Combining proteomics with transcriptomics

While proteins are chiefly responsible for most biological functions and can be seen as the ultimate executors of the information encoded in the genome, the transcription of genes as RNA plays an essential intermediate role. While post-transcriptional, translational and post-translational mechanisms all play key roles in the final concentration and biological activity of each protein, RNA measurements in the form of transcriptomics have long been used as a relevant proxy for biological output from the genome. While suitable proteomics technologies were lacking, powerful techniques such as RNAseq have enabled large scale studies of gene expression that have contributed to many systems biology studies.

Since many factors other than gene transcription are involved in protein function, however, the availability of Olink’s powerful proteomics solution can now provide the key “missing link” from genetic information to real-time biological activity. An increasing number of studies are combining transcriptomics and Olink proteomics to gain a more complete picture, leveraging on the complementary potential of these approaches, for example to study localised changes at the tissue/cellular level by RNA analysis in relation to systemic changes at the proteomics level.

Case study:  A study in collaboration with Massachusetts General Hospital Cancer Center, performed deep proteomic profiling together with single-cell RNAseq in a metastatic melanoma cohort during treatment with checkpoint inhibitor immunotherapy. Around 1500 proteins were measured, resulting in plasma protein profiles associated with both predicted treatment response and overall survival. Single-cell RNAseq data  from individual immune cells within the tumors of melanoma patients showed that differentially expressed genes between responders and non-responders were primarily derived from myeloid cells, macrophages and dendritic cells, with an excellent correlation to the plasma proteomics data. This study demonstrates how circulatory proteins may provide a roadmap to inform biological insights about the localized tumor response to therapy. Please download the full case study report using the link below:

Go to Immunotherapy Case Study

Selected publications

  • Masoudzadeh N, Östensson M, Persson J, et al. Molecular signatures of anthroponotic cutaneous leishmaniasis in the lesions of patients infected with Leishmania tropica. (2020) Scientific Reports, DOI: 10.1038/s41598-020-72671-7
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  • Harden J, Shih Y-H, Xu J, et.al.  Paired Transcriptomic and Proteomic Analysis Implicates IL-1β in the Pathogenesis of Papulopustular Rosacea. (2020) Journal of Investigative Dermatology, DOI: 10.1016/j.jid.2020.08.013
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  • Björk A, Da Silva Rodrigues R, Richardsdotter Andersson E. Interferon activation status underlies higher antibody response to viral antigens in patients with systemic lupus erythematosus receiving no or light treatment. (2020) Rheumatology, DOI: 10.1093/rheumatology/keaa611
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2947

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Protein data points generated

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Publications listed on website

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