NHLBI Clinical Proteomics Programs

NHLBI Clinical Proteomics Programs

This Request for Application (RFA) will establish Clinical Proteomics Programs to promote systematic, comprehensive, large-scale validation of existing and new candidate protein markers that are appropriate for routine use in the diagnosis and management of heart, lung, blood, and sleep diseases. These programs will facilitate validation of protein panels that may be used to predict disease susceptibility or to assist in differential diagnosis, disease staging, selection of individualized therapies, or monitoring of treatment responses. In addition, this RFA seeks to establish a high quality education and skills development program to encourage and ensure that scientists develop competencies and expertise needed to address the complex, multifaceted challenges in clinical proteomics.

Heart, lung, blood, and sleep diseases are major causes of morbidity and mortality. Cardiovascular disease is the number one killer in the United States in both men and women, across all major racial groups and totals nearly one million deaths a year. Lung diseases such as chronic bronchitis, emphysema, asthma and other obstructive or interstitial conditions account for more than 230,000 deaths annually, placing an enormous burden on our healthcare system. Blood diseases such as venous thrombosis and pulmonary embolisms are causes of significant public health concern, as well. Sleep disorders and insufficient sleep represent severe health concerns for tens of millions of Americans.

Improving patient care through the use of protein markers is well established clinically. For example, the definition of heart attack, as well as the determination of the benefit derived from antithrombotic treatments, rests on serum troponin measurement. The detection of extremely small quantities of this protein identifies patients at high risk for adverse outcomes as well those that will derive greater benefit from antithrombotic and other interventional strategies. Assay of the B-type natriuretic peptide also contributes to standard clinical information in the diagnosis of congestive heart failure. Myeloperoxidase was recently shown to help in the diagnosis of atherosclerosis and acute coronary syndromes.

The predictive values, sensitivity, and specificity of many of the individual protein markers, currently in clinical use, could potentially be enhanced if analyzed and measured in a panel. Observational studies have shown that combining protein markers troponin I, C-reactive protein and B-type natriuretic peptide into panels can provide valuable information on stratifying risk for acute coronary syndromes. Panels of protein markers, appropriately validated, could facilitate better and earlier diagnosis, improve disease staging and selection of individual therapies and lead to more reliable monitoring of treatment responses, leading to substantial improvements in public health.

The application of proteomics in the clinical environment is limited due to a lack of knowledge regarding which proteins are most useful for analysis and how data are interpreted and represented. Important research needs include the identification of panels of protein markers that are likely to provide useful clinical information, design of practical assays for these panels, and validation of these panels and assays in well characterized populations of human subjects. The emergence of clinical proteomics promises major advances in disease management, provided that a continuous channel exists for translating protein discoveries into tangible clinical benefits.

The purpose of this RFA is to establish an infrastructure for research teams to validate protein panels and to measure multiple candidate markers accurately, for heart, lung, blood, and sleep diseases. The Clinical Proteomics Programs established for this purpose will design panels of candidate proteins for disease areas, develop high throughput analytic methods, assess the predictive value of these proteomic measurements using biological specimens and clinical data from existing study populations, and establish procedures and standards for quality control.

A major shortfall of clinical proteomics is the lack of a robust infrastructure for clinical candidate panel validation. Validation is necessary to confirm the relationship to the target disease in large numbers of patient samples and requires highly standardized protein measurement systems. The samples must be derived from well characterized sample sets with associated high-quality clinical information. The validation process provides the critical evidence necessary for translating protein knowledge into practices impacting public health. A significant opportunity now exists to enhance the validation stage and help translate protein discoveries into clinical practice. Many completed and ongoing clinical trials and epidemiologic studies have disease associated biological samples in addition to detailed clinical data. Leveraging this investment will enhance validation efforts.

Panels of protein markers in the following areas would represent appropriate topics for proposed projects. This list is not intended to be all-inclusive, and other topics should be considered. 1) Predict susceptibility to coronary artery disease or acute and chronic pulmonary disease; 2) Assess the severity and rate of progression of atherosclerosis or pulmonary disease; 3) Differential diagnosis for patients presenting with shortness of breath, chest pain or elevated blood pressure; 4) Detect occult myocardial infarction and sub-clinical cardiac disease and/or damage; 5) Select optimal, individualized medical management strategies; 6) Monitor therapeutic and adverse responses to antihypertensive drugs or drugs for asthma and other lung diseases such as inhaled corticosteroids, bronchodilators, and leukotrienes; 7) Identify early stages of pulmonary disease before significant pathogenesis has occurred; 8) Evaluate risk of thrombosis in individuals with a predisposition to cardiovascular disease or stroke; 9) Evaluate risk of bleeding and appropriate management strategies in patients with bleeding disorders–hemophilia, autoimmune blood disorders, von Willebrand disease; 10) Manage anticoagulation therapy in patients with thromboembolic disorders; 11) Identify markers for early diagnosis and prognosis of heart, lung, blood, and sleep disorders; 12) Develop tests to rapidly and accurately distinguish thromboembolic stroke from hemorrhagic stroke.

Projects outside the scope of this RFA will not be considered responsive and include: 1) Studies that do not address heart, lung, blood, or sleep disorders; 2) Studies that are focused on developing new proteomic technologies to identify’ protein markers 3) Proteomic discovery efforts.

We encourage inquiries concerning this RFA and welcome the opportunity to answer questions from potential applicants. It is highly recommended that prospective applicants contact program staff (please see the “Contact” section below) about proposed projects.

A Clinical Proteomics Program should be an identifiable organizational unit formed by a single institution or a consortium of” cooperating institutions. Each Clinical Proteomics Program must provide a multidisciplinary team structure, ensuring effective coordination and integration between the selection and validation components of the Program. The team should encompass multi-disciplinary expertise and should include proteomic researchers, bioengineers, clinical chemists, protein chemists, experts in biostatistics and bioinformatics, clinical investigators, and epidemiologists.

The marker selection process should focus on the design of protein marker panels that are most useful in clinical situations with under met needs. The team should primarily be responsible for prioritizing candidate protein markers and panels for validation. The selection component should actively develop candidate protein marker panels from a wide range of sources, such as proteomic discovery efforts, published reports, differential expression based research studies and in silico sequence-based predictions.

The use of biological samples obtained by minimally invasive methods (e.g., blood, sputum, and urine) is encouraged. Samples from ongoing studies can also be used provided appropriate Institutional Review Board ORB) amendments to existing protocols have been obtained.

Since quantitative measurements of candidate markers in large and well defined clinical samples is central to the validation effort, criteria for the selection of the source material as well as the criteria for validation of the candidate markers must be specified. Where possible, existing technology platforms should be explored as multiplexing tools during panel development. Efforts to minimize sample consumption are encouraged to ensure the maximum number of assays. Emphasis will be placed on development of panels with high predictive value, specificity, and sensitivity; development of flexible assay protocols to accommodate the inclusion of newly identified proteins into ongoing validation efforts; refinement and development of innovative biostatistical tools and methods for selection of protein marker panels and for increasing the diagnostic sensitivity and specificity; and assay development applicable to clinical settings.

The multidisciplinary team will also evaluate preanalytic issues, (including those relating to sample collection, storage, processing, and handling), and set criteria, standardize, and implement preanalytic protocols prior to validation. Each Clinical Proteomics Program should have access to characterized samples with well defined clinical data and the appropriate IRB approvals before funding. Furthermore, they should operate on an ‘open source’ model system, making the data, statistical and bioinformatic tools that are generated and developed in the programs, accessible to the public domain within a time period to be determined at the first meeting of the InterProgram Steering Committee.

An Inter-Program Steering Committee (with membership from all the programs) will be appointed and will have scientific management oversight and responsibility for developing communication, coordination and collaboration among the Programs. In addition, there will be an External Scientific Panel, advisory to the National Heart, Lung and Blood Institute (NHLBI) that will evaluate the progress of the Clinical Proteomics Programs.

In order to facilitate the functions that are common to each program, one of the programs will be selected to function as an Administrative Coordinating Center (ACC) for all the programs. Therefore, applicants must include as a separate section in their proposal, a description of an Administrative Coordinating Center that will be reviewed separately, independent of the scientific application. Specification for the ACC application can be found under the section, “Packaging the Clinical Proteomics Program Application”.

Each program is expected to develop mechanisms towards education of skills necessary for clinical proteomics. Full implementation of a nationwide effort in translational research for clinical proteomics requires availability of trained M.D., M.D. /Ph.D., and Ph.D. scientists. These individuals must be knowledgeable about the diverse aspects of clinical proteomics and able to integrate the translational and clinical concepts necessary for application to heart, lung, blood, and sleep diseases. One unique feature of the Clinical Proteomics Program is to function as a spring board for advancing education, at the National level, by establishing various mechanisms, such as specialized short courses, and ‘hands on’ programs that will focus on guiding graduate students, trainees, technical personnel, M.D./Ph.D. and Ph.D. scientists in translation research for clinical proteomics. Both Clinical Proteomics Program and NHLBI-supported investigators would be eligible for these educational opportunities.

This RFA will use the National Institutes of Health (NIH) cooperative agreement (U01) award mechanism. In the cooperative agreement mechanism, the Principal Investigator retains the primary responsibility and dominant role for planning, directing, and executing the proposed project, with NIH staff being substantially involved as a partner with the Principal Investigator, as described under the section “Cooperative Agreement Terms and Conditions of Award”

Prospective applicants are asked to submit a letter of intent that includes the following information: descriptive title of the proposed research; name, address, and telephone number of the Principal Investigator; names of other key personnel participating institutions; number and title of this RFA. 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 NHLBI staff to estimate the potential review workload and plan the review.

Applications must be prepared using the PHS 398 research grant application instructions and forms (rev. 5/2001). Applications must have a Dun and Bradstreet (D&B) Data Universal Numbering System (DUNS) number as the Universal Identifier when applying for federal grants or cooperative agreements. The DUNS number can be obtained by calling 866-705-5711 or through the web site at http://www. dunandbradstreet.com/. The DUNS number should be entered on line 11 of the face page of the PHS 398 form. The PHS 398 is available at http://grants.nih. gov/grants/funding/phs398/phs398.html in an interactive format. For further assistance contact GrantsInfo, 301-435-0714, email: GrantsInfo@nih.gov.

Each application to establish a Clinical Proteomics Program must be submitted as one application by a Clinical Proteomics Program Director, who will be responsible for organizing and maintaining effective integration and interaction of the program. A clear description of interaction among the various components, plans for communication, collaboration and sharing among investigators in the Clinical Proteomics Program should be included. The Clinical Proteomics Program Director should also indicate the mechanism for handling day-to-day administrative details, program, coordination, planning and evaluation. The director will be required to have a minimum of 25 percent level of effort, and the responsibility of oversight and coordination of all projects or components of the Program, whether or not they are at his/her institution. Each program should clearly outline its administrative and organizational structure.

Applications should include appropriate budget forms providing adequate budget justification with all applicable direct and facilities and administrative costs. Estimating of staffing needs, including principal investigator, other professional and support staff must be included. During the course of the project period, it is anticipated that technologies will improve and the proposed studies may change. Accordingly, it is expected that the principal investigators will be allowed adjustments in their scientific projects to accommodate such things. Budgets should include travel costs for Awardees Meetings and Inter-Program Steering Committee Meetings, as detailed under the section titled, “Special Requirements” along with statements indicating willingness to participate in these meetings and abide by its governance.

An educational component is another integral part of each Clinical Proteomics Program. A clear description of the efforts to educate and cross train across disciplines of clinical proteomics must be outlined, including the plans for developing short courses and ‘hands on’ programs. The process of selection and monitoring of candidates for these educational activities must be portrayed as well.

A separate section not exceeding 5 pages, detailing plans for an Administrative Coordination Center, should be included in each Clinical Proteomics Program application. This section should be placed following the section on the Research Plan. The Center will facilitate functions common to all the Clinical Proteomics Programs, coordinate meetings of the awardees, the Inter-Program Steering Committee and the External Advisory Panel, and manage a Clinical Proteomics Program intranet website. The Center will also be responsible for setting up the monthly conference calls of the Steering Committee. This section should also include separate budget justification pages fur the operation of the Administrative Coordination Center not to exceed 100,000 direct costs in any year. Applications should provide adequate budget justification with all applicable direct and facilities and administrative costs, including estimated costs associated with the travel of the External Advisory Panel (6-8 members). Estimation of staffing needs and communication costs must be included. The award will be subject to administrative review annually.

Applications not conforming to these guidelines will be considered unresponsive to this RFA and will be returned without further review.

The RFA label available in the PHS 398 (rev. 5/2001) application form must be affixed to the bottom of the face page of the application. Type the RFA number on the label. Failure to use this label could result in delayed processing of the application such that it may not reach the review committee in time for review. In addition, the RFA title and number must be typed on line 2 of the face page of the application form and the YES box must be marked. The RFA label is also available at: http://grants.nih.gov/ grants/funding/phs398/labels.pdf.

The Center for Scientific Review (CSR) will not accept any application in response to this RFA that is essentially the same as one currently pending initial review, unless the applicant withdraws the pending application. However, when a previously unfunded application, originally submitted as an investigator-initiated application, is to be submitted in response to an RFA, it is to be prepared as a new application. That is, the application for the RFA must not include an Introduction describing the changes and improvements made, and the text must not be marked to indicate the changes from the previous unfunded version of the application.

Letters of intent are due 17 September 2004. Applications are due 14 October 2004. The earliest anticipated start date is July 2005.

Contact: Pothur R Srinivas, Division of Heart and Vascular Diseases, NHLBI, 6701 Rockledge Drive, Rm 10188, Bethesda, MD 20892-0001 USA, 301-435-0550, fax: 301-480-2858, email: ps241q@nih.gov; Anne P. Clark, Chief, Review Branch, Division of Extramural Affairs, NHLBI, 6701 Rock]edge Drive, Rm 7214, MSC 7924, Bethesda, MD 20892-7924 USA, Bethesda, MD 20817 (for express/courier service), 301-435-0270, fax: 301-480-0730, e-mail: ac42y@nih.gov.

Reference: RFA No. RFA-HL-04-019

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