Project Summary/Abstract: Overall
Diverse areas of cancer research have progressed to the point that it is now feasible to meaningfully integrate
research data and clinical information across the molecular, cellular, and tissue realms into a larger, more
detailed picture of the onco-dynamics of cancer, including spatial-temporal details during cancer treatment and
progression. Physicians and researchers at Washington University School of Medicine (WUSM) and the
Siteman Cancer Center (WUSM-SCC) are longtime leaders in the allied sub-disciplines of cancer, including
genomics, proteomics, imaging, functional characterization, pathology, clinical trials, and clinical care. WUSM-
SCC is an NCI-designated Comprehensive Cancer Center, which sees ~9,000 new cancer patients annually.
Building on our expertise, established infrastructure, large patient population, and extraordinary institutional
commitment, we propose to develop the Washington University Human Tumor Atlas Research Center (WU-
HTARC) within the NIH Human Tumor Analysis Network (HTAN).
We will focus on generating organ-specific human tumor atlases for three high priority cancer types associated
with exceptionally poor prognosis: the triple negative breast cancer (TNBC), glioblastoma (GBM), and
pancreatic ductal adenocarcinoma (PDAC). Collectively, we will analyze ~1,600-2000 samples collected from
spatially separated locations and at different time points along the clinical treatment course from 300-375
patients (selected from ~750 recruited patients) for the duration of the project. In addition to standard
histopathological analyses, bulk DNA/RNA sequencing, proteomics, and clinical imaging, etc., we will conduct
cutting-edge, comprehensive analyses, including single cell RNA-Seq (scRNA-Seq), multiplexed
immunofluorescent protein localization (MxIF), mass cytometry/Cytometry by Time of Flight (CyTOF) cellular
characterization, metabolomics analysis, innovative imaging, and 3-D modeling.
We have established infrastructure covering the aforementioned areas, from specimen procurement
(Biospecimen Unit), to multidisciplinary analyses modules (Characterization Unit), and to analysis pipelines
(Data Analysis Unit). Data generated from this study will be valuable for revealing the clonal evolution of the
tumor cells from longitudinally collected specimens and to reconstruct the tumor ecosystem involving non-
cancer cells and acellular structures. Our atlases will have comprehensive data integration at the 3D level over
time, providing unprecedented 4D models for the 3 selected cancer types. Our established infrastructure and
continuous efforts in incorporating new technologies in omics, imaging, and informatics, will help ensure our
atlases will be the state-of-the-art, taking full advantage of the latest progress in these fields and will continue
to evolve beyond the pilot phase to facilitate cancer research and improve clinical care.
The proposed atlases target a set of critically important clinical questions, including tumor resistance that has
long been a challenge for GBM treatment and also an important clinical problem in BRCA/TNBC and PDAC, in
which minority populations are disproportionately affected. Other emphases are BRCA response/resistance to
chemotherapy, PDAC metastasis, and GBM local recurrence in conjunction with resistance to therapy. These
atlases can cross reference each other for pan-cancer analyses. We will also seek to cooperate with any Pre-
Cancer Atlas (PCA) centers studying these disease types to maximize the temporal continuity of research on
these cancers. The similarities and differences among the three selected cancer types will provide synergy
among the three atlases and will also allow us to accumulate valuable knowledge in atlas building for other
cancer types. The data, specimens, and experience gained by our center will be shared with HTAN and the
broader research community to foster the next important discoveries in personalized cancer medicine.