RNA Microarray for Glyco-code Based Diagnostics

Similar to RNA sequencing, RNA microarray with higher throughput and higher efficiency is also one of the excellent tools in revealing glyco-code in diagnostics. With rich research experience and state-of-art equipment, Creative Biolabs provides customer-satisfied RNA microarray services for glyco-code based diagnostics.

Overview of Glyco-code in Diagnostics

The enzymatic addition of carbohydrate structures (glycans) to proteins, lipids, or other glycans is an important post-translational modification in almost every cellular process. Aberrant glycosylation is a key hallmark of carcinogenesis and is an exciting emerging field in cancer research. Thanks to recent advances in glycan profiling capabilities, knowledge of cancer glycosylation is set to explode in the coming years. Changes in the glycosylation patterns of cancer cells affect every aspect of cancer cell biology, and glycan-based therapeutic targets are attractive options for cancer drug discovery. Oncogenic changes to glycosylation pathways result in the formation of cancer-associated glycans, such as the Tn or sTn antigen, which are important biomarkers for a range of cancers. Similar to immune activation in response to neo-epitopes, these cancer-associated glycans or neo-glycans play a role in both immune recognition and evasion.

Fig.1 Therapeutic interventions that relate to the tumor glyco-code. (RodrIguez, 2018)

Introduction of RNA Microarray

A microarray contains thousands to millions of complementary DNA (cDNA) fragments or oligonucleotides (called probes) that hybridize with specific RNA molecules in a sample; the RNA has been purified, sometimes amplified, and fluorescently labeled before hybridization. Usually, hybridization is performed simultaneously with test and control RNA samples that are labeled with different dyes, to facilitate comparison between test and control. After thorough washing, fluorescence imaging reveals the expression levels of the target RNAs. The sequences of the probes are known a priori; thus, microarrays are usually designed to profile the expression levels of known genes. Alternatively, tiling arrays that include probes evenly and densely spaced across the entire genome can capture alternatively spliced exons and novel transcripts.

Fig.2 Major components of a microarray experiment. (Ahmed, 2006)

RNA Microarray for Glyco-code Based Diagnostics

RNA sequencing (RNA-Seq) workflow is divided into several steps: RNA extraction, library construction, sequencing, and data analysis. RNA-Seq offers several distinct advantages over previous hybridization-based microarray technology. In general, microarray-based gene expression profiling is limited to hybridizing gene probes to known genomic sequences within target genes of tumor specimens. Preferably, RNA-Seq enables the detection and discovery of novel gene transcripts and ncRNAs. RNA-Seq can also detect transcription boundaries with a single nucleotide resolution, reveal alternative splicing, allele-specific expression, and SNPs in the transcribed regions. RNA-Seq has remarkably low background signaling owing to its precisely mapped sequenced reads of unique genomic regions. Depending on the detected sequence, RNA-Seq provides a more precise and quantitative profile of gene expression in diverse groups or treatments.

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References

1. RodrIguez, E.; et al. The tumor glyco-code as a novel immune checkpoint for immunotherapy. Nat Rev Immunol. 2018, 18(3): 204-211.
2. Ahmed, F.E. Microarray RNA transcriptional profiling: part I. Platforms, experimental design and standardization. Expert Rev Mol Diagn. 2006, 6(4): 535-50.

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