Title Administrative Supplements for NCI-designated Cancer Centers to support pilot projects for the development and characterization of organoid/conditionally reprogrammed cell (CRC) cultures. Key Dates Announcement Release Date: May 7, 2014 Letter of Intent Request Date: May 23, 2014 Application Receipt Date: June 16, 2014 Anticipated Award Date: September 2014 Purpose The purpose of this solicitation is to request applications for CCSG administrative supplements to support pilot projects for the development and characterization of organoid cultures derived from human cancer specimens. Background Cancer is a complex set of diseases in which mutations and other genomic and epigenomic abnormalities play a role in initiation and progression. Within any cancer histological type, each tumor acquires different genetic abnormalities that may trigger similar or distinct pathways that promote the malignant phenotype. Within each tumor, so-called “driver” events that influence the phenotype must be distinguished from a larger number of “passenger” events that are of no functional consequence. Additional types of cancer heterogeneity results from subclones that comprise only a small percentage of the cells within the tumor mass at a given period of development which are defined by distinctive genetic aberrations and/or phenotypic properties. Such subclones can be easily missed by techniques that profile the tumor mass as a whole, but may play important roles in tumor maintenance, progression and/or metastasis. Current cancer models do not adequately represent the molecular and cellular diversity of human cancers. For the vast majority of the existing human cancer cell lines, the relationship to the original tumor has not been defined and detailed information regarding the clinical presentation of the cancer and its response to treatment is unavailable. Additional deficiencies in many cancer cell lines include: a) lack of genomic profiling data to define the relationship of cell lines to their corresponding primary tumors; b) absence of information regarding the phenotypic and/or genetic drift of the cell line during propagation in culture; c) inability to recapitulate the hierarchical structure of cancer in which some cells have greater tumor initiating/propagating potential than others; d) the absence of non-malignant cellular subpopulations in 2D (or 3D) cancer cell line cultures. Finally, certain cancer subtypes as well as rare cancers are underrepresented among existing cancer cell lines. Recent research may address this deficit in cancer models. Emerging culture methods for normal and malignant epithelial cells, including organoid cultures and conditionally reprogrammed cells (CRCs), offer new tools to address current gaps in our understanding of cancer processes. Organoid cultures develop structures that resemble organs in vivo whereas CRCs are propagated as stem-like cells, which can nonetheless develop organ-like structures under appropriate conditions. Most progress has been made in establishing organoids and 1 CRCs from mouse epithelial tissues but protocols for generating these cultures from human cancer specimens are being developed. The NCI wishes to develop a coordinated program to create a large number of new cancer models using these or other methods, in which the primary tumors and the models would be genetically characterized, and various clinical features and treatment response data would be associated with the models. Specifically, we plan to establish a national network for the development of robust protocols to establish human organoid/CRC cultures from a large number of cancer subtypes, create the models, and perform the molecular characterization of the organoid/CRC models and their corresponding primary tumors. NCI wants to learn which methods of cancer model generation will be the most robust for use in functional studies (e.g. validation of therapeutic target(s) by RNA interference/CRISPR technology, small molecule screens etc.). These protocols will be shared with the research community through publications and a web site. NCI plans to establish and maintain a repository of newly-generated human cancer models that would ensure quality of the materials and distribute them to the research community. To achieve these goals, we first need to explore the scientific and technical issues involved in generating and using these models. Standard operating procedures need to be developed and validated in several laboratories. The goals for this one year supplement program are 1) to perform pilot experiments that will assess the capabilities of these cancer models and 2) to identify the technical hurdles that must be overcome in order to scale up their production, maintain quality control, and create repositories for storage and distribution. We seek answers to the following questions:  What conditions favor growth of malignant over normal cells from primary human tumors and vice versa? Can standard operating procedures (SOPs) to grow the cancer models be established? Are the culture constituents reliably and reproducibly available? o Do culture conditions need to be optimized for each tumor type or subtype? o Do different culture methodologies favor outgrowth of cell subpopulations with particular phenotypic characteristics while biasing against other subpopulations that are usually found in primary tumors?  Will the 3-D position of the starting material within the patient’s tumor impact on the quality of the model in further use and if yes, how will the models generated ensure that the clonal heterogeneity of the primary tumor is represented? o Do the cultures undergo “growth constriction” and if yes, how does that impact on the genome stability?  Are hierarchical relationships between cancer propagating cells and progeny influenced by the culture conditions, including but not exclusive the presence of tumor or normal stroma?  Does the genetic and/or epigenetic make-up of the primary tumor influence its ability to be established or propagated in vitro? Administrative Supplement Requirements: To be eligible for these one-time supplementary funds, the Cancer Center must:  Obtain approval from its IRB and establish informed consent procedures to collect patient samples for the organoids/CRCs together with clinical information, as well as permission to obtain somatic and germ line DNA and RNA sequence data from the 2 organoids/CRCs and primary tumors. IRB permission and informed consent should also be obtained to store and distribute of cancer models and associated clinical and genomic data to qualified researchers through a controlled access mechanism (modeled after dbGAP (www.ncbi.nlm.nih.gov/gap)). The NCI Center for Cancer Genomics can provide templates for informed consent and IRB protocols.  Have experience in using and improving the protocols to establish organoid/CRC generation.  Obtain case matched normal tissue for each tumor accrued for organoids/CRCs production; for most cancers this would be a blood sample (lymphocytes or granulocytes are optimal); adjacent normal tissue is possibly acceptable, but if it is too close to the tumor it may have somatic mutations which would confound the mutation detection pipelines.  Propose to focus on one or a few histological subtypes in order to define optimal SOPs for generating organoids/CRCs. For the pilot phase, the NCI is interested in organoids/CRCs from any histology, but considers lung, prostate, breast, and pancreas cancers to be of great interest to investigate.  Accrue a total of 10-20 cases (the distribution per histologic subtype should be justified in the proposal) and convert into organoids/CRCs.  Participate in the kick-off meeting of investigators and in quarterly teleconferences and an end-of-project meeting (probably in person) to discuss protocols, challenges o All protocols will be shared among the participant groups. o Validated protocols will be made available to entire research community through a web-based portal.  Distribute without encumbrance all materials developed from the tissues (organoids/CRCs) and the ancillary characterization data (clinical data etc.) to the research community at the completion of the pilot. The organoids/CRCs will be maintained at an NCI-sponsored site and distributed. There will be no intellectual property associated with the submitted materials (including the clinical data). Eligible Institutions All clinical and comprehensive NCI-designated Cancer Centers are eligible to apply. Number of Applications Only one application per Center is allowed. Terms and Conditions of Funding and Allowable Costs The budget should justify all direct and the indirect costs. A maximum of $200,000 in Direct Costs will be available in these supplements for organoid/CRC generation. Tumor specimens will be collected from a minimum of 10-20 distinct patients along with concomitant samples from normal tissues (e.g. blood). It would be of considerable interest to additionally collect metastatic biopsy sample for organoids/CRCs. 3 4 Application Procedures 1. Cover Letter A cover letter should accompany each application and include: a. Request for an administrative supplement to support the project b. Title of the supplement. c. P30 grant number. d. Contact information for the center director and the project leader. e. Signatures of the center director and the authorized institutional official. 2. Application a. Standard PHS 398 (pgs 1 – 5), http://grants.nih.gov/grants/funding/phs398/phs398.html i. Item 2: check yes and provide the title indicated in the cover letter, 1.b. ii. Items 7A – 8B, denote the direct and total costs for the project. Direct costs should not exceed $200,000. iii. The authorized organization representative must sign the face page. iv. Include a detailed budget justification. v. Provide NIH biographical sketches, as appropriate, http://grants.nih.gov/grants/funding/phs398/phs398.html, for any proposed personnel. b. Summary of the Project A statement indicating that the Cancer Center agrees to perform and complete all the tasks and goals as specified above if awarded the supplement, including: 1. The informed consent process which allows collection of the tissue and clinical information which will be used for the development of the organoids/CRCs. The informed consent language needs to include text on data sharing as was developed in CCG programs (e.g. TARGET, TCGA). 2. Description of the proposed protocols and plan for improvement for a given tissue type as well as across tissue types. a. Which tumor type(s) was (were) selected and the number of cases attempted for each. The rationale for tumor type(s) has to be justified as is the use of use of successive accrual vs. enrichment of subtype(s). The Center will provide all pertinent information on quarterly basis to the NCI program office, # of cases collected, histologic type(s), age of patient, status of patient (i.e. pre or post-treatment), the status of establishment of organoids/CRCs, etc. 5 b. The organoids/CRCs established will be centralized for distribution, specifics to be determined within 6 -12 months of award. 3. Process for tracking the passage stages and freezing of adequate number of vials for distribution. The samples should be stored in N2(liq). 4. Justification of PI and staff for the study. 5. Agreement that all materials developed from samples provided using support from this supplement can be distributed without encumbrance to the extramural research community. Application Submission Letter of Intent should be sent by May 23rd to [email protected]. Applications may be submitted as a signed, scanned pdf to [email protected] and to [email protected] no later than June 16, 2014. Review Criteria All proposals will be reviewed for merit by a committee of NCI staff having expertise in Cancer Centers and PDX activities. Awards Awards will be based on responsiveness to the aims of this announcement (pp1-4) and the availability of funds. Note: IRB approvals are not required at the time of submission but will be required prior to release of funding. Reporting Requirements/Deliverables A separate supplement Progress Report must be submitted, in conjunction with the P30 CCSG parent award Annual Progress Report in T5 non-competing years years and individually in the T2 competing year. This progress report should also be submitted to Daniela S. Gerhard in the Center for Cancer Genomics, NCI ([email protected]). The progress report should include a detailed description of progress made towards the requirements indicated above. Questions Programmatic: Please contact the NCI Program Director for your P30 CCSG award, telephone number 240-276-5600. Budget: Please contact the NCI Grants Specialist for your Cancer Center at the phone number indicated on the latest Notice of award. Organoids/CRCs-specific Questions: Please contact Dr. Daniela S. Gerhard, Office of Cancer Genomics, NCI; 301-451-8027; [email protected] 6