EPEN-11. TUMOR DIFFERENTIATION IMPACTS THE BIOLOGY OF RECURRENCE IN CHILDHOOD POSTERIOR FOSSA EPENDYMOMA

Ependymoma (EPN) of childhood is curable in only 50% of cases, with recurrences in the remainder that are refractory to treatment. In recent years significant advances have been made in understanding the molecular and cellular biology of EPN. Recent studies show that PFA subgroup EPN are comprised of multiple neoplastic subpopulations that show undifferentiated, differentiated and mesenchymal characteristics. These studies focused on tumor at presentation, with recurrent EPN being less well understood. In the present longitudinal study we examine changes in neoplastic cell heterogeneity in serial presentations of PFA EPN using deconvolution (Cibersort) of bulk RNAseq data. Analysis of a cohort of 48 PFA EPN presenting at Children’s Colorado showed survival and PFA1/PFA2 subtype assignment was associated with the proportion of individual neoplastic subpopulations as determined by deconvolution. Tumors that subsequently regrew had a significantly higher estimated proportion of undifferentiated EPN cells (UEC) at presentation, than those that were non-recurrent after 5 years follow-up. This outcome association potentially age related, as UEC proportions are significantly higher in PFA arising in children < 1 year old who have a particularly poor prognosis. Changes in PFA neoplastic subpopulations at recurrence was performed in two cohorts of patients from Children’s Colorado (n=23) and Nottingham, UK (n=15). As a whole, no subpopulation proportion was significantly changed at recurrence. However, separation of PFA into subtypes PFA1 and PFA2 revealed an increase in the proportion of the cilia-differentiated EPN cell subpopulation is more frequent event in PFA1 (15/24), and rare in PFA2 (2/11). Changes in other neoplastic subpopulations at recurrence were smaller and only seen in PFA1, both UEC and mesenchymal subpopulations being lower at recurrence. In summary, only PFA1 showed dynamic changes in neoplastic subpopulation proportions at recurrence, with potential impacts on transcriptomic based-subgroup assignment, whereas PFA2 proportions remained largely stable.

Consensus molecular subtyping of colorectal cancers is influenced by goblet cell content

A critical obstacle in the field of colorectal cancer (CRC) is the establishment of precise tumor subtypes to facilitate the development of targeted therapeutic regimens. While dysregulated mucin production is a histopathological feature of multiple CRC subtypes, it is not clear how well these pathologies are associated with the proportion of goblet cells in the tumor, or whether or not this proportion is variable across all CRC. This study demonstrates that consensus molecular subtype 3 (CMS3) CRC tumors and cell lines are enriched for the expression of goblet cell marker genes. Further, the proportion of goblet cells in the tumor is associated with the probability of CMS3 subtype assignment and these CMS3 subtype tumors are mutually exclusive from mucinous adenocarcinoma pathologies. This study provides proof of principle for the use of machine learning classification systems to subtype tumors based on cellular content, and provides further context regarding the features weighing CMS3 subtype assignment.

Comparison of conventional and modern methods in determining ischemic stroke etiology by general and stroke neurologists

Background/aim: To investigate the consistency between stroke and general neurologists in subtype assignment using Trial of ORG-10172 using Acute Stroke Treatment (TOAST) and Causative Classification of Stroke (CCS) systems. Materials and methods: Fifty consecutive, acute ischemic stroke patients admitted to Stroke Unit were recruited. Patients were classified two stroke and two general neurologists, each from different medical centers, according to TOAST followed by CCS. Each neurologist was assessed for consistency and compliance in pairs. Concordance among all four neurologists was investigated and evaluated using Kappa(ĸ)-value. Results: Kappa(ĸ)-value of diagnostic compliance between stroke neurologists was 0.61 (95%CI 0.45-0.77) for TOAST and 0.78 (95%CI 0.62-0.94) for CSS-5. Kappa(ĸ)-value was 0.64 (95%CI 0.48–0.80) for TOAST and 0.75 (95%CI 0.60–0.91) for CCS-5 for general neurologists. Compliance was moderate [ĸ:0.59 (95%CI 0.52–0.65)] in TOAST and was strong [ĸ:0.75 (95%CI 0.68–0.81)] in CCS-5 for all 4 neurologists. ‘Cardioembolism’(91.04%) has reached the highest compliance in both systems. The frequency of group with ‘undetermined etiologies’ was less in CCS (26%) compared to TOAST. Conclusions: The CCS system improved the compliance in both stroke and general neurologists compared with TOAST. These suggest that automatic, evidence-based, easily reproducible CCS system was superior to TOAST system. Keywords: TOAST, CCS, Ischemic stroke, Etiology

Antiretroviral drug resistance and HIV-1 subtypes among treatment-naive prisoners in Kelantan, Malaysia

Introduction: The widespread use of highly active antiretroviral therapy (HAART) and continuous reports of HIV-1 strains developing resistance to these drugs is rather alarming, as transmission of resistant viruses to newly infected persons is possible. This study aimed to determine HIV-1 subtypes and the prevalence of primary mutations associated with antiretroviral (ARV) resistance among treatment-naive prisoners on the east coast of Malaysia. Methodology: Viral RNA was extracted from plasma samples of 21 treatment-naive prisoners. Protease (PR) and reverse transcriptase (RT) regions were amplified and sequenced. Stanford HIV database algorithms were used for interpretation of resistance, and phylogenetic analysis was performed for subtype assignment. Results: In the PR gene, no antiviral resistance-associated mutation was detected. For RT-associated mutations, K103N was the most prevalent in sequenced samples (14.3%). Genetic subtyping on the pol gene revealed that the majority of the prisoners were infected with subtype CRF33_01B (52.4%). Conclusion: Continuous surveillance of newly infected individuals is required to help strategize the best antiviral treatment for these patients.