# Biospecimen Unit

> **NIH NIH U2C** · DANA-FARBER CANCER INST · 2020 · $607,324

## Abstract

Most patients who die from cancer do so because their cancer is resistant to available therapies. Tumors are 
comprised of diverse multicellular ecosystem that include malignant and non-malignant cells. Changes in the 
cellular state, spatial organization and interaction between subsets of cells in that ecosystem are likely to be 
central to cancer progression and therapeutic resistance, but invisible by bulk analyses. Thus, there is urgent 
need to chart an atlas of the cells that compose a tumor, their spatial organization and functional relationships 
and how those features differ in tumors that are resistant to therapy. The Boston Human Tumor Atlas Network 
Research Center (HTA-RC) will create three comprehensive atlases of the cellular geography of human 
cancer to understand how changes in the tumor ecosystem lead to therapeutic resistance. The atlases 
will chart the dynamic changes associated with resistance to targeted and immune-based therapies in: (1) 
Primary and acquired resistance to CDK4/6 inhibition in breast cancer; (2) Primary and acquired resistance to 
immune checkpoint blockade in metastatic melanoma; and (3) Primary resistance to immunotherapy in 
microsatellite stable (MSS) colorectal carcinoma (CRC) compared with microsatellite instable (MSI) CRC. To 
enable these goals, the Biospecimens Unit (BSU) will provide a comprehensive, rigorous, and nimble sample 
acquisition platform that provides the bridge between the clinic and a set of state-of-the-art cellular and spatial 
analytic assays that will form data backbone for the atlases. It will provide at least 100 clinically and pathologically 
annotated samples/year to the Molecular Characterization Unit (MCU) in a manner adequate for three 
downstream measurement modalities: (1) histopathology, based on H&E stains and pathology reports; (2) 
spatial multiplex RNA and protein data (by MERFISH, IHC, CODEX, and MIBI); and (3) single-cell genomics 
data, especially single cell and single nucleus RNA-Seq (scRNA-seq, snRNA-Seq). The proposed studies build 
on an established, tight local collaboration network that has already proven as a highly effective pioneer in 
generation of pilot-scale tumor atlas datasets. expand this infrastructure and the extensive experience within 
our clinical units to assure its success in the following aims: Aim 1: Collect biospecimens from resections 
and biopsies of breast cancer, melanoma and colorectal carcinoma. The BSU will identify, procure, and 
traffic samples from surgical suite to the laboratory. Aim 2: Conduct pre-analytic processing of 
biospecimens: The BSU will perform pre-analysic processing steps of biospecimens including tissue 
dissociation, snap freezing, sectioning for spatial analysis and archiving. Rigorous SOPs and quality control 
measures for each step already well-developed and employed routinely. Aim 3: Acquire and maintain clinical 
data associated with each sample: Accurate and comprehensive clinical pathological annotati...

## Key facts

- **NIH application ID:** 9994969
- **Project number:** 5U2CCA233195-03
- **Recipient organization:** DANA-FARBER CANCER INST
- **Principal Investigator:** BRUCE E. JOHNSON
- **Activity code:** U2C (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $607,324
- **Award type:** 5
- **Project period:** 2018-09-24 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9994969

## Citation

> US National Institutes of Health, RePORTER application 9994969, Biospecimen Unit (5U2CCA233195-03). Retrieved via AI Analytics 2026-06-10 from https://api.ai-analytics.org/grant/nih/9994969. Licensed CC0.

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