# Single cell and spatial genomic analyses of specimens from patients with autoimmune diseases (Technology Core)

> **NIH AR UC2** · BRIGHAM AND WOMEN'S HOSPITAL · 2026 · $1,180,166

## Abstract

To better understand the molecular and cellular pathways driving autoimmune diseases, we propose to
deeply profile biological samples from patients with rheumatoid arthritis (RA), psoriasis (Ps), psoriatic arthritis
(PsA), primary Sjögren’s syndrome (pSS) and systemic lupus erythematosus (SLE). Working closely with the
AMP AIM network, we will focus on the cohorts and clinical questions defined by the network of clinicians,
biologists and computational biologists together with industry and non-profit partners. For our Technology
Core, we selected leading-edge multi-dimensional technologies to deeply profile end organs as well as
peripheral blood from patients with autoimmunity. We assembled a team of investigators with expertise in each
disease and tissue type, and who have already demonstrated the ability to develop and implement high-
throughput pipelines to profile tissue and blood samples. To help us design and interpret the studies, we
recruited a team of collaborators and consultants with clinical expertise in each disease, with pathology
expertise in each tissue and with technical expertise in spatial profiling methods. In the first year, we will carry
out the pilot phase to optimize pipelines for: i) preserving and disaggregating tissues; ii) profiling single cells
using scRNA-seq/CITE-seq/TCR-BCR-seq; iii) profiling single nuclei by snRNA-seq/snATAC-seq; iv) preparing
tissues for two complementary, leading-edge methods for spatial transcriptomics (Visium) and transcript
imaging (MERFISH). We will iterate the protocols to optimize cell viability and yield, technical quality metrics
specific to each technology and the representation of all cell types. In year 2, we will run the full set of scaled-
up technology pipelines using ~50 samples per tissue type, and will assess data quality, site and batch effects
and technical artifacts to inform potential modifications for the single-cell pipeline. In Years 3-5, we will profile
the remaining ~1000 biopsies and ~10

## Key facts

- **NIH application ID:** 11306983
- **Project number:** 5UC2AR081031-05
- **Recipient organization:** BRIGHAM AND WOMEN'S HOSPITAL
- **Principal Investigator:** Michael B. Brenner; Nir  Hacohen
- **Activity code:** UC2 (R01, R21, SBIR, etc.)
- **Funding institute:** AR
- **Fiscal year:** 2026
- **Award amount:** $1,180,166
- **Award type:** 5
- **Project period:** 2022-03-22T00:00:00 → 2026-12-31T00:00:00

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11306983

## Citation

> US National Institutes of Health, RePORTER application 11306983, Single cell and spatial genomic analyses of specimens from patients with autoimmune diseases (Technology Core) (5UC2AR081031-05). Retrieved via AI Analytics 2026-05-20 from https://api.ai-analytics.org/grant/nih/11306983. Licensed CC0.

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