Yoder, Sean J.

Abstract Background: Post-transplant lymphoproliferative disorder (PTLD) occurs in up to 30% of high-risk solid organ transplant recipients and is strongly associated with the intensity and duration of immunosuppression. While Epstein-Barr virus (EBV)-positive monomorphic PTLD and diffuse large B-cell lymphoma (DLBCL) share overlapping morphologic features and expression of canonical B-cell markers, they exhibit distinct EBV transcriptional programs. Immunosuppressive regimens, essential for preventing graft rejection, impair EBV-specific cytotoxic T lymphocyte (CTL) responses, thereby promoting EBV-driven lymphomagenesis. We hypothesized that these differences in viral transcription and immune evasion reflect fundamentally distinct immune microenvironments and host responses in EBV-positive PTLD compared to DLBCL. Methods This prospective, non-interventional study has been conducted at Moffitt Cancer Center since 2019. To characterize tumor-specific T-cell responses in EBV-positive PTLD versus DLBCL, peripheral blood mononuclear cells (PBMCs) from enrolled patients were infected with EBV (ATCC VR-1492) to generate autologous, immortalized lymphoblastoid B-cell lines (LCLs). EBV antigen-specific immune responses were quantified using an IFN-γ ELISpot assay targeting EBNA1, LAMP1, LAMP2A, BARF1, and a CEF peptide pool as a control. To optimize cell viability and functional readout post-thaw, we implemented an overnight resting protocol for PBMCs, which demonstrated superior IFN-γ release compared to the conventional 1-hour rest. Results We present pilot data from 11 consecutive patients (55% male; median age 63.4 years), including 3 with PTLD (2 EBV-positive; 2 monomorphic) and 8 with EBV-negative DLBCL. A total of 12 evaluable PBMC samples were analyzed: 7 pre-treatment, 1 mid-treatment, and 4 post-treatment. Successful generation of autologous LCLs was predominantly achieved using pre-treatment samples, whereas samples collected after B-cell–targeted therapy (Rituximab ± CHOP) showed reduced transformation efficiency. Notably, early pre-treatment samples exhibited a relative enrichment of CD27⁺ memory B cells. Baseline flow cytometric profiling of B cells undergoing LCL transformation revealed low CD19 expression (range <1%–15%). Repeat immunophenotyping at 3 weeks identified residual T cells within cultures, suggesting ongoing B-cell clearance. In matched flow cytometry and ELISpot assays from 7 evaluable patients with pre-treatment samples, EBV-positive PTLD cases demonstrated pronounced overexpression of PD-1 and TIM-3, but not LAG-3, alongside markedly diminished T-cell responses to EBV antigens. This distinct immunophenotypic and functional signature suggests T-cell exhaustion or dysfunction, likely driven by prior immunosuppression, which may impair immune surveillance and facilitate EBV-driven lymphomagenesis. Conclusions Our findings reveal distinct immunologic profiles in EBV-positive monomorphic PTLD compared to EBV-negative DLBCL, characterized by immune exhaustion and impaired T-cell functionality. Specifically, overexpression of PD-1 and TIM-3—but not LAG-3—in EBV-positive PTLD correlated with diminished antigen-specific T-cell responses, as measured by ELISpot, underscoring the role of prior immunosuppression in shaping ineffective tumor-specific immunity. Successful generation of autologous LCLs was predominantly achieved from pre-treatment PBMCs, highlighting the impact of B-cell–depleting therapies (Rituximab ± CHOP) on downstream immune profiling feasibility. The persistence of residual T cells in long-term LCL cultures suggests ongoing B-cell clearance and may reflect previously unrecognized immune dynamics in PTLD. Collectively, these data provide novel insights into the immune landscape of EBV-driven PTLD and support the rationale for therapeutic strategies aimed at reversing T-cell exhaustion—such as immune checkpoint blockade or adoptive T-cell therapies—to restore anti-EBV immunity in transplant recipients.

Abstract Genome-wide association studies have identified 40 ovarian cancer risk loci. However, the mechanisms underlying these associations remain elusive. In this study, we conducted a two-pronged approach to identify candidate causal SNPs and assess underlying biological mechanisms at chromosome 9p22.2, the first and most statistically significant associated locus for ovarian cancer susceptibility. Three transcriptional regulatory elements with allele-specific effects and a scaffold/matrix attachment region were characterized and, through physical DNA interactions, BNC2 was established as the most likely target gene. We determined the consensus binding sequence for BNC2 in vitro, verified its enrichment in BNC2 ChIP-seq regions, and validated a set of its downstream target genes. Fine-mapping by dense regional genotyping in over 15,000 ovarian cancer cases and 30,000 controls identified SNPs in the scaffold/matrix attachment region as among the most likely causal variants. This study reveals a comprehensive regulatory landscape at 9p22.2 and proposes a likely mechanism of susceptibility to ovarian cancer. Significance: Mapping the 9p22.2 ovarian cancer risk locus identifies BNC2 as an ovarian cancer risk gene. See related commentary by Choi and Brown, p. 439

Abstract Introduction: Mitochondria are intracellular organelles that play an important role in energy metabolism, reactive oxygen species generation, and apoptosis. They possess their own haploid genome distinct from nuclear DNA, and mutations in mitochondrial DNA (mtDNA) have previously been linked to cancer risk, disease progression, and treatment response for multiple tumor types. However, the spectrum of mtDNA variation in epithelial ovarian carcinoma (EOC) and associations with clinical characteristics have not been fully explored. Methods: We extracted mtDNA from fresh frozen EOC tumors of women diagnosed with primary invasive epithelial ovarian, fallopian tube, or peritoneal carcinoma, and performed targeted sequencing using the Illumina MiSeq Reporter mtDNA workflow. Homoplasmic and heteroplasmic SNVs and indels were called using an in-house bioinformatics pipeline. We estimated mtDNA haplogroup using Haplogrep and compared to results from available germline mtDNA SNP genotyping. We derived regional weighted variant burden scores based on mtDNA functional domains, accounting for underlying haplogroup, heteroplasmic fraction, and predicted functional impact. To assess potential differences in variant burden by histotype, we compared burden scores using Kruskal-Wallis testing. Among high-grade serous tubo-ovarian cases, we explored associations with overall survival (OS) using Cox proportional hazards regression. After quality control filtering, 389 mitochondrial genomes were analyzed, including those from 320 tubo-ovarian high-grade serous tumors, 42 endometrioid tumors, and 18 clear cell tumors. Results: Accounting for predicted haplogroup, we identified a median count of two global private heteroplasmies per tumor (range: 0-9). Elevated mutation rates were identified in the regulatory control region as well as among the various mt-tRNAs (>3 per 10kb per sample) relative to the remainder of the mtDNA. The majority of recurrent variants across tumors were also identified in the mtDNA control region. We did not observe an association with overall mtDNA variant burden and patient age at diagnosis. Regional mtDNA burden scores revealed a significant association with histotype (P<0.001) for the oxidative phosphorylation complex IV genes, with higher burden in tubo-ovarian high-grade serous and clear-cell tumors relative to endometrioid tumors. For patients with tubo-ovarian high-grade serous tumors, increased variant burden in MT-CO1 (cytochrome C oxidase I) was associated with improved OS (HR = 0.32; 95% CI = [0.14,0.70], LRT P = 0.001) after adjustment for age, stage, and debulking status. Conclusions: We demonstrate a wide range of tumor mtDNA variant patterns in the largest known collection of EOC patients. This work provides the first extensive evaluation of mtDNA variation in these diseases and highlights the potential prognostic relevance of mitochondrial dysfunction. Citation Format: Nicholas B. Larson, Stacey J. Winham, Chen Wang, Jared M. Evans, Sebastian M. Armasu, Bryan M. McCauley, Sean J. Yoder, Lan Min Zhang, Catherine M. Phelan, Ellen L. Goode. Targeted deep sequencing of mitochondrial DNA in epithelial ovarian carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 420.

Abstract An ovarian cancer Genome Wide Association Study (GWAS) identified 9p22.2 as a novel susceptibility locus with the most statistically significant single nucleotide polymorphisms (SNPs) located in an intergenic region near the Basonuclin 2 (BNC2) gene, which codes for a putative transcription regulator containing three pairs of zinc finger (ZF) domains. The minor alleles are protective in terms of ovarian cancer susceptibility. However, the molecular mechanisms by which these SNPs modify susceptibility remain largely unknown. The significant SNPs in the 9p22.2 locus lie in non-coding regions and therefore are hypothesized to affect the activity of regulatory elements and modify the expression of a target gene(s). In order to test this hypothesis we conducted fine mapping for the locus which delimited a ∼74kb region containing SNPs with a p-value less than 10-8. FAIRE-Seq and ChIP-Seq experiments for histone markers conducted in immortalized ovarian surface epithelial cells (IOSE) and fallopian tube epithelial cells (IFTE) were used to prioritize functional SNP candidates which overlap with regulatory elements. Luciferase assays tested the ability of these regulatory elements to activate transcription. Chromosome conformation capture (3C) experiments demonstrate a physical interaction between the BNC2 promoter and candidate regulatory elements containing risk-associated SNPs. Methylation Quantification at Trait Loci (mQTL) revealed an association between decreased methylation at the BNC2 promoter and the protective minor alleles. Expression analysis shows decreased expression of BNC2 in cancer versus normal tissue implicating tumor suppressor function of BNC2. Therefore the protective minor allele likely increases expression of BNC2 which in turn contains tumor suppressing properties that decrease ovarian cancer risk. BNC2 protein is in complex with transcriptional regulatory proteins, in particular the NURD complex components. Moreover, BNC2 acts as a transcriptional repressor in in vitro transfection assays indicating that it functions in transcriptional repression. We then used protein binding microarrays and CHIP-Seq experiments to identify its putative DNA binding motifs and its downstream target genes. Analysis of this data suggests that BNC2 functions in a regulatory transcription network that impacts on genes implicated in ovarian cancer with enrichment for genes in the TGF-beta response pathway. Citation Format: Melissa A. Buckley, Howard C. Shen, Gustavo A. Mendoza-Fandino, Nicholas T. Woods, Anxhela Gjyshi, Juliet French, Kate Lawrenson, Honglin Song, Jonathan Tyrer, Renato S. Carvalho, Alexandra Valle, Ann Chen, Sean Yoder, Gregory Bloom, Ya-Yu Tsai, Ally Yang, Timothy R. Hughes, Xiaotao Qu, Mine Cicek, Melissa Larson, Ellen Goode, Brooke Fridley, Susan Ramus, Georgia Chenevix-Trench, Paul Pharoah, Thomas A. Sellers, Simon Gayther, Alvaro N.A. Monteiro, Ovarian Cancer Association Consortium. Functional analysis of the 9p22 locus implicates the transcriptional regulation of BNC2 as a mechanism in ovarian cancer predisposition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3285. doi:10.1158/1538-7445.AM2014-3285