Genomic Profiling of Patient-Derived Xenografts for Lung Cancer Identifies B2M Inactivation Impairing Immunorecognition

Abstract

Purpose: We aimed to maximize the performance of detecting genetic alterations in lung cancer using high-throughput sequencing for patient-derived xenografts (PDXs). Experimental Design: We undertook an integrated RNA and whole-exome sequencing of 14 PDXs. We focused on the genetic and functional analysis of b2-microglobulin (B2M), a component of the HLA class-I complex. Results: We identified alterations in genes involved in various functions, such as B2M involved in immunosurveillance. We extended the mutational analysis of B2M to about 230 lung cancers. Five percent of the lung cancers carried somatic mutations, most of which impaired the correct formation of the HLA-I complex. We also report that genes such as CALR, PDIA3, and TAP1, which are involved in the maturation of the HLA-I complex, are altered in lung cancer. By gene expression microarrays, we observed that restitution of B2M in lung cancer cells upregulated targets of IFNa/IFNg. Furthermore, one third of the lung cancers lacked the HLA-I complex, which was associated with lower cytotoxic CD8 þ lymphocyte infiltration. The levels of B2M and HLA-I proteins correlated with those of PD-L1. Finally, a deficiency in HLA-I complex and CD8 þ infiltration tended to correlate with reduced survival of patients with lung cancer treated with anti-PD-1/anti-PD-L1. Conclusions: Here, we report recurrent inactivation of B2M in lung cancer. These observations, coupled with the mutations found at CALR, PDIA3, and TAP1, and the downregulation of the HLA-I complex, indicate that an abnormal immunosurveillance axis contributes to lung cancer development. Finally, our observations suggest that an impaired HLA-I complex affects the response to anti-PD-1/anti-PD-L1 therapies. Clin Cancer Res; 23(12);

A Gene Signature Predicting Natural Killer Cell Infiltration and Improved Survival in Melanoma Patients

“…1F) has one of the most negative hazard coefficients, likely reflecting its role in MHC class I antigen presentation of neoantigens to CD8 þ T cells and consistent with reports of this process for immune control of tumors (54). Further, a truncation mutant of B2M can confer resistance to PD-1 blockade in melanoma (55), and mutations in B2M have been shown to disrupt immune surveillance in lung cancer (56). The large negative hazard coefficient associated with HAPLN3, encoding a hyaluronan and proteoglycan link protein, suggests that this gene may warrant further investigation in the context of immune recognition and targeting.…”

MET-Oncogenic and JAK2-Inactivating Alterations Are Independent Factors That Affect Regulation of PD-L1 Expression in Lung Cancer

“…References concerning the antibodies and scoring systems used, as well as the details and concentrations of the various treatments are presented in Supplementary Table S2. Western blots and immunohistochemistry were performed using previously described protocols (4). We used previously described criteria to determine B2M, HLA-I, and PD-L1 levels by immunohistochemistry (4).…”

“…These include defects in tumor immunorecognition, such as downregulation of the HLA-I complex due to gene alterations of its components (either B2M or HLA-A) or at molecules involved in its maturation process (e.g., CALR, TAP1/2, and TAPBP; refs. [2][3][4]. An abnormal increase in the expression of negative controllers of the immune response, such as constitutively high levels of programmed death ligand-1 (PD-L1) expression, also contributes to immune tolerance (1).…”

“…This clinical benefit makes it crucial to identify factors that determine the sensitivity or refractoriness to immune checkpoint inhibitors (ICI). Several functionally interrelated tumor biomarkers have been proposed as predictors of the response to ICIs, including high tumor mutational load, DNA mismatch repair deficiency, strong intratumoral T-cell infiltration, and a high level expression of PD-L1 and of the HLA-I-class complex (4,(6)(7)(8)(9). In addition, inactivating mutations of JAK2 in melanoma, involved in IFNg signaling, and of B2M in melanoma and in lung cancer, account for primary and acquired resistance to these treatments (4,10,11).…”

Resistance mechanisms in melanoma to immuneoncologic therapy with checkpoint inhibitors

“…A late relapse patient with metastatic melanoma resistant to CTLA-4 inhibition was found to have biallelic loss of b-2-microglobulin [29,110] . Zaretsky et al [29] also identified a patient with homozygous frameshift deletions of b-2-microglobulin that had developed resistance to PD-1 blockade [28][29][30]192] . Five patients treated with immunotherapy were found to have reduced MHC expression and were not recognized by effector T cells due to loss of b-2-microglobulin expression.…”