Comprehensive characterization of programmed death ligand structural rearrangements in B-cell non-Hodgkin lymphomas

Abstract

Key Points• Capture sequencing reveals that PDL SRs cluster into 2 discrete breakpoint regions.• PDL SRs are significantly associated with increased protein expression and limit T-cell activation.Programmed death ligands (PDLs) are immune-regulatory molecules that are frequently affected by chromosomal alterations in B-cell lymphomas. Although PDL copy-number variations are well characterized, a detailed and comprehensive analysis of structural rearrangements (SRs) and associated phenotypic consequences is largely lacking. Here, we used oligonucleotide capture sequencing of 67 formalin-fixed paraffin-embedded tissues derived from primary B-cell lymphomas and 1 cell line to detect and characterize, at base-pair resolution, SRs of the PDL locus (9p24.1; harboring PDL1/CD274 and PDL2/ PDCD1LG2). We describe 36 novel PDL SRs, including 17 intrachromosomal events (inversions, duplications, deletions) and 19 translocations involving BZRAP-AS1, CD44, GET4, IL4R, KIAA0226L, MID1, RCC1, PTPN1 and segments of the immunoglobulin loci. Moreover, analysis of the precise chromosomal breakpoints reveals 2 distinct cluster breakpoint regions (CBRs) within either CD274 (CBR1) or PDCD1LG2 (CBR2). To determine the phenotypic consequences of these SRs, we performed immunohistochemistry for CD274 and PDCD1LG2 on primary pretreatment biopsies and found that PDL SRs are significantly associated with PDL protein expression. Finally, stable ectopic expression of wild-type PDCD1LG2 and the PDCD1LG2-IGHV7-81 fusion showed, in coculture, significantly reduced T-cell activation. Taken together, our data demonstrate the complementary utility of fluorescence in situ hybridization and capture sequencing approaches and provide a classification scheme for PDL SRs with implications for future studies using PDL immune-checkpoint inhibitors in B-cell lymphomas. (Blood. 2016;128(9):1206-1213

Prevalence ofPDL1Amplification and Preliminary Response to Immune Checkpoint Blockade in Solid Tumors

“…Similar alterations have been observed in many tumor types and correlate with increased PD-L1 expression, presumably via loss of inhibitory micro RNA binding sites. 31 , 44 , 45 This patient achieved a partial response that lasted 9 months with a durvalumab (anti-PD-Ll)-based regimen. The other alteration, with a PKD1P1-PDCD1LG2 rearrangement, has not been previously reported or characterized.…”

Biology and therapy of primary mediastinal B‐cell lymphoma: current status and future directions

“…PD‐L1/2 overexpressing malignant cells increase the co‐inhibitory pathways leading to hypo‐responsive T‐cells known as T‐cell anergy (Wang et al , ). PD‐L1/2 expression is aberrant in malignant B cells through a combination of somatically acquired copy‐number gains and chromosomal rearrangements (Chong et al , ). CD274 (previously termed PD‐L1 ) and PDCD1LG2 are located on chromosome 9p24.1.…”

Immune checkpoint inhibitors in Hodgkin and non-Hodgkin lymphoma: how they work and when to use them

“…The hope for effective clinically relevant biomarkers is fueled by the finding that PDL1 and PDL2 expression is heterogeneous in specific lymphoma entities [20][21][22][23][24], and abundance and spatial patterns of PD1 expressing (exhausted) T cells have been reported as variable and correlated with treatment outcome [25,26]. Moreover, in a subset of B cell lymphomas, including CHL, PMBCL, and diffuse large B cell lymphoma (specifically primary central nervous system lymphoma and primary testicular lymphoma), structural genomic alterations (copy number amplification, translocations, and intrachromosomal rearrangements) are correlated with elevated gene expression of PDL1 and PDL2 [22,27,28], suggesting that these somatically acquired changes underlie an immune privilege phenotype that might be preferentially targetable with immune checkpoint inhibition in the subset of patients with PDL1 and PDL2 alterations.…”