KIF15 missense variant is associated with the early onset of idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease that is accompanied by respiratory symptoms, primarily dyspnoea, and a poor quality of life. The impacts of current antifibrotic therapies are limited, and the prognosis has not improved sufficiently [1, 2].

Studies are slowly unravelling the aetiology of IPF with evidence of genetic susceptibility combined with external risk factors and possible exposure. More than 25 different genetic regions and numerous variants have been reported to be involved in IPF [3‐7]. Although data on genetic variants are abundant, little is known about their clinical significance. The clinical aspects have been best described in variants in the telomerase and promoter regions of MUC5B. A common variant in MUC5B has the largest effect on IPF risk, but rare variants, such as TERT, are considered more important in disease pathogenicity [5, 7, 8]. Variants in non-telomerase-related genes, such as SDPL1, KIF15, and surfactant-related genes, have recently been suggested to be of importance in IPF [5, 7, 9‐11]. These single studies focused on genetic data with limited clinical features. There is a lack of studies where detailed clinical data are presented along with the genetic variants.

A recent large-scale meta-analysis of IPF genetics suggested causal coding variants at three loci –TERT, SPDL1, and KIF15, in the FinnGen IPF (FinnIPF) population [12]. The unique genetic background of an isolated population in Finland has provided a special basis for several genetic research studies [13, 14]. Using data from the national biobank and large GWAS studies, we aimed to correlate this genetic data with a well-defined clinical cohort of 138 patients with IPF.

We studied the effects of the predicted rare causal variants of TERT, SPDL1, and KIF15 and the common variant of MUC5B on the clinical phenotype and disease course of patients with IPF.

The FinnishIPF study is a nationwide epidemiological registry study [15]. The inclusion criteria are written informed consent and a diagnosis of IPF according to the ATS/ERS criteria [16]. FinnGen (https://​www.​finngen.​fi/​en) is a large biobank study in which diagnoses are based on ICD codes. FinnGen samples were genotyped using multiple Illumina and Affymetrix arrays (Illumina, San Diego, CA, USA and Thermo Fisher Scientific, Santa Clara, CA, USA, respectively), filtered, and imputed with a population-specific reference panel as previously described [15].

In 2017, a subgroup of patients in the FinnishIPF study was contacted to collect DNA and serum samples and was included in the FinnGen analysis (FinnIPF cohort, N = 235). Our study cohort consisted of FinnishIPF study patients who were followed up at the Helsinki University Hospital (N = 138).

In the present study, causal variants predicted by fine-mapping in the FinnGen study, two TERT loss of function (Lof) and missense variants (rs770066110 and rs776981958) and SPDL1 (rs116483731) and KIF15 missense (rs138043992) variants, were included in the analyses [12]. We also analysed the most well-known genetic variant for IPF, MUC5B (rs35705950) [4, 9, 17]. Due to the extremely high prevalence (97/138), the patients with the MUC5B variant were investigated separately.

The patient characteristics of the variant groups are shown in Table 1. Most patients were male and smokers with no family history of pulmonary fibrosis. Comorbidities included hypertension, hyperlipidaemia, coronary artery disease, obesity, type 2 diabetes mellitus, and hypothyroidism, and 33 patients had cancer: 12 lung, 11 prostate, 6 gastrointestinal tract, 4 bladder, 3 breast, 1 cervix, and 1 renal cancer. The variant groups differed, especially in variables relating to treatment and prognosis, such as the probability of lung transplantation, age at diagnosis, or death (Table 1).

We investigated the possibility of defining a clinical IPF phenotype based on distinct genetic variants associated with IPF susceptibility. To the best of our knowledge, this is one of the first studies in which systematically collected clinical characteristics were compared with a detailed genetic evaluation.

The studied KIF15 missense variant causes a nucleotide substitution from arginine to leucine at the 501st amino acid (p.Arg501Leu). Hence, it could affect the stability and function of the KIF15 protein. KIF15 is a motor protein involved in mitotic spindle assembly and affects cell proliferation. It is upregulated in various cancers, including breast and gastric cancer. Overexpression of KIF15 promotes lung carcinogenesis and cancer cell proliferation and is associated with a poor prognosis in non-small cell lung carcinoma [18‐20]. Several KIF15 variants (missense, Lof, and intron) have also been associated with IPF risk, but their impact on disease course and phenotype remains unclear [4, 10, 11].

The KIF15 variant in this study was suggested to be causal in the fine-mapping of the FinnGen IPF population [12]. It was recently observed that variants in the Finnish population that were enriched by more than twofold were 1.7-fold more likely to be associated with a phenotype expected by chance [14]. Allelic frequency (AF) in our IPF cohort was 0.018, which showed a twofold increase compared with that of the reference Finnish population (AF 0.009), over fourfold compared with that of the non-Finnish Europeans (AF 0.004), and sixfold compared with that of ALL individuals (AF 0.003) based on the whole genome variant set version 3.1.2 of the Genome Aggregation Database (GnomAD). This shows that the KIF15 missense variant allele is enriched in the Finnish population and could be a possible causal variant for IPF, as shown earlier [12].

Our main finding was that patients with the KIF15 missense variant were diagnosed at a substantially younger age than other patients. The difference in the median diagnosis age between the KIF15 variant carriers and others was large (over 10 years) and not explained by family history of IPF or statistical outliers. The proportion of KIF15 variant carriers was ninefold higher in patients aged < 55 years. Our findings imply a potential link between the early onset of disease and the KIF15 missense variant. Among the three earlier studies reporting on KIF15 and IPF, only Zhang et al. reported the median age of the patients [4, 10, 11]. In their study, the median age of patients with KIF15 variants (stop gain, missense, splice acceptor, and frameshift) was 64 years (N = 12), and that of all patients was 67 years. The study included both patients with IPF and other interstitial lung diseases [11]. It is important to note that the comprehensive KIF15 mutation variant list in the Zhang data doesn’t include our KIF15 variant found in an all-Finnish population.

Our KIF15 missense variant patients received transplantation or died at a younger age than other patients. This was probably explained by the early onset of the disease and increased morbidity. Patients diagnosed at a younger age are more likely to meet the requirements for lung transplantation, and human lifespan is limited and influenced by many factors other than the variants (such as the presence and severity of comorbid conditions, smoking, and exposures). Hence, the large difference in the timing of disease onset has the potential to mask the effects of the variant on overall survival. Some results might suggest that the KIF15 variant impacts the disease course. Patients with the KIF15 variant needed oxygen therapy markedly more often than the others. Previously, Allen et al. reported an association between lower pulmonary function and the KIF15 variant, rs78238620 [4]. In our study, the KIF15 missense group performed the worst in pulmonary function tests, but probably due to the sample size, the results did not reach statistical significance. This might also obscure the finding that none of the patients with the KIF15 missense variant had a known family history of pulmonary fibrosis despite the early onset of the disease. More studies on the possible effects of KIF15 variants on disease course, mortality, and familial forms of the disease are needed.

Considering the notable effect on disease onset and the possible effect on disease progression, our findings support the view of Moss and Rosas, who highlighted that KIF15 has the potential to uncover disease mechanisms and even contribute to drug discovery [7]. Many centres employ genetic panels for clinical diagnosis, and the identified mutations influence clinical decisions [21, 22]. Our findings suggest that KIF15 could be included in genetic screening panels.

The findings on the other, better-described variants (in TERT, SPDL1, and MUC5B) were in line with earlier studies. Telomerase reverse transcriptase (TERT) maintains telomere length by adding nucleotides to the ends of telomeres and plays a role in cellular senescence and cancer development. Shorter telomere lengths have been associated with IPF and poor survival [23‐25]. The TERT variant was also associated with worse outcomes in our study. SPDL1 variants are reportedly upregulated in the lung tissue of patients with IPF [9]. We did not find a distinct clinical phenotype for the SPDL1 variant. Previously, Dhindsa et al. reported a summary of the clinical features of 26 IPF patients with the SPLD1 variant without a clear or significant difference from other study patients. These results suggest that the SPDL1 variants do not have any major impact on the clinical phenotype of IPF. The best-known single genetic risk factor for IPF is a variant in MUC5B, which is present in more than half of the patients with IPF and has been associated with susceptibility to IPF and a mild disease course [26‐29]. In our study, 70% of the patients carried the MUC5B variant, and these patients needed lung transplantation at an older age than other patients. The other variants did not affect this result.

Our study has several strengths. Repeated genetic bottlenecks and isolation from other countries create a distinct genetic profile for the Finnish people, providing a unique setting for genetic studies. Patient samples were genotyped as part of a large FinnGen IPF study, and all patients had IPF and met the ATS/ERS criteria for the disease. We had access to detailed clinical histories of all patients, and all data were reviewed by two pulmonologists specialising in IPF care. The number of patients was limited, but the statistical assumptions were met, and there were no distinct outliers in any of the variant groups. The number of censored patients in the survival analyses was minimal.

Our study also has limitations. Our patient population was relatively small and from a single university hospital. Only four variants were analysed; therefore, the significance of other potentially significant variants remains unknown. The small number of patients in some variant groups limits the possibilities of adjusting the analyses with confounding factors, such as disease severity, sex, age, and comorbidities, that are known to influence IPF survival. It was not possible to analyse the association between genetic variants and pulmonary function over time. The observatory and exploratory nature of the study limit final conclusions regarding distinct phenotypes. Larger confirmatory studies within multi-ancestry genetic populations and multiple cohorts are needed to confirm these results and detect possible milder effects caused by other variants.

Our study highlights the importance of connecting clinical characteristics to genetic data. We found that the KIF15 missense variant is associated with a remarkably early onset of the disease, leading to transplantation and death at an early age. Our findings suggest the potential of KIF15 to be used in diagnostic procedures, patient monitoring, and screening, especially among young patients. We also confirmed the previously identified clinical phenotypes of TERT variants and that many patients with IPF are genetically susceptible to the disease. In the future, larger studies on KIF15 focusing on clinical aspects, especially disease course and survival, are needed to confirm its significance.