Projects

The Data Library hosts a series of research projects containing multi-omic data and de-identified clinical data. Project data is shared in our research community to best leverage these rich datasets toward biological discovery.

ImmunoX CoProjects

Human-Mouse Cancer Translator

Human-Mouse Cancer Translator (HuMu)

Overview

The Human-Mouse Cancer Translator Project aims to immunoprofile a series of common and exceptional models of cancer in mice. Models will be studied in various environment backgrounds such as variation in diet and age. The goal of the project is to create a rational translation between the classes of immune systems in cancers as revealed in Immunoprofiler and other UCSF datasets.

Data Types

CyTOF, single-cell RNAseq

PIs

Max Krummel, Matthew Spitzer, Peter Turnbaugh

Immune Cell Census

Data Library

Immune Cell Census

Overview

The Immune Cell Census aims to determine how much variation exists in normal immune systems, and importantly - how much variation exists in even a single person’s immune system at various times. We'll be profiling transcriptomes, epigenomes, and a subset of the proteome at the single cell level to understand the composition and function of individual immune systems.

Data Types

CITEseq, , single-cell RNAseq, VDJ sequencing

PI

Jimmie Ye

Chronic Viral Infection

Data Library

Chronic Viral Infection

Overview

The Chronic Viral Infection project aims to evaluate the immunological context of anti-viral and anti-tumor immune response by assessing local (liver) and peripheral (PBMC) immune repertoires in uninfected patients, patients with active viral replication (HBV, HCV) and patients with drug induced viral suppression and/or clearance in the presence and absence of liver cancer. We'll be profiling transcriptomes and a subset of the proteome both in bulk and at the single cell level to identify novel targets for therapy to augment viral clearance in chronic viral infection and control of liver cancer through immunomodulation.

Data Types

single-cell RNAseq, CyTOF, bulk RNAseq

PI

Jody Baron, Stewart Cooper

Colorectal Cancer Organoids

Data Library

Colorectal Cancer ImmunoPLUS Organoids

Overview

The Colorectal Cancer ImmunoPLUS Organoids Project aims to determine how colorectal cancer (CRC) escapes immune surveillance and coopts a tumor microenvironment (TME) to promote tumor growth and metastasis. We are profiling TME cells and transcriptomes of CRC patients at the single cell level and engineering data-driven, patient-derived organoids co-cultured with autologous immune cells to understand and perturb tumor immune microenvironments.

Data Types

Imaging, flow cytometry, single-cell RNAseq

PI

Jeroen Roose

ImmunoMicrobiome

Data Library

ImmunoMicrobiome

Overview

The ImmunoMicrobiome project aims to integrate high-dimensional immune system profiling with microbiome tracking in healthy individuals toward an understanding of the interaction of the two systems. We are building a reference of paired immune (from blood) and microbiome samples (from several body sites) from healthy individuals to explore the relationship between the microbiome and systemic immunity

Data Types

CyTOF, single-cell RNAseq, metagenomic sequencing, metabolomics

PIs

Matthew Spitzer, Gabi Fragiadakis

Fetal-Immune Response to Pathogens in Utero

Data Library

Fetal-Immune Response to Pathogens in Utero

Overview

The aim of this project is to characterize the fetal immune response to two in utero pathogen exposures, malaria and congenital CMV. CyTOF and scRNAseq will be performed on banked cord blood cells from an extremely well-characterized cohort of Ugandan infants. Cytof will be used to broadly examine differences in immune cell populations in cord blood (including activation/maturation/differentiation), while scRNAseq will be used to identify transcriptional changes in response to infection. Given the dearth of information currently available about fetal immune system, these results will markedly advance what is known about how the fetus responds to infection

Data Types

CyTOF, Bulk RNAseq, CITEseq, Demographics & Clinical Features

PI

Margaret Feeney

Frontotemporal lobar degeneration

Data Library

Innate Immunity and Neurodegeneration

Overview

The brain has long been thought to be an immune-privileged organ, shielded from the peripheral immune system. However, emerging evidence indicates that brain’s own innate immunity, which consists of microglia and astrocytes, play major roles in promoting neurodegeneration in the aging brain. The goal of our project is to investigate the role of microglia and astrocytes in neurodegeneration in a common familial form of frontotemporal dementia (FTD) caused by mutations in the human progranulin (GRN) gene. In addition, we have ongoing collaborations with other investigators at ImmunoX to determine the role of GRN mutations in the peripheral immunity, focusing on autoimmunity dysfunction and immune-mediated tumorigenesis.

Data Types

single-cell RNAseq

PI

Eric Huang

Consortia Projects

COMET

Data Library

COVID-19 Multi-Phenotyping for Effective Therapies (COMET)

Overview

The COMET study collects biological samples of blood, respiratory secretions, and viral shedding in nasal secretions from COVID-19 coronavirus patients at UCSF and ZSFG hospitals in order to identify immunophenotypic features for the development of effective therapeutic interventions. The COMET study is closely aligned with the multi-center IMPACC study funded by the NIH’s National Institute of Allergy and Infectious Diseases (NIAID), and eligible participants from COMET will be included in IMPACC.

Data Types

single-cell RNAseq, CyTOF, bulk RNAseq, serology, disease biomarkers

PI and leadership

Carolyn Calfee, COMET leadership team

Immunoprofiler

Data Library

The Immunoprofiler Initiative

Overview

The UCSF Immunoprofiler Initiative coordinates the handling of valuable human biopsy samples taken from cancer patients, and performs a series of tests for immune composition, immune cell gene expression, and immune interaction biology. We propose that cancers are discrete forms of immunopathologies. By understanding the nature of the immune response, we will determine how to treat cancers and provide new targets for the next round of immunotherapies.

Data Types

Flow Cytometry, RNA-Seq, Imaging

PI

Max Krummel

Autoimmunoprofiler

Data Library

Autoimmunoprofiler

Overview

AutoImmunoprofiler is a consortium project with the objective to profile a range of autoimmune diseases using a combination of proteomic, transcriptomic, epigenomic, and structural analyses. Emphasis will be on freshly collected tissue samples with matched peripheral blood samples from select clinically well-annotated patients. Overall goals include to better understand the underlying mechanisms of autoimmune diseases, identify the relationship between diseased tissue and peripheral compartment, elucidate novel pathways and targets for therapeutic intervention, and to guide the selection of patients and indications for existing drugs.

Data Types

single-cell RNAseq/CITE-seq; snATACseq

PIs

Max Krummel, Jeroen Roose, David Erle, Alexis Combes, Gabi Fragiadakis

The UCSF Data Library

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Projects

The Data Library hosts a series of research projects containing multi-omic data and de-identified clinical data. Project data is shared in our research community to best leverage these rich datasets toward biological discovery.

ImmunoX CoProjects

Human-Mouse Cancer Translator (HuMu)

Immune Cell Census

Chronic Viral Infection

Colorectal Cancer ImmunoPLUS Organoids

ImmunoMicrobiome

Fetal-Immune Response to Pathogens in Utero

Innate Immunity and Neurodegeneration

Consortia Projects

COVID-19 Multi-Phenotyping for Effective Therapies (COMET)

The Immunoprofiler Initiative

Autoimmunoprofiler