Targeted epigenome modification grant with Charlie Gersbach and Greg Crawford funded

Genome sequencing and the identification of epigenetic marks by projects such as ENCODE and the Epigenomics Roadmap Project have transformed biomedical research. Technologies for targeted manipulation of these epigenetic properties are necessary to transform the knowledge gained from these projects into tangible scientific advances and benefits for human health, such as gene therapies that modify the epigenetic code at targeted regions of the genome and the engineering of epigenome-specific drug screening platforms. To address this technology gap, we are developing a suite of well-characterized tools for custom locus- and cell type-specific modification of any epigenomic property.

Gestational diabetes grant with Bill Lowe to be funded by NIDDK

Glucose levels in mothers during pregnancy have important implications for the offspring, as exposure of the developing fetus to high glucose levels is associated with adverse outcomes at birth as well as obesity and abnormal glucose metabolism later in childhood and adulthood. Factors regulating glucose levels during pregnancy are not well understood. The goal of this five-year project is to define genetic factors that impact glucose levels and metabolism in mothers during pregnancy.http://upload.wikimedia.org/wikipedia/commons/4/43/NIH_logo.svg

Astronaut Jessica Meir visits ReddyLab

Jessica Meir, one of eight new astronauts selected by NASA this year, stopped by to visit the ReddyLab on her way to astronaut training in Houston. Prior to becoming an astronaut, Jessica excelled in her research of how animals can survive in extreme environments including below the ice in Antarctica and above the mountains in the Himalayas. We were thrilled Jessica was able to visit our lab, and we wish her all the best in her exploration of the most extreme environment yet, outer space!

Read more about Jessica here: http://www.nasa.gov/astronauts/2013_meir.html

Gestational Diabetes paper published in Diabetes

Identification of HKDC1 and BACE2 as Genes Influencing Glycemic Traits During Pregnancy Through Genome-Wide Association Studies.

Hayes MG, Urbanek M, Hivert MF, Armstrong LL, Morrison J, Guo C, Lowe LP, Scheftner DA, Pluzhnikov A, Levine DM, McHugh CP, Ackerman CM, Bouchard L, Brisson D, Layden BT, Mirel D, Doheny KF, Leya MV, Lown-Hecht RN, Dyer AR, Metzger BE, Reddy TE, Cox NJ, Lowe WL Jr; for the HAPO Study Cooperative Research Group. 

Maternal metabolism during pregnancy impacts the developing fetus, affecting offspring birth weight and adiposity. This has important implications for metabolic health later in life (e.g., offspring of mothers with pre-existing or gestational diabetes mellitus have an increased risk of metabolic disorders in childhood). To identify genetic loci associated with measures of maternal metabolism obtained during an oral glucose tolerance test at ∼28 weeks' gestation, we performed a genome-wide association study of 4,437 pregnant mothers of European (n = 1,367), Thai (n = 1,178), Afro-Caribbean (n = 1,075), and Hispanic (n = 817) ancestry, along with replication of top signals in three additional European ancestry cohorts. In addition to identifying associations with genes previously implicated with measures of glucose metabolism in nonpregnant populations, we identified two novel genome-wide significant associations: 2-h plasma glucose and HKDC1, and fasting C-peptide and BACE2. These results suggest that the genetic architecture underlying glucose metabolism may differ, in part, in pregnancy.

CAS9-VP64 activation paper in Nature Methods

RNA-guided gene activation by CRISPR-Cas9–based transcription factors.

Pablo Perez-Pinera, D Dewran Kocak,Christopher M Vockley, Andrew F AdlerAmi M Kabadi, Lauren R Polstein, Pratiksha I Thakore, Katherine A Glass, David G Ousterout, Kam W Leong, Farshid Guilak, Gregory E Crawford, Timothy E Reddy, Charles A Gersbach 

Technologies for engineering synthetic transcription factors have enabled many advances in medical and scientific research. In contrast to existing methods based on engineering of DNA-binding proteins, we created a Cas9-based transactivator that is targeted to DNA sequences by guide RNA molecules. Coexpression of this transactivator and combinations of guide RNAs in human cells induced specific expression of endogenous target genes, demonstrating a simple and versatile approach for RNA-guided gene activation.

GRHL2 paper published in PNAS →

Evidence for multiple roles for grainyheadlike 2 in the establishment and maintenance of human mucociliary airway epithelium.

Gao X, Vockley CM, Pauli F, Newberry KM, Xue Y, Randell SH, Reddy TE, Hogan BL. 

Most of the airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated basal progenitor cells. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia, there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in coordinating multiple cellular processes required for epithelial morphogenesis, differentiation, remodeling, and repair. However, only a few target genes have been identified, and little is known about GRHL function in the adult lung. Here we focus on the role of GRHL2 in primary human bronchial epithelial cells, both as undifferentiated progenitors and as they differentiate in air-liquid interface culture into an organized mucociliary epithelium with transepithelial resistance. Using a dominant-negative protein or shRNA to inhibit GRHL2, we follow changes in epithelial phenotype and gene transcription using RNA sequencing or microarray analysis. We identify several hundreds of genes that are directly or indirectly regulated by GRHL2 in both undifferentiated cells and air-liquid interface cultures. Using ChIP sequencing to map sites of GRHL2 binding in the basal cells, we identify 7,687 potential primary targets and confirm that GRHL2 binding is strongly enriched near GRHL2-regulated genes. Taken together, the results support the hypothesis that GRHL2 plays a key role in regulating many physiological functions of human airway epithelium, including those involving cell morphogenesis, adhesion, and motility. 

Fetal Adiposity paper in HMG →

The chromosome 3q25 genomic region is associated with measures of adiposity in newborns in a multi-ethnic genome-wide association study.

 Urbanek M, Hayes MG, Armstrong LL, Morrison J, Lowe LP, Badon SE, Scheftner D, Pluzhnikov A, Levine D, Laurie CC, McHugh C, Ackerman CM, Mirel DB, Doheny KF, Guo C, Scholtens DM, Dyer AR, Metzger BE, Reddy TE, Cox NJ, Lowe WL Jr; for the HAPO Study Cooperative Research Group.

Newborns characterized as large and small for gestational age are at risk for increased mortality and morbidity during the first year of life as well as for obesity and dysglycemia as children and adults. The intrauterine environment and fetal genes contribute to the fetal size at birth. To define the genetic architecture underlying the newborn size, we performed a genome-wide association study (GWAS) in 4465 newborns in four ethnic groups from the Hyperglycemia and Adverse Pregnancy Outcome Study. We tested for association with newborn anthropometric traits (birth length, head circumference, birth weight, percent fat mass and sum of skinfolds) and newborn metabolic traits (cord glucose and C-peptide) under three models. Model 1 adjusted for field center, ancestry, neonatal gender, gestational age at delivery, parity, maternal age at oral glucose tolerance test (OGTT); Model 2 adjusted for Model 1 covariates, maternal body mass index (BMI) at OGTT, maternal height at OGTT, maternal mean arterial pressure at OGTT, maternal smoking and drinking; Model 3 adjusted for Model 2 covariates, maternal glucose and C-peptide at OGTT. Strong evidence for association was observed with measures of newborn adiposity (sum of skinfolds model 3 Z-score 7.731, P = 4.29×10-16, and to a lesser degree fat mass and birth weight) and a region on Chr3q25.31 mapping between CCNL and LEKR1. These findings were replicated in an independent cohort of 2296 newborns. This region has previously been shown to be associated with birth weight in Europeans. The current study suggests that association of this locus with birth weight is secondary to an effect on fat as opposed to lean body mass.