Gene Co-Expression in Breast Cancer: A Matter of Distance

Gene regulatory and signaling phenomena are known to be relevant players underlying the establishment of cellular phenotypes. It is also known that such regulatory programs are disrupted in cancer, leading to the onset and development of malignant phenotypes. Gene co-expression matrices have allowed us to compare and analyze complex phenotypes such as breast cancer (BrCa) and their control counterparts. Global co-expression patterns have revealed, for instance, that the highest gene-gene co-expression interactions often occur between genes from the same chromosome (cis-), meanwhile inter-chromosome (trans-) interactions are scarce and have lower correlation values. Furthermore, strength of cis- correlations have been shown to decay with the chromosome distance of gene couples. Despite this loss of long-distance co-expression has been clearly identified, it has been observed only in a small fraction of the whole co-expression landscape, namely the most significant interactions. For that reason, an approach that takes into account the whole interaction set results appealing. In this work, we developed a hybrid method to analyze whole-chromosome Pearson correlation matrices for the four BrCa subtypes (Luminal A, Luminal B, HER2+ and Basal), as well as adjacent normal breast tissue derived matrices. We implemented a systematic method for clustering gene couples, by using eigenvalue spectral decomposition and the k–medoids algorithm, allowing us to determine a number of clusters without removing any interaction. With this method we compared, for each chromosome in the five phenotypes: a) Whether or not the gene-gene co-expression decays with the distance in the breast cancer subtypes b) the chromosome location of cis- clusters of gene couples, and c) whether or not the loss of long-distance co-expression is observed in the whole range of interactions. We found that in the correlation matrix for the control phenotype, positive and negative Pearson correlations deviate from a random null model independently of the distance between couples. Conversely, for all BrCa subtypes, in all chromosomes, positive correlations decay with distance, and negative correlations do not differ from the null model. We also found that BrCa clusters are distance-dependent, meanwhile for the control phenotype, chromosome location does not determine the clustering. To our knowledge, this is the first time that a dependence on distance is reported for gene clusters in breast cancer. Since this method uses the whole cis- interaction geneset, combination with other -omics approaches may provide further evidence to understand in a more integrative fashion, the mechanisms that disrupt gene regulation in cancer.

Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes

Background Autism spectrum disorder (ASD) is a neurodevelopmental disorder with complex heritability and higher prevalence in males. The neonatal epigenome has the potential to reflect past interactions between genetic and environmental factors during early development and influence future health outcomes. Methods We performed whole-genome bisulfite sequencing of 152 umbilical cord blood samples from the MARBLES and EARLI high-familial risk prospective cohorts to identify an epigenomic signature of ASD at birth. Samples were split into discovery and replication sets and stratified by sex, and their DNA methylation profiles were tested for differentially methylated regions (DMRs) between ASD and typically developing control cord blood samples. DMRs were mapped to genes and assessed for enrichment in gene function, tissue expression, chromosome location, and overlap with prior ASD studies. DMR coordinates were tested for enrichment in chromatin states and transcription factor binding motifs. Results were compared between discovery and replication sets and between males and females. Results We identified DMRs stratified by sex that discriminated ASD from control cord blood samples in discovery and replication sets. At a region level, 7 DMRs in males and 31 DMRs in females replicated across two independent groups of subjects, while 537 DMR genes in males and 1762 DMR genes in females replicated by gene association. These DMR genes were significantly enriched for brain and embryonic expression, X chromosome location, and identification in prior epigenetic studies of ASD in post-mortem brain. In males and females, autosomal ASD DMRs were significantly enriched for promoter and bivalent chromatin states across most cell types, while sex differences were observed for X-linked ASD DMRs. Lastly, these DMRs identified in cord blood were significantly enriched for binding sites of methyl-sensitive transcription factors relevant to fetal brain development. Conclusions At birth, prior to the diagnosis of ASD, a distinct DNA methylation signature was detected in cord blood over regulatory regions and genes relevant to early fetal neurodevelopment. Differential cord methylation in ASD supports the developmental and sex-biased etiology of ASD and provides novel insights for early diagnosis and therapy.

Bulked segregant analysis RNA-seq (BSR-Seq) validated a stem resistance locus in Aegilops umbellulata, a wild relative of wheat

Many disease resistance genes that have been transferred from wild relatives to cultivated wheat have played a significant role in wheat production worldwide. Ae. umbellulata is one of the species within the genus Aegilops that have been successfully used as sources of resistance genes to leaf rust, stem rust and powdery mildew. The objectives of the current work was to validate the map position of a major QTL that confers resistance to the stem rust pathogen races Ug99 (TTKSK) and TTTTF with an independent bi-parental mapping population and to refine the QTL region with a bulk segregant analysis approach. Two F2 bi-parental mapping populations were developed from stem rust resistant Ae. umbellulata accessions (PI 298905 and PI 5422375) and stem rust susceptible accessions (PI 542369 and PI 554395). Firstly, one of the two populations was used to map the chromosome location of the resistance gene. Later on, the 2nd population was used to validate the chromosome location in combination with a bulk segregant analysis approach. For the bulk segregant analysis, RNA was extracted from a bulk of leaf tissues of 12 homozygous resistant F3 families, and a separate bulk of 11 susceptible homozygous F3 families derived from the PI 5422375 and PI 554395 cross. The RNA samples of the two bulks and the two parents were sequenced for SNPs identification. Stem rust resistance QTL was validated on chromosome 2U of Ae. umbellulata in the same region in both populations. With bulk segregant analysis, the QTL position was delimited within 3.2 Mbp. Although there were a large number of genes in the orthologous region of the detected QTL on chromosome 2D of Ae. tauschii, we detected only two Ae. umbellulata NLR genes which can be considered as a potential candidate genes.

HPCDb: an integrated database of pancreatic cancer

We have established a database of Human Pancreatic Cancer (HPCDb) through effectively mining, extracting, analyzing, and integrating PC-related genes, single-nucleotide polymorphisms (SNPs), and microRNAs (miRNAs), now available online at http://www.pancancer.org/. Data were extracted from established databases, ≥5 published literature (PubMed), and microarray chips (screening of differentially expressed genes using limma package in R, |log2 fold change (FC)| > 1). Further, protein–protein interactions (PPIs) were investigated through the Human Protein Reference Database. miRNA–target relationships were also identified using the online software TargetScan. Currently, HPCDb contains 3284 genes, 120 miRNAs, 589 SNPs, 10,139 PPIs, and 3904 miRNA–target pairs. The detailed information on PC-related genes (e.g., gene identifier (ID), symbol, synonyms, full name, chip sets, expression alteration, PubMed ID, and PPIs), miRNAs (e.g., accession number, chromosome location, related disease, PubMed ID, and miRNA–target interactions), and SNPs (e.g., SNP ID, allele, gene, PubMed ID, chromosome location, and disease) is presented through user-friendly query interfaces or convenient links to NCBI GEO, NCBI PubMed, NCBI Gene, NCBI dbSNP, and miRBase. Overall, HPCDb provides biologists with relevant information on human PC-related molecules at multiple levels, helping to generate new hypotheses or identify candidate markers.

Abstract 309: A Female Myh11-CreER T2 Mouse Line Resulting from Y to X Chromosome-translation

The Myh11-CreER T2 mouse line ( Cre +/ ) provides a powerful tool for studying the role of smooth muscle cells (SMCs) in the pathogenesis of vascular diseases. The Cre allele was initially inserted into Y chromosome, and thus excluded its inheritance by female mice. However, a number of vascular diseases exhibit sexual dimorphism in development and progression, and the underlying mechanisms may involve regulation of SMC biology by the dosage-effects of sex-linked genes and gender. A Cre line that induces SMC-specific gene deletion in female mice would complement the existing Cre +/ line to address this critical issue. Our lab established the Cre +/ colony with one male ancestor and it spontaneously separated to two subcolonies during subsequent breeding. One subcolony produced only male Cre +/ progenies, but the other produced both male and female Cre +/ progenies, indicating chromosome-translocation of the Cre allele. In view of this observation, we mapped the chromosome-location of the Cre allele for these subcolonies with cross-breeding experiments. The 1 st experiment crossed two Cre +/ males from the first subcolony with four Cre -/ females. Of the produced progenies, all males ( n =9) carried and all females ( n =22) did not carry the Cre allele, which favors Y chromosome- ( Y Cre+ ) over autosome-location of the Cre allele in this subcolony (Bayes Factor>1000). In the 2 nd experiment, a Cre +/ female from the second subcolony was bred with a Cre -/ male. Then, a Cre +/ male progeny of these breeders was mated with a Cre -/ female. The former breeding pair exhibited equal inheritance of the Cre allele by its male and female offspring. The latter breeding pair showed that all female progenies ( n =8) did, but all male progenies ( n =4) did not, carry the Cre allele. The data favors X chromosome- ( X Cre+ ) over autosome-location of the Cre allele in this subcolony (Bayes Factor>1000). To assess the recombination driven by Cre +/ allele with different chromosome-location, we crossed X Cre+ and Y Cre+ strains with R26R reporter mice. Robust Cre activity (x-gal staining) was observed in vascular SMCs of Y Cre+ and X Cre+ mice. The X Cre+ mice generated via Y to X chromosome-translocation thus represents a novel strain that is suitable for inducible gene deletion in SMCs of female mice.