Targeted Transcriptomic in Investigation of Genetic Diversity in Mouse Responses to Differentiation and Chemical Exposure

**THIS IS A REQUEST FOR INFORMATION ONLY** This exchange is being issued in accordance with Federal Acquisition Regulation (FAR) 15.201(e) as a Request for Information (RFI). The purpose of this RFI is for the National Institute of Environmental Health Sciences (NIEHS) to gain both subject-matter knowledge and industry feedback concerning the subject requirement. This RFI may also be used to identify qualified and interested business concerns. This exchange is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this exchange is to obtain information regarding: (1) the availability and capability of qualified small business sources; (2) whether they are small businesses; HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. I. BACKGROUND The Division of the National Toxicology Program (NTP) is building on the substantial progress we have made in characterizing biological responses to chemical exposures through the first two phases of our Tox21 high throughput screening program for compound toxicity profiling. In the next phase of Tox21, we will expand our interrogation of global biological pathway responses to chemical exposures using a variety of methods including transcriptomic analysis of human cell lines, based on a selected set of genes (referred to as the S1500 gene set), following exposures to large numbers of chemicals over multiple doses and times. The efforts in human cells will include studies with induced pluripotent stem cell (iPS)-derived neuronal cells, consistent with our strong interest in interrogating developmental processes and the genes and pathways that actively regulate them. Reflective of our interest in developmental pathways, we also have several lines of investigation utilizing zebrafish as a model system for investigating the effects of environmental chemicals on developmental processes. Because genetic diversity in human populations is likely to be an important factor in regulation of developmental processes and in response to environmental exposures, we want to investigate the impact that genetic diversity has on developmental processes, particularly those that involve neuronal cell differentiation. Neurological conditions and diseases are appearing at a dramatically increasing frequency in human populations and environmental exposures are often invoked as causative factors in the observed increases. To gain additional insight into the relationship between neuronal cell development, environmental exposures, and the role that genetic diversity plays in this dynamic process, the NTP plans to utilize embryonic stem (ES) and iPS cells derived from the powerful genetic model system represented by the diversity outbred mouse model. It is anticipated that studies using this mouse model will greatly expand our understanding of neuronal cell differentiation pathways and the critical factors that can influence them. II. REQUIREMENT DESCRIPTION: In the studies that are the subject of this solicitation, the NTP will apply transcriptomic interrogation to mouse embryonic stem (ES) cell lines derived from Diversity Outbred (DO) mice and iPS-like neuronal progenitor cell (NPC) lines derived from these same ES cell lines and relate these to functional parameters assessed by measuring alterations in proliferation and outgrowth. This effort will allow identification and interrogation of genetic factors that contribute to the developmental transitions that neuronal lineages undergo and potentially allow for identification of specific genetic loci or genes responsible for the diversity observed in the developmental processes of neural progenitor cell (NPC) lines, by utilizing transcriptomic data to identify significant eQTLs and perhaps genetic determinates that have gender as a covariate. Mouse neuronal progenitor cells will be treated with vehicle, potential and known neurotoxicants, and non-neurotoxic compounds to determine what portion of diversity in biological response diversity is due to genetic determinants, reflected both in transcriptomic profiles as well as alterations in proliferation, neurite outgrowth, and cell viability, parameters that will be measured using a variety of tools, including high content imaging. The hypothesis under test for this project is as follows: ES and iPS cells from genetically diverse male and female DO mice will be pushed along normal neuronal cell differentiation pathways, and transcriptomic profiles generated for each cell line during this transition period will identify both the common genetic determinants of neuronal differentiation among all cell lines as well as genetic determinants that may be associated with differential responses reflected in well-defined functional parameters such as rates of cell proliferation, neurite outgrowth, and cell viability. Furthermore, because the identified pathways and genes critical for neuronal differentiation may be affected by exposure to environmental chemicals, resulting in alterations in the differentiation process as evidenced by both transcriptomics profiles and functional parameters, the specific genetic targets of the environmental chemicals will be identified. Requirement Schedule. - Select and culture 100 male and 100 female DO ES cell lines. - Derive neural progenitor cell (NPC) lines from the male and female DO ES lines [100 cell lines per sex]. - Measure a variety of growth parameters, focusing on those reflective of neuronal cell proliferation, differentiation, and functions. - Generate transcriptomic profiles for each cell line using Next Generation RNA-Seq approaches. - Integrate various growth characteristics, genotype information, and transcriptomic data in order to mine for genetic determinates of growth and differentiation. - Treat NPC lines with vehicle control and 6 chemicals, selected by NTP scientists, at 4 concentrations per chemical and harvest cell lysates for subsequent transcriptome analysis. Requirement Deliverables. The deliverables to NTP shall be: a. RNA extracts from each of 100 male and 100 female DO ES cell lines selected for study b. Neural progenitor cell (NPC) lines derived from 200 DO ES cell lines c. Detailed report on growth parameters including proliferation characteristics, neurite outgrowth, stains for neuronal-specific markers, and cell viability d. RNA extracts from each of the 200 NPC lines derived from the 200 ES cell lines e. mRNA RNA-Seq profiles for each of the 400 RNA samples (ES + NPC) f. Alignment of RNA-Seq reads to DO mouse genomes/transcriptomes g. QTL analysis on neurite differentiation characteristics that show significant variance across the 200 NPC lines h. eQTL analysis on genes with sufficient counts for use with quantitative trait mapping in (g.) i. Frozen RNA lysates from 200 NPC lines treated with 6 compounds at 4 concentrations plus vehicle control each Place and Period of Performance. All work is expected to be conducted at the contractor's facility or at a designated and approved subcontractor facility. Government Furnished Information. The government will supply compounds to be used in the treatment of the NPC lines. Government scientists will contribute to the selection of the ES cell lines to be used in this study and will have final approval authority on any and all protocol modifications. III. INFORMATION SOUGHT: Interested organizations are required to submit their capability statements and should not exceed ten (10) pages in length; not including a standard product brochure that clearly details the ability to perform the aspects of the notice described above and should be tailored to the "Project Requirements" as concise as possible. Each response should also include the following business information: a. DUNS number b. Organization Name c. Company Address d. Point of Contact (including name, title, addresses, telephone number, fax number and Email address) e. Business size f. Socio-economic status g. Teaming Agreements (if necessary) Standard product brochures will not be considered a sufficient response to this RFI. IV. RESPONSE INSTRUCTIONS: The descriptive literature provided in response to this RFI shall not exceed 10 pages. Disclaimer and Important Notes. This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received a Request for Proposal (RFP) may be published. However, responses to this notice will not be considered adequate responses to an RFP. Confidentiality. No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).