Association of maternally inherited GNAS alleles with African-American male birth weight

Increased copy number of imprinted genes in the chromosomal region 20q11-q13.32 is associated with resistance to antitumor agents in cancer cell lines

BACKGROUND

Parent of origin-specific allelic expression of imprinted genes is epigenetically controlled. In cancer, imprinted genes undergo both genomic and epigenomic alterations, including frequent copy number changes. We investigated whether copy number loss or gain of imprinted genes in cancer cell lines is associated with response to chemotherapy treatment.

RESULTS

We analyzed 198 human imprinted genes including protein-coding genes and noncoding RNA genes using data from tumor cell lines from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We examined whether copy number of the imprinted genes in 35 different genome locations was associated with response to cancer drug treatment. We also analyzed associations of pretreatment expression and DNA methylation of imprinted genes with drug response. Higher copy number of BLCAP, GNAS, NNAT, GNAS-AS1, HM13, MIR296, MIR298, and PSIMCT-1 in the chromosomal region 20q11-q13.32 was associated with resistance to multiple antitumor agents. Increased expression of BLCAP and HM13 was also associated with drug resistance, whereas higher methylation of gene regions of BLCAP, NNAT, SGK2, and GNAS was associated with drug sensitivity. While expression and methylation of imprinted genes in several other chromosomal regions was also associated with drug response and many imprinted genes in different chromosomal locations showed a considerable copy number variation, only imprinted genes at 20q11-q13.32 had a consistent association of their copy number with drug response. Copy number values among the imprinted genes in the 20q11-q13.32 region were strongly correlated. They were also correlated with the copy number of cancer-related non-imprinted genes MYBL2, AURKA, and ZNF217 in that chromosomal region. Expression of genes at 20q11-q13.32 was associated with ex vivo drug response in primary tumor samples from the Beat AML 1.0 acute myeloid leukemia patient cohort. Association of the increased copy number of the 20q11-q13.32 region with drug resistance may be complex and could involve multiple genes.

CONCLUSIONS

Copy number of imprinted and non-imprinted genes in the chromosomal region 20q11-q13.32 was associated with cancer drug resistance. The genes in this chromosomal region may have a modulating effect on tumor response to chemotherapy.

Differences of DNA methylation patterns in the placenta of large for gestational age infant

To investigate the molecular mechanisms of later metabolic health changes in large for gestational age (LGA) newborns by analyzing deoxyribonucleic acid (DNA) methylation patterns in the placenta of LGA and appropriate for gestational age (AGA) newborns.A total of 6 placentas of LGA and 6 placentas of AGA newborns were enrolled as LGA group and AGA group. DNA methylation was analyzed using the Illumina Infinium Human MethylationEPIC BeadChip microarrays and verified via pyrosequencing and reverse transcription-quantitative real-time polymerase chain reaction. Functional enrichment analysis were constructed by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis based on the differentially methylated regions between LGA and AGA groups.Clinical investigation showed that LGA newborns had significantly lower hemoglobin and blood glucose compared to AGA newborns. Birth weight was negatively correlated to hemoglobin and blood glucose. Genome-wide DNA methylation analysis identified 17 244 methylation variable positions achieving genome-wide significance (adjusted P < .05). 34% methylation variable positions were located in the gene promoter region. A total of 117 differentially methylated regions were revealed by bump hunting analysis, which mapped to 107 genes. Function analysis showed 13 genes enriched in "adhesion and infection process, endocrine and other factor-regulated calcium reabsorption, calcium signaling pathway and transmembrane transport". Four genes linked to type II diabetes mellitus. Among the 13 genes, we selected GNAS and calcium voltage-gated channel subunit alpha1 G for independent verification of pyrosequencing, and the messenger ribonucleic acid levels of guanine nucleotide binding protein, calcium voltage-gated channel subunit alpha1 G, DECR1, and FK506 binding protein 11 were verified by reverse transcription-quantitative real-time polymerase chain reaction.DNA methylation variation and gene expression differences in placental samples were associated with LGA newborns, which linking the effect of intrauterine environment to regulation of the offspring's gene expression. Furthermore, pathway analysis suggested that intrauterine environment affecting fetal growth might had a functional impact on multiple signaling pathways involved in fetal growth, metabolism, and inflammation. Further studies were required to understand the differences of methylation patterns.

Development of an Integrated Platform Using Multidisciplinary Real-World Data to Facilitate Biomarker Discovery for Medical Products

Translational multidisciplinary research is important for the Center for Devices and Radiological Health's efforts for utilizing real‐world data (RWD) to enhance predictive evaluation of medical device performance in patient subpopulations. As part of our efforts for developing new RWD‐based evidentiary approaches, including in silico discovery of device‐related risk predictors and biomarkers, this study aims to characterize the sex/race‐related trends in hip replacement outcomes and identify corresponding candidate single nucleotide polymorphisms (SNPs). Adverse outcomes were assessed by deriving RWD from a retrospective analysis of hip replacement hospital discharge data from the National Inpatient Sample (NIS). Candidate SNPs were explored using pre‐existing data from the Personalized Medicine Research Project (PMRP). High‐Performance Integrated Virtual Environment was used for analyzing and visualizing putative associations between SNPs and adverse outcomes. Ingenuity Pathway Analysis (IPA) was used for exploring plausibility of the sex‐related candidate SNPs and characterizing gene networks associated with the variants of interest. The NIS‐based epidemiologic evidence showed that periprosthetic osteolysis (PO) was most prevalent among white men. The PMRP‐based genetic evidence associated the PO‐related male predominance with rs7121 (odds ratio = 4.89; 95% confidence interval = 1.41−17.05) and other candidate SNPs. SNP‐based IPA analysis of the expected gene expression alterations and corresponding signaling pathways suggested possible role of sex‐related metabolic factors in development of PO, which was substantiated by ad hoc epidemiologic analysis identifying the sex‐related differences in metabolic comorbidities in men vs. women with hip replacement‐related PO. Thus, our in silico study illustrates RWD‐based evidentiary approaches that may facilitate cost/time‐efficient discovery of biomarkers for informing use of medical products.

GWAS of DNA Methylation Variation Within Imprinting Control Regions Suggests Parent-of-Origin Association

Imprinting control regions (ICRs) play a fundamental role in establishing and maintaining the non-random monoallelic expression of certain genes, via common regulatory elements such as non-coding RNAs and differentially methylated regions (DMRs) of DNA. We recently surveyed DNA methylation levels within four ICRs (H19-ICR, IGF2-DMR, KvDMR, and NESPAS-ICR) in whole-blood genomic DNA from 128 monozygotic (MZ) and 128 dizygotic (DZ) human twin pairs. Our analyses revealed high individual variation and intra-domain covariation in methylation levels across CpGs and emphasized the interaction between epigenetic variation and the underlying genetic sequence in a parent-of-origin fashion. Here, we extend our analysis to conduct two genome-wide screenings of single nucleotide polymorphisms (SNPs) underlying either intra-domain covariation or parent-of-origin-dependent association with methylation status at individual CpG sites located within ICRs. Although genome-wide significance was not surpassed due to sample size limitations, the most significantly associated SNPs found through multiple-trait genome-wide association (MQFAM) included the previously described rs10732516, which is located in the vicinity of the H19-ICR. Similarly, we identified an association between rs965808 and methylation status within the NESPAS-ICR. This SNP is positioned within an intronic region of the overlapping genes GNAS and GNAS-AS1, which are imprinted genes regulated by the NESPAS-ICR. Sixteen other SNPs located in regions apart from the analyzed regions displayed suggestive association with intra-domain methylation. Additionally, we identified 13 SNPs displaying parent-of-origin association with individual methylation sites through family-based association testing. In this exploratory study, we show the value and feasibility of using alternative GWAS approaches in the study of the interaction between epigenetic state and genetic sequence within imprinting regulatory domains. Despite the relatively small sample size, we identified a number of SNPs displaying suggestive association either in a domain-wide or in a parent-of-origin fashion. Nevertheless, these associations will require future experimental validation or replication in larger and independent samples.

Newborn umbilical cord blood DNA methylation and gene expression levels exhibit limited association with birth weight

Most cases of fetal growth retardation are unexplained. These newborns are at high risk of serious illness or death in the neonatal period and exhibit significantly increased risk of specific chronic illnesses later in life. While there are several hypotheses to explain the well-established association between low birth weight and later risk of disease, the true etiology is unknown. To search for molecular patterns that may explain the biological basis for reduced fetal growth in a clinically normal cohort, and possibly provide clues for the lifelong increased risk of disease, we surveyed genome-wide DNA methylation and gene expression patterns in the umbilical cord blood of newborns born in Shelby County, TN. While we did not find genome-wide significant associations of birth weight with either leukocytic gene expression or DNA methylation, we did find suggestive associations in several genes with known effects on pre- or postnatal growth and health. As with previous molecular epidemiological studies of birth weight, we did not sample the most biologically relevant tissues in the newborn. However, our discovery of biologically plausible associations in a peripheral tissue suggests that further studies of tissues key to fetal growth regulation are warranted.

Association of birth weight with polymorphisms in the IGF2, H19, and IGF2R genes

There is a substantial genetic component for birth weight variation. We tested 18 single nucleotide polymorphisms (SNPs) in the IGF2, H19, and IGF2R genes for associations with birth weight variation in 342 mother-newborn pairs (birth weight 2.1-4.7 kg at term) and 527 parent-newborn trios (birth weight 2.1-5.1 kg) across three localities. SNPs in the IGF2R (rs8191754; maternal genotype), IGF2 (rs3741205; newborn genotype), and 5' region of the H19 (rs2067051, rs2251375, and rs4929984) genes were associated with birth weight. Detailed analyses to distinguish direct maternal, direct newborn, and parent of origin effects for the most strongly associated H19 SNP (rs4929984) determined that the association of maternal genotype with newborn birth weight was due to parent of origin effects not direct maternal effects. That SNP is located near the CTCF binding sites that influence expression of the maternally imprinted IGF2 and paternally imprinted H19 locus, and there are statistically significant and independent opposite effects of the same rs4929984 allele, depending on the parent from which it was inherited.