CoProjects RFP Requirements

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How CoProjects Works

A funded CoProject typically consists of a standard set of high-dimensional assays for a fixed number of samples over an approximate time period. Non-standard assays (either novel or developmental) can also be proposed, but may require external funding or an agreement to share and implement the assay within the UCSF CoLabs. All standard assays require adherence to a set of standard operating procedures (SOPs) to ensure highly consistent and high-quality data across datasets.

Day-to-day operations are managed and run through the UCSF CoLabs. Each funded CoProject is driven by a 3-person team: an embedded researcher, a technician, and a data scientist. As a sample comes through the pipeline, the technician processes it, while the data scientist curates and stores it in the UCSF Data Library. The embedded researcher works alongside the technician and data scientist to process and analyze the data. A set embargo period is placed on the data to give the investigator and her team a “first-pass” opportunity to mine it and make discoveries. After the embargo period is lifted, the data becomes open-access to all ImmunoX members in the ImmunoX Data Library for analysis and cross-comparison with other open-access datasets.

What is CoLabs

CoProjects is the funding mechanism for ImmunoX projects; CoLabs is the technology and infrastructure that supports the CoProjects. CoLabs is funded by institutional support and serves a user base across the entire UCSF community, not just the CoProjects.

Unlike fragmented “cores,” which age and become obsolete over time, CoLabs revitalizes the model for central lab resources by capitalizing on critical personnel and cutting-edge technologies, and driving collaboration across disciplines.

The model will house all CoLabs in a contiguous space and create a set of common pipelines and workflows in one centralized locale. It will recruit and retain world-class staff through project engagement, backstopped “tenure,” and annual operational funds. And it will develop and invest in transformative methods and technologies.

In its current form, CoLabs consolidates three existing groups and establishes two new ones under one roof:

Disease to Biology CoLab: A new CoLab that specializes in consistent and high-quality human specimen processing. Technicians associated with ImmunoX CoProjects are housed here and are responsible for coordinating specimen processing and data analysis workflows with other CoLabs.

Flow Cytometry CoLab: A CoLab that integrates the existing Parnassus Flow Cytometry Core and specializes in counting, sorting, and analyzing suspensions of cells using advanced cell sorting and cytometric analyses technologies.

Biological Imaging Development CoLab: A CoLab that integrates the existing Biological Imaging Development Center and specializes in assembling, testing, and applying emerging light microscopy techniques and technologies.

Genomics CoLab: A Colab that integrates existing but fragmented units at UCSF. It specializes in performing single-cell gene transcript sequencing and developing and deploying innovative methods for analyzing and modifying gene function.

Data Sciences CoLab: A new CoLab to develop bioinformatic frameworks for curating, storing, analyzing, and sharing access to data produced through the CoLabs pipeline. It will also house bioinformaticians and computational biologists to drive ImmunoX CoProjects.

Funding and Infrastructure Support

CoProjects and the use of the interactive CoLabs are either subsidized or fully-funded through the Bakar ImmunoX Initiative and through institutional support.

A standard budget for a single CoProject should not exceed $1 million, barring extraordinary circumstances. A single CoProject is typically between one to three years.

Each CoProject includes appropriate FTE support for an embedded researcher, technician, and data scientist in the CoLabs:

Embedded researcher, typically an Ph.D.- or M.D.-level, is nominated by the investigator
Technician is hired into the Disease to Biology (D2B) CoLab and directly supervised by the D2B CoLab Director
Data scientist is hired into the Data Sciences (DS) CoLab and directly supervised by the DS CoLab Director

Please note: CoProjects does not fund investigator salaries or benefits, except under extraordinary circumstances.

Disease Types

CoProjects aims to sample across a wide spectrum of normal and diseased blood and tissues. Proposals are evaluated based on how differentially arrayed and novel the immune system’s response is in the proposed disease types compared to diseases already profiled. At this time, we encourage applicants to apply for, but are not limited to, the following immune-mediated topics:

Local and systemic immunity at sites of chronic infection
Local and systemic immunity at sites in neuroinflammation
Wound healing and fibrosis
Local and systemic immunity in autoimmunity
Local and systemic immunity in aging, with emphasis on wound healing and anti-cancer responses

Population-level variations in “normal” immune responses in blood and tissues

Data Ownership & Embargo

There is a standard 18-month embargo on data generated in the CoProjects. This timeline is negotiable based on sample enrollment and completion schedules. Following the defined embargo period, CoProjects data becomes available to other members of the ImmunoX community. Investigators who want to access to a CoProject must first contact the CoProject Principal Investigator and Bakar ImmunoX Chief Strategist. Investigators who use data on any publication must offer middle authorship to the CoProjects Principal Investigator and acknowledge ImmunoX CoProjects as a partial or full source of support.

Specimen Availability and Requirements

CoProjects requires specimens at least 0.5 grams in size for tissue or at least 10 ml in volume for blood. It is highly recommended that a CoProjects pilot study is completed in advance of a full proposal to determine feasibility. We also ask that the proposal include evidence of live specimen availability at UCSF from previous years of clinical records. The live specimen must be able to be transported to the D2B CoLab within 2 hours on ice. At present, CoProjects requires the investigator to either have an IRB approved at inception or use the universal Biospecimen Resources (BIOS) IRB.

Standard Assays

Standard assays for CoProjects include:

Diseased or adjacent normal tissue:

2 panels for mass cytometry (CyTOF)
Standard panels are available shown on the RFP; open channels allow for 2-3 investigator-specific antibodies
2 pre-sorted populations for single-cell sequencing (ssSeq)
Lymphocyte and non-lymphocyte or myeloid-enriched populations
Embedded fixed-formalin paraffin-embedded (FFPE) blocks
Two 5-color immunofluorescence imaging panels or 20-color multiplex ion beam imaging (MIBI) panels (in development)

Blood

2 panels for mass cytometry (CyTOF)
Standard panels are available shown on the RFP; open channels allow for 2-3 investigator-specific antibodies
2 pre-sorted populations for single-cell sequencing (ssSeq)
Lymphocyte and non-lymphocyte or myeloid-enriched populations

Non-standard assays for CoProjects include but are not limited to:

5 panels of 17-colors each for standard flow cytometry
5 population bulk RNA sequencing
Organoids
Live biopsy imaging
Microbiome analysis
Serum proteomics for mass spectrometry

Each of these options should be discussed with the Bakar ImmunoX Chief Strategist and D2B CoLab Director prior to application. SOPs are available upon request.

Pilots Versus Full Study CoProjects

Pilots are defined as ≤12 cases in order to generate feasibility and diligence data for larger cohort studies, as well as for hypothesis testing and development. Pilots are usually collected within one year of start date but may be extended based on circumstance.

Full studies are typically larger cohorts >12 cases and may include longitudinal or multi-year case. Full studies are assigned to three-person teams, whereas pilots utilize effort from current D2B and DS CoLabs personnel, based on allocation by Directors.

Three-Person CoProject Teams

Full studies result in the allocation of effort for a 3-person team:

The embedded researcher, typically Ph.D./M.D.-level, is expected to keep a major footprint in the CoLabs during ongoing studies and work alongside the technician and data scientist to accomplish the aims of the CoProjects proposal. The embedded researcher is given bench space within the Disease to Biology (D2B) CoLab and is expected to occasionally process a sample and attend or present regular updates at CoLabs meetings.
The technician is hired directly into the D2B CoLab, and his or her direct supervisor is the D2B CoLab Director. The D2B CoLab Director is in charge of the technician’s hiring, supervision, and allocation. At least 80% technician effort is allocated towards the CoProject, but 20% technician effort is reserved for pilots and other D2B responsibilities.
Similarly, the data scientist is hired directly into the Data Sciences (DS) CoLab and his or her director supervisor is the DS CoLab Director. The data scientist is usually assigned to 2 CoProjects, with additional responsibilities towards pilots, pipeline development, and walk-in support.

Together, this creates a three-person team for each CoProject. It is typical to offer co-authorship to ImmunoX and CoLabs personnel involved in the study and include them in good faith in ongoing studies. It is a requirement that published studies acknowledge ImmunoX and CoLabs for all publications that use CoProjects-generated data.

Selection and Awards

The ImmunoX Research Committee is responsible for reviewing and selecting full-study CoProject proposals for funding. The primary criteria to evaluate proposals include but are not limited to:

Proven ability to provide samples in a timely manner to the CoLabs and to process samples using standard CoProjects pipelines and assays
Novelty of the sample type and its potential ability to illuminate new immune states not already profiled in the ImmunoX Data Library
Novelty of non-standard assays, if applicable, with regard to their potential ability to understand new immune states

CoProject proposals are awarded one term of 1-2 years for sample acquisition, processing, and analysis. A second term of funding can be requested, contingent upon progress. The start of a project should begin within 6 months of a decision, contingent upon sample streams and hiring and allocation of CoLabs personnel.

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For additional inquiries or questions contact vincent.chan@ucsf.edu

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Intro

ImmunoX proposes an innovative concept in collaborative sciences, seeking to keep scientists engaged in their personal missions, while sharing their methods and technologies and adding wide-sweeping value to a common database called the ImmunoX Data Library.

The core concept is a series of ImmunoX CoProjects located within CoLabs space to survey the immune contexture of varying degrees of “normalness” and diseased states.

The underlying hypothesis is the existence of a finite number of immunological themes of cellular composition, positioning, and gene expression patterns within normal and diseased tissues. The process of finding and exploiting them for diagnostic and therapeutic purposes benefits from a common platform and shared database. We anticipate that this form of collaboration will accelerate cures for diseases ranging from cancer to autoimmunity. We also anticipate that new discoveries of methods to exploit these immunological themes may be serendipitous, conceivably from piloting rare cases or diseases. Finding these cases requires a wide net and a pipeline that can take in large cohorts as well as new pilots.