instability. Quantifying telomere dysfunction using the TeloView technology showed utility in risk stratification of cancer patients, particularly hematological malignancies. In this study, we analyzed 168 SMM patients. We report an AUC in ROC analysis of 0.8 using a subset of the patients as a training dataset. We then conducted a blind validation on a different cohort and demonstrated a positive predictive value of 85% and negative predictive value of 73%, with sensitivity and specificity of 83% and 76%, respectively. We examined the correlation between the TeloView prediction and the 20-2-20 scoring system, and cytogenetic abnormalities. We report a correlation of 53% with the 20-2-20 scores and over 60% correlation with cytogenetic abnormalities. The result of this study presents the telomere profiling as an effective biomarker able to stratify SMM patients to their respective risk groups with high sensitivity and specificity.

Abstract Despite major advances in the treatment of breast cancer (BC), it remains the most diagnosed and second deadliest cancer among American women. BC consists of distinct clinical subtypes, including estrogen receptor or HER2 receptor-positive and triple-negative breast cancer (TNBC) that lacks these receptors preventing the use of established precision therapies and the standard of care remains neoadjuvant chemotherapy (NACT), followed by surgery, radiation and emerging combinations with immunotherapy. While NACT is effective in some patients, up to 50% of patients are intrinsically unresponsive or acquire resistance. These patients demonstrate the highest rates of recurrence and distant metastasis. It is known that chemotherapies can effectively eliminate proliferating tumor cells, but a small population of drug-tolerant persister (DTPs) cells can remain and are thought to play a key role in relapse and resistance. We hypothesized that chemotherapy influences TNBC tumor plasticity by exerting selective pressures leading to the outgrowth of resistant subpopulations with the greatest survival advantage. To evaluate this hypothesis, we generated in vivo models of disease progression and chemotherapy resistance and investigated the plasticity of tumor cell subpopulations by single-cell RNA sequencing. We developed PDX models from a multi-drug resistant primary TNBC treated with standard-of-care chemotherapy and its patient-matched lung metastasis. To model response and resistance at the metastatic stage, we challenged this metastasis PDX with several cycles of Gemcitabine. We obtained residual disease that relapsed and eventually developed resistance, mirroring the patient response. We performed single-cell RNA sequencing (scRNAseq) of these models using a droplet-based technology from 10X Genomics. This scRNAseq data was used to compare the changes in the proportions of cellular subpopulations in each model. Our data show that the rebound model presents greater similarity to the untreated metastasis, while the resistant model significantly differs in cell population expression profiles. Interestingly, the residual disease demonstrates an intermediated state with similarities to both the untreated metastasis and the resistant model. We identified populations with hypoxic signatures in the primary tumor, its matched metastasis and the residual, rebound and resistant models. Immunohistochemistry and Nanostring GeoMx Digital Spatial Profiler validated these populations in these models. In addition, we have identified other varying populations and are currently investigating their cellular mechanisms and gene expression patterns. Using scRNA-sequencing to understand the clonal expansion of resistant subpopulations following chemotherapy reveals distinctive resistant cell features enabling the identification of the vulnerabilities of these tumors. Citation Format: Sandrine Busque, Constanza Martinez Ramirez, Ariel Madrigal Aguirre, Paul Savage, Anie Monast, Anne-Marie Fortier, Gerardo Zapata, Atilla Omeroglu, Jamil Asselah, Nathaniel Bouganim, Sarkis Meterissian, Francine Tremblay, Ari Meguerditchian, Yasser Riaz Alhosseini, Hamed S. Najafabadi, Hellen Kuasne, Morag Park. Identification of Gemcitabine-resistant Populations using scRNA-Sequencing in Triple Negative Breast Cancer Patient-Derived Xenografts [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B067.