Highly parallel genome-wide expression analysis of single mammalian cells.

BACKGROUND: We have developed a high-throughput amplification method for generating robust gene expression profiles using single cell or low RNA inputs. METHODOLOGY/PRINCIPAL FINDINGS: The method uses tagged priming and template-switching, resulting in the incorporation of universal PCR priming sites at both ends of the synthesized cDNA for global PCR amplification. Coupled with a whole-genome gene expression microarray platform, we routinely obtain expression correlation values of R(2)~0.76-0.80 between individual cells and R(2)~0.69 between 50 pg total RNA replicates. Expression profiles generated from single cells or 50 pg total RNA correlate well with that generated with higher input (1 ng total RNA) (R(2)~0.80). Also, the assay is sufficiently sensitive to detect, in a single cell, approximately 63% of the number of genes detected with 1 ng input, with approximately 97% of the genes detected in the single-cell input also detected in the higher input. CONCLUSIONS/SIGNIFICANCE: In summary, our method facilitates whole-genome gene expression profiling in contexts where starting material is extremely limiting, particularly in areas such as the study of progenitor cells in early development and tumor stem cell biology.

miRNA expression profiling using Illumina Universal BeadChips.

We have developed a highly sensitive, specific, and reproducible method for microRNA (miRNA) expression profiling, using BeadArray technology. This method incorporates an enzyme-assisted specificity step, a solid-phase primer extension to distinguish between members of miRNA families. In addition, a universal PCR is used to amplify all targets prior to array hybridization. Using this method, highly reproducible miRNA expression profiles were generated with 100-200 ng total RNA input. The method has a 3.5-4 log (10(5)-10(9) molecules) dynamic range and is able to detect 1.2- to 1.3-fold differences between samples. Expression profiles generated by this method are highly comparable to those obtained with RT-PCR (R (2) = 0.85-0.90) and direct sequencing (R = 0.87-0.89). This method should prove useful for high-throughput expression profiling of miRNAs in large numbers of tissue samples.

Gene expression profiling in formalin-fixed, paraffin-embedded tissues using the whole-genome DASL assay.

Here, we provide a detailed technical description of a gene expression assay (Whole-Genome DASL (WG-DASL)), which not only enables whole-genome transcriptional profiling of degraded material, such as formalin-fixed, paraffin-embedded tissues, but is also capable of generating robust profiles with low input intact RNA. The WG-DASL assay combines target-specific annealing, extension, and ligation events followed by universal PCR and labeling steps to generate highly multiplexed Cy3-labeled products. These short products, which are single-stranded, are directly hybridized to a whole-genome expression BeadChip (HumanRef-8) containing probe content corresponding to ∼24 K RefSeq transcripts. After washing and imaging, fluorescence emissions are quantitatively recorded for each probe using high-resolution confocal scanners and imaging software. GenomeStudio software allows direct analysis of mRNA expression data and provides results in standard file formats that can be readily exported and analyzed with most standard gene expression analysis software programs. This technology is particularly useful for genome-wide expression profiling in degraded, archived material, including limited quantities of clinical samples, such as microdissected and biopsied materials.

Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform.

BACKGROUND: The cDNA-mediated Annealing, extension, Selection and Ligation (DASL) assay has become a suitable gene expression profiling system for degraded RNA from paraffin-embedded tissue. We examined assay characteristics and the performance of the DASL 502-gene Cancer Panel v1 (1.5K) and 24,526-gene panel (24K) platforms at differentiating nine human epidermal growth factor receptor 2- positive (HER2+) and 11 HER2-negative (HER2-) paraffin-embedded breast tumors. METHODS: Bland-Altman plots and Spearman correlations evaluated intra/inter-panel agreement of normalized expression values. Unequal-variance t-statistics tested for differences in expression levels between HER2 + and HER2 - tumors. Regulatory network analysis was performed using Metacore (GeneGo Inc., St. Joseph, MI). RESULTS: Technical replicate correlations ranged between 0.815-0.956 and 0.986-0.997 for the 1.5K and 24K panels, respectively. Inter-panel correlations of expression values for the common 498 genes across the two panels ranged between 0.485-0.573. Inter-panel correlations of expression values of 17 probes with base-pair sequence matches between the 1.5K and 24K panels ranged between 0.652-0.899. In both panels, erythroblastic leukemia viral oncogene homolog 2 (ERBB2) was the most differentially expressed gene between the HER2 + and HER2 - tumors and seven additional genes had p-values < 0.05 and log2 -fold changes > |0.5| in expression between HER2 + and HER2 - tumors: topoisomerase II alpha (TOP2A), cyclin a2 (CCNA2), v-fos fbj murine osteosarcoma viral oncogene homolog (FOS), wingless-type mmtv integration site family, member 5a (WNT5A), growth factor receptor-bound protein 7 (GRB7), cell division cycle 2 (CDC2), and baculoviral iap repeat-containing protein 5 (BIRC5). The top 52 discriminating probes from the 24K panel are enriched with genes belonging to the regulatory networks centered around v-myc avian myelocytomatosis viral oncogene homolog (MYC), tumor protein p53 (TP53), and estrogen receptor α (ESR1). Network analysis with a two-step extension also showed that the eight discriminating genes common to the 1.5K and 24K panels are functionally linked together through MYC, TP53, and ESR1. CONCLUSIONS: The relative RNA abundance obtained from two highly differing density gene panels are correlated with eight common genes differentiating HER2 + and HER2 - breast tumors. Network analyses demonstrated biological consistency between the 1.5K and 24K gene panels.

Distinct pigmentary and melanocortin 1 receptor-dependent components of cutaneous defense against ultraviolet radiation.

Genetic variation at the melanocortin 1 receptor (MC1R) is an important risk factor for developing ultraviolet (UV) radiation-induced skin cancer, the most common form of cancer in humans. The underlying mechanisms by which the MC1R defends against UV-induced skin cancer are not known. We used neonatal mouse skin (which, like human skin, contains a mixture of melanocytes and keratinocytes) to study how pigment cells and Mc1r genotype affect the genome-level response to UV radiation. Animals without viable melanocytes (Kit(W-v)/Kit(W-v)) or animals lacking a functional Mc1r (Mc1r(e)/Mc1r(e)) were exposed to sunburn-level doses of UVB radiation, and the patterns of large-scale gene expression in the basal epidermis were compared to each other and to nonmutant animals. Our analysis revealed discrete Kit- and Mc1r-dependent UVB transcriptional responses in the basal epidermis. The Kit-dependent UVB response was characterized largely by an enrichment of oxidative and endoplasmic reticulum stress genes, highlighting a distinctive role for pigmented melanocytes in mediating antioxidant defenses against genotoxic stresses within the basal epidermal environment. By contrast, the Mc1r-dependent UVB response contained an abundance of genes associated with regulating the cell cycle and oncogenesis. To test the clinical relevance of these observations, we analyzed publicly available data sets for primary melanoma and melanoma metastases and found that the set of genes specific for the Mc1r-dependent UVB response was able to differentiate between different clinical subtypes. Our analysis also revealed that the classes of genes induced by UVB differ from those repressed by UVB with regard to their biological functions, their overall number, and their size. The findings described here offer new insights into the transcriptional nature of the UV response in the skin and provide a molecular framework for the underlying mechanisms by which melanocytes and the Mc1r independently mediate and afford protection against UV radiation.

Skin layer-specific transcriptional profiles in normal and recessive yellow (Mc1re/Mc1re) mice.

The melanocortin 1 receptor (Mc1r) plays a central role in cutaneous biology, but is expressed at very low levels by a small fraction of cells in the skin. In humans, loss-of-function MC1R mutations cause fair skin, freckling, red hair, and increased predisposition to melanoma; in mice, Mc1r loss-of-function is responsible for the recessive yellow mutation, associated with pheomelanic hair and a decreased number of epidermal melanocytes. To better understand how Mc1r signaling affects different cutaneous phenotypes, we examined large-scale patterns of gene expression in different skin components (whole epidermal sheets, basal epidermal cells and whole skins) of neonatal (P2.5) normal and recessive yellow mice, starting with a 26K mouse cDNA microarray. From c. 17 000 genes whose levels could be accurately measured in neonatal skin, we identified 883, 2097 and 552 genes that were uniquely expressed in the suprabasal epidermis, basal epidermis and dermis, respectively; specific biologic roles could be assigned for each class. Comparison of normal and recessive yellow mice revealed 69 differentially expressed genes, of which the majority had not been previously implicated in Mc1r signaling. Surprisingly, many of the Mc1r-dependent genes are expressed in cells other than melanocytes, even though Mc1r expression in the skin is confined almost exclusively to epidermal melanocytes. These results reveal new targets for Mc1r signaling, and point to a previously unappreciated role for a Mc1r-dependent paracrine effect of melanocytes on other components of the skin.