Attachment 1 - HCR FISH Statement of Work.pdf

STATEMENT OF WORK

HCR FISH detection of cryptic RNAs

1. INTRODUCTION AND BACKGROUND

TDP-43 is an RNA-binding protein that plays a key regulatory role in ALS and FTD cases.

The field is currently able to detect and quantify TDP-43 pathology only by assessing brains post-mortem and attempts to directly measure TDP-43 in biofluids have not yet been successful.

The Inherited Neurodegenerative Disease Section (INDS) developed an ultra-sensitive modified smFISH technique to detect cryptic exons in proteins regulated by TDP-43 in fixed human mutated iPSC neurons. We hypothesize that brain-derived extracellular vesicles (EV) carry these cryptic exons and may serve as a reservoir of these biomarkers at distant body sites, such as within the cerebrospinal fluid (CSF) or the bloodstream. To this end, we plan to develop methods to detect EV-associated cryptic exons, first in iPSC neuron models and ultimately in CSF and blood samples.

The contractor shall assist in applying the ultra-sensitive platform technology for capture and imaging of single extracellular vesicles (EVs), as well as optimize smFISH technology developed by INDS.

2. SCOPE AND REQUIREMENTS

In the performance of the Tasks specified, the Contractor shall be responsible for properly protecting all information used, gathered, or developed as a result of the Statement of Work (SOW). The Contractor shall establish and implement appropriate administrative, technical, and physical safeguards to ensure the security and confidentiality of sensitive data, including personal protected identification.

To achieve our aim, the Contractor shall:

1. Manage the receiving of (up to 200) CSF samples, and provide safe storage at vendor’s facility, including keeping all samples at -80C and preventing repeated freeze/thaw cycles.

2. The contractor should provide a research fellow at 30% effort for 6 months per year and a research assistant at 100% effort for 12 months per year to perform the work associated with this contract.

3. Provide relevant protocols and material lists associated with the Government’s samples to the Inherited Neurodegenerative Disease Section.

4. Provide regular updates on processing of Government’s samples to ensure adequate progress is being made.

5. Provide the analyzed data in electronic form and associated summary reports as specified under “Reporting Requirements and Deliverables”.

3. WORK TO BE PERFORMED

Independently, and not as an agent of the US Government, the Contractor shall provide all necessary personnel, facilities, supplies and services (except for those to be furnished by the US Government as specified elsewhere in this contract) to perform the work required by this contract.

A. Apply methods to fix and permeabilize EVs for RNA labeling and imaging inside programmable microchannels. Optimize fixative selection and duration of fixation to improve sensitivity of cryptic exon detection.

B. Apply methods to detect EV-associated cryptic exons in STMN2 with fluorescent dye-conjugated RNA probes using iPS cell-derived neuron models with or without TDP-43 depletion via CRISPR inhibition. The primary modality for RNA detection is HCR FISH. Team will test combinations of single probes and multiple probes to identify parameters that result in the highest sensitivity of cryptic exon detection, ideally with co-detection of the native transcript for the CE gene.

Additional parameters to optimize include temperature at different steps of the procedures, durations of individual steps, washing parameters, and imaging parameters.

C. Apply these methods to detect the STMN2 cryptic exons in CSF samples from patients with ALS or FTD compared to age-matched control patients. These experiments will leverage methodological details that are defined in A and B, but will be adjusted as needed to improve sensitivity and specificity of CE detection in CSF. Initial optimizations will be performed on pooled samples from cases and controls.

D. Apply these methods to detect the STMN2 cryptic exons in plasma samples from patients with ALS or FTD compared to age-matched control patients. These experiments will leverage methodological details that are defined in A and B, but will be adjusted as needed to improve sensitivity and specificity of CE detection in CSF. Additional variables to test include optimization of EV capture, including the use of antibodies that enrich/select for CNS-derived EVs. Initial optimizations will be performed on pooled samples from cases and controls.

E. Based on the results of the initial 200 CSF samples, an additional 100 samples may need to be analyzed in the same fashion as the original 200.

4. ANTICIPATED PERIOD OF PERFORMANCE

The anticipated period of performance consists of a base year with one 12-month option period as follows:

Base year: 4/29/2024 – 4/28/2025 Option Period 1: 4/29/2025 – 4/28/2026

5. REPORTING REQUIREMENTS AND DELIVERABLES

A. Reports

The contractor shall prepare and submit an annual progress report detailing updates on each phase of the project outlined in the “Work to be Performed” above. All reports shall be submitted electronically either as a Word document of PDF file or Excel file, as appropriate.

6. DATA MANAGEMENT SYSTEM

Vendor shall transfer the data to Government via Google Cloud.

7. SECTION 508 REQUIREMENTS

This language is applicable to Statements of Work (SOW) or Performance Work Statements (PWS) generated by the Department of Health and Human Services (HHS) that require a contractor or consultant to (1) produce content in any format that could be placed on a Department-owned or Department-funded Web site; or (2) write, create or produce any communications materials intended for public or internal use; to include reports, documents, charts, posters, presentations (such as Microsoft PowerPoint) or video material that could be placed on a Department-owned or Department-funded Web site.

Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. 794d) requires Federal agencies to purchase electronic and information technologies (EIT) that meet specific accessibility standards. This law helps to ensure that federal employees with disabilities have access to, and use of, the information and data they need to do their jobs. Furthermore, this law ensures that members of the public with disabilities have the ability to access government information and services.

There are three regulations addressing the requirements detailed in Section 508. The Section 508 technical and functional standards are codified at 36 CFR Part 1194 and may be accessed through the Access Board’s Web site at http://www.access-board.gov. The second regulation issued to implement Section 508 is the Federal Acquisition Regulation (FAR). FAR Part 39.2 requires that agency acquisitions of Electronic and Information Technology (EIT) comply with the Access Board’s standards. The entire FAR is found at Chapter 1 of the Code of Federal Register (CFR) Title 48, located at http://www.acquisition.gov. The FAR rule implementing Section 508 can be found at http://www.section508.gov. The third applicable regulation is the HHS Acquisition Regulation (HHSAR).

Regardless of format, all Web content or communications materials produced for publication on or delivery via HHS Web sites - including text, audio or video - must conform to applicable Section 508 standards to allow federal employees and members of the public with disabilities to access information that is comparable to information provided to persons without disabilities. All contractors (including subcontractors1) or consultants responsible for preparing or posting content intended for use on an HHS-funded or HHS-managed Web site must comply with applicable Section 508 accessibility http://www.access-board.gov/ http://www.acquisition.gov/ http://www.section508.gov/ standards, and where applicable, those set forth in the referenced policy or standards documents below. Remediation of any materials that do not comply with the applicable provisions of 36 CFR Part 1194 as set forth in the SOW or PWS, shall be the responsibility of the contractor or consultant retained to produce the Web-suitable content or communications material.

The following Section 508 provisions apply to the content or communications material identified in this SOW:

•36 CFR 1194.21 (all)

References:

1)HHS Policy for Section 508 Electronic and Information Technology (E&IT) (January2005): http://www.hhs.gov/od/Final_Section_508_Policy.html

2)HHS Section 508 Web site: http://508.hhs.gov/

3)HHS ASPA Web Communications Division Web site:

http://www.hhs.gov/web/policies/index.html

4)US General Services Administration (GSA) Section 508 Web site:

http://www.section508.gov/index.cfm http://www.hhs.gov/od/Final_Section_508_Policy.html http://508.hhs.gov/ http://www.hhs.gov/web/policies/index.html http://www.section508.gov/index.cfm