Primary fibroblasts, EBV-immortalized B-cells and T-cells from 75 umbilical cords were used to examine gene expression-relevant cis expressive quantitative trait loci (eQTLs). The authors used Illumina’s WG-6 v2 BeadExpression array and 550K SNP array. They found 8.5% of 1,007 genes with cis eQTLs in all three cell types, 12% in two types, and 79% that were cell-type specific. These correlated positively with transcript number per gene. They suggested that “the majority of cell type specificity is due to cell type-specific use of regulatory elements.”

Following infection some CD8+ effector cytotoxic lymphocytes (CTLs) retain memory properties. The authors investigated the transcriptional repressor Blimp-1 (encoded by Prdm1) using P14 chimeric mice. Following infection with lymphocytic choriomeningitis virus they found upregulation of Prdm1 mRNA in day 8 effector CTLs, but lowering of expression between day 40-100. This was mirrored by Blimp-1 expression. Analysis utilized Illumina Sentrix MouseRef-8 Expression BeadChips.

Here the authors tested both a developmental issues—how TNF-alpha affects Schwann cell-axon interactions—and a computational one—how to analyze limited microarray datasets. They used Illumina Mouse-8 BeadChips to assess gene expression in an in vitro dorsal root ganglia model where a TNF-neutralizing antibody was applied. Results showed the necessity of TNF-alpha in Schwann cell envelopment of axons and the utility of “maximum-entropy network-based methods for analysis of microarray data.”

The authors utilized ten cell lines to investigate resistance and sensitivity to chemotherapy drugs in pancreatic cancer. They investigated epithelial to mesenchymal transition (EMT) using Illumina Human-6v2 BeadChips and the BeadStation 500X. When exposed to gemcitabine they found five sensitive and five resistant cells lines. The former five were more sensitive to 5-FU and cisplatin compared to the latter. Gene expression clarified the separation between the two groups. EMT was predominantly regulated by the balance between the transcription suppresser Zeb-1 and E-cadherin.

The authors used a number of techniques to investigate possible new immunosuppressants. They utilized in vitro bone marrow-derived dendritic cells (DCs) and investigated the actions of crassin acetate (CRA), a coral-derived cembrane diterpenoid. Gene expression in the DCs incubated with CRA was investigated using Illumina’s Sentrix Mouse-6 Array. Compared to controls there was s significant increase in the expression of an isoform of the heme degradation protein Heme oxygenease—HO-1.

HIV-1 can be endocytosed by dendritic cells (DCs) and can then replicate inside them. The authors examined gene expression in DC during these phases utilizing Illumina’s Sentrix Human-6 BeadChips. DC were exposed to purified HIV-1 envelope proteins, HIV-1, or inactivated virus. They found differential gene expression depending on endocytosis or HIV-1 replication stages, as well as to active or inactivated virus. Many immune regulation genes were up-regulated while lysosomal enzyme-encoding genes were down-regulated, postulated to be associated with “HIV-1 survival and transfer.”

Estrogen receptor (ER)alpha regulates most of the effects of estrogens. The authors examined this in the liver and uterus of k/o mice lacking a functional ERalpha DNA binding-domain (DBD). They utilized the Illumina Mouse Sentrix WG-6v1.1 BeadChips and the BeadStation 500X and found “a near-complete loss of estrogen-dependent gene regulation in comparison with the wild type”. This impacted both uterine and liver development and function.