Sponsored by The Cancer Cell Map Initiative, UCSF and UC San Diego Health Sciences

Overview

The Cancer Cell Map Initiative is pleased to accept applications for our Cancer Systems Biology Training Program. Applications are solicited from graduate students, postdoctoral fellows and senior scientists (titles such as project scientist or research scientist) at UCSF wishing to develop and apply systems biology approaches to address a compelling biomedical question in cancer research. Proposals are welcome from trainees in CCMI-funded labs or from trainees proposing a collaborative project with at least one CCMI faculty member.

The CCMI will provide funds to support up to 50% of the awardee’s salary. Funds will be provided for one year with the ability to re-apply for future years. 

Goals of the Program

The mission of CCMI is to enable a new era of cancer discovery and treatment, based on the complete elucidation of the molecular networks underlying cancer. Medical research increasingly depends on knowledge of molecular networks of multiple types; such networks define a hierarchy of structures and processes in a cancer cell. To interrogate these networks, the CCMI leverages interactomics, imaging and computational tools at the University of California, San Francisco (UCSF), UC San Diego and Stanford University. 

This program is intended to support the short-term exploration of innovative, high-risk concepts that complement existing CCMI research (more details are available at www.ccmi.org/research and bit.ly/CCMI2pubs).

Possible topics of notable interest are as follows:

• Technologies for large-scale gene editing in primary cells, 3D tissue models or similar
• Technology development of large-scale advanced phenotype readouts like cell migration or similar
• Mechanistic studies involving patient-derived models
• Development and implementation of data integration methods leveraging machine-learning approaches
• Studies exploring cancer and immune cells interactions

Required Application Components 

• Using the NIH’s structure (Significance, Innovation and Approach) or a similar format the proposal should include a succinct description of the research plan along with proposed experiments, methods and analysis and detailed milestones.
  – Describe a single Specific Aim in two pages or less (page limit includes Figures but not References). Proposals should clearly state the significance of the biomedical problem in cancer, why it will benefit from a systems biology approach and how this work will support the applicant’s future career.
  – Describe the available reagents and assays needed to support the research or describe what will need to be developed.
  – Applicants must provide a statement of the roles of collaborating CCMI Investigator(s) and how the project fits into the larger umbrella of the CCMI research program.
  
  
• Letter(s) of Support from (a) faculty research mentor(s), commiting to guidance throughout the duration of the proposed project.
  – At least one of the mentors has to be a CCMI faculty member (at the full professor level), while the other can come from any institution and should be recognized as an accomplished investigator in cancer research.
  – For proposals from trainees in CCMI-funded labs, a single mentor is sufficient. For trainees outside the CCMI proposing a collaborative project, biosketches and letters of support should be provided from both their main faculty mentor and the collaborating CCMI faculty member.
  
  
• NIH format biosketches of the applicant and mentors 
  
  
• Brief informal budget, indicating the applicant’s current salary and fringe benefit rates.
  – For applications outside of UCSF: Institutional F&A negotiated rate agreement

All documents should be submitted as one PDF with the subject line “CCMI CSBT Application” to hello@ccmi.org by 11 AM PT Monday, August 7, 2023. Please also direct any questions to hello@ccmi.org.

Review Criteria

Applications will be initially screened by an appointed group of trainees working in CCMI-funded labs. Each reviewer will read multiple applications using an NIH review criteria: (1) Significance; (2) Approach; (3) Innovation; (4) Investigator; and (5) Environment. Both raw scores and rank- normalized scores will be used to identify top-scoring proposals. These will then be further reviewed by the CCMI’s Co-Directors, Assistant Director and assigned contacts in the Administrative Core. Final decisions will take into account not only the above criteria, but also how well a proposal fits within the CCMI’s broader research capabilities and long-term research interests.

Progress Reporting And Expectations 

Awardees will be asked to submit a brief progress report one month prior to the Center’s NIH progress reporting date (April/May) and at the end of the project period (Aug). Progress and final reports will be provided to the Center Director and the NIH program office. 

Trainees will also be required to participate in the CCMI’s annual External Advisory Committee Meeting, every other month All Hands Meetings and other CCMI events. 

About The Cancer Cell Map Initiative (CCMI)

The CCMI is generating comprehensive maps of the key protein-protein and genetic interactions underlying cancer, and is developing computational methods using these maps to identify new drug targets and groups of patients with shared outcomes (Fig. 1). Protein-protein interaction maps – the complete set of proteins that bind to another protein – tell us about the physical structure of cancer cells. Genetic interaction maps – knowing how deleting one gene impacts how cells respond to the loss of another gene – tell us about how groups of genes function as pathways and networks. New drug targets and patient subtypes will then be identified using a variety of machine learning algorithms. Unsupervised methods such as clustering and network propagation will be used to identify patient subtypes and drug targets, respectively, and supervised methods like neural networks will be trained to predict outcomes based genetic information.

The CCMI was originally founded in 2015 by Trey Ideker (UCSD) and Nevan Krogan (UCSF) who had worked for more than a decade, often in collaboration, to establish fundamental experimental, computational and conceptual frameworks for mapping molecular networks. The first iteration of the CCMI as an NCI-funded CancerSystems Biology Consortium culminated in comprehensive protein networks for breast and head-and-neck squamous cell carcinoma. For the second round of NCI funding through CCMI 2.0, we have elected to extend our comprehensive network mapping to central pathways important to many cancer types, beginning with the PI3K/AKT/mTOR axis and TP53, and to a third cancer type, lung squamous cell carcinoma (Fig. 1). We are expanding our network mapping pipeline, originally based on affinity purification mass spectrometry (AP-MS), by protein immunofluorescent imaging, covering physical scales in the 0.05 – 500 μm range, and cryo-EM, covering physical scales in the 1 – 50 nm range. With these additional data we aim to create spatiotemporal models of stable and transient protein interactions involved in cancer.