Frequently Asked Questions about DF/HCC Breast Data and Specimen Use

What is the DF/HCC Breast Users Committee?- What are the policies for DF/HCC Breast data and specimen use?

o Policies Publication Policies

What are the sources of DF/HCC Breast data and specimens for research?How do I submit a research proposal?How do I register for OncDRS?How do I create a project team on OncDRS?What are the different projects within the DF/HCC Breast SPORE grant?

The DF/HCC Breast Users Committee

Composition: The Breast Users Committee is the supervising body for use of the breast cancer data and/or specimens from the DF/HCC. The Users Committee will be composed of at least one member from each participating organization which includes Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Massachusetts General Hospital, representing the disciplines of pathology, surgery, and medical oncology, radiation oncology and biostatistics. Members will be appointed by the chairs with no pre-specified term limits. The current membership is presented below.

Purpose: The members of the DF/HCC Breast Users Committee are charged with reviewing the feasibility and scientific validity of proposed clinical and health services research and/or qualitative improvement (QI) projects and translational and laboratory-based projects using the specimens and clinical data available through DF/HCC research protocols which govern its collection.

Scope: All research using clinical data and/or biospecimens from breast cancer patients treated at any of the participating institutions must be reviewed by the Users Committee and is subject to a required annual renewal process for ongoing projects. Generally exempt from this scope are studies that are pre-specified in prospective therapeutic clinical trials. For example, use of archival tissue specimens for the purpose of assessing a pre-specified biomarker to determine eligibility into an IRB-approved clinical trial does not require additional Users Committee approval to proceed. In contrast, secondary use of clinical data and/or biospecimens from clinical trials not explicitly specified in the original IRB-approved protocol is subject to Users Committee review.

Policies: For DFCI/BWH, all biospecimens are banked in the DFCI/BWH tissue bank (Bank Director: Dr. Deborah Dillon). All requests for biospecimens housed within the DF/BWH tissue bank must be approved by the DF/HCC Breast Users Committee prior to release, as do requests for curated clinical data. If the samples need to be sent out of DFCI/BWH to another institution, a Material Transfer Agreement (MTA) will also need to be signed and approved by Office of General Counsel before clinical data and/or specimens are released. Researchers can

1

request de-identified tissue or blood samples and linked clinical data from the bank without obtaining additional IRB approval for the specific research question. Users must sign a data use agreement stating that the bank will not provide, and the user will not attempt to learn, the identity of the patients. Please note that there may be additional time and/or funding required depending on the scope of the tissue and/or clinical data request, and not all requests will be deemed feasible. If an identified data set (e.g. a data set that contains patient names, medical record numbers, etc) or a limited data set (e.g. a data set that contains dates of treatment) is requested, then DF/HCC IRB approval specific to the project must be obtained by the requesting researcher before release of clinical data or specimens. Consultation with the Co-Chairs of the Breast Data/Tissue Users Committee is available to researchers prior to IRB submission and during the IRB approval process. The Users Committee will require documentation of IRB approval (if needed) prior to release of tissue or clinical data. Administrative staff will maintain a flow sheet to follow the progress of each request and maintain contact with the investigators during the review process. The administrative staff forwards the proposal to all members of the Users Committee (detailed below) for review and comment.

For proposals for DFCI/BIDMC: All requests for biospecimens housed at DFCI/BIDMC must be approved by the DF/HCC Breast Users Committee prior to release, as do requests for curated clinical data. If the samples need to be sent out of DFCI/BIDMC to another institution, a Material Transfer Agreement (MTA) will also need to be signed and approved by Office of General Counsel before clinical data and/or specimens are released.

Publication and authorship policies:

Prior to abstract or manuscript submission, investigators should notify the Breast Users Committee for guidance regarding authorship and funding acknowledgements. In general, an investigator from each institution represented in the analysis of clinical data and/or specimens should be included in the authorship. In addition, for publications that include curated clinical data (i.e. from a cohort database), the PI/leaders of the relevant database should be included as an author(s). For publications including biospecimens, the bank director should generally be included as an author. For secondary use of an existing clinical trial’s clinical data or biospecimens, the trial PI should be included as an author. Failure to adhere to the publication policy may result in loss of privileges to access clinical data or biospecimens for research.

All manuscripts which include the use of bio-specimens or clinical data abstracted from Protocols 93-085, 09-204 and/or 05-246 should reach out to the Users Committee to discuss acknowledgements, as funding sources have varied over time. In particular, it is important that all manuscripts express acknowledgement of the contribution to the DF/HCC Breast SPORE: Specialized Program of Research Excellence (SPORE), An NCI funded program, Grant 1P50CA168504.

2

Research that has used tissue and/or blood samples collected under DF/HCC Protocol #05-246 should acknowledge:-Dana-Farber Harvard Cancer Center SPORE grant #P50CA168504. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health/NCI.-ACT-NOW Fund at Dana-Farber Cancer Institute

Depending on the samples and annotated clinical data required, the research may also need to acknowledge:-Breast Cancer Research Foundation-National Comprehensive Cancer Network Oncology Research Program (in collaboration with Pfizer Independent Grants for Learning & Change)-Fashion Footwear Association of New York-Friends of Dana-Farber Cancer Institute

Please check with the study PI (Nancy U. Lin, MD) prior to manuscript submission to confirm the correct acknowledgements are included.

DF/HCC Breast Users Committee Members (as of January 1, 2017)

CO-CHAIRSNANCY LIN, MD; DFCI

DEBORAH DILLON, MD; BWHLAURA COLLINS, MD; BIDMC

USERS COMMITTEE MEMBERSWILLIAM BARRY, PHD; DFCIJENNIFER BELLON, MD; DFCIMYLES BROWN, MD; DFCI

LEIF ELLISEN, MD PHD; MGHJUDY GARBER, MD, MPH; DFCIMEHRA GOLSHAN, MD; BWH

MICHAEL HASSETT, MD, MPH; DFCISTEVEN ISAKOFF, MD, PHD; MGH

TARI KING, MD; BWHIAN KROP, MD, PHD; DFCIBEVERLY MOY, MD; MGH

ANN PARTRIDGE, MD, MPHSTUART SCHNITT, MD; BIDMCBARBARA SMITH, MD; MGHNADINE TUNG, MD; BIDMC

3

ERIC WINER, MD; DFCIJULIA WONG, MD, DFCIJEAN ZHAO, PHD, DFCI

Proposals Involving Use of Oncomap/Oncopanel Data:

A smaller subset of the DFHCC Breast Users Committee will review all proposals involving use of Oncomap and/or Oncopanel data in breast cancer patients.

This committee is structured as follows:

Co-chairs: Nancy Lin, MD and Deborah Dillon, MD

Members:Eric Winer, MD

William Barry, PhDIan Krop, MD, PhD

Tari King, MD

Ad-hoc Members:Jennifer Bellon, MD (as needed for proposals involving local therapy questions)

Judy Garber, MD, MPH (as needed for germline genetics expertise)

FEE STRUCTURE: There may be fees associated with requests for clinical data, tissue/blood specimens and pathology services. Details will be sent upon approval of proposals. For outside tissue block requests, there are additional fees (including requests for BWH).

Sources of DF/HCC Breast Data and Specimens for Research

93-085: Project SHARE (Specimens Help All Research Efforts) Collection of Specimen and Clinical Data for Patients with Breast Cancer or High Risk for Breast Cancer Principal Investigator: Nancy Lin, MD/DFCI

Overall accrual: 22,487 as of March 1, 2017

Blood collection includes blood samples that are only drawn on those patients scheduled to have a blood draw for routine clinical purposes at a time period soon after patient consents.

4

Ten mL blood will be drawn into EDTA containing test tube, and whole blood will be aliquoted into cryovials. Five mL will be drawn into a blue topped tube. Plasma will be separated from cellular component by centrifugation and aliquoted into cryovials. Blood collection is catalogued in caTissue. Note not all patients have a blood sample drawn since patients may not come back to be treated. Only one blood sample per patient is collected and the timing of the blood collection is not based on timing before or after surgery, progression, or treatment switch.

Tissue collection are obtained only when a procedure is planned for clinical reasons and would normally be discarded following routine pathological procedures, mainly among patients with new diagnosis of primary breast cancer. Tissue collection will be catalogued in caTissue. Fresh/frozen tissue will be then be banked and stored under the Breast Tissue Bank under Dr. Deborah Dillon.

1997-2011 – No strict eligibility criteria for collection during this time period 700-800 breast cancer tumor samples from patients consented under 93-085 to

allow for linkage with detailed clinical annotation in CRIS data. Basic retrospective specimen-level annotation in caTissue ongoing and includes pathologic tumor size, number of positive lymph nodes, histologic grade, hormone receptor status, HER2 status

Approximately 750 anonymized samples collected under Partners #1148. For more information, contact Deborah Dillon directly.

2015-present- Eligibility criteria - >=1.5 cm and/or neoadjuvant chemotherapy patients with at

least >1.0 cm residual disease. 87 breast cancer tumors collected to date. Basic retrospective specimen-level annotation in caTissue ongoing and includes

pathologic tumor size, number of positive lymph nodes, histologic grade, hormone receptor status, HER2 status. Also includes whether specimen was obtained after neoadjuvant therapy and whether it is linked to a specific tissue collection sub-study (i.e. inflammatory breast cancer, clinical trial, etc.)

Can be linked to RedCAP data for detailed clinical annotation.

BOC Clinical Databases

Demographic, clinical and treatment data

1997-2012 Demographic, clinical, and treatment data of patients with newly diagnosed breast cancer and received some or all of their treatment for breast cancer at Dana-Farber Cancer

5

Institute and Massachusetts General Hospital from July 1997 to August 2012. Data was collected in the CRIS database.

4937 and 2590 patients at DFCI and MGH, respectively with data and follow-up up until 2012.

Data are collected in Clinical Research Information System (CRIS) database. The following clinical information will be collected on each study participant:

Demographic (age at initial dx, race/ethnicity) Primary breast cancer history: stage, histology, grade, hormone receptor status

and HER2 status Treatment history: adjuvant chemotherapy, adjuvant hormone therapy, adjuvant

radiation therapy Metastatic breast cancer history: date of recurrent or metastatic disease;

location; sites and dates of radiation therapy, dates of systemic therapy (lines of therapy and first and last does; response)

Please note that patients who had surgery and drug therapy elsewhere and subsequently were seen at DFCI for the first time after a diagnosis of metastatic breast cancer was made are NOT included in this database.

Follow-up data until 2012

2013 – 2015- No data collected during this time period

2016 – present - Collection of demographic, clinical and treatment data of patients with newly diagnosed breast cancer and underwent surgery at DF/BWCC as of January 1, 2016. Data is being collected in a RedCAP database.

The following clinical information will be collected on each study participant: Demographic (age at initial dx, race/ethnicity) Primary breast cancer history: stage, histology, grade, hormone receptor status

and HER2 status Treatment history: adjuvant chemotherapy, adjuvant hormone therapy, adjuvant

radiation therapy Metastatic breast cancer history: date of recurrent or metastatic disease Please note that patients who had surgery and drug therapy elsewhere and

subsequently were seen at DFCI for the first time after a diagnosis of metastatic breast cancer was made are NOT included in this database.

Long-term follow-up data

Table 1. Examples of patient inclusion within BOC clinical databases

Patient vignette 1997-2012 (CRIS) 2016- (RedCAP)

New diagnosis of stage I-III breast cancer, surgery at BWH, chemotherapy at DFCI

Yes Yes

6

New diagnosis of stage I-III breast cancer, surgery at MGH, chemotherapy at MGH

Yes No

New diagnosis of stage I-III breast cancer, surgery at outside hospital, chemotherapy at DFCI

Yes No

New diagnosis of stage I-III breast cancer, second opinion only, not treated at DFCI or MGH

No No

New diagnosis of stage I-III breast cancer, surgery at Faulkner Hospital, chemotherapy at DFCI

Yes Yes

New diagnosis of stage I-III breast cancer, surgery at Faulkner Hospital, no treatment at DFCI or BWH main campus

No Yes

New diagnosis of de novo metastatic breast cancer, treated at DFCI

Yes Yes

New diagnosis of recurrent metastatic breast cancer, previous treatment for stage II breast cancer at outside hospital

No No

Presenting for second opinion for second line therapy for metastatic breast cancer, consult only

No No

Presenting for second opinion for second line therapy for metastatic breast cancer (treated elsewhere prior), and subsequently transfers care to DFCI

No No

11-104: Profile - Research on Clinically Acquired Patient Material in CancerPrincipal Investigator – Bruce Johnson, MD

Overall Accrual: 594 - Oncomap testing, 1,130 - Oncopanel testingAccrual of patients with primary diagnosis of breast cancer: XX

11-104 (Profile) is the umbrella protocol for clinical data, tissue collection and genomic testing of tumors across DFCI, BWH, and Boston’s Children’s Hospital. Patients have been consented since 2011. There have been different versions of the assay used since 2011. The Oncomap assay was used from 8/01/2011 through the end of September 2013 from DFCI (adult and pediatric), BWH (Adults) and consult patients referred from other hospitals to DFCI and BWH are included. Three versions of OncoPanel tests are included in the database:OncoPanel Version 1 (v1) data includes patients sequenced between 6/26/2013 and 8/6/2014. Oncopanel v1 includes an initial 275 cancer genes and 91 introns across 30 genes for rearrangement detection. Implemented on August 7 of 2014, Version 2 of OncoPanel expands on the initial

7

version to include the exonic regions of an additional 25 genes associated with disease and drug response, intronic regions of an additional 4 genes, as well as other non-coding regions across several other genes. Version 3 of Oncopanel went live on October 4, 2016.

All DFCI patients are approached at registration for consent to the protocol. The consent rate, however, has varied and overall within breast cancer patients has been less than 50 percent. The Breast Oncology Center has prioritized approach and consent for 11-104 in patients with metastatic breast cancer on the clinical floors. Oncomap/Oncopanel testing has been ordered primarily on patients with metastatic breast cancer and the consent rate for these patients is higher, based on targeted consent efforts in the breast oncology clinic for these patients. In addition, it is important to note that because of the targeted metastatic population, analyses examining disease-free survival and recurrence rates are not be feasible in the breast cancer dataset.

As of Jan 1, 2017, a total of 594 patients have undergone Oncomap testing and a total of 1,130 patients have undergone Oncopanel testing. Of these, 321 patients had metastatic disease at the time of Oncomap testing, and 888 had metastatic disease at the time of Oncopanel testing. Please note that a mix of primary tumors and metastatic tumors were tested in those patients with metastatic breast cancer.

There are some non-curated clinical data elements that can be linked to Oncomap/Oncopanel results available in OncDRS (for example, age, race, sex, chemotherapy ordered within EPIC), however, detailed curated clinical data, including ER, PR, and HER2 status, and any information from outside records, are not available through OncDRS for breast cancer patients. Other data sources outlined in this document will need to be used to obtain this type of clinical data and use of this data requires formal collaboration with Dr. Eric Winer, Dr. Nancy Lin, and Dr. Deborah Dillon.

09-204: EMBRACE: Ending Metastatic Breast Cancer for EveryonePrincipal Investigator: Nancy Lin, MD/DFCI

Overall accrual: 1623 metastatic breast cancer patients

Demographic, clinical, and treatment data of patients with metastatic breast cancer enrolled in the study and have a baseline blood draw dating from January 8, 2010 to present. The study enrolls patients seen at least once at DFCI for a diagnosis of metastatic breast cancer and who consent to the study. In contrast to the 93-085 databases, patients seen as consults only and patients who received part or all of their treatment at outside institutions may be included in this study, if consented.

1074 patients with baseline data and 395 patients with follow-up data. Data is collected in INFORM electronic case report form. A plan to shift to a RedCAP

database will be implemented in early 2017.

8

The following clinical information will be collected on each study participant: Demographic (age at initial dx, race/ethnicity) Primary breast cancer history: stage, histology, grade, hormone receptor status

and HER2 status Treatment history: adjuvant chemotherapy, adjuvant hormone therapy, adjuvant

radiation therapy Metastatic breast cancer history: date of recurrent or metastatic disease;

hormone receptor and HER2 status; location; sites and dates of radiation therapy, dates of systemic therapy (lines of therapy and first and last dose)

RECIST response data is NOT available. Archival scans are also not collected nor catalogued prospectively.

Long-term follow-up data

Blood collection includes:

For all consented patients, blood is collected: At baseline: 10 mL into EDTA tube and 10 mL into CPT tube At time of first treatment switch: 10 mL into EDTA tube and 10 mL into CPT tube At 4 to 6 weeks after treatment switch: 10 mL into EDTA tube and 10 mL into

CPT tube In June 2015, all consented patients also had a blood sample at baseline and at each

progression event for the analysis of cfDNA (One 10 mL sample in CPT tube) and then blood draws every three months at time of clinical blood draws (Two 10 mL samples into EDTA-containing or CellSave tubes).

984 patients have completed their baseline draw, 336 participations have completed their first treatment switch draw, and then 278 patients have completed their 4-6 week after treatment switch draw.

Tissue collection: The consent includes permission to request archival tissue specimens for research purposes. At present, no on-site bank of stored archival specimens exists though there are discussions under way to create one.

05-246: Collection of Specimens and Clinical Data for Patients with Breast CancerPrincipal Investigator: Nancy Lin, MD/DFCI

Total accrual: 547 breast cancer patients

This study allows us to collect research specimens in the preoperative, neoadjuvant, and locally advanced and metastatic settings. If a patient has consented to the study, any patient with suspected and confirmed breast cancer at all stages of disease can consent to providing tissue samples by undergoing a research biopsy – either at the time of a clinical biopsy or independent

9

of the timing of a clinical biopsy. The study also allows for serial biopsies to be performed. Biopsy material is fresh-frozen.

In terms of blood collection, samples will be collected to match the time of biopsy for isolation of CTCs, germline DNA and cfDNA. Serial blood draws are available for a subset of patients.

In addition, there is a substudy under 05-246 as part of the Center for Cancer Precision Medicine (substudy being led by Dr. Nick Wagle) that is focused primarily on whole exome and transcriptome sequencing of tumor samples from patients with metastatic breast cancer. Tissue collection will undergo a different process that those consented under 05-246 (3-6 cores will be collected: 1 for clinical pathology (FFPE) to be used for H&E and clinical testing first and then once clinical testing is complete, Oncopanel; remaining cores will be frozen in OCT and if clinical testing is completed, remaining cores will be sent to the Broad Institute). In addition to the initial blood draw at time of biopsy, blood collection will also occur at time of first treatment switch, 4-6 weeks after treatment switch and at time of tumor progression and/or at regular three month intervals.

Blood Catalogue

The Users Committee maintains a catalogue of blood samples (whole blood, serum, plasma) collected from both industry-sponsored clinical trials (IST) and investigator-initiated/cohort studies within the breast oncology group. This information was compiled from CaTissue and the planned specimen collections and time points listed in the study protocols. We have also compiled the breast cancer sub-types, types of patients (i.e. menopausal or not), and setting (neoadjuvant, adjuvant, metastatic).

If you wish to use the archival blood samples for research questions, you may use this catalogue to get a sense of what is available for your research question. If you wish to access the samples, we recommend the following:

1. Reach out to the PI(s) of the relevant studies to evaluate whether a collaboration would be possible, the proposed question is feasible and of interest, and there is potentially sufficient leftover material for your proposed studies.

2. If the PI is in agreement, submit a research proposal through the DFHCC Breast Users Committee. The study PI must be listed as a co-investigator on the users committee application.

3. Whether or not your project will require submission of a separate IRB protocol will depend upon the exact language of the parent clinical trial consent form. The combination of the study PI and Users Committee chairs can guide you in navigating this question.

4. If the proposal is approved by the Users Committee and once necessary IRB clearances are in place, you may then work with the Director of the Bank and/or his/her delegates to access the samples.

10

06-169: Helping Ourselves, Helping Other: The Young Women’s Breast Cancer StudyPrincipal Investigator: Ann Partridge, MD, MPH/DFCI

Overall accrual (as of June 2016): 1302 young women (diagnosed age 40 or younger) with breast cancer

Study includes blood and tissue collection, medical record abstraction and serial questionnaires (women are surveyed every 6 months for the first 3 years after diagnosis, then yearly after for an additional 7 years). There are plans to continue the survey component of this study beyond the initial 10 years. Clinical and treatment data is abstracted via medical record review.

656 patients with baseline data fully extracted (extraction ongoing). Data is collected in a Microsoft Access database. Some survey data (year 7 is

manually entered by staff, years 8,9,10 can be accessed directly by the patient) is collected in Redcap (online survey portal)

The following clinical information is collected on each study participant: Demographic (age at initial dx, race/ethnicity) Primary breast cancer history: stage, histology, grade, hormone receptor status

and HER2 status Treatment history: (neo-)adjuvant chemotherapy, adjuvant hormone therapy,

surgical history Metastatic breast cancer history data is abstracted based on patient self-

reported survey data: date of recurrent or metastatic disease Long-term follow-up data

Blood collection includes:

For all consented and active patients (as of June 21, 2016, of the 1116 eligible, we have at least 1 sample from 91% of our patients. As of 6/21/16, 837 patients have completed their baseline draw, 984 patients have completed their 1 year draw, and 356 patients have completed their 4 year draw.). Blood is requested at the following time points:

At baseline (Enrollment to 9 months post-dx) 1 year from diagnosis (9 months to 2 years post-dx) 4 years from diagnosis (3.5 years to 5 years post-dx) If collected, 2 (10 mL) EDTA tubes are taken at each time point

10 mL tubes yield 6 cryovials 4(~2mL each) aliquots of whole blood 2(~2mL each) aliquots of plasma

*Note the above time ranges are guidelines. The protocol only specifies that blood will be requested at 3 different time points. There are some existing draws that were collected outside of these ranges.

11

Tissue collection: for all consented patients (98% of our cohort)we pursue the following: original H&E Stained slides from all specimens and tissue blocks stored in paraffin.Central pathology review and individuals with tumor blocks banked: As of June 28th, 2016, (867/68%) and 734/57%, respectively

11-035: Inflammatory Breast Cancer OutcomesPrincipal Investigator: Beth Overmoyer, MD, FACP/DFCI

Overall accrual: 372 inflammatory breast cancer patients

Demographic, clinical, and treatment data of patients with inflammatory breast cancer enrolled in the study. The study enrolls patients seen at least once at DFCI since 1997 for a diagnosis of IBC and who consent to 93-085. In contrast to the other 93-085 databases, patients seen as consults only and patients who received part or all of their treatment at outside institutions may be included in this study, if consented.

414 patients with retrospective data. Data is collected in RedCAP electronic case report form. The following clinical information will be collected on each study participant:

Demographic (age at initial dx, race/ethnicity, family history) Primary breast cancer history: stage, histology, grade, hormone receptor status

and HER2 status Initial presentation of IBC (symptoms and imaging studies) Treatment history: adjuvant chemotherapy, adjuvant hormone therapy, adjuvant

radiation therapy Longitudinal followup: date and sites of recurrent or metastatic disease;

hormone receptor and HER2 status; location; lines of systemic therapy Long-term follow-up data

12-156: Clinical and Pathological Correlation of Inflammatory Breast Cancer ImagingPrincipal Investigator: Eren Yeh, MD/DFCI, BWH

Overall accrual: 414 inflammatory breast cancer patients

This study reviews imaging data on the characteristics of inflammatory breast cancer patients treated at the Dana-Farber Cancer Institute. The study enrolls patients seen at least once at DFCI for a diagnosis of IBC, consent to 93-085, are included in 11-035 (the retrospective IBC database), and whose imaging is available through the DFCI/BWH radiologydigital imaging archives since 1997 as part of their routine clinical care. In contrast to the other 93-085 databases, patients seen as consults only and patients who received part or all of their treatment at outside institutions may be included in this study, if consented.

12

94-138/13-325: SEARCH: Hereditary and Other Risk Factors for CancerPrincipal Investigator: Judy Garber, MD, MPH/DFCI

Overall accrual: 6387 high risk patients

Demographic, clinical, family history information is collected on all participants. Participants meet one of the following eligibility requirements:

Known cancer susceptibility gene mutation Anyone having genetic testing for a known cancer susceptibility gene mutation Personal history of multiple primary cancers Personal or family history suggestive of inherited predisposition such as young age of

cancer diagnosis, multiple primary cancers, or rare growth/malignancies Members of a group known or suspected to have increased risk of cancer

Blood collection includes: For all consented patients, blood or saliva kit is collected:

o One time blood draw of 10 mL into EDTA tube and 5 mL into CPT tube oro One time saliva donation of 2 mL

Greater than 3672 patients have completed their specimen donation.

Tissue collection will soon include archival tissue to bank for future studies

10-458: ACT: Tissue Repository for Individuals at High Risk for CancerPrincipal Investigator: Judy Garber, MD, MPH/DFCI

Overall accrual: Greater than 283 high risk patients

Demographic, clinical, family history information is collected on all participants. Participants meet one of the following eligibility requirements:

Known cancer susceptibility gene mutation Anyone having genetic testing for a known cancer susceptibility gene mutation Personal history of multiple primary cancers Personal or family history suggestive of inherited predisposition such as young age of

cancer diagnosis, multiple primary cancers, or rare growth/malignancies Members of a group known or suspected to have increased risk of cancer

Tissue collection 2-4 fresh frozen blocks are collected per side. 186 patients have completed tissue collection.

Summary:

13

The following clinical information will be collected on each study participant (via the 09-204 database for patients who are consented to both studies. For patients who decline 09-204, the information is collected and stored in a separate file maintained by the study CRC).

Demographic (age at initial dx, race/ethnicity) Primary breast cancer history: stage, histology, grade, hormone receptor status

and HER2 status Treatment history: adjuvant chemotherapy, adjuvant hormone therapy, adjuvant

radiation therapy Metastatic breast cancer history: date of recurrent or metastatic disease;

location; sites and dates of radiation therapy, dates of systemic therapy (lines of therapy and first and last dose)

RECIST response data is NOT available. Archival scans are also not collected nor catalogued prospectively. Clinical response data is annotated when available as best response as ascertained by review of the medical record(e.g. Response, Stable Disease, Progressive Disease, Unevaluable, Unknown).

Long-term follow-up data

Data from OncDRSOn an institute-wide level, various types of data are also available through OncDRS (see below). The table below presents the type and source of data and the number of patients across DFCI that have data available through OncDRS. All OncDRS data is updated every two weeks and new data elements will be included over time. For more information on specific data elements, please refer to OncDRS Data Guide. Important note: ER, PR and HER2 data, as well as other curated data are not available through OncDRS. In addition, tumor registry data, particularly prior to 2016, do not include the majority of breast cancer patients seen at DFCI.

DFCI tumor registry data, particularly prior to 2016, do not include the majority of breast cancer patients seen at DFCI because the DFCI tumor registry included cases who were seen at DFCI for their first course of treatment. If breast cancer patients are seen and treated at either BWH or Faulkner Hospital prior to coming to DFCI, these patients are included in the other institutions’ Tumor Registries. Starting in 2016, the DFCI Tumor Registry began to include any patient seen at the DFCI at least 3 times to increase the numbers of newly diagnosed patients in the DFCI Tumor Registry.

Data Type Source(s) Approx Number Patients, 2/1/16 Approximate Number of Patients 2/23/2017

Demographics Epic 285,500 310,900Patient Vital Status

Epic, Cancer Registry 281,500 310,900

Visit Diagnosis Epic 246,600 269,400Cancer Registry

Cancer Registry 67,200 73,100

14

Diagnosis

Oncology Medications

Epic, Pre-Epic Pharmacy, Pre-Epic COE, Pre-Epic LMR

53,000 (not including Epic & LMR data)

105,100 (All Sources)

Oncology Treatment Plan

Epic, COE 39,600 ( not including Epic data)42,200 (All Sources)

Lab Results – Chemistry & Hematology

Sunquest Lab 118,500128,300

Encounters Epic 281,500 310,900OncoPanel Genetic Test Results from Tumor Specimens

CAMD 6,600

13,400

OncoMap Genetic Test Results from Tumor Specimens

CAMD 4,900

4,900

11-104 Protocol Consent

OnCore, Epic 62,50079,500

Protocol Registration OnCore 115,582 132,800

DF/HCC Breast Data and Specimen Use Policy

Scope: All publications using DF/HCC data and specimens must be based on research proposals that were approved or deemed exempt by the Users Committee. Examples of publications deemed exempt would be those resulting from prospective, DF/HCC IRB-approved therapeutic clinical trials. The process of submission, review and approval of research proposal are described below.

All proposals that require the use of curated data (for example, collected as part of 93-085 CRIS or REDCAP database, 09-204 metastatic database, or proposed secondary analysis previously unplanned as part of a therapeutic clinical trial) must also be approved by the relevant study PI, who will be a study collaborator.

All proposals for secondary use of clinical data or samples collected under an existing DF/HCC IRB-approved therapeutic clinical trial must also be approved by the relevant study PI.

15

Submission policy: Investigators within DF/HCC must submit a proposal form directly to the Breast Users Committee via email directly to the project manager or via OncDRS for access to data and/or specimens. Please see below for guidance as to whether to use the proposal form and/or OncDRS submission process. Investigators must come from an institution in which significant contribution is being made in terms of specimen and/or clinical data collection in order to submit a research proposal using that resource(s). Investigators that are external to DF/HCC must have an investigator (collaborator) that is a faculty member at DF/HCC to submit on his/her behalf. The project manager for the Users Committee will ensure distribution of the research proposal to the members of the Users Committee for review and comment via email. Members will reply with a decision whether to 1) approve, 2) reject; or 3) request revision and resubmission. The project manager will convey the decision and/or any questions from the Users Committee to the investigator, generally within 4 weeks after the proposal is distributed to members for review.

Approval policy: When making final approval of a research proposal, all efforts will be made to come to consensus. If needed, simple majority voting will be used and quorum will be at least half of all active Users Committee participants and 2 of the 3 co-chairs. Each of the co-chairs has veto power if a proposal has a major flaw and can re-route the proposal to the full Users Committee for additional consideration. Once approved by the committee and the DF/HCC IRB if required, the project manager will forward the investigator a letter stating the users’ committee final approval. The project manager then will work with the appropriate staff to identify and generate datasets and collection of specimens based on the cohort specifications. All approved research proposals are catalogued in the Breast Users Committee log for reference.

Annual Renewal Policy: As of March 2016, we have initiated a required annual review of previously approved projects.

The goals of an annual review are as follows: To receive a progress report on the projects that have been previously approved To understand how the specimens and/or data has been used in each project To determine whether any publications have been generated from each project To assess whether projects have been completed or are still on-going, and ongoing,

what the timeline is for completion.

The annual renewal form should be submitted to the project manager each year until the project is completed. An updated approval letter will be distributed upon re-review and approval by the Users Committee.

Grant Policy: Feasibility requestsIf an investigator is preparing a grant proposal, aggregate data and/or de-identified data to determine feasibility can be provided for the application, if available. We encourage

16

investigators to reach out in advance to the co-chairs of the Users Committee to determine whether the desired biospecimens/clinical data are available and the timeline for turnaround of a feasibility request. More details on this process can be found here.

Letters of supportUpon receipt of a brief synopsis, listing of specific aims, and if relevant enumeration of types and amount of tissue/blood/clinical data required for the proposed study, the Users Committee is able to provide a generic letter of support to investigators in good standing within DF/HCC, which outlines the relevant clinical data and biospecimens that could be available and indicates the process by which a concept is vetted by the Users Committee. A sample approval letter can be found here. The turnaround time for this letter is two weeks. Investigators who wish to attach a letter for a grant application with a firmer commitment (e.g. Users Committee ‘pre-approval’) must submit a full Users Committee application at least four weeks before the grant deadline.

Documentation of IRB ApprovalRecently, studies and/or proposals supported with NCI or DOD grant funding have required documentation of IRB approval and review of the grant proposal/application by the IRB. For studies using clinical data and/or specimens collected under any of the data sources outlined above, the aims of the study outlined in the grant proposal will need to be approved by the Users Committee and/or OHRS (depending on the nature of the study and need for identified data or not).

In terms of OHRS review, you may contact OHRS as to their requirements for reviewing the grant proposal to meet the NIH or DOD policies. In some circumstances, IRB approval of the data and tissue collection ‘umbrella protocol’ and documentation of approval through the Users Committee mechanism will fulfill NCI/DOD requirements. However, increasingly, granting agencies are requiring documentation of IRB review of the specific research proposal in the grant, even it is using de-identified samples and de-identified clinical data obtained from an IRB-approved ‘umbrella protocol’. Please also note that amendments to the existing cohort study protocols will not be submitted for each proposed individual grant proposal. Instead, investigators will need to submit a low-risk protocol application summarizing the proposed work to the DF/HCC IRB. Please refer to the OHRS website for details of submission and application templates for IRB review of low risk protocols.

How do I submit a research proposal?

Depending on the request type for clinical data and/or tissue, the submission of your research proposal to Users Committee (and IRB if applicable) will have different requirements.

17

Please refer to the section, “Do I need to submit through OncDRS, the Users committee, or both” for additional details.

Request Type for clinical data and/or specimens

OncDRS Request form

Users Committee (paper application)

IRB

Aggregate data (e.g. number of eligible patients with clinical data/specimens)

No, can either directly access OncDRS aggregate query tool or complete Clinical Research Data Request form.

No No

De-identified data for feasibility analysis

Yes NoMust agree not to publish or identify patients without Users Committee approval

No

De-identified clinical data

Yes, an option for DFCI based investigators, and replaces users committee paper application

Yes. (Note, if OncDRS is used, an additional paper application is not required)

No

Identified Retrospective data, discrete data elements

Yes, an option for DFCI based investigators, and replaces users committee paper application

Yes. (Note, if OncDRS is used, an additional paper application is not required)

Yes. Either complete OncDRS application which will then automatically route to IRB after users committee approval is granted (only available for DFCI-based investigators). Or, submit users committee application by email and a separate IRB protocol. http://www.dfhcc.harvard.edu/research/clinical-research-support/office-for-human-research-studies/oncpro/

Identified data (which may or may not require retrospective data), with plan for continued prospective data collection for additional data elements

No Yes Yes. Studies that intend to collect data from identified patients (for example, a prospective cohort study) require an IRB protocol and approval and cannot be submitted solely through OncDRS. Complete users committee application and complete “New Project Application: Research use of retrospective medical records or previously collected specimens.”

Any study requiring patient contact and/or prospective collection of new biospecimens, whether or not minimal risk

No Yes Yes

De-identified biospecimens

No Yes No

18

Identified biospecimens No Yes Yes. Studies that required identified biospecimens require an IRB approved protocol to specify the types of PHI and clinical data which will be collected and the individuals who will have access to PHI. In some cases, this can occur under an existing cohort or banking study, depending upon the research question and composition of the collaborating investigators.

Secondary use of de-identifiedProspective/Clinical Trial data or specimens

No Yes Depends. The consent form of the clinical trial will need to be reviewed to determine whether the proposed research falls within the boundaries of the consent language. If yes, then no additional IRB protocol is required. If no, then complete “New Project Application: Research use of retrospective medical records or previously collected specimens.”

Secondary use of identifiedProspective/Clinical Trial data or specimens

No Yes Yes. Complete users committee application and complete “New Project Application: Research use of retrospective medical records or previously collected specimens.” The exception to this is if the parent clinical trial is still open for data collection/analysis and the only individuals allowed access to PHI are listed as investigators with PHI access as part of the parent trial.

Aggregate patient data/specimens or de-identified data/specimens for feasibility study: If you are interested in obtaining aggregate patient data/specimens or de-identified data/specimens for feasibility study, you do not need Users Committee approval since data will be either provided in aggregate as a patient count or de-identified and will never be published. For data available in OncDRS – you can use the Aggregate Query Tool with OncDRS. For data that is not available in OncDRS (CRIS, caTissue, data from breast oncology cohort studies (e.g. 09-204, 05-246) or you need assistance with OncDRS, complete the Clinical Data Request Form. Once you wish to move ahead with the formal study, you will need to submit a full research proposal to the users’ committee.

Research project on deidentified data/specimens: If you are interested in obtaining deidentified data and/or specimens, you will need to submit a research proposal to the Users Committee for approval.

Research project on identified data (retrospective or prospective): If you are interested in obtaining identified retrospective data (e.g. chart review), you will need to submit a research proposal to the Users Committee for approval. In addition, the investigator will need to submit a protocol to the IRB for the study. Approval from the Users Committee is contingent on IRB approval. If you submit your proposal via OncDRS, you will also automatically be submitting the application to the IRB (OHRS). The review of your proposal by the IRB will be an ‘expedited review”, which will likely take 2-3 days. For prospective studies, it is required to complete “New Project Application: Prospective Collection of Human Material and/or Clinical Data for Research Purposes” found on the OHRS website.

Other types of proposals:

Operational and quality improvement data: If the goal is to examine operational, clinical or data quality improvement, with no intent to publish - you can just request a report using the following links:

19

a. For research operational tasks such as data quality on CRIS, research statistics or consenting reports - use this link: http://dfcionline.org/departments/informationsystems/clinres/coris/

b. For clinical operations tasks such as clinical operations management or clinical quality improvement use this link: http://dfcionline.org/managerstoolkit/dart/

Note on clinical trials: The Users Committee mechanism is not intended to be used for the implementation of clinical trials. If you are interested in starting a clinical trial, please refer to the OHRS website: http://www.dfhcc.harvard.edu/research/clinical-research-support/

Do I need to submit an application to OncDRS, Users Committee, or both?

Investigators outside of DFCI must submit all requests via the Users Committee application form (i.e. “paper form”), via email to the Users Committee administrator, Lauren Knelson: laurenp_knelson@dfci.harvard.edu.

OncDRS may be used to submit requests for clinical data projects in lieu of the “paper form”. This service is only available to DFCI investigators. The advantage of submission through OncDRS is that a single application serves as the document for both Users Committee and IRB review. Otherwise, investigators must submit an application to the Users Committee and a separate low risk protocol application to the IRB.

OncDRS applications may also be submitted for the following: Any study that includes use of Oncomap or Oncopanel data must be submitted through

OncDRS Investigators may also choose to submit proposals through OncDRS in order to gain

access to specific data elements. Whether or not a separate IRB protocol is also required depends upon the project (see Table above). Examples of OncDRS requests include but are not limited to:

o an identified list of all patients who received trastuzumab at DFCIo an identified list of all patients with a billing diagnosis of breast cancer seen at

DFCI over a specific time frame

Requests for use of archival biospecimens should be done through the “paper form”, as the paper application includes additional details regarding the types and quantities of biospecimens requested.

How do I register for OncDRS?

Staff Requester RegistrationTo sign up for a New User Account:At the SPARKS Web Portal Login screen, click the Register now! live link.

20

Enter your Partners username and password, and click Next.

Select your Institution, Department, and Appointment from the drop-down lists on the Registration page.

Read and accept the User Agreement

21

A confirmation message appears once your registration submission is successful. This may take a few moments. The confirmation message also states that you must be added to a project team by a Faculty Requester before you can start using the OncDRS applications.

Click OK to return to exit the registration page and return to the main OncDRS portal page.Once a Faculty Requester has added you to a project team, you can log in using your Partners credentials and use OncDRS applications as a member of a project team.

How do I create a Project Team on OncDRS?

1. Select ‘Manage Project Teams’ from the SPARKS>OncDRS menu

22

2. In the new window that appears, type in a new project team name in the box ‘Add New Project Team:’ at the bottom right of the screen and click ‘Add’ to create new team.

3. Click on the newly created team and a new window will appear. Team members can be added by typing in their last name and clicking on the search button (magnifying glass to the right). Click on the User ID name, the row will highlight blue. Click ‘Add’ and then ‘Save’. Team members can be added, activated, or deactivated at any time.

4. The new Project Team is now available for selection when running Aggregate Queries (See Aggregate Query Tool Instructions)

DF/HCC Breast SPORE Grant

1) Project #1- Androgens, androgen receptor signaling and breast carcinogenesis. Myles Brown, MD & Rulla Tamimi, ScD.

Specific aims: Aim 1. Evaluate the role of androgen and AR signaling in breast cancer risk in the NHS. Aim 2. Evaluate the role of androgens and AR signaling on breast cancer prognosis in the

NHS. Aim 3. Use breast cancer subtype specific AR-target gene sets to confirm AR signaling as

a predictor of prognosis in ER+ and ER-/HER2+ breast cancer in BIG-198 and NeoAlto.

2) Project #2- Overcoming Resistance to HER2-Directed Therapies for Breast Cancer. Thomas Roberts, PhD & Ian Krop, MD, PhD

Aim 1. To use genetically engineered mouse (GEM) models to evaluate PI3K-targeted treatment strategies for HER2+ breast cancer Aim 1A. To compare the effects of p110 isoform-specific and pan-PI3K inhibitors in

conjunction with HER2-directed therapy in GEM models of HER2 driven breast tumors.Aim 1B. To examine the response to HER2- and PI3K-targeted combination therapies of

HER2 tumors with concomitant PIK3CA mutations or PTEN loss.

23

Aim 2. To identify and test resistance mechanisms to HER2- and PI3K-targeted therapies in GEM modelsAim 2A. To test the ability of recently identified mechanisms of resistance to PI3K

inhibitors to block response to combinations of HER2 and PI3K targeted therapiesAim 2B. To identify genes capable of conferring resistance to HER2-targeted inhibition in

a GEM model

Aim 3. To evaluate the role of PI3K inhibition in conjunction with HER2-targeted therapy in patients with HER2+ breast cancer Aim 3A. To test the hypothesis that the addition of a PI3K inhibitor overcomes resistance

to preoperative pertuzumab/trastuzumab based therapy Aim 3B. To identify PI3K-dependent and PI3K-independent resistance pathways enriched

in residual tumors after preoperative HER2- and PI3K-directed therapyAim 3C. To assess PI3K-dependent and PI3K-independent pathways associated with

resistance to HER2- and/or PI3K-directed therapies in human breast cancer specimens.

3) Project #3- Novel Strategies to extend DNA Repair Therapies for Triple Negative Breast Cancer. Alan D’Andrea, MD & Judy Garber, MD, MPH

The overarching goal of the project is to utilize novel strategies to disrupt homologous recombination (HR) repair in BRCA-proficient triple-negative breast cancers (TNBC) in order to sensitize them to poly (ADP-ribose) polymerase (PARP) inhibition. The Project includes preclinical work in TNBC cell lines and patient-derived (PDX) models with ultimate translation to clinical trial.

Specific Aim 1. Evaluate the combination of a CDK1 inhibitor (dinaciclib) and a PARP inhibitor (veliparib/ABT-888) in the treatment of BRCA-proficient Triple Negative Breast Cancer

Specific Aim 2. Evaluate the combination of a PI3K inhibitor (BYL719) and a PARP inhibitor (olaparib) in the treatment of BRCA-proficient Triple Negative Breast Cancer (see modifications of original aims described below)

4) Project #4- BET bromodomain proteins as novel therapeutic targets in Triple Negative Breast Cancer. Kornelia Polyak, MD, PhD, Eric Winer, MD

Aim 1. To define and characterize the drug target and downstream targets of JQ1/BET bromodomain inhibitors in TNBCs.

Aim 1A. To identify key mediators of JQ1’s effects in TNBCs by global tagged-compound-binding assays (Chem-seq).

Aim 1B. To analyze the gene expression profiles of TNBCs following JQ1/BET bromodomain inhibitor treatment and after downregulation of BRD4 or other relevant bromodomain proteins.

Aim 1C. To perform ChIP-seq for BRD4 or other relevant bromodomain proteins in TNBC to identify JQ1/BET bromodomain inhibitor genomic targets.

24

Aim 1D. To integrate analysis of all genomic data to define major downstream mediators of response to JQ1/BET bromodomain inhibitors in TNBCs.

Aim 2. To conduct a clinical trial to test JQ1/ BET bromodomain inhibitors in TNBC patients.Aim 2A. To conduct a phase II trial of JQ1/BET bromodomain inhibitors in patients

with metastatic TNBC. The primary objective of the trial is to detect a signal of response to a bromodomain inhibitor in metastatic TNBC. Baseline, on treatment, and post-progression (in responding patients) tumor biopsies will be performed to facilitate mechanistic studies and the development of pharmacodynamic biomarkers and biomarkers predictive of clinical response.

Aim 2B. To analyze the expression of the targets of JQ1/BET bromodomain inhibitors in primary human breast tumor samples. We will analyze the expression of direct drug targets, critical downstream effectors, and predictors of response identified in Aim 1 by immunohistochemistry and multi-color immunofluorescence.

Aim 2C. To derive xenograft models from biopsies of patients enrolled in the clinical trial. These will be used to test hypotheses regarding biomarkers, targets, resistance mechanisms, and combination therapies.

Aim 3. To develop cell lines resistant to bromodomain inhibitors and characterize combination therapies to improve therapeutic responses and overcome acquired.

Aim 3A. To develop resistant cell lines. We will start with sensitive TNBC cell lines and develop resistant derivatives by prolonged growth in gradually increasing JQ1 concentrations in cell culture or xenograft-bearing mice.

Aim 3B. To investigate whether combining G2/M arrest inducing-drugs or targeted agents effective in TNBC with JQ1/BET bromodomain inhibitors leads to more efficient pre-clinical therapeutic responses.

SPORE Career Enhancement Program (CEP) & Developmental Research Program (DRP)

CEP Projects

Awarded 2016:Harnessing tumor associated macrophages for breast cancer therapyInvestigator: Jennifer Guerriero, PhD (DFCI)Aim 1: Test the hypothesis that TMP195 treatment enhances hormone and monoclonal antibody therapy in the MMTV-PyMT mouse model of breast cancer. Test the hypothesis that TMP195 treatment will enhance anti-estrogen therapy in the MMTV-PyMT mouse model of breast cancer. Test the hypothesis that TMP195 treatment will enhance anti-HER-2/neu monoclonal antibody therapy in the MMTV-PyMT mouse model of breast cancer. Aim 2: Test the hypothesis that TMP195-activated TAMs will benefit patients with triple negative breast cancer. Test the hypothesis that TMP195 induces tumor regression in a mouse model of triple negative breast cancer. Test the hypothesis that TMP195 will enhance PARP inhibitor therapy in a mouse model of triple negative breast cancer.

25

Breast cancer subtype specific risk prediction models to inform precision medicineapproaches to prevention and early detectionInvestigator: Anne Marie McCarthy, PhD (MGH)Existing breast cancer risk models do not consider tumor subtype and have limited predictive ability. Improving risk prediction models to estimate subtype specific risk using epidemiological, clinical, and imaging features could enable prediction of aggressive tumors and be used to guide more intensive prevention and screening strategies for women at high risk for poor prognosis cancers. Aim 1: Examine the relationship of epidemiologic risk factors and imaging features (e.g. breast density, mass characteristics, calcifications, asymmetry, architectural distortions) with aggressive breast cancer subtypes (TNBC, HER2+) among women undergoing routine screening mammography. Aim 2: Adapt existing breast cancer risk prediction models to generate subtype specific risk estimates.

Etiology and prevention of breast and ovarian cancersInvestigator: Megan Rice, ScD (MGH)Breast cancer is the most commonly diagnosed cancer among US women and is the leading cause of cancer death for women <45y of age. Pregnancy prior to age 35 confers a long-term protective effect against breast cancer, with a greater benefit for women who were younger at first birth. Despite the risk reduction, pregnancy is associated with a transient increase in breast cancer risk; the magnitude and duration of this increased risk is greater in older first-time mothers. Aim 1: Investigate the association between lifestyle factors related to inflammation, specifically sedentary behavior and a pro-inflammatory diet pattern, and risk of breast cancer diagnosed ≤10 years after childbirth. Secondarily, we will compare the strength of association between these factors and total breast cancer risk stratified by parity and time since childbirth in premenopausal women (i.e., nulliparous, ≤10 years, >10 years). Aim 2: Assess the relationship between aspirin and non-aspirin NSAIDs use and risk of breast cancer diagnosed ≤10 years after childbirth. Secondarily, we will compare the strength of the association between NSAIDs use and total breast cancer risk stratified by parity and time since childbirth in premenopausal women. Aim 3: Compare the expression of inflammation pathway markers in breast tumor tissue from women diagnosed ≤10 years since childbirth to tissue from those diagnosed >10 years since childbirth or to nulliparous women.

Awarded in 2015

Minority Supplement AwardInvestigator: Shawn Johnson, PhDThe goal of this project was to further characterize the ability of CDK12 inhibition to sensitize triple negative breast cancer (TNBC) models, both BRCA-wildtype and –mutated, to PARP inhibitors. Aim 1: Further elucidate the structural mechanism by which dinaciclib, a pan-CDK inhibitor, inhibits CDK12 with greater efficacy than other known CDK9 inhibitors. Aim 2: Improve in vivo pharmacodynamic assays for assessing homologous recombination (HR) in FFPE-samples. Specifically, the quantification of RAD51 foci induction in FFPE-samples from patient derived xenografts (PDX) models. Aim 3: Develop and characterize novel covalent

26

CDK12 inhibitors in collaboration with the Nathaneal Grey lab. Aim 4: Finalize and submit manuscript detailing combined CDK12/PARP inhibitor combination preclinical work.

Awarded in 2014

Integrative Subtype-Specific Prognostic Models for Precision Breast Cancer DiagnosticsInvestigator: Andrew H Beck, MD, PhD (BIDMC)We hypothesize that the expression of molecular signatures and morphologic phenotypes drive breast cancer progression in a subtype-specific manner. To discover morphologic phenotypes associated with breast cancer progression, we developed the Computational Pathologist (C-Path) system. To identify robust molecular signatures associated with breast cancer progression, we developed Significance Analysis of Prognostic Signatures (SAPS). In the current project, we will integrate the unique strengths of these methods and apply them to a large and well-annotated collection of breast cancer samples to build robust, biologically informative, data-driven tools for precision breast cancer diagnostics. The goal of this project is to identify morphological and molecular biomarkers of invasive breast cancer (IBC) prognosis in breast cancer molecular subtypes and to construct integrative subtype-specific prognostic models. Aim 1: To discover morphologic biomarkers associated with patient prognosis in breast cancer molecular subtypes. Aim 2: To validate subtype-specific prognostic expression biomarkers in breast cancer molecular subtypes. Aim 3: To build integrative subtype-specific prognostic models comprised of morphologic phenotypes, expression biomarkers, and host lifestyle factors to predict survival in breast cancer molecular subtypes.

Estrogen receptor mutations: the functional roles in endocrine resistance and potential as a therapeutic targetInvestigator: Rinath Jeselsohn, MD (DFCI)The estrogen receptor is a nuclear transcription factor that drives proliferation and growth of luminal type breast cancers and is the major target of hormone-based therapies for breast cancer. We have identified ESR1 mutations in up to 20% of metastatic endocrine resistant tumor samples. These mutations are all clustered in the ligand-binding domain and our functional studies indicate that these mutations confer constitutive activity and relative resistance to endocrine treatments. Aim 1: Establish stable cell lines and patient derived xenografts harboring the ESR1 mutations and determine the functional roles of the ER mutations in tumor growth, invasiveness, metastasis and endocrine resistance.Aim 2: Decipher the molecular mechanisms mediating the phenotype of the ESR1 mutations.Aim 3: Test the efficacy of estrogen receptor degraders combined with PI3K, CDK4/6 or HSP90 inhibitors to inhibit ESR1 mutational driven tumor growth in pre-clinical models.

Sapacitabine and Seleciclib in BRCA-Deficient Breast CancerInvestigator: Sara Tolaney MD, MPH (DFCI)The specific aims of our proposal focus on assessing homologous recombination (HR) proficiency in clinical samples of BRCA carrier patients enrolled to the sapacitabine/seliciclib

27

combination trial. Enrollment to this cohort has not yet begun, so we have not been able to begin work on either of the specific aims to date.Aim 1: Assess HR proficiency of tumor samples using the Myriad Genetics HR-deficiency (HRD) assayAim 2: Perform whole exome sequencing to determine the mutational signature of tumor samples

Assessing methods to improve the efficacy of PI3K inhibitors in PIK3CA mutated breast cancersInvestigator: Sadhna Vora, MD (MGH)The goal of this project is to improve the efficacy of PI3K inhibitors (PI3Ki) in breast cancers driven by the oncogenic mutation of the PIK3CA gene. Our preliminary data suggested that either mTORi or CDKi, when combined with PI3Ki, could overcome resistance to single agent PI3Ki. Our work over the first year of the grant term has focused more on CDK/PI3Ki than mTOR/PI3Ki due to findings from the clinic of toxicities associated with the mTOR/PI3Ki combination (notably hyperglycemia and gastrointestinal issues).Aim 1: In vivo studies of PI3K inhibition with either mTORC or CDK 4/6 inhibitors to determine which treatment strategy is a more effective initial PI3Ki based therapy.Aim 2: Perform pooled shRNA screen on de novo resistant established and patient derived PIK3CA cell lines.Aim 3: to assess patient samples for biomarkers of resistance to PI3K inhibitors.

Identifying resistance mechanisms in ER+ breast cancer by translational genomicsInvestigator: Nikhil Wagle, MD (DFCI)The goal of this research is to apply both comprehensive genomic profiling and systematic functional approaches to test the hypothesis that somatic genetic differences may contribute to endocrine-resistance in breast cancer.Aim 1: to conduct a near-genome scale lentiviral open reading frame (ORF) screen for genes whose overexpression is sufficient to confer resistance to anti-estrogen therapy in breast cancer cell lines.Aim 2: To perform comprehensive genomic characterization of pre-treatment and post-progression breast cancer samples obtained from patients who have developed resistance to hormonal therapy.

DRP Projects

Awarded in 2016

Award 8: Supramolecular nanotherapeutics for preferential immune modulation of the tumorMicroenvironmentInvestigator: Ashish Kulkarni, PhD (BWH)Aim 1: Use SNPs to switch immunosuppressive M2 to cytotoxic M1 macrophages, and study the effect inbreast cancer. Based on preliminary observations, we will (a) use a syngeneic immunocompetent 4T1 and an athymic MDAMB-231 TNBC xenograft murine model to test the efficacy of the SNP vs a CSFR1 antibody and small molecule inhibitors of CSF1R; and (b) dissect the mechanisms underlying the switch

28

from a M2 to an M1 subtype in response to SNP mediated sustained CSF1R inhibition; Aim 2: Test for synergy between the SNP and an immune checkpoint inhibitor in a breast cancer model. More specifically, we will test the hypothesis that a combination of a CSF1R-inhibiting SNP and an immune checkpoint inhibitor, administered in the right temporal sequence can result in an enhanced outcome in terms of survival.

Award 9: Rapid functional analysis of BRCA1 VUS alleles Investigator: Nicholas Willis, PhD (BIDMC)The project will test the hypothesis that Suppression of aberrant DSB repair contributes to BRCA1 tumor suppressor function. Aim1: Perform a genetic analysis of a panel of BRCA1 variants in HR repair and LTGC suppression. Survey the remaining BRCA1 VUS alleles for suppression of LTGC. Generate and test efficacy of RFP-SCR breast cancer HR reporter cell lines. Aim 2: Relate HR functions of VUS alleles to PARPi sensitivity and cisplatin sensitivity. Study the impact of BRCA1 variants in reversal of PARP inhibitor sensitivity of BRCA1 mutant cells.

Awarded in 2015

Complimenting BMN-673 with PD-1 Pathway Blockade to Improve Responses Against Brca1 -/- Breast CancerInvestigator: Michael Goldberg, PhD (DFCI)Immunotherapy can address refractory disease and represents an exciting approach to achieve durable responses. While the antitumor effects of conventional therapies – such as radiation and chemotherapy – are generally attributed to their cyotoxicity, their efficacy is at least partly attributable to their partial induction of antitumor immunity. Still, even immunotherapy has demonstrated only modest benefit against advanced breast cancer to date. A combination of cancer cell-intrinsic and -extrinsic interventions may be required to improve outcomes. The goal of this SPORE project is to confirm that combining the PARP1 inhibitor BMN-673 with anti-PD-1 or anti-PD-L1 will yield a synergistic antitumor response against breast tumors that exhibit impaired homologous recombination, a common feature of triple-negative breast cancer.We are the first to show that, BMN-673 has immunoregulatory effects, providing a mechanistic rationale for the proposed combination. We identified several immunoregulatory genes that are upregulated following treatment with BMN-673 and hypothesized that BMN-673 may influence the composition and function of immune cells in the tumor microenvironment. We confirmed that BMN-673 significantly increases the number of tumor-associated CD8+ T cells and NK cells as well as their production of IFN-γ and TNF-α. These data suggest that BMN-673 may therefore serve as an adjuvant therapy to immunotherapy in mice– and ultimately patients– whose tumors harbor defects in homologous recombination. To test this hypothesis, we will complete the following Aims: 1) confirm synergy between BMN-673 and anti-PD-1/PD-L1 in Brca1-/- breast tumors, and 2) define mechanism of cooperativity between PARP inhibition and PD-1 pathway checkpoint blockade. This project is well aligned with the scope, investigators, and project selection of the SPORE in Breast Cancer. The work is highly complementary to Project 3 (Novel Strategies to Extend DNA Repair Therapies for Triple-Negative Breast Cancer). If successful, the approach described herein could be replicated with inhibitors from Project 4 (BET Bromodomain Proteins as Novel Therapeutic Targets in Triple-Negative Breast Cancer). We will work with Core D (Tissue and Pathology Core) and hope to work with Core C (Clinical Trials Core).

Neutralization of BCL2/BCL-XL enhances the cytotoxicity of T-DM1 in vivo Investigator: Jason Zoeller, PhD (HMS)

29

Resistance to T-DM1 represents a major obstacle in the effective treatment. Using two PDX models of advanced HER2+ resistant disease, we obtained preliminary evidence demonstrating that blockade of BCL2/BCL-XL anti-apoptotic activity dramatically enhances the effectiveness of T-DM1. This proposal will characterize this combination treatment in additional models of advanced and/or metastatic HER2+ breast cancer, to address its effectiveness in distinct ER tumor subtypes, characterize the need for BCL2- and/or BCL-XL-specific inhibition, and assess tumor response at the primary and secondary sites. Such insight could inform a future clinical trial. Improving the initial cytotoxic effectiveness of T-DM1 may provide a therapeutic approach to reduce and/or eliminate drug resistance in the clinic. Aim 1. To evaluate the effectiveness of T-DM1 plus BCL2/BCL-XL inhibition across multiple models of HER2+ resistant disease. For T-DM1/ABT-263 in vivo experiments, PDX tumor fragments or cells will be transplanted into the mammary fat pad of female NOD/SCID mice. Mice with hormone receptor positive tumors will require sub-cutaneous implantation of a slow-release estrogen pellet. The BCL2/BCL-XL inhibitor ABT-263 will be administered, and pathological response will be determined via analysis of the H&E stained sections. Tumor cells will be visualized by HER2 IHC. Tumors will also be analyzed for markers of cell proliferation (Ki67) and cell death (cleaved caspase-3). Aim 2. To determine the effectiveness of combination T-DM1 plus BCL2- or BCL-XL-selective inhibitors. We will initiate these studies in HER2+ER- PDX12 and HER2+ER+ PDX5. Experiments will include eight treatment arms: (1) T-DM1, (2) BCL2/BCL-XL inhibitor ABT-263, (3) BCL2 inhibitor ABT-199, (4) BCL-XL inhibitor ABT-133, (5) T-DM1 + ABT-263, (6) T-DM1 + ABT-199, (7) T-DM1 + ABT-133 and (8) placebo controls. ABT-133 will be provided through collaboration with Abbvie. Blood and tumors will be collected and analyzed at the 14-day endpoint as described above.

Discovering how Phosphoinositide 3-Kinase (PI3K) regulates DNA synthesis and repair, and exploiting this dual function of PI3K to design combination treatments for triple-negative breast cancerInvestigator Gerburg Wulf, MD, PhDAim 1: Nucleoside synthesis downstream from PI3K is not regulated via AKT but via the Rac/PAK axis and ultimately regulation of glycolytic flux. PI3K directly coordinates glycolysis with cytoskeletal dynamics in an AKT-independent manner. Growth factors or insulin stimulate the PI3K-dependent activation of Rac, leading to disruption of the actin cytoskeleton, release of filamentous actin-bound aldolase A and an increase in aldolase activity. Consistently, PI3K-, but not AKT-, SGK- or mTOR-inhibitors, cause a significant decrease in glycolysis at the step catalyzed by aldolase, while activating PIK3CA mutations have the opposite effect.Aim 2: DNA damage induced by PI3K inhibitors is a consequence of impaired production of nucleotides needed for DNA synthesis and DNA repair. Inhibition of PI3K causes a reduction in all four nucleotide triphosphates, while inhibition of AKT is less effective than inhibition of PI3K in suppressing nucleotide synthesis and inducing DNA damage. Carbon flux studies reveal that PI3K-inhibition disproportionately affects the non-oxidative pentose phosphate pathway (non-ox PPP) that delivers ribose-5-posphate required for base ribosylation. In vivo in a mouse model of BRCA1-linked triple-negative breast cancer (K14-Cre BRCA1f/fp53f/f) the PI3K-inhibitor BKM120 led to a precipitous drop in DNA synthesis within 8 hours of drug treatment, while DNA synthesis in normal tissues was less affected. In this mouse model combined PI3K- and PARP-inhibition was superior to either agent alone to induce durable remissions of established tumors.

30

Awarded in 2014

Developing microRNA ‘signatures’ as biomarkers for optimal therapeutic use of PARP inhibitors in Triple Negative Breast Cancer (TNBC)Investigator: Dipanjan Chowdhury, Ph.D. (DFCI) Aim 1 is to assess the ability of SENSMiRNAs to abrogate HR-mediated DSB repair using two complementary assays which have been optimized in my laboratoryAim 2 is focused on understanding the mechanism by which these miRNAs influence HR, that is, identify HR pathway members that may be regulated by SENSMiRNAs.Aim is to assess the ability of SENSMiRNAs to enhance sensitivity to PARP inhibitors alone and in combination with CDK inhibitor in vitro in TNBC lines.Aim 4 is to assess whether expression of SENSMiRNAs are associated with response to PARPi/CDK inhibitor (Phase II trial, SPORE program) or with cisplatin (Phase II trial, Myriad Genetic Laboratories) in tumor specimens from TNBC patients.

Identifying Disseminated Triple Negative Breast Tumor Cells that are Responsible for Disease Relapse Investigator: Sandra S. McAllister, PhD (BWH)Aim 1 is to Identify disseminated tumor cells that respond to systemic signals to form overt lung metastasesAim 2 is to obtain molecular signatures of disseminated tumor cells before and after they form overt tumors.

Palbociclib in Breast Cancer: Resistance Mechanisms and Synthetic Lethality with NHEJ Inhibition Investigator: Geoffrey Shapiro, M.D., Ph.D. (DFCI)Aim 1: determine the mechanisms of resistance to the CD4/6 inhibitor palbociclib in breast cancer cell lines and investigate strategies to overcome resistanceAim 2: assess the combined inhibition of CDK4/6 and non-homologous end joining (NHEJ) in breast cancer cells

Elucidation of the role of MELK, a novel oncogenic kinase, in basal-like breast cancer Investigator: Jean Zhao, PhD (DFCI)Aim 1: To determine the mechanism(s) underlying the oncogenic role of MELK in basal-like breast cancer.Aim 2: To evaluate the role MELK in the tumorigenesis of basal-like breast cancer in a GEM model.Aim 3: To develop a GEM model of breast tumor driven by overexpression of MELK.

31