Aeirtec combines clinical study Targeted RNA-seq gene expression with their patented multiplexed High Sensitivity Proteomics, 5 color Fluorescent Immunohistochemistry and Biostatistics

Examining RNA-seq immune signatures for prediction of response to therapy through AI and machine learning

Skin : Invasive melanoma (lower green)

Routine Sample RNA QC

Aeirtec have combined their modular service of clinical study biopsy and blood sample multiplexed immune and immune-oncology-targeted gene expression (RNAseq) (eg 100-700 targeted genes) and multiplex immunoassay of a wide range of secreted immune / inflammatory markers.

Enabling measurement of biopsy transcriptomics, multi-colour immunohistochemstry and circulating secreted and immune cellular  biomarkers of immune response in clinical study samples of immunomodulating therapeutic candidates.

Providing comprehensive covering of immune status in immune-oncology and immune conditions.

  • The service is part of our modular provision, including multiplexed proteomics, biostatistics and bioinformatics.

  • As with our proteomics activity, we assist in design of subpanels for analysis within the available targeted RNA-Seq libraries, with customization where required.

  • Aeirtec applies their 30 years of experience in separate clinical study conduct to assist clients and investigator sites in correct sample acquisition for security in RNA acquisition. Aeirtec uses optimized sample processing for parallel NGS and IHC.

  • Aeirtec has state of the art facilities for complex biomarker strategies, including several NGS systems, 5 color fluorescent IHC systems, multiplexed proteomics systems, flow cytometry, ELISPOT, micro to high volume sample ultracentrifuges.

RNA-Seq quality and cell count normalization

As with our proteomics service, the next generation sequencing (RNA-Seq) is built on a platform of guaranteeing quality of study sample measurement.

  • Quality commences with ensuring that investigator sites use the best sample acquisition protocols including blood capturing system for RNA preservation.

  • Following the subsequent RNA extraction by the optimal system, each individual study subject’s RNA sample quality is confirmed by ‘lab on a chip’ automated analysis and confirmation RNAse removal.

  • To ensure extraction is controlled, we add known quantities of spike non-mammalian targets, providing correct normalization at data analysis.

  • Observed significant changes in expression are validated by qPCR.

For immune targeted RNA-Seq in both frozen and formalin-fixed biopsy and peripheral blood mononuclear cell (PBMC), quantitation of immune cell subsets (eg through Quantiseq deconvolution) is complimented with several rounds of multi fluorescent color immunohistochemistry (IHC) or the study hematology data for PBMC. So, lymphocyte and monocyte/macrophage RNA levels also incorporate the IHC cell counts and study entry/final visit hematology cell counts, giving cell and ‘per cell’ RNA quantitation.

Our facilities include several Illumina sequencers for NGS, automated fluorescence imaging systems (EVOS M7000, Biotek Cytation, Nikon TE2000 and Delta Vision) for same sample repeated rounds of 5 fluorescence color imaging for high multiplexing frozen and formalin-fixed immunohistochemistry, our proprietary patented high sensitivity multiplex bead-based proteomics, Flow cytometers/ELISPOT and both micro and large volume ultracentrifuges to ensure non-aggregated purification.