While genomic data uncovers the potential genetic drivers of cancer (tumor), proteomic data profiles the patient’s (host) immune response to the cancer. Both are critical elements for interpreting the real-time complexity of the cancer disease state (cancer ecosystem).

 

The Cancer Ecosystem

“Together, cancer cells and host cells form an ecosystem. Initially, the cancer cells are an invasive species to a new niche or environment. Eventually, the cancer-cell [to] host-cell interactions create a new environment. Ask not just what the cancer is doing to you. Ask what you are doing to the cancer.”

– DR. KENNETH PIENTA, MEDICAL ONCOLOGIST AT JHU
MUKHERJEE S. “CANCER’S INVASION EQUATION.” THE NEW YORKER, SEPTEMBER 2017.

THE TUMOR

  • Driver Mutations
  • Tumor Mutation Burden
  • Microsatellite Instability
  • PD-L1 Expression
  • MHC Expression
  • Metabolic Factors
  • Tumor Microenvironment
  • Cancer Staging (tumor, nodes, metastases)

THE HOST

  • Systemic Immunity (innate and adaptive immune systems) Circulating Proteins
  • Environmental Factors: hormone levels, microbiome (e.g. hormone levels, microbiome)
  • ECOG Performance Status
  • Patient Demographics (e.g. age, smoking status)

 

 

Biodesix is the leader in discovering and commercializing clinically relevant proteomic diagnostic tests using mass spectrometry in combination with machine learning. ​

 

Proteomic Technology Platforms

MALDI-ToF Mass Spectrometry

Biodesix uses Matrix Assisted Laser Desorption/ Ionization Time of Flight (MALDI-ToF) mass spectrometry to broadly interrogate the circulating proteome without the need to identify specific proteins in advance. ​

LEARN MORE ABOUT OUR APPLICATIONS OF MALDI-TOF  
Liquid Chromatography (LC-MS) Mass Spectrometry

Biodesix uses LC-MS for targeted and discovery proteomics:

  1. Quantification of predefined highly-multiplexed sets of proteins (MRM mass spectrometry).
  2. Unbiased discovery proteomics (SWATH / DIA mass spectrometry)
LEARN MORE ABOUT OUR APPLICATIONS OF LC-MS  

Biodesix uses mass spectrometry to decipher the circulating proteome with both top-down and bottom-up approaches​

Top-Down Proteomics:​ Intact protein analysis
  • Highly multiplexed & high throughput​
  • Identifies splice variants & PTMs​
  • Highly reproducible
  • Established clinical diagnostic with VeriStrat®
LEARN MORE ABOUT MALDI  
Bottom-Up Proteomics: ​Peptide analysis
  • Quantitative and precise
  • Highly multiplexed targeted proteomics​
  • Eliminates need for expensive antibody development​
  • Established clinical diagnostic with BDX-XL2
LEARN MORE ABOUT LC-MS  
Image Source: N.L. Anderson and N.G. Anderson. The Human Plasma Proteome. Molecular and Cellular Proteomics (2002); 1:845-867. ​

 

 

“We’ve tended to focus on the cancer, but its host tissue —“soil,” rather than “seed”—that could help us predict the danger it poses……The seed was the cancer cell; the soil was the local ecosystem where it flourished, or failed to.”

-MUKHERJEE S. “CANCER’S INVASION EQUATION.” THE NEW YORKER, SEPTEMBER 2017.

Get in touch

Contact us