GWA analyses
Six SNPs showed evidence for an association with early-life TL (Table 3, Fig. 4), with a Bonferroni corrected threshold (nominal P<0.05 and P≤2.77x10-7 at the genome-wide P-value threshold) and a genomic inflation factor λ=1.0476±0.0002 (Fig. S2.3). Seven SNPs that showed weak evidence for an association with TL (nominal 0.05<P<0.10) are also shown in Table 3. Using the annotated house sparrow genome, a total of sixteen genes on four chromosomes were found to be located within proximity (±100 kb) of four of the six top SNPs (Table 4). Among five of the seven SNPs with weak evidence for an association with TL we identified 10 genes within ±100 kb on three chromosomes (Table S2.5).
SNPa429690 is located on chromosome 2 within the Aquaporin-1 (AQP1) gene, which encodes the AQP1 water channel membrane protein. The AQP1 protein is abundant in erythrocytes (where TL is measured) and important in regulating body water transport and balance (Nielsen et al., 2002), but also in a range of other physiological functions including cell migration, wound healing, fat metabolism and oxidative stress (Saadoun, Papadopoulos, Hara-Chikuma, & Verkman, 2005; Verkman, Anderson, & Papadopoulos, 2014). The same SNP is located 39 kb from the growth hormone-releasing hormone receptor (GHRHR), which controls body growth (Mullis, 2005), and has been associated with telomerase activity (Banks et al., 2010), lifespan (Soerensen et al., 2012) and the progression of several types of cancer (Chu et al., 2016; Schally et al., 2018; Villanova et al., 2019). Humans with over-expression of growth hormones and consequently insulin-like growth factor 1 (IGF-1) have shorter telomeres (Aulinas et al., 2013; Deelen et al., 2013; Matsumoto et al., 2015; Monaghan & Ozanne, 2018). SNPa17235 was close (11 kb) to FRMD4B (FERM domain-containing protein 4B), which is involved in epithelial cell polarity that is important in tissue morphogenesis (Ikenouchi & Umeda, 2010). This SNP was also near other genes related to cell proliferation (UBA3 and TMF1), skeletal muscle organization (LMOD3) and oxidative stress (ARL6IP5, see Table 4). SNPa108592 was in the vicinity (43-84 kb) of several genes on chromosome 15 linked to cell proliferation, ubiquitination and immune response (Table 4). SNPa450086 was 76 kb from OXR1 (oxidation resistance protein 1) that regulates expression of several antioxidant enzymes (Volkert, Elliott, & Housman, 2000).
Among the SNPs with weak evidence for an association with TL, SNPa34968 was close (11 kb) to the ZBED1 (zinc finger BED domain-containing protein 1) gene that is involved in cell proliferation and DNA replication (Ohshima, Takahashi, & Hirose, 2003; Hansen, Traynor, Ditzel, & Gjerstorff, 2018), and may also regulate telomere length inDrosophila flies (Silva-Sousa, Varela, & Casacuberta, 2013). Expression of the SCN4A gene (68 kb from SNPa491204) has previously been correlated with TL in human stem cells (Wang et al., 2017). SNPa491204 was also near (49 kb) the growth hormone gene GH (which is linked to TL as described above, see also Pauliny, Devlin, Johnsson, & Blomqvist, 2015) and WNT9B (40 kb) of the Wnt/β-catenin signaling pathway, which is modulated by telomerase (Park et al., 2009). SNPi16410 was closest to SHCBP1 (70 kb) and CDCA4 (76 kb), which are both involved in cell proliferation and probably apoptosis (Wang et al., 2008; Asano et al., 2014; Xu, Wu, Li, Huang, & Zhu, 2018; Zou et al., 2019). SHCBP1 is upregulated by growth factor stimulation (Schmandt, Liu, & McGlade, 1999). CDCA4 is likely involved in the regulation of hematopoietic stem cells from where erythrocytes (reflecting TL) are derived (Abdullah, Jing, Spassov, Nachtman, & Jurecic, 2001).
Searching beyond the ±100 kb limits, the top marker, SNPa223513, was found closest (106 kb) to the SAMD5 (sterile alpha motif domain-containing protein 5) gene, which function is unknown, but may play a role in tumorigenesis (Sa, Lee, Hong, Kong, & Nam, 2017), cancer cell proliferation (Matsuo et al., 2014) or tumor suppression in the cytoplasm (Yagai et al., 2017). SNPa108592 is 263 kb from LRRC43 (leucine-rich repeat-containing protein 43) that belongs to a class of poorly known proteins often associated with innate immunity (Ng & Xavier, 2011). Members of the LRRC superfamily have previously been associated with TL variation in humans (Codd et al., 2010). The same SNP is 363 kb from ZCCHC8 (zinc finger CCHC domain-containing protein 8) that is required for telomerase functioning (Gable et al., 2019).
When not controlling for the effect of tarsus length on TL, the same six top SNPs were identified as in the analysis above including tarsus length (Table S2.6). In addition, SNPa208275 was associated with TL and found 47 kb from FGFR2 encoding a tyrosine-protein kinase that is a receptor for fibroblast growth factors that regulates several aspects of cell proliferation and bone morphogenesis (Table S2.7, Katoh, 2009).