Exome sequencing identifies PD-L2 as a potential predisposition gene for lymphoma

Abstract

To investigate germline predisposition in lymphoma, we performed whole-exome sequencing and discovered a novel variant (c.817-1G>T) in programmed cell death 1 ligand 2 (PD-L2) in a family with early-onset lymphomas and other cancers. The variant was present in the proband with follicular lymphoma and his son with Hodgkin's lymphoma. It was in the terminal splice acceptor site of PD-L2 and embedded in a putative enhancer of Janus kinase 2 (JAK2) and programmed cell death 1 ligand (PD-L1). We also found that gene expression of PD-L2, PD-L1, and JAK2 was significantly increased. Using 3' rapid amplification of cDNA ends (3' RACE), we detected an abnormal PD-L2 transcript in the son. Thus, the c.817-1G>T variant may result in the elevated PD-L2 expression due to the abnormal PD-L2 transcript and the elevated PD-L1 and JAK2 expression due to increased enhancer activity of PD-L1 and JAK2. The PD-L2 novel variant likely underlies the genetic etiology of the lymphomas in the family. As PD-L2 plays critical roles in tumor immunity, identification of PD-L2 as a germline predisposition gene may inform personalized immunotherapy in lymphoma patients.

Keywords: PD-L2; germline predisposition; lymphoma.

FIGURE 1

Pedigree of the family with the PD‐L2 novel variant. Arrow indicates the proband. +: positive for PD‐L2 c.817‐1G>T variant; ‐: negative for PD‐L2 c.817‐1G>T variant. Dx: diagnosis

FIGURE 2

PD‐L2 alterations identified in patients. PD‐L2 c.817‐1G>T variant identified by whole‐exome sequencing (WES) shown in Integrated Genomics Viewer (A) and by Sanger sequencing for confirmation (B). (C) RNA expression of PD‐L2 in the son compared to the control. One pair of primers was designed on exons 3 and 4; the other was designed on exons 6 and 7. Two‐tailed p values were calculated between the son and the control from three independent experiments using Student's t‐test. **, p < 0.01; ***, p < 0.001. (D), Electrophoresis of 3′ RACE polymerase chain reaction product. HDLM‐2, a cell line with high expression of PD‐L2, was used as a control. The fragment with a box with red dashed lines was from the abnormal PD‐L2 transcript. (E) PD‐L2 variant is located in a putative enhancer predicted by Roadmap Epigenomics Project. Data visualization was performed using WashU Epigenome Browser. CB: cord blood. HSC: hematopoietic stem cells. PB: peripheral blood. (F) RNA expression of PD‐L1 and JAK2 in the son compared to the control. Two‐tailed p values were calculated between the son and the control from three independent experiments using Student's t‐test. ***, p < 0.001