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Open AccessArticle

RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens

1
Institute of Personalized Medicine, I.M. Sechenov First Moscow State Medical University, 119048 Moscow, Russia
2
Omicsway Corp., Walnut, CA 91789, USA
3
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
4
Karelia Republic Oncological Hospital, 185000 Petrozavodsk, Russia
5
Vitamed Oncological Clinical Center, 121309 Moscow, Russia
6
Faculty of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
7
Kaluga Regional Oncological Hospital, 248007 Kaluga, Russia
8
Oncological Dispensary of the Republic of Karelia, 185002 Petrozavodsk, Russia
9
Moscow Institute of Physics and Technology, 141701 Moscow, Russia
*
Author to whom correspondence should be addressed.
Biomedicines 2020, 8(5), 114; https://doi.org/10.3390/biomedicines8050114
Received: 29 March 2020 / Revised: 2 May 2020 / Accepted: 7 May 2020 / Published: 9 May 2020
(This article belongs to the Section Cancer Therapeutics)
RNA sequencing is considered the gold standard for high-throughput profiling of gene expression at the transcriptional level. Its increasing importance in cancer research and molecular diagnostics is reflected in the growing number of its mentions in scientific literature and clinical trial reports. However, the use of different reagents and protocols for RNA sequencing often produces incompatible results. Recently, we published the Oncobox Atlas of RNA sequencing profiles for normal human tissues obtained from healthy donors killed in road accidents. This is a database of molecular profiles obtained using uniform protocol and reagents settings that can be broadly used in biomedicine for data normalization in pathology, including cancer. Here, we publish new original 39 breast cancer (BC) and 19 lung cancer (LC) RNA sequencing profiles obtained for formalin-fixed paraffin-embedded (FFPE) tissue samples, fully compatible with the Oncobox Atlas. We performed the first correlation study of RNA sequencing and immunohistochemistry-measured expression profiles for the clinically actionable biomarker genes in FFPE cancer tissue samples. We demonstrated high (Spearman’s rho 0.65–0.798) and statistically significant (p < 0.00004) correlations between the RNA sequencing (Oncobox protocol) and immunohistochemical measurements for HER2/ERBB2, ER/ESR1 and PGR genes in BC, and for PDL1 gene in LC; AUC: 0.963 for HER2, 0.921 for ESR1, 0.912 for PGR, and 0.922 for PDL1. To our knowledge, this is the first validation that total RNA sequencing of archived FFPE materials provides a reliable estimation of marker protein levels. These results show that in the future, RNA sequencing can complement immunohistochemistry for reliable measurements of the expression biomarkers in FFPE cancer samples. View Full-Text
Keywords: transcriptomics; RNA sequencing; immunohistochemistry; molecular diagnostics; biomarkers detection; clinical oncology; targeted therapies; personalized medicine; lung cancer; breast cancer; trastuzumab; NCT03521245; bioinformatics transcriptomics; RNA sequencing; immunohistochemistry; molecular diagnostics; biomarkers detection; clinical oncology; targeted therapies; personalized medicine; lung cancer; breast cancer; trastuzumab; NCT03521245; bioinformatics
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Sorokin, M.; Ignatev, K.; Poddubskaya, E.; Vladimirova, U.; Gaifullin, N.; Lantsov, D.; Garazha, A.; Allina, D.; Suntsova, M.; Barbara, V.; Buzdin, A. RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens. Biomedicines 2020, 8, 114.

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