The Impact of Interferon-alpha2 on HLA-Genes in Patients with Polycythemia Vera and Related Neoplasms
Authors: Skov Vibe , Riley Caroline H , Thomassen Mads , Kjær Lasse , Larsen Thomas Stauffer , Jensen Morten K , Bjerrum Ole Weis , Kruse Torben A , Hasselbalch Hans Carl 
Published: October 2019

Abstract
Introduction
Gene expression profiling studies in the Philadelphia-negative chronic myeloproliferative neoplasms (MPNs) have unraveled significant deregulation of several immune and inflammation genes of potential importance for clonal evolution (Skov V et al., Eur J Haematol 2011; Leuk Res 2012; Exp Hematol 2012). Other mechanisms might be downregulation of major histocompatibility (MHC) class I and II genes, which are used by tumor cells to escape antitumor T-cell-mediated immune responses. In a previous study, several genes encoding human leukocyte antigen (HLA) class I and II molecules, beta2microglobulin and members of the antigen processing machinery of HLA class I molecules (LMP2, LMP7, TAP1, TAP2 and tapasin) have been shown to be significantly downregulated (Skov V, Leuk Lymphoma 2012). Upregulation of HLA-genes is considered one of the mechanisms of action of interferon-alpha2 (IFN-alpha2) but regulation of these genes during IFN-alpha2 treatment of patients with MPNs has never been studied. The purpose of this study was to assess the regulation of several HLA genes before and during treatment with IFN-alpha2, the hypothesis being that IFN-alpha2 - as in other cancers - may restore downregulation of HLA genes in MPNs as well.
Patients and Methods
Using Affymetrix HG-U133 2.0 Plus microarrays, gene expression profiling have been performed on whole blood from patients with ET (n =8), PV (n = 21), and PMF (n = 4) before and after 3 months of treatment with IFN-alpha2. Background correction, normalization, and gene expression index calculation were performed with the robust multi-array (rma) method. The regularized t-test limma for pairwise data was used to calculate differences in gene expression between patients before and after treatment with IFN-alpha2. A p-value < 0.05 was considered significant.
Results
Statistical analysis of all 54,675 probe sets on the microarray revealed 6261, 10,008, 2828, and 12,390 probe sets to be significantly differentially expressed in ET, PV, PMF, and MPNs as a whole, respectively, in response to treatment with IFN-alpha2 (P-value <0.05). To examine if treatment with IFN-alpha2 restores preexisting abnormalities of HLA genes in MPNs, pretreatment vs. posttreatment gene expression changes of MPNs were analyzed. Several HLA genes were significantly deregulated. Of 23 HLA major histocompatibility complex (MHC) class I and II genes and 26 HLA associated and complex group genes, 15, 24, 6 and 24 genes were significantly deregulated in ET, PV, PMF, and MPNs as a whole, respectively (P<0.05). In ET patients, BAT4, HCG26, HCP5, HLA-B, HLA-C, HLA-F, HLA-G, TAP1, and PSMB9 were significantly upregulated and BAT5, CIITA, HCG11, HLA-DOA, HLA-DQA1, and HLA-DRB4 were significantly downregulated. In PV patients, the significantly upregulated genes included CD74, HCG26, HCG8, HCP5, HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, HLA-DOB, HLA-DPA1, HLA-DRB1, HLA-DRB5, HLA-DRB6, MR1, TAP1, TAP2, TAPBPL, PSMB8, and PSMB9 and the significantly downregulated genes included CITTA, HLA-DOA, and HLA-DPB2. In PMF, HCP5, HLA-DOA, and HLA-DQA1 were significantly upregulated and HCP5, TAP1, and PSMB9 significantly downregulated. In MPNs as a whole, BAT4, HCG26, HCG8, HCP5, HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, HLA-DOB, HLA-DPA1, HLA-DRB1, HLA-DRB5, HLA-DRB6, MR1, TAP1, TAP2, TAPBPL, PSMB8, and PSMB9 were significantly upregulated and CIITA, HLA-DOA, and HLA-DPB2 were significantly downregulated (all P<0.05).
Conclusions: Whole blood transcriptional profiling has unraveled that IFN-alpha2 potently up-regulates several HLA-genes of importance for tumor immune surveillance. Our findings may be crucial for the efficacy of IFN-alpha2 in the treatment of MPNs, since the potential of cytotoxic immune cells for tumor killing is likely by this mechanism significantly enhanced and the path towards induction of minimal residual disease accordingly improved as well.

Disclosures
Bjerrum: Bristoll Myers Squibb, Novartis and Pfizer: Other: educational activities. Hasselbalch:Novartis: Research Funding.