FOXP1 suppresses immune response signatures and MHC class II expression in activated B-cell-like diffuse large B-cell lymphomas.

The FOXP1 (forkhead box P1) transcription factor is a marker of poor prognosis in diffuse large B-cell lymphoma (DLBCL). Here microarray analysis of FOXP1-silenced DLBCL cell lines identified differential regulation of immune response signatures and major histocompatibility complex class II (MHC II) genes as some of the most significant differences between germinal center B-cell (GCB)-like DLBCL with full-length FOXP1 protein expression versus activated B-cell (ABC)-like DLBCL expressing predominantly short FOXP1 isoforms. In an independent primary DLBCL microarray data set, multiple MHC II genes, including human leukocyte antigen DR alpha chain (HLA-DRA), were inversely correlated with FOXP1 transcript expression (P<0.05). FOXP1 knockdown in ABC-DLBCL cells led to increased cell-surface expression of HLA-DRA and CD74. In R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine and prednisone)-treated DLBCL patients (n=150), reduced HLA-DRA (<90% frequency) expression correlated with inferior overall survival (P=0.0003) and progression-free survival (P=0.0012) and with non-GCB subtype stratified by the Hans, Choi or Visco-Young algorithms (all P<0.01). In non-GCB DLBCL cases with <90% HLA-DRA, there was an inverse correlation with the frequency (P=0.0456) and intensity (P=0.0349) of FOXP1 expression. We propose that FOXP1 represents a novel regulator of genes targeted by the class II MHC transactivator CIITA (MHC II and CD74) and therapeutically targeting the FOXP1 pathway may improve antigen presentation and immune surveillance in high-risk DLBCL patients

Characterization of programmed death ligands in B-cell non-Hodgkin lymphomas

Non-Hodgkin lymphomas constitute a conglomerate of malignancies that originate from a population of white blood cells termed lymphocytes. Lymphoid cancers are a significant health burden in Canada, with over 9,200 new diagnoses in 2018. Of those newly diagnosed, roughly 40% will die within five years. Studying a subpopulation of aggressive B-cell derived non-Hodgkin lymphomas with both high-throughput sequencing and conventional research techniques, we identified recurrent, somatic aberrations in two genes that are contributors to lymphoma pathogenesis: programmed death ligands 1 (CD274) and 2 (PDCD1LG2). In healthy individuals, programmed death ligands are central to maintaining peripheral tolerance and preventing autoimmune disease. However, we establish that malignant B-cells hijack this axis to suppress the antitumor immune response.Within this dissertation, we report on the frequency of programmed death ligand structural genomic rearrangements in seven different B-cell lymphoma entities and demonstrate the effects of structural genomic rearrangements on gene expression. Additionally, we evaluate ectopic cytokine stimulation, copy number variations, DNA methylation, and micro RNA regulation as additional mechanisms of deregulating programmed death ligand expression. Using novel, capture-based high-throughput techniques, we characterize, at base-pair resolution, the subtypes, cluster locations, and partners of programmed death ligand structural genomic rearrangements. We go on to demonstrate the effects of protein expression and characterize the functional impairment resulting from deregulated programmed death ligand binding in both B and T-cell populations using retroviral cell line models. Finally, in evaluating flanking breakpoint sequences of programmed death ligand structural genomic rearrangements, we propose the molecular mechanisms involved in producing these aberrations. Taken together, our work informs on relevant components of B-cell non-Hodgkin lymphoma pathogenesis and substantiates the effectiveness of molecularly precise therapies targeting the programmed death ligand axis, as they become mainstays of lymphoma treatment.Medicine, Faculty ofPathology and Laboratory Medicine, Department ofGraduat

Summary findings derived from factor analysis for the three outcome variables and a summary of the model features.

<p>Likert responses from 135 MD/PhD program graduates who answered all three questions were analyzed to confirm the one factor structure and quantify the reliability of measuring MD/PhD program satisfaction.</p

The characteristics of surveyed Canadian MD/PhD alumni (n = 139).

<p>n is the number of survey respondents providing a response pertaining to the specified variable. IQR denotes the interquartile range.</p

Logistic regression for outcome measures of satisfaction with physician-scientist training and independent variables.

<p>Data was derived from the surveyed Canadian MD/PhD alumni cohort (n = 139); data presented as odds ratio (95% confidence intervals), and (*) <i>P</i> < 0.05; (**) <i>P</i> < 0.01. N/A denotes independent variables that are not applicable to outcome measures.</p

Summary findings derived from factor analysis for the three outcome variables and a summary of the model features.

<p>Likert responses from 135 MD/PhD program graduates who answered all three questions were analyzed to confirm the one factor structure and quantify the reliability of measuring MD/PhD program satisfaction.</p

The contrasting role of nasopharyngeal angiotensin converting enzyme 2 (ACE2) transcription in SARS-CoV-2 infection : A cross-sectional study of people tested for COVID-19 in British Columbia, Canada

Background: Angiotensin converting enzyme 2 (ACE2) protein serves as the host receptor for SARS-CoV-2, with a critical role in viral infection. We aim to understand population level variation of nasopharyngeal ACE2 transcription in people tested for COVID-19 and the relationship between ACE2 transcription and SARSCoV-2 viral load, while adjusting for expression of: (i) the complementary protease, Transmembrane serine protease 2 (TMPRSS2), (ii) soluble ACE2, (iii) age, and (iv) biological sex. The ACE2 gene was targeted to measure expression of transmembrane and soluble transcripts. Methods: A cross-sectional study of n = 424 “participants” aged 1 104 years referred for COVID-19 testing was performed in British Columbia, Canada. Patients who tested positive for COVID-19 were matched by age and biological sex to patients who tested negative. Viral load and host gene expression were assessed by quantitative reverse-transcriptase polymerase chain reaction. Bivariate analysis and multiple linear regression were performed to understand the role of nasopharyngeal ACE2 expression in SARS-CoV-2 infection. Findings: Analysis showed no association between age and nasopharyngeal ACE2 transcription in those who tested negative for COVID-19 (P = 0092). Mean relative transcription of transmembrane (P = 000012) and soluble (P<00001) ACE2 isoforms, as well as TMPRSS2 (P<00001) was higher in COVID-19-negative participants than COVID–19 positive ones, yielding a negative correlation between targeted host gene expression and positive COVID-19 diagnosis. In bivariate analysis of COVID-19-positive participants, transcription of transmembrane ACE2 positively correlated with SARS-CoV-2 viral RNA load (B = 049, R² =014, P<00001), transcription of soluble ACE2 negatively correlated (B= -085, R² = 026, P<00001), and no correlation was found with TMPRSS2 transcription (B= -0042, R² =<010, P = 069). Multivariable analysis showed that the greatest viral RNA loads were observed in participants with high transmembrane ACE2 transcription (B= 089, 95%CI: [059 to 118]), while transcription of the soluble isoform appears to protect against high viral RNA load in the upper respiratory tract (B= -0099, 95%CI: [-018 to -0022]). Interpretation: Nasopharyngeal ACE2 transcription plays a dual, contrasting role in SARS-CoV-2 infection of the upper respiratory tract. Transcription of the transmembrane ACE2 isoform positively correlates, while transcription of the soluble isoform negatively correlates with viral RNA load after adjusting for age, biological sex, and transcription of TMPRSS2. Funding: This project (COV-55) was funded by Genome British Columbia as part of their COVID-19 rapid response initiative.Medicine, Faculty ofNon UBCPathology and Laboratory Medicine, Department ofPopulation and Public Health (SPPH), School ofReviewedFacultyGraduat

Genomic rearrangements involving programmed death ligands are recurrent in primary mediastinal large B-cell lymphoma

The pathogenesis of primary mediastinal large B-cell lymphoma (PMBCL) is incompletely understood. Recently, specific genotypic and phenotypic features have been linked to tumor cellim mune escape mechanisms in PMBCL. We studied 571 B-cell lymphomas with a focus on PMBCL. Using fluorescence in situ hybridization here, we report that the programmed death ligand (PDL) locus (9p24.1) is frequently and specifically rearranged in PMBCL (20%) as compared with diffuse large B-cell lymphoma, follicular lymphoma, and Hodgkin lymphoma. Rearrangement was significantly correlated with overexpression of PDL transcripts. Utilizing high-throughput sequencing techniques, we characterized novel translocations and chimeric fusion transcripts involving PDLs at base-pair resolution. Our data suggest that recurrent genomic rearrangement events underlie an immune privilege phenotype in a subset of B-cell lymphomas