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Analytical tools for studying the tumor microenvironment leveraging spatial transcriptomics

Award Number: U01CA274489
ORGANIZATION: NATIONAL CANCER INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2022
PERIOD OF PERFORMANCE END DATE: 08/31/2025

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Analytical tools for studying the tumor microenvironment leveraging spatial transcriptomics - PROJECT SUMMARY/ABSTRACT Understanding the tumor microenvironment (TME) heterogeneity and architecture are key to stratify cancer patients responsive to immunotherapy and clinical outcome. Single-cell RNA sequencing (scRNAseq) is a powerful tool for studying the TME at the single-cell level, however, spatial information between single cells was not preserved in this technology, which is vital in studying the TME. In contrast, use of spatially resolved transcriptomics holds the promise in the understanding of the spatial contexture of the TME because of its power to capture the location of individual cells within the larger tissue architecture. Recently, commercialization of spatial transcriptomic (ST) technologies have allowed researchers to study at an unprecedented level the spatial architecture of the TME. Similar to other “omics” technologies, novel computational tools are urgently needed to decipher and infer biological meaning for these high-dimensional ST data. In addition to the need for methods for analyzing and visualizing ST data in its current form, there is the need to develop methods for the future state of ST, whereby the level of cellular resolution is vastly decreasing to the single cell level. Moreover, the application of multiple assays to one tissue sample is also producing multiple modalities measured on the same sample (e.g., scRNAseq, image-based cytometry methods such as multiplex immunofluorescence) which requires effective methods for data integration. Lastly, many ST studies are completed on multiple samples simultaneous with the goal of correlating TME features with clinical outcome, thus requiring computational tools to unravel the impact of the spatial architecture of the TME on clinical response. In the proposed research, we will tackle these challenges by implementing state-of- the-art statistical and computational methods that account for and leverage the spatial information present in ST data to understanding the TME. We will develop innovative methods for assessing the TME’s composition (Aim 1) and studying co-localization and spatial heterogeneity (Aim 2), along with hardening of the analytical software, spatialGE, for the analysis and visualization of ST data (Aim 3). The statistical and bioinformatics analytical approaches implemented in spatialGE will allow cancer researchers to easily leverage these methods in their studies of the TME. These analytical methods, along with the developed software tools (spatialGE R/Bioconductor package along with web-based software), will be established in collaboration with clinical, translational, and basic science cancer investigators to ensure usability and interpretability of the developed approaches.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = -$4,751 )
2026	2024	H. LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE HOSPITAL, INC.	12902 USF MAGNOLIA DR	TAMPA	FL	33612	HILLSBOROUGH	USA	Cancer Biology Research	000	3	1/30/2026	NON-COMPETING CONTINUATION	-$4,751
														Subtotal = -$4,751

Issue Date FY: 2024 ( Subtotal = $397,545 )
2024	2024	H. LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE HOSPITAL, INC.	12902 USF MAGNOLIA DR	TAMPA	FL	33612	HILLSBOROUGH	USA	Cancer Biology Research	002	3	8/15/2024	NON-COMPETING CONTINUATION	$397,545
2024	2023	H. LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE HOSPITAL, INC.	12902 MAGNOLIA DR	TAMPA	FL	33612	HILLSBOROUGH	USA	Cancer Biology Research	000	2	12/19/2023	NON-COMPETING CONTINUATION	$0
2024	2023	H. LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE HOSPITAL, INC.	12902 USF MAGNOLIA DR	TAMPA	FL	33612	HILLSBOROUGH	USA	Cancer Biology Research	001	2	7/24/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $397,545

Issue Date FY: 2023 ( Subtotal = $405,558 )
2023	2023	H. LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE HOSPITAL, INC.	12902 MAGNOLIA DR	TAMPA	FL	33612	HILLSBOROUGH	USA	Cancer Biology Research	000	2	8/25/2023	NON-COMPETING CONTINUATION	$405,558
														Subtotal = $405,558

Issue Date FY: 2022 ( Subtotal = $415,728 )
2022	2022	H. LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE HOSPITAL, INC.	12902 MAGNOLIA DR	TAMPA	FL	33612	HILLSBOROUGH	USA	Cancer Biology Research	000	1	9/1/2022	NEW	$415,728
														Subtotal = $415,728

Grand Total All Awards = $1,214,080

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Analytical tools for studying the tumor microenvironment leveraging spatial transcriptomics

Award Number: U01CA274489

ORGANIZATION: NATIONAL CANCER INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/01/2022

PERIOD OF PERFORMANCE END DATE: 08/31/2025

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