Interferon-lambda (IFNL) germline variations and their significance for HCC and PDAC progression: an analysis of The Cancer Genome Atlas (TCGA) data

Hepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (PDAC) are leading causes of cancer-related deaths [1]; they belong to the most lethal malignancies with 5-yr survival rates < 20% [2, 3]. According to Hanahan and Weinberg, dysregulated cellular pathways that transform growth of normal cells into neoplasms are regarded as ‘hallmarks of cancer’ [4]. The evasion of the host’s immune defense, later on, has been recognized as one further principle of promoting malignant growth [4]. The impact of the host’s immune system for disease progression is underscored by the recent successful clinical translation of immunotherapeutic strategies [5].

Understanding that not all patients benefit from cancer immunotherapy, the term ‘cancer immune responsiveness’ (CIR) has been coined [6]. Germline genetic variants have been proposed to contribute to CIR including those in IFN signaling genes [6]. IFNs and their effectors have been known for long not only to mediate antiviral but also to edit antitumor host responses [7, 8]. They divide into type I (IFN-α_n/β), type II (IFN-γ) and type III (IFN-λ_1–4). Among the genes encoding IFN species, only one, type III IFNL4, harbors a common exonic gain-or-loss-of-function variation: while the phylogenetically older variant ΔG enables functional IFN-λ₄ protein expression, the knockout variant TT causes a frameshift thereby disrupting the open reading frame and preventing translation [9, 10]. This germline dinucleotide polymorphism, IFNL4 rs368234815 [TT/ΔG] (merged into IFNL4 rs11322783) thus reflects the ongoing process of pseudogenization dividing human beings into those who are predisposed to express IFN-λ₄ protein and into those who are not [11]; it associates with clearance of hepatitis C virus (HCV) and a variety of other disease conditions (reviewed in [12]).

In the context of viral infections, generally, an IFN-λ₄ creating genetic background rather was found to be unfavorable for the host. This counter-intuitive relationship was first recognized for HCV infection, when the IFN-λ₄ creating genotypes were shown to be in LD with those IFNL variants that had been identified before to be correlated with poor clearance of HCV infection in genome wide association studies (GWAS) on main ethnic populations [10, 13]. Similarly, in human immunodeficiency virus (HIV) infection, the IFN-λ₄ creating genotype was found to be associated with a higher prevalence of AIDS [14] while the non-encoding genotype associates with a lower probability to acquire HIV [15, 16]. Also cytomegalovirus (CMV) reactivation is described to be more prevalent in patients encoding for a functional IFN-λ₄ protein [17, 18].

The availability of collaborative comprehensive data repositories enables analyses of patient material on a whole genome scale and on large sample sizes. The Cancer Genome Atlas (TCGA) database provides datasets on more than 11,000 cancer patients across 33 tumor entities to the scientific community. Besides demographic and clinical data, TCGA comprises whole exome DNA and RNA sequencing data not only of tissue samples derived from primary tumors but also from corresponding non-malignant material, the latter giving rise to patients’ germline genetic background.

By employing TCGA datasets, this study aimed at finding clinical evidence for or against an impact of IFNL germline variations for HCC or PDAC progression. Using the Kaplan-Meier estimator, disease progression was assessed by (i) the length of the specific progression-free interval (PFI) and by (ii) the overall survival (OS) time as two clinical outcome endpoints. A multivariate Cox proportional-hazards model was applied considering patients’ age, tumor grade, and tumor stage as covariates along with IFNL genotypes.

Based on TCGA datasets, this study revealed significant associations between IFNL germline variations and progression of PDAC in terms of the length of the specific PFI and the OS time as two clinical endpoints. These IFNL variations are in nearly complete LD to a dinucleotide polymorphism that controls IFNL4 gene expression (IFNL4 rs368234815). By performing a multiple regression analysis including patients’ age at diagnosis, tumor stage, and tumor grade as further covariates, IFNL variation was proven to be an independent parameter for the length of the specific PFI (p = 0.02) and with a tendency to significance also for OS time (p = 0.09). This relationship was not observed for a cohort of patients matched for ethnicity but diagnosed for HCC.

A genetic background corresponding to the ability to express a functional IFN-λ₄ protein, i.e. carriers of the IFNL4 rs368234815 creating ΔG allele, was found to be related to a delayed progression of PDAC disease, i.e. being favorable. As outlined above, in the context of viral diseases, an IFN-λ₄ creating genetic background – in general – is unfavorable for the host.

This disadvantage is also seen in the context of some cancer diseases, in particular for cancer entities with a virus related etiology. For instance, the IFNL4 rs368234815 ΔG allele was shown to be associated with prostate cancer among men at increased risk of sexually transmitted infections [21]. In an independent study, this allele was shown to be related to significant decreased overall survival of African-American men with prostate cancer [22]. Moreover, susceptibility to AIDS-related Kaposi’s sarcoma was also found to be associated with genotypes predicted to produce an active IFN-λ₄ [23].

In contrast, for PDAC, an entity for which no virus-related etiology is supposed, we found the genetic predisposition to encode for IFN-λ₄ to be favorable for the outcome in terms of the length of the specific PFI and of the OS time. Even if biology of IFN-λ species is not yet completely understood, this is in accordance with the supposed general antitumor activity of type III IFNs [24, 25].

TCGA also provides information on cancer treatments. Where available, data comprise the type of the therapy, its starting date and duration, and the response to it. All of the HCC patients included into our analysis are documented to have received surgery, i.e. liver lobectomy or segmentectomy. Some of them received ablation (n = 40), adjuvant radiation (n = 7), or one or several regimens of chemotherapy (n = 12). Likewise, all of the PDAC cases under investigation were subjected to partial or total pancreatectomy. Some of them received adjuvant radiation therapy (n = 37) or adjuvant chemotherapy (n = 109). Our analyses were performed disregarding therapeutic schemes or their outcomes, which is a limitation. However, our analyses focusing on disease outcome in terms of the length of the specific PFI and OS time, are based on the assumption that patients were receiving the best possible care according to their individual health conditions. Nevertheless, the significant but weak association between IFNL genotype and clinical outcome for PDAC patients in the whole cohort might mask stronger associations within subgroups, e.g. among patients who are responding or non-responding to a cytostatic therapy. Data thus might reflect therapy responsiveness that, in turn, might translate into disease outcome. Accordingly, this association between IFNL variants and disease progression might be more prominent for PDAC than for HCC patients due to a higher proportion of patients subjected to chemotherapy, i.e. 109/162 (73.3%) vs 12/187 (6.4%), respectively. Whether treatment response is underlying the association between IFNL genotypes and cancer disease progression needs to be addressed in a separate analysis with a higher sample number. Alternatively, the lack of a relationship between IFNL genotypes and HCC progression might be related to that proportion of cases with viral etiology that distinguishes the HCC cohort from the PDAC cohort. The HCC cohort under study includes more than half of the patients (61%) with HBV infection (n = 42), with HCV infection (n = 31) or with HBV/HCV coinfections (n = 41).

By employing a collaborative oncologic data repository with a given number of cases, TCGA facilitated the exploratory mining of clinical evidence suggestive for of an impact of IFNL germline variations on PDAC cancer progression. An IFNL haplotype predisposing for IFNL4 gene expression appeared to be favorable for the host, which is in line with the concept of antitumor activities of type III IFNs. Further analyses will regard therapeutic interventions as additional variates.