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Request for Scientific Services to Conduct In-depth Cell Characterization for the NIH Regenerative Medicine Innovation Project

Request for Scientific Services to Conduct In-depth Cell Characterization for the NIH Regenerative Medicine Innovation Project

Section I. Purpose

Regenerative Medicine (RM) using adult stem cells is an emerging area of science that holds great promise for treating and curing a variety of injuries and diseases.  While our understanding of adult stem cell biology is progressing rapidly, the need for a more complete understanding of the biological attributes of stem cell products is widely acknowledged, as it may enable the correlation of clinical outcomes with particular cell characteristics, inform future product development, help improve product safety and efficacy, and enhance reproducibility of studies. The purpose of this announcement is to solicit applications from providers of technology platforms and scientific research services to perform high quality in-depth cell characterization (IDCC) assays as outlined below in support of the Regenerative Medicine Innovation Project (RMIP) and to collaborate in the development of approaches for IDCC involving regenerative medicine clinical products.

Section II. Background 

The 21st Century Cures Act, passed in 2016, includes several provisions, pertinent to RM clinical research,  that apply to the National Institutes of Health (NIH), the U.S. Food and Drug Administration (FDA), and the National Institute of Standards and Technology (NIST).  One such provision is that NIH, in coordination with the FDA, award grants and contracts for clinical research to further the field of RM using adult stem cells.  In response, the Regenerative Medicine Innovation Project (RMIP) was launched to support late-stage pre-clinical and IND/IDE-enabling studies, as well as carefully selected clinical trials that will significantly advance the field of RM.  NIH and FDA co-hosted a workshop in December 2017 to explore the state of RM science involving adult stem cells, with a focus on approaches to the development of safe and effective RM products. Through this and other national and international expert forums on RM, NIH identified several critical challenges in the advancement of stem cell research. These challenges include the following: limited understanding of the identity and nature of stem cell products used in clinical applications, difficulties in preparation of cGMP-compliant stem cell products, and need for regulatory support to enable submission of well-developed IND/IDE applications.  To address these challenges, the NIH, in consultation with the FDA and NIST, established the Regenerative Medicine Innovation Catalyst (RMIC) to provide critical support services for RM research that include IDCC to describe the molecular and biological attributes of source stem cells and stem cell-derived products. Furthermore, the RMIC will develop ways to optimize the sharing and utilization of IDCC data in order to address gaps in knowledge and further the field of RM. The RMIC, through its collaborative network of entities, is designed to address these aforementioned critical challenges and will:

  • Provide in-depth and independent characterization of the source stem cell line and stem cell-derived products being developed,
  • Provide a platform for sharing and analysis of clinical trial (if applicable) and cell product characterization data, thereby potentially enabling correlation of stem cell-derived product attributes with clinical outcomes, and
  • Create a foundation for enhancing our understanding of clinical outcomes, refining production methods, and informing future RM product development.

Importantly, the RMIC will promote transparency and ultimately may contribute to reproducibility and standardization of clinical grade stem cell-derived products.

A key component of the RMIC is the In-depth Cell Characterization (IDCC) Hub, administered by the Progenitor Cell Translational Consortium (PCTC) – University of Maryland, Baltimore. The IDCC Hub is the administrative and coordinating support center responsible for soliciting and managing IDCC services to support RMIP awardees. IDCC is defined as the performance of a suite of assays aimed at describing the structural and biological attributes of single cells or cell populations that characterize their identities and are predictive of their functions. The IDCC assays will be performed in parallel with the RMIP study or post-hoc as feasible and appropriate. Because IDCC assays may identify cellular attributes for which the clinical significance is not currently known, these results are not intended necessarily to inform decisions during the conduct of the study, nor are they intended to factor into the normative oversight requirements and processes for the source study. Final assay results will also be returned to the RMIP study investigators as they become available. In order to accelerate the field and inform oversight of future studies, assay results will be made available to the broader research community via the RMIC one year following the end of RMIP awards (or as appropriate).

 

Section III. Financial and Cost Matching Requirements

Applicants funded under this announcement are required to match these federally awarded dollars (total costs: direct costs and indirect costs including facilities and administrative costs) with at least an equal amount (1:1) of non-Federal contributions, as mandated by the 21st Century Cures Act. Qualifying non-Federal contributions may include state and local funding not originating from Federal funds, private-sector investments, in-kind contributions, and donations from foundations. See 45 CFR 75.306, as well as relevant FAQs, for additional details. Applicants will be required to demonstrate that funds and in-kind contributions are committed or available at the time of, and for the duration of, the award. Applications must identify the source, type, and amount of funds proposed to meet the matching requirement and explain how the value of in-kind contributions was determined.  Applications must also include letter(s) of support confirming that the required matching contributions (cash or in-kind contributions such as salary, consultant costs, equipment) are available.

The total of all proposed matching contributions of funds, equipment, and services must at least equal the federal award under this solicitation and contribute to at least 50% of total project costs.  Any potential contribution of services should be estimated on a time and material basis, and must include an average labor rate, fringe rate, and overhead rate.  Any equipment used as an in-kind contribution must have been purchased with private funds and not obtained with a prior federal award.  All funded applicants shall have a government-approved or industry standard accounting system by which actual project costs are tracked and reported pursuant to the Cost Share Standard Operating Process/Procedures.  This is an absolute requirement to be sure that cost matching obligations are met.

 

Section IV. Focus of Solicitation

This Solicitation focuses on the large-scale in-depth cell characterization function of the RMIC for a wide range of cells which includes induced pluripotent stem cells, mesenchymal stem cells, placental cells, bone-marrow derived mononuclear cells, and retinal pigment epithelial cells. Proposals to provide scientific research services for the items listed below will be considered. Strong applications will address each of the following items:

  • Qualitative and quantitative analysis of cells and the cellular phenotype, biological function, and multi-omic approaches using one or more of the diverse set of cell attributes outlined in Table 1 below (Strong applications will provide a comprehensive approach for evaluating cell attributes and conducting IDCC);
  • Infrastructure and capacity for IDCC of the aforementioned wide range of cell types and sufficient to carry out the characterization of up to 50 individual cell samples or cell-derived products simultaneously per year;
  • Use of procedures that accommodate and document incoming sample quarantine, storage, handling and transport;
  • In partnership with the IDCC Hub, development of IDCC workflow to support test sample runs, pilot cell characterization studies, and ultimately IDCC assays of source stem cell and final clinical-grade product for RMIP studies; and
  • Management, processing, analysis, and visualization of large data sets from disparate analytical platforms (e.g., flow cytometry, mass spectrometry, gas chromatography, PCR, plate-based assays, high-throughput screening).

 

Table 1: List of key cell attributes and suggested assays for In-depth Cell Characterization

Cell Attributes

Example Assays

Rationale

Source Stem cell

Final Clinical-grade Product

Safety (Donor eligibility determination, sterility, adventitious agent, pyrogenicity-endotoxin, and mycoplasma testing)

Donor Eligibility Determination:         In accordance with 21 CFR 1271 and FDA guidance using FDA licensed, approved, cleared test kits in a qualified laboratory

Critical for product safety verification and mitigating risk of infectious disease to patient (Required under regulation for allogeneic cellular products)

 

X

 

Microbiology / Sterility Testing:      USP <71> Membrane Filtration, Bacteriostasis and Fungistasis, Direct Inoculation; Rapid Microbial Detection assays (ATP-based bioluminescence, fluorescent labeling, electrical resistance, nucleic acid probes) of acceptable specificity, sensitivity, and accuracy

Critical for product safety verification and mitigating risk of infectious disease to patient (Required under regulation for cellular products)

X

X

Pyrogenicity / Endotoxin Testing:   USP <85> Limulus Amebocyte Lysate (LAL) Assay (Kinetic turbidimetric, Chromogenic , Gel-clot)

X

X

Virology/Adventitious Agents (Master Cell Bank, Working Cell Bank, End-of-Production): ICH Q5A Viral Safety Evaluation, Retrovirus (cell culture infectivity assays / electron microscopy); in vitro-based assays using susceptible indicator cell cultures (range of human and relevant animal viruses); in vivo, animal-based inoculation assays (viruses not able to grow in cell culture); species-specific antibody production testing; PCR-based direct-testing of cells

X

X

Mycoplasma Testing:                        USP <63> culture-based detection; PCR-based testing (demonstrate comparability to compendial culture-based method)

 

X

X

Identity (Species determination) and Sex (Male/Female)

PCR-based assays, Flow cytometry

 

Species determination used as an additional check to confirm authenticity

 

Sex determination provides for      confirmation of authenticity, may be useful for purposes of identification post-administration to assess distribution and possible cell migration

X

 

Purity and Heterogeneity

Single-cell RNA-seq, Single cell ATAC-seq, Flow cytometry, Mass cytometry

 

Used to evaluate the composition profile of cellular preparations and to identify presence of non-target cell types that may pose risks to subjects receiving a cellular product

X

X

Viability

Trypan Blue Dye exclusion assay, Acridine Orange and Propidium Iodide (AOPI) staining, MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) tetrazolium reduction assay, Electrical potential and Morphometric assays, apoptosis assays, mitochondrial membrane potential-dyes, luminescence ATP assay, oxygen consumption and glycolysis activity

Critical for determining safety and efficacy of cellular products intended for patient administration (Required under regulation for cellular products)

X

X

Senescence

Telomere length assay

 

For limited replication capacity cell phenotypes with functional proper-ties that degrade with increasing passage number as proliferation limits are reached

X

X

Genetic Stability

Karyotyping, Southern blot analysis, FISH assays

 

For cellular phenotypes exhibiting a high proliferative capacity that may accumulate genetic mutations over extended periods in culture that impact functional properties or pose a safety risk if given to patients

X

X*

Cell Proliferation

MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) tetrazolium reduction assay, Alamar Blue, detection of cellular proliferation markers (Ki-67, PCNA [proliferating cell nuclear antigen], topoisomerase IIB), luminescence ATP assay

Serve to identify cellular products that could pose a safety risk to subjects.  Typically performed in conjunction with preclinical toxicology testing

 

X

Clonal Capacity

 

In vitro single-cell clonogenic assays

Determine ability of stem cell self-renewal and generation of differentiating lineages

X

 

Pluripotency/ Multipotency

 

Quantitative RT-PCR assessment of Oct4, Sox2, Lin28, Klf4, and c-Myc genes among others; Flow cytometric assessment of Oct4, Lin28, SSEA4, TRA-1-81, TRA-1-60, Sox17 proteins among others

 

Quantitative assessment of differentiation capacity; Embryoid body formation, embryonic lineage commitment, specific lineage differentiation (i.e., cardiac, neuronal etc.); Retinal pigment epithelium commitment; Adipogenesis, chondrogenesis, or osteogenesis for MSCs

Provide useful    information concerning a  key attribute of starting cellular material for the purpose of establishing whether there is a safety risk that may be posed by the presence of residual, non-target pluripotent stem cells in the final clinical-grade product

 

Provide quantitative assessment of specific function

 

X

X

Tumorigenicity

 

OncoPanel assay and FDA-approved F1CDx and MSK-IMPACT Next Generation Sequencing (NGS) to detect tumor gene alterations (MSK-IMPACT is a single-site assay performed at Memorial Sloan Kettering Cancer Center)

Provide information concerning the potential for a final clinical-grade cellular product to exhibit neoplasia following administration to subjects.  Confirm results through preclinical toxicology testing

X

X

Transcriptome

 

Single-cell RNA-seq, Single molecule-FISH

Use information to correlate with quantitative biological function and clinical outcome assessments

X

X

Epigenome

 

ATAC-seq, ChIP-seq, Methylome assays

Use information to correlate with quantitative biological function and clinical outcome assessments

X

X

Genome

 

Next Generation Sequencing (NGS), including assays to detect SNP and SNV

Assess or compare genetic stability

X

X

Proteome

 

Liquid Chromatography Mass Spectrometry (LC-MS), Nuclear Magnetic Resonance (NMR) spectroscopy, Gas Chromatography Mass Spectrometry (GC-MS), Mass cytometry, CyTOF

Use information to correlate with quantitative biological function and clinical outcome assessments

 

X

Lipidome and Metabolome

 

Mass spectrometry and Mass cytometry-based assays

Use information to correlate with quantitative biological function and clinical outcome assessments

 

X

Comprehensive Assessment of Cellular Markers (intracellular and cell surface).

Flow cytometry (Including but not limited to assessment of markers that are critical for cell survival and engraftment, immune suppression and evasion, and differentiation), Electron microscopy (SEM/TEM) to characterize apical/basolateral morphology

 

Useful for the  stereotypic identification of cellular phenotype(s) based on assessment of select markers associated with critical functional attributes indicative of biologic activity or indices of risk posed to subject safety. Also, can correlate with other transcriptome and possibly other omics analysis

X

X

Potency

 

Examples of cell-specific functional assays include cytokine secretion profile analysis, flow cytometry for canonical cell markers, cell polarization, electrical resistance and stereotypic morphometric analysis

Critical for determining efficacy of cellular products intended for patient administration (Required under regulation for cellular products)

 

X

* One-time testing of final clinical-grade cellular products requiring additional cell expansion from each Working Cell Bank

 

Furthermore, applicants must address the following criteria for assuring quality and comparability of generated assay data:

  • Demonstrate strategies for achieving comparability/benchmarking so that different assays, samples, labs, and processing times can be compared (e.g., use of stable reference sample materials that produce known outcomes for the assay and consider in-process benchmarks for assays as needed to establish confidence in the analytical process);
  • Establish and report detailed criteria for results, including cut-off and discrimination criteria (e.g.,  quantifying relative density of cell surface markers and percentage of labeling in population, percentage of cells containing dye above a stated threshold to determine viability, binning criteria for flow cytometry and other methods);
  • Collect and provide raw unprocessed data where applicable (e.g., raw flow cytometry data without binning);
  • Establish and report detailed protocols for handling materials and for all steps of assays including full details on manual steps (e.g., including ranges for variables such as time, temperature, etc., and in-process quality metrics when possible);
  • Delineate model-dependent analyses for nucleic acid sequence analysis, image processing and analysis, etc. (e.g., qualify and quantify accuracy and precision of the analytical pipeline with a test data set);
  • Follow a consensus data storage format for each measurement type for easy comparison of datasets;
  • Adhere to agreed upon requirements for storing and reporting metadata;
  • Adhere to the procedures and policies of the RMIC, and
  • Provide all available metadata information on reagents such as antibodies, and independent qualifying data if available (e.g., protein concentration, binding constant, purity, stoichiometry of fluorophores, storage conditions).

 

Applicants must be willing to confer with the National Institute of Standards and Technologies (NIST) to identify measurement science and measurement assurance strategies for each of the measurement platforms so that appropriateness of the assay method and confidence in the assay result can be determined. Please see https://www.nist.gov/mml/bbd/cell-measurements/advanced-therapies-cellular-and-gene-therapy-and-regenerative-medicine-2 for more details on NIST’s biosystems and biomaterials measurement assurance programs.

 

Section V. Data Standards

To ensure that data can be shared broadly across databases and optimally used across research, it is important for applicants to utilize appropriate data standards and common data elements to the extent possible which would help to maximize the value and interoperability of data in advancing research.  Accordingly, when developing and collecting data and data sets, awardees should consider following the NIH resource guide document which provides sample tools and information for identifying and utilizing certain data standards and common data elements in NIH programs. Furthermore, awardees are expected to adhere to data standards that are developed in collaboration between IDCC Hub, RMIC, NIH, FDA, and NIST.

 

Section VI. Data Stewardship

Applicants must accept that ownership of the provided data is retained by the originating entity. Service providers will not use, release, reproduce, distribute, or publish any of the data produced in the conduct of IDCC assays, nor authorize others to do so, without written permission of the NIH or other named entities. The awardees will be expected to follow all applicable NIH regulations, policies, and expectations concerning sharing research data, biomedical materials, and publication, as well as any specific requirements within the RMIP funding opportunity announcements and the terms of individual awards. Furthermore, awardees are expected to follow NIH standards for overall data quality, transfer, and management.

Section VII. Submission Process

The purpose of the submission is to provide the IDCC Hub with information on proposed capabilities and scope of services. A solicitation timeline is included below. Instructions on what to include in the application, and the technical evaluation criteria by which submissions will be assessed are found in the Submission Evaluation Criteria section.

Letter of Intent 

Prospective applicants are asked but not required to submit a letter of intent that includes the following information:

  • Descriptive title of proposed research
  • Name, address, and telephone number of the Principal Investigator
  • Names of other key personnel
  • Participating institutions

Although a letter of intent is not required, is not binding, and does not enter into the review of a subsequent application, the information that it contains allows IDCCH staff to estimate the potential review workload and plan the review. 

The letter of intent is to be sent by August 15, 2020, as a pdf attached to an email to mterrin@som.umaryland.edu with cc to alefever@som.umaryland.edu   and litang@som.umaryland.edu

 

Activity

Proposed Dates

Solicitation Announced:

July 13, 2020

Letter of Intent Due:

August 15, 2020

Application Submission Due:

September 14, 2020

Review of Applications:

November 26, 2020

Estimated Award Date:

December 15, 2020 (earliest possible)

 

Section VIII. Submission Instructions

Use of the submission template will facilitate technical evaluation.  The submission will capture the information outlined below. Please use the Solicitation Submission Template outline below to complete your submission:

  • Title Page containing a 100 word executive summary
  • Table of contents
  • Facilities and infrastructure
  • Mechanisms for incoming sample quarantine, storage, handling and transport
  • Laboratory space, including dimensions, BSL level, CLIA, GLP or GMP status
  • Equipment, including qualification, validation and calibration schedule
  • Resources and personnel budgets, including current capabilities and needed hires
  • Biosketches of key personnel
  • Description of the methodology for the proposed assays
  • Assay validation or qualification of assays
  • Assay costs per sample
  • Plan for progress (technical and fiscal) reports every six months
  • Letters of reference or evidence of track record to perform work
  • Letter(s) of support confirming that the required matching contributions (cash or in-kind contributions such as salary, consultant costs, equipment) are available

Applications will be accepted electronically up to 5:00 PM Eastern time on the due date specified. An acknowledgement email will be sent immediately after receipt. Questions and completed Intent to Submit and completed Proposals should be submitted to mterrin@som.umaryland.edu with copy to alefever@som.umaryland.edu and litang@som.umaryland.edu.  Proposals that do not follow the submission TEMPLATE will not be accepted.

 

Section IX. Submission Evaluation Criteria

Submissions will be evaluated using NIH review criteria – Significance, Investigators, Innovation, Approach and Environment -- and prioritized by scientific and technical merit for each of the cell attribute characterization assays offered in the Approach; facilities that include a central facility for performance of characterizations, dedicated space for staff and equipment, and an offsite facility for backup of data; resources to ensure secure internet access; track record and qualifications of the scientific leadership, i.e., principal investigator(s) in performance of in-depth cell characterizations; electronic specimen tracking system; quality management plan; proposed site organization and time lines; and, cost.

Section X. Confidential Information

Applicants should not include confidential or proprietary information in their applications that they do not want shared within the IDCC Hub. If there is a need to include confidential or proprietary information, please contact us at mterrin@som.umaryland.edu (cc: aminul.islam@nih.gov) to schedule a phone call to discuss further. The IDCC Hub recognizes that commercialization is important to developing products that will ultimately be made available to the public, and thus any proprietary information provided by the applicants or RMIP awardees will be protected to the extent possible under the law.

 

Section XI. Contact Information

Communication and questions during the solicitation period (including both submission and evaluation steps) should be directed by email to Dr. Michael Terrin (mterrin@som.umaryland.edu) with copy to Dr. Aminul Islam (aminul.islam@nih.gov) . If the communication/question pertains to a specific proposal under review please provide the proposal title and name of the applicant.

 

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