Bedell, Victoria

Introduction: HIV-associated diffuse large B-cell lymphoma (HIV-DLBCL) is a significant complication in HIV-positive individuals, presenting unique clinical challenges and a poorer prognosis compared to patients with de novo DLBCL. Epstein-Barr Virus (EBV) status is a critical factor influencing the pathogenesis, clinical behavior, and therapeutic responses in these lymphomas. Plasmablastic lymphomas (PBL) have shared some overlapping genomic abnormalities with HIV-DLBCL including MYC rearrangements. This study aims to elucidate the differences in the genetic profiles and pathway activations between EBV(+) and EBV(-) HIV-DLBCL through comprehensive genomic profiling. Methods: Cases of DLBCL were identified in patients living with HIV from a multi-institute cooperative group. Cases of Burkitt lymphoma and PBL were excluded. We performed whole exome sequencing (WES) on 106 tumors of HIV-DLBCL and RNA sequencing on 39 tumors and mapped the reads to hg38 reference genome using BWA and STAR, respectively. EBV status of cases was determined by in situ hybridization and/or reads mapped on EBV genome in sequencing data. Somatic mutations were identified using variant callers (Strelka2, Mutect2) with WES data. For those mutated genes in COSMIC, allele frequency cutoff was set at 0.03. Mutations with an artifact score larger than 0.7 in SOBDetector and those located in segmental duplications were further removed. They were annotated with Ensembl Variant Effect Predictor, manually checked, and plotted with maftools. RNAseq read counts aligned to each gene were obtained by featureCounts and DEseq2 was used for differential expression (DE) analysis between EBV positive and negative groups. Pathway analysis with the DE genes was performed using GSEA. FISH analysis was performed using MYC, BCL2, and BCL6 break-apart probes. Results: There were 41 cases of EBV(+) HIV-DLBCL and 65 cases of EBV(-) HIV-DLBCL. FISH of EBV(+) HIV-DLBCL identified 42% (3/7) with MYC rearrangement (MYCr), none with BCL2 rearrangements (BCL2r) (0/6), and 33% (2/6) positive for BCL6 rearrangement (BCL6r) with 1 tumor having a MYCr/BCL6r. For EBV(-) HIV-DLBCL, there were 35% with a MYCr (6/17), 18% with BCL2r (2/11), and 27% with a BCL6r (3/11) with 2 tumors with MYCr/BCL6r, and 1 tumor with MYCr/BCL2r/BCL6r. The most frequent mutations seen in EBV(+) HIV-DLBCL were STAT3 (32%), DDX3X (22%), and TP53 (15%). For EBV(-) HIV-DLBCL, the most frequent mutations were KMT2D (25%), TP53 (23%), GNA13 (22%), and TET2 (22%). Pathways that were most commonly associated with EBV(+) HIV-DLBCL were JAK/STAT (42%) (STAT3, JAK1) and NF-kB (39%)(DDX3X, TNFAIP3) while EBV(-) HIV-DLBCL was associated with epigenetic modifiers (62%)(KMT2D, TET2, EP300), JAK/STAT (45%)(SOCS1, JAK3) and PI3K/mTOR (40%)(GNA13, MTOR). Significant disparities between EBV(+) and EBV(-) were KMT2D (24% vs 50%, P=0.0025), TET2 (10% vs 26%, P=0.008), SOCS1 (29% vs 39%, P=0.04), DDX3X (15% vs 5%, P=0.03), and GNA13 (5% vs 24%, P=0.001). RAS mutations (KRAS, NRAS) were infrequent in HIV-DLBCL (EBV(+), 12%; EBV(-), 6%), in contrast to prior studies of PBL. Gene expression profiling showed enrichment of MYC targets, oxidative phosphorylation, and the mTORC pathway in EBV(+) as compared to EBV(-) HIV-DLBCL. Conclusion: EBV(+) HIV-DLBCL show a distinct mutational profile compared to EBV(-) HIV-DLBCL, with EBV(+) cases showing frequent mutations with STAT3 and DDX3X in contrast to EBV(-) cases with frequent mutations associated with epigenetic modification pathways (KMT2D, TET2). These genetic profiles underscore the need for tailored therapeutic approaches depending on EBV status. Although the analysis is limited and requires confirmation in a larger cohort, this is the largest study at present evaluating these tumors.

11051 Background: A serious complication associated with breast cancer treatment is the increased risk for development of therapy-related acute myeloid leukemia (t-AML). To evaluate and possibly identify patients (pts) at high risk for development of t-AML, the Southwest Oncology Group asked whether dose-intensive adjuvant regimens for high risk breast cancer pts induced genetic damage to hematopoietic stem cells (HSC), defined by the emergence of clonal hematopoiesis, an early marker of HSC damage. Methods: 274 pts consented to the clonal hematopoiesis study objective of S0012, a randomized clinical trial of standard doxorubicin and cyclophosphamide followed by weekly paclitaxel (arm 1, 129 pts) vs. weekly doxorubicin and daily oral cyclophosphamide plus G-CSF followed by weekly paclitaxel (arm 2, 145 pts) as neoadjuvant therapy for inflammatory and locally advanced breast cancer. Two different clonality assays were used: the HUMARA (HUMan Androgen Receptor) Assay to estimate the incidence of early genetic damage by clonal proliferation and microsatellite instability (MSI) testing at 5 loci (Bat 26, Bat 40, APC, Mfd, D2S123), common ‘hotspots‘ in t-AML, to screen for loss of heterozygosity or defective DNA mismatch repair mechanisms. Blood samples were evaluated prior to treatment and at 6 and 12 mos post-surgery for emergence of clonal hematopoiesis. Results: Of the 274 pts enrolled, follow-up clonal hematopoiesis samples were available for 195 pts; 96 pts on arm 1 and 99 pts on arm 2. Both HUMARA and MSI results were negative for clonal hematopoiesis in 96% of samples analyzed. In 14 cases, the HUMARA assay suggested that a clonal population was present, but MSI analysis was negative. No cases were HUMARA+/MSI+. With a median follow-up of 19.6 mos, only one pt has developed t-AML 3 yr 5 mos post randomization. Her clonal hematopoiesis test samples at 6 and 12 mos following treatment were negative. Conclusions: Clonal hematopoiesis assays performed within the first year following neoadjuvant therapy and surgery on S0012 failed to identify an emerging clonal HSC population. Longer clinical follow-up will be necessary to define the positive predictive value of detecting clonal hematopoiesis in the 14 HUMARA+/MSI- cases as a harbinger of t-AML. No significant financial relationships to disclose.