Profiling of the metabolic transcriptome via single molecule molecular inversion probes

Area of Science:

• Biochemistry
• Molecular Biology
• Oncology

Background:

• Cancer cells exhibit unique metabolic alterations, presenting potential therapeutic targets.
• Identifying these cancer-specific metabolic pathways requires robust and accessible methods.
• Current methods like 13C-tracing are costly and complex, limiting their clinical use.

Purpose of the Study:

• To validate a novel metabolic profiling technique using multiplex targeted next-generation RNA sequencing with single molecule molecular inversion probes (smMIPs).
• To assess the utility of smMIP-profiling for measuring the activity and mutations of genes encoding metabolic enzymes.
• To evaluate the potential of this method for routine patient care.

Main Methods:

• Multiplex targeted next-generation RNA sequencing utilizing single molecule molecular inversion probes (smMIPs).
• Profiling of an isogenic cell line pair with differing Von Hippel Lindau protein expression.
• Measurement of gene activity and mutations in genes encoding metabolic enzymes.

Main Results:

• smMIP-profiling successfully provided relevant information on active metabolic pathways.
• The technique demonstrated its ability to measure gene activity and mutations in metabolic enzymes.
• The method is cost-effective and suitable for medium-to-high throughput analysis.

Conclusions:

• smMIP-based targeted RNA sequencing is a validated, cost-effective method for metabolic profiling.
• This approach can identify active metabolic pathways and gene alterations in cancer.
• Its suitability for medium-high throughput analysis makes it promising for routine patient care and cancer metabolism research.