Expired PA-14-014: Functional Genetics, Epigenetics, and Non-coding RNAs in Substance Abuse (R01)

Part 1. Overview Information

Participating Organization(s)	National Institutes of Health (NIH)
Components of Participating Organizations	National Institute on Drug Abuse (NIDA)
Funding Opportunity Title	Functional Genetics, Epigenetics, and Non-coding RNAs in Substance Abuse (R01)
Activity Code	R01 Research Project Grant
Announcement Type	Reissue of PA-11-033
Related Notices	February 8, 2017 - This PA has been reissued as PA-17-155. NOT-OD-16-004 - NIH & AHRQ Announce Upcoming Changes to Policies, Instructions and Forms for 2016 Grant Applications (November 18, 2015) NOT-OD-16-006 - Simplification of the Vertebrate Animals Section of NIH Grant Applications and Contract Proposals (November 18, 2015) NOT-OD-16-011 - Implementing Rigor and Transparency in NIH & AHRQ Research Grant Applications (November 18, 2015) June 4, 2014 - Notice NOT-14-074 supersedes instructions in Section III.3 regarding applications that are essentially the same.
Funding Opportunity Announcement (FOA) Number	PA-14-014
Companion Funding Opportunity	PA-14-013, R21 Exploratory/Developmental Grant
Number of Applications	See Section III. 3. Additional Information on Eligibility.
Catalog of Federal Domestic Assistance (CFDA) Number(s)	93.279
Funding Opportunity Purpose	Genetic and genomic studies have identified genes and gene variants that potentially modulate the fundamental biological mechanisms underpinning addictive processes. Discovery of these genes/variants, while extremely valuable, is only a first step in understanding molecular mechanisms of addiction. This Funding Opportunity Announcement encourages basic functional genetic and genomic research in two areas: 1. functional validation to determine which candidate genes/variants/epigenetic/non-coding RNA features have an authentic role in addictive processes, and 2. detailed elucidation of the molecular pathways and processes modulated by candidate genes/variants, particularly for those genes with an unanticipated role in addiction.

Key Dates

Posted Date	December 5, 2013
Open Date (Earliest Submission Date)	January 5, 2014
Letter of Intent Due Date(s)	Not Applicable
Application Due Date(s)	Standard dates apply, by 5:00 PM local time of applicant organization. Applicants are encouraged to apply early to allow adequate time to make any corrections to errors found in the application during the submission process by the due date.
AIDS Application Due Date(s)	Standard AIDS dates by 5:00 PM local time of applicant organization. Applicants are encouraged to apply early to allow adequate time to make any corrections to errors found in the application during the submission process by the due date.
Scientific Merit Review	Standard dates apply
Advisory Council Review	Standard dates apply
Earliest Start Date	Standard dates apply
Expiration Date	January 8, 2017
Due Dates for E.O. 12372	Not Applicable

Required Application Instructions

It is critical that applicants follow the instructions in the SF424 (R&R) Application Guide, except where instructed to do otherwise (in this FOA or in a Notice from the NIH Guide for Grants and Contracts). Conformance to all requirements (both in the Application Guide and the FOA) is required and strictly enforced. Applicants must read and follow all application instructions in the Application Guide as well as any program-specific instructions noted in Section IV. When the program-specific instructions deviate from those in the Application Guide, follow the program-specific instructions. Applications that do not comply with these instructions may be delayed or not accepted for review.

Table of Contents

Part 1. Overview Information
Part 2. Full Text of the Announcement
Section I. Funding Opportunity Description
Section II. Award Information
Section III. Eligibility Information
Section IV. Application and Submission Information
Section V. Application Review Information
Section VI. Award Administration Information
Section VII. Agency Contacts
Section VIII. Other Information

Part 2. Full Text of Announcement

Section I. Funding Opportunity Description

Purpose

Genetic and genomic studies have identified genes and gene variants that potentially modulate the fundamental biological mechanisms underpinning addictive processes. Discovery of these genes/variants, while extremely valuable, is only a first step in understanding molecular mechanisms of addiction. This Funding Opportunity Announcement (FOA) encourages basic functional genetic and genomic research in two areas: 1. functional validation to determine which candidate genes/variants/epigenetic/non-coding RNA features have an authentic role in addictive processes, and 2. detailed elucidation of the molecular pathways and processes modulated by candidate genes/variants, particularly for those genes with an unanticipated role in addiction.

Background

Genes. Addiction to, or dependence on, drugs of abuse (including prescription drugs, nicotine, methamphetamine, cannabis, opioids, stimulants, and inhalants) is a major public health and economic problem. Candidate genes/variants that play a role in addictive processes have been identified using methods such as human or animal genome-wide association scans, QTL characterization, gene expression profiling, forward or reverse genetic screens, proteomics, or through epigenomic analyses. Genes and variants identified by these methods are priority targets for functional validation. Other candidate genes/variants include genes relevant to co-occurring psychiatric disorders and social behaviors relevant to drug addiction, as well as genes relevant to other areas of NIDA’s mission, including pain and HIV/AIDS susceptibility and progression.

Functional Validation. The most desirable functional validation would be demonstration of an epigenetic or genetic variant’s effect on a human phenotype relevant to addiction. Effects of copy number variation, modified chromatin states, methylation patterns, higher order chromatin structure, transcriptional regulation and how these changes are influenced by genetic variation are of interest. An epigenetic or genetic variant could manifest itself phenotypically at the level of a molecular pathway, cell, circuit, organism, or social interaction, leading to phenotypic differences in protein function, cell morphology, neural connectivity, behavioral responses to an addictive drug, or behavioral responses to social cues. Validation studies are encouraged at any of these levels to identify phenotypic differences relevant to addictive processes and further elucidate the driving molecular pathways that converge to elicit biobehavioral changes. Some human functional validation studies may not be feasible or ethical, necessitating the use of in vivo animal models or in vitro strategies.

Resources. There are numerous public and private resources available to facilitate functional validation of genes/variants involved in addiction. NIDA promotes the mining of databases (containing information such as model organism phenotypes, physically interacting proteins, Roadmap Epigenomics Program and ENCODE datasets, eQTL data, and gene expression levels with respect to brain anatomy) to obtain insight into the molecular mechanisms of epigenetic or genetic variant function in addictive processes. Publicly available mutants in yeast, C. elegans, Drosophila, zebrafish, mouse, and other models can be used for functional tests. For example, to test hypotheses about gene function and addiction, the Knock Out Mouse Project (KOMP) provides ES cells that can be used to generate knockout animals. Reagents for RNA knockdown of genes are available for functional validation studies. Researchers may also exploit iPS cells, human tissue banks, and post-mortem tissue collections for validation studies. For many available resources see Neuroscience Information Framework (http://www.neuinfo.org/).

Potential Research Areas and Approaches

Applicants proposing to functionally validate genetic findings or to elucidate functional mechanisms for putative substance abuse relevant genes are encouraged to apply to this FOA. Applicants proposing discrete projects with substantial preliminary data are encouraged to submit an R01 grant application, while applicants proposing high risk/high payoff exploratory/developmental research projects with limited preliminary data are encouraged to submit an R21 grant application using the companion R21 FOA. Applicants proposing to discover new genes or gene variants involved in substance abuse may also apply using the related NIDA FOA "Discovering Novel Targets: The Molecular Genetics of Drug Addiction and Related Co-Morbidities." Applications submitted to this FOA can vary greatly in depth and breadth of analysis. They may investigate a single high priority epigenetic or genetic variant in detail (e.g. using transgenic mouse approaches) or test several hundred genes/variants rapidly (e.g. using high throughput RNA knockdown).

NIDA seeks to understand addiction to abused substances such as prescription drugs, nicotine, methamphetamine, cocaine, cannabis, opioids, and inhalants. Applicants should therefore focus on one or more NIDA-relevant substances of abuse. Applicants proposing to investigate alcohol in concert with one or more NIDA-relevant drugs may also submit their CRAN-related project to this FOA, since NIDA is a member of the Collaborative Research Activity on Addiction at NIH (CRAN). Applicants investigating only the effects of alcohol should submit using an appropriate NIAAA FOA.

The following list highlights some areas of functional genetic/genomic research that would be of interest.

Human Studies. Functional validation studies could use human DNA samples from phenotypically well-characterized individuals to correlate a gene variant with a particular phenotype and/or endophenotype. Similarly, post-mortem tissue could be used for allele-specific gene expression, epigenomic mapping, or other studies. Researchers performing assays that measure epigenomic or somatic genomic features are encouraged to focus on tissues directly relevant to the disease being investigated. Some applicants may wish to propose epigenomic investigations of blood to identify potential biomarkers for chronic exposure to abused substances or as a potential indicator of addiction trajectory. For blood studies, it may be prudent to propose to collect multiple samples over time from the same individual and to consider assaying only the most relevant cell type(s) contained within the sample. Induced pluripotent stem cells (iPS cells) and neurons or other cell types derived from these cells may be useful for investigating the function of a genetic variant.

Comparison of Wild type and Gene Variant Functions. The molecular alteration associated with a gene variant frequently does not reveal whether the function of a particular gene is increased, decreased, or leads to unexpected functional consequences. Yet this information is critical if one wishes to exploit a gene variant to develop a therapeutic approach. Approaches using in vivo transgenes, in vitro biochemical assays, or other validation methods that can address these issues will help to identify the most promising molecular targets for therapeutic interventions to treat addictions.

Addictive behavior. Approaches that can ascribe a functional role to an epigenetic and/or genetic variant with respect to a particular aspect of addictive behavior (e.g. drug reinforcement, tolerance, withdrawal, craving, reinstatement) are of great interest, as are strategies to identify epigenetic and/or genetic variant effects on behavioral responses to other drugs or addictive stimuli, stress, changes in social situations, food, other natural rewards, or other environmental stimuli. In general, applicants are advised to carefully consider their selection of a behavioral model of drug exposure or addiction and to justify why this behavioral model is the most compelling choice for the proposed aims of their application.

Genetic Models. Established genetic models (such as yeast, C. elegans, sea slug, Drosophila, zebrafish, mouse, and primate) as well as emerging genetic models (such as rat) can be used to examine in vivo epigenetic and/or genetic variant function. Strategies could include exploitation of available genetic knockouts or other mutants, knockin of gene variants, or conditional reduction or overexpression of wild type and variant alleles. Since some model organism genomes (e.g. C. elegans and Drosophila) do not encode obvious opioid or cannabinoid receptors, functional validation studies involving these pathways would need to use genetic models such as zebrafish or mouse. Cross-species validation of functional alleles is encouraged, as are studies investigating sex differences with respect to epigenetic and/or genetic variant function. Functional validation approaches that could lead to the development of in vivo models of addictive processes or could facilitate future screening for therapeutic agents are of great interest.

Genomic Manipulation. Depletion of candidate gene mRNAs in cells, tissues, brain regions, or whole organisms using RNA interference or related approaches can be used to discover or validate phenotypes. These phenotypes could range from the cellular (e.g. changes in morphology or function of synapses, dendritic spines, or neurons) to the organismal (e.g. changes in behavioral responses to drugs). Similarly, applicants may wish to exploit locus-specific genome editing approaches such as the use of TALE, CRISPR or related strategies to address genetic or epigenetic function. Strategies to investigate the effects of genetic or epigenetic variants in specific cell types or during specific temporal windows using opto-epigenetic or chemo-epigenetic approaches are also encouraged.

Epigenetics and Epigenomics. Identification of cell type-specific epigenomic features associated with addictive processes as well as functional validation of epigenetic mechanisms of gene regulation in the context of neuroscience or addiction biology are encouraged as are studies aiming to discover or better characterize histone or DNA modifications important for neuronal signal transduction or regulation of gene expression. Exploitation of chromatin structure assays (e.g. Hi-C, ChIA-PET) or microscopy techniques to explore chromatin dynamics in response to substances of abuse are also of interest.

Somatic Genomic Variation and Regulatory Elements. Studies investigating somatic genomic variation and its regulation and function in the nervous system and in response to drugs of abuse (including the role of repetitive DNA, retrotransposons, and other sources of somatic genomic variation as well as their potential functional effects on gene expression, alternative splicing, or chromatin state) are encouraged. Studies exploiting artificial somatic genomic variation such as DNA barcoding to tag brain cells for cell censuses, connectivity studies, or functional characterization are also of interest. Studies to assign drug abuse-related function to variants in non-coding RNAs, microRNAs, gene regulatory elements, transposable elements, or other putative non-protein coding regions of the genome are appropriate.

Non-coding RNAs and RNA Modifications. Studies to identify and characterize non-coding RNAs relevant to neuroscience and addictive processes are encouraged. Applicants might wish to investigate the role of miRNA regulation in substance abuse, especially the identification of miRNA targets and associated mechanistic pathways. Investigations into novel and poorly understood classes of regulatory non-coding RNAs such as circular RNAs (circRNAs), long non-coding RNAs (lncRNAs), or RNAs associated with chromatin are of great interest. Applications investigating the potential functional roles of RNA modifications in mRNAs or regulatory RNAs in the nervous system are also encouraged.

Systems-level Approaches. Bioinformatic resources can be mined to identify causal genes or gene variants or to generate testable hypotheses concerning the function of candidate genes and groups of genes. Some data types that could be used include: gene expression, epigenomic, transcription factor binding information, proteomic, metabolomic, interactome, functional genomic, in silico mapping data, connectome, or neuroanatomical expression. Studies could test to see if sets of candidate disease genes are co-expressed in a particular brain region or cell type, or function together in a signal transduction cascade.

Cellular or Circuit-level Approaches. Studies comparing epigenetic and/or genetic variant functional consequences at the cellular and circuit levels, especially with respect to drug challenge are encouraged. Such outcomes may include, but are not limited to, studies of differences in neurotransmission, intracellular trafficking of proteins or RNAs, neurophysiology, signal transduction, as well as synaptic and dendritic physiology or morphology. Functional responses to changes in the neural environment due to steroid hormones, cytokines and chemokines, neuropeptides or neurotransmitter imbalance are also sought.

Developmental and Transgenerational Studies. Investigations into the functional effects of genes/variants on organism development in the context of drug exposure and addiction pathways are also of great interest. Approaches investigating epigenetic and/or genetic variant roles in neuronal differentiation, brain patterning, circuit formation, plasticity of brain circuitry during adolescence, gene x environment, gene x development, or gene x environment x development functional effects are all appropriate. In addition, there are some indications that parental exposure to certain drugs of abuse may lead to transgenerational phenotypic effects. Studies exploring these effects, including whether or not these effects are inherited through epigenetic or non-epigenetic mechanisms, are encouraged.

Imaging Strategies. Studies to identify in vivo human or animal gene/variant/epigenetic effects on neuronal activity or brain functions relevant to addiction are appropriate. These may include specific behaviors associated with addictive processes that are influenced by neurocircuitry or neuroconnectivity that may be assessed by imaging techniques such as fMRI, DTI, MRS, or PET. Studies in live, behaving animals that examine brain function in response to commonly abused drugs are encouraged, especially in animal models of adolescent drug exposure.

Brain Energetics. Studies investigating the functional interplay between molecular regulation of brain energy utilization and brain and/or behavioral changes resulting from chronic exposure to abused substances are of interest.

Extracellular Vesicles. Secreted extracellular vesicles (EVs) such as exosomes and microvesicles play an important role in many biological processes. EVs appear to play several interesting roles in the nervous system and may function in 1. neuronal-glial communication, 2. synaptic plasticity, and 3. immune surveillance. Potential studies could include: 1. the functional role of EVs and their cargoes in the nervous system, particularly with respect to neuroplastic processes and substance abuse exposures, 2. whether or not EVs in serum, cerebral spinal fluid, or other body fluids might be useful biomarkers for substance abuse exposure or addiction trajectory, and 3. whether or not EVs might have therapeutic utility for cell-specific treatment of substance abuse.

HIV/AIDS. Functional genetic and genomic studies relevant to HIV/AIDS infection and/or progression, including molecular regulation of HIV latency are encouraged.

Translational. The use of functionally validated gene variants, RNAs, or proteins for clinical applications or as validated biomarkers to predict phenotypes are of interest, as is the development of cell-type specific targeting approaches to deliver DNA, RNA, protein or other potentially therapeutic cargoes.

Special Considerations

HIV/AIDS Counseling and Testing Policy for the National Institute on Drug Abuse: In light of recent significant advances in rapid testing for HIV and in effective treatments for HIV, NIDA has revised its 2001 policy on HIV counseling and testing. NIDA-funded researchers are strongly encouraged to provide and/or refer research subjects to HIV risk reduction education and education about the benefits of HIV treatment, counseling and testing, referral to treatment, and other appropriate interventions to prevent acquisition and transmission of HIV. This policy applies to all NIDA funded research conducted domestically or internationally. For more information see https://grants.nih.gov/grants/guide/notice-files/NOT-DA-07-013.html.

National Advisory Council on Drug Abuse Recommended Guidelines for the Administration of Drugs to Human Subjects: The National Advisory Council on Drug Abuse (NACDA) recognizes the importance of research involving the administration of drugs with abuse potential, and dependence or addiction liability, to human subjects. Potential applicants are encouraged to obtain and review these recommendations of Council before submitting an application that will administer compounds to human subjects. The guidelines are available on NIDA's Web site at http://www.drugabuse.gov/funding/clinical-research/nacda-guidelines-administration-drugs-to-human-subjects

Points to Consider Regarding Tobacco Industry Funding of NIDA Applicants: The National Advisory Council on Drug Abuse (NACDA) encourages NIDA and its grantees to consider the points it has set forth with regard to existing or prospective sponsored research agreements with tobacco companies or their related entities and the impact of acceptance of tobacco industry funding on NIDA's credibility and reputation within the scientific community. Please see http://www.drugabuse.gov/about-nida/advisory-boards-groups/national-advisory-council-drug-abuse-nacda/council-statements/points-to-consider-regarding- for details.

Data Harmonization for Substance Abuse and Addiction via the PhenX Toolkit: NIDA strongly encourages investigators involved in human-subjects studies to employ a common set of tools and resources that will promote the collection of comparable data across studies and to do so by incorporating the measures from the Core and Specialty collections, which are available in the Substance Abuse and Addiction Collection of the PhenX Toolkit (www.phenxtoolkit.org). Please see NOT-DA-12-008 (https://grants.nih.gov/grants/guide/notice-files/NOT-DA-12-008.html) for further details.

Section II. Award Information

Funding Instrument	Grant: A support mechanism providing money, property, or both to an eligible entity to carry out an approved project or activity.
Application Types Allowed	New Renewal Resubmission Revision The OER Glossary and the SF424 (R&R) Application Guide provide details on these application types.
Funds Available and Anticipated Number of Awards	The number of awards is contingent upon NIH appropriations and the submission of a sufficient number of meritorious applications.
Award Budget	Application budgets are not limited but need to reflect the actual needs of the proposed project.
Award Project Period	The maximum project period is 5 years.

NIH grants policies as described in the NIH Grants Policy Statement will apply to the applications submitted and awards made in response to this FOA.

Section III. Eligibility Information

1. Eligible Applicants

Eligible Organizations

Higher Education Institutions

Public/State Controlled Institutions of Higher Education
Private Institutions of Higher Education

The following types of Higher Education Institutions are always encouraged to apply for NIH support as Public or Private Institutions of Higher Education:

Hispanic-serving Institutions
Historically Black Colleges and Universities (HBCUs)
Tribally Controlled Colleges and Universities (TCCUs)
Alaska Native and Native Hawaiian Serving Institutions
Asian American Native American Pacific Islander Serving Institutions (AANAPISIs)

Nonprofits Other Than Institutions of Higher Education

Nonprofits with 501(c)(3) IRS Status (Other than Institutions of Higher Education)
Nonprofits without 501(c)(3) IRS Status (Other than Institutions of Higher Education)

For-Profit Organizations

Small Businesses
For-Profit Organizations (Other than Small Businesses)

Governments

State Governments
County Governments
City or Township Governments
Special District Governments
Indian/Native American Tribal Governments (Federally Recognized)
Indian/Native American Tribal Governments (Other than Federally Recognized)
Eligible Agencies of the Federal Government
U.S. Territory or Possession

Other

Independent School Districts
Public Housing Authorities/Indian Housing Authorities
Native American Tribal Organizations (other than Federally recognized tribal governments)
Faith-based or Community-based Organizations
Regional Organizations
Non-domestic (non-U.S.) Entities (Foreign Institutions)

Foreign Institutions

Non-domestic (non-U.S.) Entities (Foreign Institutions) are eligible to apply.
Non-domestic (non-U.S.) components of U.S. Organizations are eligible to apply.

Foreign components, as defined in the NIH Grants Policy Statement, are allowed.

Required Registrations

Applicant Organizations

Applicant organizations must complete and maintain the following registrations as described in the SF 424 (R&R) Application Guide to be eligible to apply for or receive an award. All registrations must be completed prior to the application being submitted. Registration can take 6 weeks or more, so applicants should begin the registration process as soon as possible. The NIH Policy on Late Submission of Grant Applications states that failure to complete registrations in advance of a due date is not a valid reason for a late submission.

Dun and Bradstreet Universal Numbering System (DUNS) - All registrations require that applicants be issued a DUNS number. After obtaining a DUNS number, applicants can begin both SAM and eRA Commons registrations. The same DUNS number must be used for all registrations, as well as on the grant application.
System for Award Management (SAM) (formerly CCR) Applicants must complete and maintain an active registration, which requires renewal at least annually. The renewal process may require as much time as the initial registration. SAM registration includes the assignment of a Commercial and Government Entity (CAGE) Code for domestic organizations which have not already been assigned a CAGE Code.
NATO Commercial and Government Entity (NCAGE) Code Foreign organizations must obtain an NCAGE code (in lieu of a CAGE code) in order to register in SAM.
eRA Commons - Applicants must have an active DUNS number and SAM registration in order to complete the eRA Commons registration. Organizations can register with the eRA Commons as they are working through their SAM or Grants.gov registration. eRA Commons requires organizations to identify at least one Signing Official (SO) and at least one Program Director/Principal Investigator (PD/PI) account in order to submit an application.
Grants.gov Applicants must have an active DUNS number and SAM registration in order to complete the Grants.gov registration.

Program Directors/Principal Investigators (PD(s)/PI(s))

All PD(s)/PI(s) must have an eRA Commons account and should work with their organizational officials to either create a new account or to affiliate an existing account with the applicant organization’s eRA Commons account. If the PD/PI is also the organizational Signing Official, they must have two distinct eRA Commons accounts, one for each role. Obtaining an eRA Commons account can take up to 2 weeks.

Eligible Individuals (Program Director/Principal Investigator)

Any individual(s) with the skills, knowledge, and resources necessary to carry out the proposed research as the Program Director(s)/Principal Investigator(s) (PD(s)/PI(s)) is invited to work with his/her organization to develop an application for support. Individuals from underrepresented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH support.

For institutions/organizations proposing multiple PDs/PIs, visit the Multiple Program Director/Principal Investigator Policy and submission details in the Senior/Key Person Profile (Expanded) Component of the SF424 (R&R) Application Guide.

2. Cost Sharing

This FOA does not require cost sharing as defined in the NIH Grants Policy Statement.

3. Additional Information on Eligibility

Number of Applications

Applicant organizations may submit more than one application, provided that each application is scientifically distinct.

NIH will not accept any application that is essentially the same as one already reviewed within the past thirty-seven months (as described in the NIH Grants Policy Statement), except for submission:

To an RFA of an application that was submitted previously as an investigator-initiated application but not paid;
Of an investigator-initiated application that was originally submitted to an RFA but not paid; or
Of an application with a changed grant activity code.

Section IV. Application and Submission Information

1. Requesting an Application Package

Applicants must download the SF424 (R&R) application package associated with this funding opportunity using the Apply for Grant Electronically button in this FOA or following the directions provided at Grants.gov.

2. Content and Form of Application Submission

It is critical that applicants follow the instructions in the SF424 (R&R) Application Guide, except where instructed in this funding opportunity announcement to do otherwise. Conformance to the requirements in the Application Guide is required and strictly enforced. Applications that are out of compliance with these instructions may be delayed or not accepted for review.

For information on Application Submission and Receipt, visit Frequently Asked Questions Application Guide, Electronic Submission of Grant Applications.

Page Limitations

All page limitations described in the SF424 Application Guide and the Table of Page Limits must be followed.

Required and Optional Components

The forms package associated with this FOA includes all applicable components, required and optional. Please note that some components marked optional in the application package are required for submission of applications for this FOA. Follow all instructions in the SF424 (R&R) Application Guide to ensure you complete all appropriate optional components.

Instructions for Application Submission

The following section supplements the instructions found in the SF424 (R&R) Application Guide and should be used for preparing an application to this FOA.

SF424(R&R) Cover