Special_Notice_FBO_75N91019Q00063.pdf

Document Title: The Creation of Breast Cancer Organoids for Preclinical Testing of Tumor Necrosis Factor Related Apoptosis Inducing Ligand (TRAIL).

Document Type: Special Notice

Solicitation Number: 75N91019Q00063

Proposed Posted Date: July 12, 2019

Proposed Response Date: July 26, 2019

Classification Code: Q3 – Lab Testing Service

NAICS Code: 621511 – Medical Laboratories

Business Size Standard: $32.5 Million

Contracting Office Address

Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Room 1E126, Bethesda, MD

20852, UNITED STATES.

Description

The National Cancer Institute (NCI), Center for Cancer Research (CCR), Womens Malignancies Branch (WMB) plans to procure on a sole source basis the testing of Tumor Necrosis Factor Related Apoptosis Inducing Ligand (TRAIL) agonists on a panel of human derived breast cancer organoids from Tempus Labs, Inc., 600 W. Chicago Avenue, Suite 510, Chicago, IL 60654- 2282.

This acquisition will be processed in accordance with simplified acquisition procedures as stated in FAR Part 13.106-1(b)(1) and is exempt from the requirements of FAR part 6.

Only one award will be made as a result of this solicitation. This will be awarded as a severable firm fixed price type contract.

The services acquired under this contract are severable services. Funds are only available for use for the contract line item (CLIN) to which they are obligated. Unused funds from one CLIN may not rollover for use in other periods.

The North American Industry Classification System code is 621511 and the business size standard $32.5 Million.

The anticipated period of performance shall consist of a base period of 12 months, plus two (2) 12-month option periods as follows:

Base Period: August 5, 2019 – August 4, 2020 Option Period One: August 5, 2020 – August 4, 2021 Option Period Two: August 5, 2021 – August 4, 2022

It has been determined there are no opportunities to acquire green products or services for this procurement.

1.0 BACKGROUND

The Women's Malignancies Branch (WMB) conducts basic, translational and clinical research on the mechanisms of cancer with emphasis on those that only or primarily affect females such as breast and ovarian cancer. Research in the laboratories of the Branch covers subjects including growth factor receptor signaling, cell survival and the induction of apoptosis, metastasis, and DNA repair and cell cycle check points. The research links basic and translational experimental cancer biology and clinical investigation.

A major goal of the NCI, Women’s Malignancies Branch (WMB) laboratory is to develop Tumor Necrosis Factor Related Apoptosis Inducing Ligand (TRAIL)-receptor targeted therapies for breast cancer. The NCI has studied TRAIL for several years, both in the lab and the clinic, and have made great strides. The NCI has shown that Triple Negative Breast Cancer (TNBC) with mesenchymal features are the most sensitive to TRAIL-mediated apoptosis and that both chemotherapeutic drugs and pathway-targeted drugs can enhance TRAIL-mediated killing of breast and ovarian cancer cells. More recently, the NCI has demonstrated that a high potency TRAIL agonist (MEDI3039) can kill orthotopic xenografts and prevent metastatic outgrowths in mice from a mesenchymal TNBC cell line. Yearly, the goal is to closely relate the work in the lab to the clinical setting in order to achieve better outcomes for patients.

2.0 OBJECTIVE

The NCI’s objective is to be able to generalize laboratory findings to patient samples and confirm observations using data base of analyzed patient samples. The NCI wants to be able to test TRAIL agonists on a panel of human derived breast cancer organoids developed by the Contractor. The NCI wants to look at the comparison of the genomics of TRAIL sensitive and resistant organoids directly to patient samples in a data base. In order to do this, the NCI needs a reliable source of data on human patient samples for comparison provided by the Contractor.

3.0 SCOPE

Specific Aim 1: Create a panel of breast cancer organoids and characterize the genome and transcriptome.

In collaboration with the Contractor, tissue from breast cancer patients seen at the NCI Women’s Malignancies Branch (WMB) at the Center for Cancer Research or a source provided by the

Contractor, will be used to create breast cancer organoids. The organoids will undergo genome panel and transcriptome sequencing, using the same methods performed on patient samples.

Specific Aim 2: Test the sensitivity of the organoids to TRAIL ligands. Once a library of organoids representative of the different breast cancer subtypes is created by the Contractor, the ability of TRAIL ligands to kill the organoids will be tested. This will allow the NCI to test across a breast cancer representative panel of organoids much more rapidly and broadly than intended with patient derived xenografts. Once sensitivity/resistance to TRAIL ligands is established, the genomic, transcriptomic, and clinical features of the organoids that are sensitive or resistant to TRAIL can be compared to the broader database that the Contractor has developed on patient samples.

Ultimately, this information can be used to develop clinical trials of TRAIL ligands that target the patients that are most similar to the responsive organoids. The organoids will be shared with the laboratories in the WMB so that the NCI will have an ongoing repository of the organoid library for future experiments looking at developing other drug therapy; in addition to TRAIL and for other women’s malignancies in addition to breast cancer.

4.0 CONTRACTOR REQUIREMENTS

At the request of the NCI laboratory, the Contractor shall provide genomic sequencing of the organoids using the Tempus xT panel in addition to full transcriptome sequencing. The Contractor shall provide the NCI with all accumulated data and analysis as well as provide portions of the organoids created from the patient tissues.

4.1 The Contractor shall attempt to develop up to 50 Organoid Models/three-dimensional (3D) culture established from breast cancer biospecimen samples provided by the NCI or by other sites contributing to the Contractor’s biospecimen repository. For each successfully developed Organoid Model, the Contractor shall provide a frozen aliquot to the NCI Technical Point of Contact (TPC).

4.2 The Contractor shall provide screening of organoids with up to three TRAIL inhibitor drug candidates (in triplicate). For each Organoid Model, the Contractor shall provide the NCI with drug screening Organoid Screening Services and deliver the following reports:

4.2.1 Representative images of Organoid Model

4.2.2 Cell apoptosis results by Annexin V or equivalent assay and results interpretation

4.2.3 Cell proliferation results by MTS or equivalent assay and results interpretation

4.2.4 General project conclusions

4.3 For each Organoid Model, the Contractor shall provide genomic sequencing using the Tempus xT panel and full transcriptome sequencing. FASTQ, VCF or BAM files and mutational burden reports will be transferred via a secure website or server.

4.4 The Contractor shall provide genomic analysis of human tumors for clinical and research use.

4.5 The Contractor shall have extensive genomic and clinical data on each patient that is analyzed.

4.6 The Contractor shall create breast cancer organoids, 3D cultures derived directly from patient samples, that recapitulate the tumor phenotypes and are comprised of tumor cells, stromal cells, and immune cells, thereby more accurately reflecting tumor biology.

5.0 PLACE OF PERFORMANCE

All services including organoid development and genomic analysis shall be performed at the Contractor’s laboratory.

6.0 Report(s)/Deliverables and Delivery Schedule

DELIVERABLE DELIVERABLE DESCRIPTION / FORMAT

REQUIREMENTS DUE DATE

Successfully developed Organoid (Refer to Section 4.1)

Frozen aliquot of each successfully developed organoid delivered under proper storage conditions

At completion of all screening, which is every 6 months after date of award

Screening Service for Drug Candidates (Refer to Section 4.2)

Screening results of up to 3 drug candidates which will include images of organoid, apoptosis assays, proliferation assays, and project conclusions electronically delivered via secure website

Based on Successful organoid creations, which is every 6 months after date of award

Genomic Sequencing (Refer to Section 4.3)

Full Transcriptome sequencing for each organoid with BAM file and burden reports transferred via secure website.

Based on Successful organoid creations, which is every 6 months after date of award

All of the required deliverables are indicated in Section 4.0 above. The length of time for the creation of the organoid will vary from specimen to specimen as will the time necessary to produce and analyze all of the data. However, all reports from the required screenings will be delivered in a timely manner with respect to the work being performed. Electronic copies will be delivered to the NCI Technical Point of Contact (TPC).

7.0 Section 508 Compliance

Training material guidelines of the revised 508 Standards apply as follows:

E.205 Electronic Content

E205.3 Agency Official Communication. Electronic content that is not public facing shall conform to the accessibility requirements specified in E205.4 when such content constitutes official business and is communicated by an agency through one or more of the following:

A. An emergency notification;

B. An internal or external program or policy announcement;

C. A notice of benefits, program eligibility, employment opportunity, or personnel action;

D. A formal acknowledgement of receipt;

E. Educational or training materials; or F. Intranet content designed as a Web page.

EXCEPTION: Records maintained by the National Archives and Records Administration (NARA) pursuant to Federal recordkeeping statutes shall not be required to conform to the Revised 508 Standards unless public facing.

E205.4 Accessibility Standard. Electronic content shall conform to Level A and Level AA Success Criteria and Conformance Requirements in WCAG 2.0 (incorporated by reference, see 702.10.1).

See the details at https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-ict-refresh/final-rule/text-of-the-standards-and-guidelines#E205-content

Electronic and Information Technology Accessibility, Section 508 Compliance is applicable to this notice and the following information is provided to assist:

8.0 CLAUSES

FAR 52.217-8 Option to Extend Services (Nov 1999)

The Government may require continued performance of any services within the limits and at the rates specified in the contract. These rates may be adjusted only as a result of revisions to prevailing labor rates provided by the Secretary of Labor. The option provision may be exercised more than once, but the total extension of performance hereunder shall not exceed 6 months. The Contracting Officer may exercise the option by written notice to the Contractor within 30 days.

https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-ict-refresh/final-rule/text-of-the-standards-and-guidelines#E205-content https://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-ict-refresh/final-rule/text-of-the-standards-and-guidelines#E205-content

(End of Clause) FAR 52.217-9 Option of Extend the Term of the Contract (March 2000)

(a) The Government may extend the term of this contract by written notice to the Contractor within 30 days; provided that the Government gives the Contractor a preliminary written notice of its intent to extend at least 30 days before the contract expires. The preliminary notice does not commit the Government to an extension.

(b) If the Government exercises this option, the extended contract shall be considered to include this option clause.

(c) The total duration of this contract, including the exercise of any options under this clause, shall not exceed 36 months.

(End of clause)

This is not a solicitation for competitive quotations. However, if any interested parties, especially small businesses, believe they can meet the above requirement, they may submit a statement of capabilities. All information furnished must be in writing and must contain sufficient detail to allow the NCI to determine if it can meet the above unique specifications described herein. A copy of the capability statement must be received in the NCI Office of Acquisition on or before 10:00 AM EST on July 26, 2019. All questions must be in writing and emailed to Kathy Elliott, Contract Specialist at Elliottk@mail.nih.gov. A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. In order to receive an award, contractors must have valid registration and certification on Sam.gov, www.sam.gov. No collect calls will be accepted. Please reference solicitation number 75N91019Q00063 on all correspondence.