Solving the sensitivity challenge in the quest for blood-based protein biomarkers

By Anna Berdine

Proteomics holds great promise in the discovery and profiling of biomarkers for early detection of disease and monitoring of therapeutic response.  Circulating proteins found in body fluids such as blood, CSF and urine represent ideal candidates as they are relatively simple to collect through non-invasive procedures.  However, blood-based liquid biopsy analysis is challenged by the wide dynamic range that exists within the proteome, in which highly abundant proteins such as immunoglobulin mask the detection of lower abundance protein biomarkers. This results in thousands of clinically relevant proteins which reside in lower concentrations below the detection limit of many traditional proteomics platforms 1,2,3

Recently, new technologies have emerged that are capable of the exquisite sensitivity and broad dynamic range required to accurately detect and quantify changes in protein levels in a highly multiplexed format.  In a recent pre-print publication, the NULISA Assay demonstrated the ability to detect proteins from plasma at attomolar levels with 10 logs of dynamic range4, providing evidence of its utility in future protein biomarker studies across a variety of disease states.

Evidence of the clinical significance of detecting changes in these low abundant proteins is emerging across many areas of human disease. Cytokine profiling is increasingly standard practice in clinical research due to their involvement in various diseases and potential as therapeutic targets5.  However, the measurement of some of the most critical cytokines such as IL4, IL1B, IFN alpha, can be challenging due to their low abundance and short half-life6,7.

Neurodegenerative disorders are another area where advances in protein biomarker detection provide hope for earlier diagnosis and better therapeutic outcomes.  A review by Zetterburg et al8 describes the current state of biomarkers for Alzheimer’s Disease and the potential of a combined protein biomarker analysis including Aβ, p-tau, and makers of inflammation to facilitate the development and clinical implementation of novel drug candidates against AD8.  A high sensitivity protein assay is required to detect these changes in blood and avoid the highly invasive and costly procedures involved in CSF collection or PET imaging.

NULISA solves the sensitivity issue by removing sources of background noise from the sample matrix.  Compared to other existing technologies, NULISA demonstrated increased sensitivity for detection of low abundant targets4.  Furthermore, the combination with NGS readout allows the NULISA technology to have high multiplexing- from 1-1000’s of plex- and a high throughput capability of 96 – 288 samples per run.  By enabling ultra-sensitive, high plex analysis of the blood proteome, technologies such as the NULISA assay unlock the potential of liquid biopsy to improve human health.  

References
  • Anderson, N. L. & Anderson, N. G. The Human Plasma Proteome: History, Character, and Diagnostic Prospects *. Molecular & Cellular Proteomics 1, 845–867 (2002).
  • Uhlén, M. et al. The human secretome. Sci Signal 12, eaaz0274 (2019). Williams, S. A. et al. Plasma protein patterns as comprehensive indicators of health. Nat Med 25, 1851–1857 (2019)
  • Melani, R. D. et al. The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells. https://www.science.org.
  • Feng W, Beer J, Hao Q, Ariyapala IS, Sahajan A, Komarov A, Cha K, Moua M, Qiu X, Xu X, Iyengar S, Yoshimura T, Nagaraj R, Wang L, Yu M, Engel K, Zhen L, Xue W, Lee CJ, Park CH, Peng C, Zhang K, Grzybowski A, Hahm J, Schmidt SV, Odainic A, Spitzer J; Bonn COVIMMUNE Consortium; Buddika K, Kuo D, Fang L, Zhang B, Chen S, Latz E, Yin Y, Luo Y, Ma XJNULISA: a novel proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing. bioRxiv [Preprint]. 2023 Apr 10:2023.04.09.536130. doi: 10.1101/2023.04.09.536130. PMID: 37090549; PMCID: PMC10120728.
  • Matthew C MatsunagaPaul S Yamauchi. IL-4 and IL-13 Inhibition in Atopic Dermatitis. J Drugs Dermatol.2016 Aug 1;15(8):925-9. PMID: 27537991
  • Interleukin-17 family members in health and diseaseSoo-Hyun Chung1Xiao-Qi Ye 1Yoichiro Iwakura 1  Int Immunol 2021 Nov 25;33(12):723-729. doi: 10.1093/intimm/dxab075.
  • Milena Iwaszko1Sylwia Biały 1Katarzyna Bogunia-Kubik 1Significance of Interleukin (IL)-4 and IL-13 in Inflammatory Arthritis PMID: 34831223. PMCID: PMC8616130. DOI: 3390/cells10113000
  • Henrik ZetterbergBarbara B Bendlin  Biomarkers for Alzheimer’s disease-preparing for a new era of disease-modifying therapies. Mol Psychiatry. 2021 Jan;26(1):296-308. doi: 10.1038/s41380-020-0721-9. Epub 2020 Apr 6.