Molecular techniques and technologies to probe alterations in gene and protein expression that may contribute to the development, progression, prognosis, heterogeneity, therapeutic options, and drug-resistance of cancers and tumor types are an increasingly important part of the clinician’s diagnostic toolbox.
Researchers and clinicians alike are relying on sequencing technology and genomic, proteomic, and metabolomic strategies to identify biomarkers with the potential for use in diagnostics, drug discovery and development, and patient stratification for clinical drug testing.
Commenting on the recent AACR meeting, analysts from Mizuho Securities observed that molecular diagnostics are “clearly an essential part of oncology,” with “a lot of optimism around cancer genome sequencing, even if most attendees do not think it will replace existing diagnostics in the near future.” They report “significant need for better biomarkers and companion diagnostics,” with biomarkers and diagnostics “being used earlier in development, but still under-utilized.” Additionally, “genomics is clearly driving many aspects of oncology R&D,” the Mizuho analysts explained.
Several presentations at the AACR meeting highlighted the application of molecular diagnostic tools in cancer R&D and product development for the oncology diagnostics market.
Mirza Peljto and co-authors from Flagship Biosciences and Affymetrix/Panomics described a method for the quantitative in situ assessment of oncogene RNA and protein expression in human clinical tumor tissue for use in biomarker and diagnostics development. In breast cancer, the Her2 oncogene is amplified or overexpressed in about 30% of breast cancers, but the correlation between Her2 gene expression and protein expression in these tumors is not well understood.
The researchers used chromogenic RNA in situ hybridization (CISH) and immunohistochemistry (IHC) to develop a quantitative image analysis-based assay in which the levels of Her2 protein and RNA can be compared in situ within tissue context. This approach allows for the measurement and correlation of Her2 RNA and membrane protein expression across an entire tissue section. “It improves diagnostic concordance by relying on an automated method and also improves confidence in interpretation by assessing every tumor cell across the whole slide,” said Peljto.
The authors were able to distinguish high- from low-expressing biopsy samples using the CellMap™ algorithm to analyze the digital images produced, to differentiate tumor cells from the normal surrounding tissue, and to transform the images into cell and biomarker maps and quantify the levels of RNA and protein biomarkers.
The authors reported 79% concordance between Her2 RNA and Her2 protein expression. The study results “suggest the potential use of RNA CISH in assessment of Her2 status in conjunction and/or parallel to IHC.” The authors drew the following conclusions: “We demonstrated practical feasibility of combined molecular and image analysis for analyzing clinical tumor samples. The inclusion of automated, whole-slide IHC and CISH interpretation for molecular assessment for companion diagnostics may help solve the long-standing problem of manual pathologist assessments and improve concordance with the inclusion of an RNA-based readout simultaneous to an IHC-based readout.”