Distinct Molecular Landscape of Epstein–Barr Virus Associated Pulmonary Lymphoepithelioma-Like Carcinoma Revealed by Genomic Sequencing

Abstract

Pulmonary lymphoepithelioma-like carcinoma (LELC) is a subtype of non-small cell lung cancer (NSCLC) characterized by marked lymphocytic infiltration and association with Epstein–Barr virus (EBV). The molecular basis underlying the disease remains unclear. We sought to study the molecular landscape by multiple approaches including whole genomic sequencing, capture-based targeted sequencing, fluorescent in situ hybridization and immunohistochemistry. Tumor cells from 57 EBV-positive pulmonary LELCs were isolated by careful microdissection prior to genomic sequencing. Integrated analysis revealed a distinct genomic landscape of low TP53 mutation rate (11%), low incidence of known drivers in the RTK/RAS/RAF (11%) and PI3K/AKT/mTOR pathways (7%), but enriched for loss-of-function mutations in multiple negative regulators of the NF-κB pathway. High level programmed cell death ligand-1 (PD-L1) expression was shown with 47% and 79% of the cases showing positive PD-L1 immunoreactivity at ≥50% and ≥1% tumor proportion score, respectively. Subsets of the patients with actionable fibroblast growth factor receptor 3 (FGFR3) aberrations (4%) and mismatch repair deficiency (4%) were potentially eligible for precision medicine. Pulmonary LELC showed a distinct genomic landscape, different from major NSCLC subtypes but resembled that of EBV-associated nasopharyngeal carcinoma. Our work facilitated the understanding of molecular basis underlying pulmonary LELC to explore potential therapeutic options.

Molecular characteristics of primary pulmonary lymphoepithelioma-like carcinoma based on integrated genomic analyses

“…Similar to previous studies by Hong et al and Xie et al, 11,12,37 TP53 mutation was also detected in our study. Except for TP53, no other common FMGs were observed within these studies, but a variety of similar CNVs were identified at both the segment and gene levels.…”

“…7 However, the prognostic significance of PD-L1 expression in pLELC is still completely controversial [8][9][10] In recent years, a few studies have reported the mutational landscape of pLELC using multiple approaches, including wholeexome sequencing, targeted deep sequencing, and singlenucleotide polymorphism (SNP) arrays. 11,12 However, analysis at the RNA level, e.g., transcriptome sequencing, seems to be absent in relevant research. In addition, Epstein-Barr virus (EBV), which has been detected in various tumors, such as Burkitt's lymphoma, EBV-associated gastric cancer, and nasopharyngeal carcinoma (NPC), 2 as well as pLELC, 5 either exists typically as an episome in cells or tends to integrate into the host genome.…”

PD-1 and PD-L1 Expression on Circulating Lymphocytes as a Marker of Epstein-Barr Virus Reactivation-Associated Proliferative Glomerulonephritis

“…It is worth noticing, that EBV is enumerated among human viruses with a proven role in oncogenesis, and the development of autoimmune disorders, as well as immunosuppression [40][41][42][43]. The life cycle of EBV is particularly complex and the virus undergoes the latency phase during which it expresses several genes impacting oncogenesis [44][45][46][47]. Recent studies have shown that EBV DNA is present in large quantities in patients with autoimmune diseases of several etiologies [48,49].…”

Pathogenic Role of Epstein–Barr Virus in Lung Cancers

“…The latest literature search was performed in March 2021. Having carefully evaluated the extracted studies, we selected 42 relevant studies and the EBV status in LCs was summarized in Table 2 [ 12 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 ].…”

“…Indeed, elevated levels of multiple immune checkpoint molecules, such as indoleamine 2,4-dioxygenase (IDO), programmed cell death 1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), lymphocyte-activation gene 3 (LAG3), B and T lymphocyte attenuator (BTLA), and v-domain Ig suppressor of T cell activation (VISTA) were also detected in EBV(+) LCs [ 12 ]. Further, several studies have reported that high levels of programmed death-ligand 1 (PD-L1) were observed in EBV(+) LCs [ 64 , 66 ]. These immune inhibitors may contribute to EBV-associated tumor immune tolerance.…”