Abstract 2748: Integrative analysis of 3D chromatin organization revealed regulation mechanisms in angioimmunoblastic T-cell lymphoma
Authors: Makoto Iwasaki, Caroline MacVicar, Anna Baird Rider, Aliyah Sohani, Valentina Nardi, Josie Ford, Kusha Chopra, Eric Jacobsen, Jeffrey Barnes, Salvia Jain
Journal: Cancer Research (2025)

Abstract Molecular studies have highlighted recurrent alterations in epigenetic modifier genes, including TET2, DNMT3A, and IDH2, in angioimmunoblastic T-cell lymphoma (AITL). However, the direct impact of gene regulatory elements on gene expression changes leading to T-cell lymphomagenesis remains poorly understood. We focus on 3D chromatin organization. Hi-C and RNA sequencing was performed on diagnostic FFPE tumor samples from seventeen patients with AITL. Two CD4+ T cells from individual donors and one follicular helper T cells (TFH) from four donors were used as controls. To annotate AITL-specific loops in association with enhancer status, we identified H3K27ac histone marks in TFH cells using CUT&amp;Tag. Promoter-super enhancer (P-SE) loops or stripes were defined as those with non-promoter anchors containing SE predicted by ROSE. In comparison to normal CD4+ T-cell controls, recurrent AITL-specific alterations in A/B (active/inactive) compartments, topologically associating domains (TADs), and chromatin loops were identified. Principal-component analysis (PCA) of genome-wide compartment scores indicated AITL samples and normal CD4+ T cells clearly separated by the first two components. On average, there was 3.5% (range: 2.0-5.3) A-to-B compartment switch and 1.9% (range: 0.8-4.8) B-to-A switch when comparing AITL samples with normal CD4+ T cell controls (p=5.17 × 10-5, two-sided paired t-test). Alterations in TADs were recurrently observed in 434 of 743 cancer census genes in COSMIC, including MYC, TCL1A, and RHOA. On average, 60.1% of loops include promoters in at least one anchor. Genes within AITL-specific loops exhibited significantly higher expression than those outside of loop regions (p=7.39 × 10-88, Kruskal-Wallis test). Genes within P-SE loops/stripes showed significantly higher expression than those within promoter-inactive enhancer (P-IE) loops/stripes, which were defined by ENCODE as enhancers without TFH SE (loops: p = 5.17 × 10-5, stripes: p=1.55e-15, Kruskal-Wallis test). Based on the differential loop analysis using diffpeakachu, significant chromatin loops were observed in the MYC region and genes associated with pathways related to MYC, such as the Wnt signaling pathway. AITL-specific loops in the MYC region were observed in eight of seventeen patients. Recurrent MYC promoter-TFH SE loop (chr8:127730000-127740000, chr8:127960000-127970000) was located between ME1 and ME2 of MYC enhancer in AML (Pulikkan et al., 2018). Our findings indicate that AITL exhibits unique chromatin conformations, suggesting the formation of a lymphoma-specific gene regulatory landscape. Recurrent changes in chromatin conformation involve MYC. Distinct gene regulatory elements associated with enhancer regions in AITL is implicated. Correlation of the regulatory candidates with their mutational signature is underway and will be reported at the meeting. Citation Format: Makoto Iwasaki, Caroline MacVicar, Anna Baird Rider, Aliyah Sohani, Valentina Nardi, Josie Ford, Kusha Chopra, Eric Jacobsen, Jeffrey Barnes, Salvia Jain. Integrative analysis of 3D chromatin organization revealed regulation mechanisms in angioimmunoblastic T-cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2748.