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.
- Driver Mutations
- Tumor Mutation Burden
- Microsatellite Instability
- PD-L1 Expression
- MHC Expression
- Metabolic Factors
- Tumor Microenvironment
- Cancer Staging (tumor, nodes, metastases)
- 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. HOW WE APPLY MALDI-TOF
Liquid Chromatography (LC-MS) Mass Spectrometry
Biodesix uses LC-MS for targeted and discovery proteomics:
- Quantification of predefined highly-multiplexed sets of proteins (MRM mass spectrometry).
- Unbiased discovery proteomics (SWATH / DIA mass spectrometry)
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®
Bottom-Up Proteomics: Peptide analysis
- Quantitative and precise
- Highly multiplexed targeted proteomics
- Eliminates need for expensive antibody development
- Established clinical diagnostic with BDX-XL2
“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.