The Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO) network

The Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO) network is a collaboration between the National Cancer Institute (NCI), the Department of Defense (DoD), and the Department of Veterans Affairs (VA). This network aims to incorporate proteogenomics into patient care as a way of looking beyond the genome, to the activity and expression of the proteins that the genome encodes.

The emerging field of proteogenomics aims to better predict how patients will respond to therapy by screening their tumors for both genetic abnormalities and protein information. Advances in proteomic technology have made this approach possible in recent years.

Screening a patient’s proteogenome may enable researchers to more precisely match their tumor types to targeted therapies than screening for genomic mutations alone. Proteogenomics may also help researchers more completely characterize the biologic pathways of cancer development, metastasis, and treatment resistance. Multiple pilot studies have shown that, across tumor types, proteogenomics identifies additional biology, beyond standard genomics alone.

Since most cancer drugs target proteins, combining protein analysis with gene analysis is expected to improve the ability to predict tumor response to treatment and eventually match the tumor with the right drug.

Deepening Understanding of Proteogenomics

The APOLLO network was launched in 2016 in response to the Cancer Moonshot (White House Fact Sheet), which challenged federal agencies to work closely together to hasten the progress of cancer research. The network speeds the pace of proteogenomics research and increases the resources devoted to it. By partnering with the nation’s two largest health systems – DoD and VA – the NCI can study a larger number of patients and obtain results faster and more efficiently than conducting tissue-based proteogenomics and clinical trials on its own.

APOLLO's focus is on full proteogenomic profiling of cancer biospecimens from a wide variety of organ sites acquired from DoD and other medical facilities, with the goal of bringing the proteogenomics research workflow into the DoD and VA clinical systems for routine genomic and proteomic profiling that will ultimately enable matching tumor types to targeted therapies.

Data include medical images, including CT and MRI scans, obtained before and during treatment that can be connected to the patient’s genomic, proteomic, and clinical data.

APOLLO aims to make all data available publicly through the Genomic Data Commons, the Proteomic Data Portal, and the Cancer Imaging Archive. Using all of the available data (analytical, invasive, noninvasive, and clinical) will enable researchers to study the relationships among these data, validate results, and develop predictive and prognostic models to improve patient care.

The DoD agency leading the APOLLO network is the Murtha Cancer Center at the Uniformed Services University of the Health Sciences (USUHS) in Bethesda, Maryland. DNA sequencing and RNA sequencing will be performed by The American Genome Center at USUHS. Using CPTAC’s analytical workflows, the APOLLO network represents a continuous dedication to multidisciplinary research and team science that brings together leading cancer centers and organizations to study the molecular basis of cancer through proteogenomics.