International Agency for Research on Cancer workshop on 'Expression array analyses in breast cancer taxonomy'

Wide clinical spectrum in ALG8-CDG: clues from molecular findings suggest an explanation for a milder phenotype in the first-described patient

BACKGROUND

Congenital disorders of glycosylation (CDG) includes ALG8 deficiency, a protein N-glycosylation defect with a broad clinical spectrum. If most of the 15 previously reported patients present an early-onset multisystem severe disease and early death, three patients including the cas princeps, present long-term survival and less severe symptoms.

METHODS

In order to further characterize ALG8-CDG, two new ALG8 patients are described and mRNA analyses of the ALG8-CDG cas princeps were effected.

RESULTS

One new patient exhibited a hepato-intestinal and neurological phenotype with two novel variants (c.91A > C p.Thr31Pro; c.139dup p.Thr47Asnfs*12). The other new patient, homozygous for a known variant (c.845C > T p.Ala282Val), presented a neurological phenotype with epilepsy, intellectual disability and retinis pigmentosa. The cas princeps ALG8-CDG patient was reported to have two heterozygous frameshift variants predicted to be without activity. We now described a novel ALG8 transcript variant in this patient and the 3D model of the putative encoded protein reveals no major difference with that of the normal ALG8 protein.

CONCLUSION

The description of the two new ALG8 patients affirms that ALG8-CDG is a severe disease. In the cas princeps, as the originally described frameshift variants are degraded, the novel variant is promoted and could explain a milder phenotype.

Genome wide identification and expression profile in epithelial cells exposed to TiO₂ particles

Environmental particles are believed to provoke airway inflammation in susceptible individuals by stimulating epithelial cells to release mediators that exacerbate lung diseases. Here, we sought to identify genes expressed throughout the genome by epithelial cells stimulated with TiO2 particles. A human bronchial epithelial cell line, BEAS-2B, was stimulated with or without 40 µg TiO2 for 2 h. RNA was purified from cells and subjected to microarray analysis. Genes exhibiting more than a twofold change in RNA expression were selected. Candidate genes were then analyzed using bioinformatics tools, including pathway, ontology, and network analyses. ITGAV mRNA expression levels were measured in BEAS-2B cells using real-time polymerase chain reaction. Among 37,803 genes, 92 genes displayed more than a twofold change in mRNA levels according to the microarray analysis; 87 genes were upregulated while five genes were downregulated. The 92 genes were classified based on functional annotation using a protein information resource database search for biological processes and a pathway search using the KEGG pathway database. These genes are related to macromolecule biosynthesis, metabolic processes and, in particular, RNA metabolism. When genes with more than a threefold change were analyzed, KIF11, ITGAV, SEMA3C, IBTK, and DEK were selected as candidate genes induced by TiO2 -stimulated BEAS-2B cells. To validate these results, BEAS-2B cells stimulated with 40 µg TiO2 expressed threefold higher ITGAV mRNA levels compared to those without TiO2 particle stimulation. We conclude that KIF11, ITGAV, SEMA3C, IBTK, and DEK are candidate genes expressed by epithelial cells when stimulated with TiO2 particles.

Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples

The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as “warm ischemia”. Current practice advocates cryopreservation of biosamples within 30 minutes of resection, but this recommendation has not been systematically validated by measurements of mRNA decay over time. Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analyzed gene expression variation in samples of 3 hepatocellular carcinomas (HCC) and 3 lung carcinomas (LC) cryopreserved at times up to 2 hours after resection. RNA Integrity Numbers (RIN) revealed no significant deterioration of mRNA up to 2 hours after resection. Genome-wide transcriptome analysis detected non-significant gene expression variations of −3.5%/hr (95% CI: −7.0%/hr to 0.1%/hr; p = 0.054). In LC, no consistent gene expression pattern was detected in relation with warm ischemia. In HCC, a signature of 6 up-regulated genes (CYP2E1, IGLL1, CABYR, CLDN2, NQO1, SCL13A5) and 6 down-regulated genes (MT1G, MT1H, MT1E, MT1F, HABP2, SPINK1) was identified (FDR <0.05). Overall, our observations support current recommendation of time to cryopreservation of up to 30 minutes and emphasize the need for identifying tissue-specific genes deregulated following resection to avoid misinterpreting expression changes induced by warm ischemia as pathologically significant changes.

Genomic predictors of outcome and treatment response in breast cancer

Despite advances in breast cancer treatment and outcome over the last two decades, women continue to relapse and die of advanced disease. Historically, estrogen and progesterone receptor expression, HER2 overexpression and clinico-pathologic parameters have guided therapeutic decision making. However, there are limits to the risk estimation provided by these parameters, leading to potential overtreatment of low-risk disease and undertreatment of poor-risk disease. Genomic technologies now provide the opportunity to refine our therapeutic approach by individualizing treatment to patients' individual tumor profiles. Gene profiles or signatures are groupings of genes that are differentially expressed between tumors, reflecting differences in biologic behavior. Prognostic gene signatures stratify breast cancer patients by tumor natural history, regardless of the treatment employed. Currently, there are three commercially available prognostic gene signatures: Oncotype DX (Genomic Health, Inc.), MammaPrint (Agendia BV), and the HOXB13/IL17BR (H/I) ratio; (Theros H/ISM; bioTheranostics). Others under development include the Intrinsic Gene Set, the Rotterdam Signature, the Wound Response Indicator, and the Invasive Gene Signature. Predicative signatures classify patients based on responsiveness to specific therapies. Of the prognostic signatures, Oncotype DX has been shown to have predictive value for the incremental benefit of chemotherapy when added to a hormonal therapy regimen. Additional genetic profiles under development predict response to specific hormonal therapies, anthracyclines, and taxanes. Gene signatures have the potential to transform breast cancer treatment as it becomes tailored to each patient's tumor expression profile and significantly improve the outcomes of this disease.