Proteomics is the large scale study of proteins. Biodesix uses mass spectrometry for the analysis of circulating proteins in blood, which allows for identification of clinically relevant proteomic differences in patient populations.
WHY PROTEOMICS?
 

While genomic data reveal the “blueprint” of cancer, proteomic profiling reveals the real-time complexity of disease and the immune response. Measuring the circulating proteins in blood allows a deeper understanding of the patient or host’s response to their tumor.

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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 / MSI
  • PD-L1 Expression
  • MHC Expression
  • Metabolic Factors
  • Tumor Microenvironment
  • Cancer Staging (tumor, nodes, metastases)

THE HOST

  • Systemic Immunity (innate and adaptive immune systems) -> regulated by Circulating Proteins
  • Environmental Factors: hormone levels, microbiome
  • ECOG Performance Status
  • Patient Demographics (e.g., age, smoking status)
Source: Image adapted from Chen and Mellman 2016 for educational purposes.

“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.

BIODESIX’S PROTEOMIC TESTS CAPTURE THE SYSTEMIC
ECOSYSTEM OF A PATIENT BY:

MASS SPECTROMETRY

Taking a biologically agnostic snapshot of the circulating proteome using MALDI-ToF mass spectrometry.

MACHINE LEARNING TEST DESIGN

Converting the acquired molecular data into a clinical test using modern machine learning.

BIOLOGICAL MECHANISM

Interpreting the host’s biology using multiple assessment methods

Host Biology: The Circulating Proteome

Biodesix develops multivariate proteomic tests that can measure protein abundance to gain a real-time comprehensive view of a patient’s changing disease state and immune profile. Blood-based proteomic analyses reflect innate and/or adaptive immune responses that may affect clinical outcomes on immunotherapy and other treatments. The ImmunoStrat® suite of prototype and development tests have been designed to interrogate a patient’s circulating proteome with the goal of predicting response to various immunotherapies across multiple tumor types. Please contact the Biodesix Business Development team for more information.

“Cancer is no more a disease of cells than a traffic jam is a disease of cars. Studying cars alone won’t work—they’re necessary, but not sufficient—jams are higher-level relational contextual phenomena. Likewise gene-level thinking can “mistake the music for the piano.”

-SMITHERS, D. W., “CANCER: AN ATTACK ON CYTOLOGISM” LANCET, 1962.

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