Association of a common LAMA5 variant with anthropometric and metabolic traits in an Italian cohort of healthy elderly subjects

A Pilot Study of Blood-Based Methylation Markers Associated With Pancreatic Cancer

Over the past several decades in the United States, incidence of pancreatic cancer (PCa) has increased, with the 5-year survival rate remaining extremely low at 10.8%. Typically, PCa is diagnosed at an advanced stage, with the consequence that there is more tumor heterogeneity and increased probability that more cells are resistant to treatments. Risk factors for PCa can serve as a way to select a high-risk population and develop biomarkers to improve early detection and treatment. We focus on blood-based methylation as an approach to identify a marker set that can be obtained in a minimally invasive way (through peripheral blood) and could be applied to a high-risk subpopulation [those with recent onset type 2 diabetes (DM)]. Blood samples were collected from 30 patients, 15 had been diagnosed with PCa and 15 had been diagnosed with recent onset DM. HumanMethylationEPIC Beadchip (Illumina, CA, United States) was used to quantify methylation of approximately 850,000 methylation sites across the genome and to analyze methylation markers associated with PCa or DM or both. Exploratory analysis conducted to propose importance of top CpG (5'-C-phosphate-G-3') methylation site associated genes and visualized using boxplots. A methylation-based age predictor was also investigated for ability to distinguish disease groups from controls. No methylation markers were observed to be significantly associated with PCa or new onset diabetes compared with control the respective control groups. In our exploratory analysis, one methylation marker, CpG04969764, found in the Laminin Subunit Alpha 5 (LAMA5) gene region was observed in both PCa and DM Top 100 methylation marker sets. Modification of LAMA5 methylation or LAMA5 gene function may be a way to distinguish those recent DM cases with and without PCa, however, additional studies with larger sample sizes and different study types (e.g., cohort) will be needed to test this hypothesis.

Evolutionary conserved networks of human height identify multiple Mendelian causes of short stature

Height is a heritable and highly heterogeneous trait. Short stature affects 3% of the population and in most cases is genetic in origin. After excluding known causes, 67% of affected individuals remain without diagnosis. To identify novel candidate genes for short stature, we performed exome sequencing in 254 unrelated families with short stature of unknown cause and identified variants in 63 candidate genes in 92 (36%) independent families. Based on systematic characterization of variants and functional analysis including expression in chondrocytes, we classified 13 genes as strong candidates. Whereas variants in at least two families were detected for all 13 candidates, two genes had variants in 6 (UBR4) and 8 (LAMA5) families, respectively. To facilitate their characterization, we established a clustered network of 1025 known growth and short stature genes, which yielded 29 significantly enriched clusters, including skeletal system development, appendage development, metabolic processes, and ciliopathy. Eleven of the candidate genes mapped to 21 of these clusters, including CPZ, EDEM3, FBRS, IFT81, KCND1, PLXNA3, RASA3, SLC7A8, UBR4, USP45, and ZFHX3. Fifty additional growth-related candidates we identified await confirmation in other affected families. Our study identifies Mendelian forms of growth retardation as an important component of idiopathic short stature.

Association of the Laminin, Alpha 5 (LAMA5) rs4925386 with height and longevity in an elderly population from Southern Italy

Studies in animal models and humans suggest that reduced growth and adult stature are associated with lifespan extension. Moreover, epidemiological studies reported a positive association between adult height and risk of multiple cancers. Yet, it is unclear which factors mediate these relationships. Laminins are major components of the basement membranes and cooperate with growth factors and matrix-dependent receptors in cell proliferation and differentiation. Previously, we reported the association of rs659822-C/T in LAMA5, encoding the laminin-α5 chain, with weight and height in a cohort of healthy 64-107 aged Italian individuals. Notably, two independent meta-analyses of genome-wide association studies found the C-allele of LAMA5 rs4925386-C/T correlated with the risk of colorectal cancer. We tested additional SNPs within the LAMA5 gene for association with anthropometric traits and longevity in our cohort of elderly subjects (N=624). Under an additive model, the rs2427283-C allele (P=0.02) and the rs4925386-T allele (P=0.01) were associated with shorter stature. Age-stratified analyses showed that the rs4925386-T allele was also positively associated with longevity (P=0.001). The association of LAMA5 rs4925386 alleles with both inter-individual differences in height and in longevity suggests that laminins may be among the factors linking stature and cancer susceptibility.

Metabolism and successful aging: Polymorphic variation of syndecan-4 (SDC4) gene associate with longevity and lipid profile in healthy elderly Italian subjects

Evidences from model systems and humans have suggested that genetic alterations in cell-ECM interactions and matrix-mediated cellular signaling cascades impact different aspects of metabolism and thereby life span. In this frame, a genetic variant (rs1981429) in the SDC4 gene encoding for syndecan-4, a central mediator of cell adhesion, has been associated with body composition in children and coronary artery disease in middle-age subjects. In order to test the hypothesis that syndecans might affect life span by affecting metabolic endophenotypes, 11 SNPs within the SDC4 gene were tested for association with longevity in a cohort of 64-107 aged individuals. We then determined whether the longevity-associated SNPs were correlated with metabolic parameters in the age group 64-85 years. RobustSNP association tests showed that rs1981429 was negatively associated with longevity (Theop=0.028), but also with high levels of triglyceride (Theop=0.028) and low levels of low-density lipoprotein-cholesterol (LDL-C) (Theop=0.009). On the other hand, rs2251252 was found to be positively correlated with longevity (Theop=0.018) and high LDL-C (Theop=0.022). On the whole, our results suggest that SDC4 alleles affect lipid profile in elderly subjects and may in part mediate the link between LDL-C and longevity.

Common variants in the LAMA5 gene associate with fasting plasma glucose and serum triglyceride levels in a cohort of pre-and early pubertal children

Laminins are large glycoproteins found in basement membranes where they play a vital role in tissue architecture and cell behavior. Previously, we reported the association of two LAMA5 polymorphisms (rs659822 and rs944895) with anthropometric traits, fasting lipid profile, and plasma glucose levels in pre-menopausal women and elderly subjects. Furthermore, earlier work in mice showed that Lama5 is involved in organogenesis and placental function during pregnancy. The objective of this study was to investigate whether LAMA5 rs659822 or rs944895 are associated with inter-individual variability in birth weight as well as anthropometric, fasting lipid profile, and fasting glucose levels in children. Two hundred and eighty nine healthy children aged 7-12 years of European, Hispanic, and African-American ancestry were studied. Co-dominant models adjusted for genetic admixture, age, gender, and stages of puberty were used to test for the association of the polymorphisms with each trait. Our analysis showed significant associations of rs659822 with fasting plasma glucose levels (p = 0.0004) and of rs944895 with fasting serum triglycerides (p = 0.004) after Bonferroni correction for multiple testing. Our results corroborate our previous findings that genetic variants in LAMA5 contribute to variation in metabolic phenotypes and provide evidence that this may occur early in life.

Spatial localization of genes determined by intranuclear DNA fragmentation with the fusion proteins lamin KRED and histone KRED und visible light

The highly organized DNA architecture inside of the nuclei of cells is accepted in the scientific world. In the human genome about 3 billion nucleotides are organized as chromatin in the cell nucleus. In general, they are involved in gene regulation and transcription by histone modification. Small chromosomes are localized in a central nuclear position whereas the large chromosomes are peripherally positioned. In our experiments we inserted fusion proteins consisting of a component of the nuclear lamina (lamin B1) and also histone H2A, both combined with the light inducible fluorescence protein KillerRed (KRED). After activation, KRED generates reactive oxygen species (ROS) producing toxic effects and may cause cell death. We analyzed the spatial damage distribution in the chromatin after illumination of the cells with visible light. The extent of DNA damage was strongly dependent on its localization inside of nuclei. The ROS activity allowed to gain information about the location of genes and their functions via sequencing and data base analysis of the double strand breaks of the isolated DNA. A connection between the damaged gene sequences and some diseases was found.