Genetic Analysis in Blood and Tumor Samples From Patients With Advanced or Metastatic Estrogen Receptor Positive and HER2 Negative Breast Cancer Receiving Palbociclib and Endocrine Therapy

PRIMARY OBJECTIVES:

I. Identify novel genomic variants and pathways associated with early progression
(progression within 12 months) among women with advanced hormone positive breast cancer
treated with palbociclib and endocrine therapy.

SECONDARY OBJECTIVES:

I. To assess whether time to progression differs with respect to SNAIL expression and other
markers of EMT.

II. To assess whether time to progression differs with respect to genetic alterations known
to be associated with endocrine monotherapy resistance (e.g. ESR1 mutations/fusions, AKT,
HER2, estrogen receptor [ER]alpha, etc.).

III. To tabulate the number of patients who have targetable mutations found in the baseline
tumor and assess their subsequent treatment regimen following progression on palbociclib and
endocrine therapy.

IV. To assess whether time to progression differs with respect to biomarkers associated with
the CD44high/CD24/low/ERlow cancer stem cell-like phenotype, ERalpha downregulation and
resistance to endocrine therapy and palbociclib [expression of total and phosphorylated
AURKA, breast cancer stemness biomarkers (CD44, CD24, ALDH1) EMT transcription factors
(SMAD5, SOX2), cyclin E, cyclin A and phosphorylated retinoblastoma (Rb)].

V. To generate patient derived xenograft (PDX)s from the baseline tumor biopsy (Rochester
only) test novel endocrine therapy combinations in PDXs generated from the baseline tumor
biopsy.

TERTIARY OBJECTIVES:

I. To compare and contrast the spectrum of ESR1 mutations identified in tissue, circulating
cell free deoxyribonucleic acid (DNA) (cfDNA), and circulating tumor cell (CTC) derived DNA.

II. To compare and contrast the actionable genomic alterations found in cfDNA or CTC derived
DNA that are not found in tumor tissue.

III. To assess whether genetic alterations known to be associated with endocrine monotherapy
resistance is seen in cfDNA and CTC derived DNA.

IV. To examine shifts in the populations of epithelial like CTCs and stem cell like CTCs
during the course of endocrine therapy with palbociclib.

V. To assess CTC expression of ER, HER2, and other markers of endocrine resistance.

VI. To explore the proteomics of ER-positive breast cancer and identify biomarkers associated
with early progression and neutropenia.

OUTLINE:

Patients undergo collection of blood at baseline and on day 1 of each treatment cycle.
Patients also undergo tumor biopsy at baseline and 2 months. Biopsy samples are analyzed for
genetic profile via next generation sequencing and ribonucleic acid (RNA) sequencing. Biopsy
samples are also used for the generation of xenograft mice model.

After completion of study, patients are followed up for 3 years.

Inclusion Criteria:

- PRE-REGISTRATION INCLUSION CRITERIA

- Women who have disease that is amenable to biopsy and agree to undergo a standard of
care core biopsy of recurrent or metastatic breast cancer, and to collect additional
core samples for research purposes

- Patients must satisfy one of the following criteria for prior therapy:

- First line setting: No prior endocrine therapy in the metastatic setting with no
more than one prior line of chemotherapy in the advanced/metastatic setting

- Second line setting: Progression on one prior line of endocrine based therapy
monotherapy either in the adjuvant or advanced/metastatic setting. Either one or
two prior lines of chemotherapy in the advanced setting are allowed

- Note: Patients receiving bisphosphonate or denosumab therapy prior to
registration may continue at the same intervals used prior to study registration

- First line therapy setting only: Palbociclib and letrozole is recommended for locally
advanced or metastatic breast cancer

- Second line therapy setting only: Palbociclib and fulvestrant is recommended (after
progression on first line endocrine therapy) for metastatic breast cancer

- Measurable disease as defined by Response Evaluation Criteria in Solid Tumors (RECIST)
criteria or bone only disease are eligible.

- Note: Those patients with both non-measurable disease and bone metastases are
eligible

- Note: Patients are not allowed to begin a new systemic anti-cancer therapy during
pre-registration with the exception of bisphosphonate or denosumab; palliative
radiation is allowed during pre-registration

- No current evidence of visceral crisis or lymphangitic spread

- History of central nervous system metastasis are allowed provided they have been
treated (i.e., surgery, radiation, and/or radiosurgery) =< 12 weeks prior to
registration and have stable neurologic function, including no requirement for
medication(s) to control symptoms for at least 2 weeks; Note: patients with known
leptomeningeal disease are not eligible

- Women who are premenopausal must agree to begin or continue an LHRH agonist (goserelin
preferred)

- NOTE: A woman is considered premenopausal if menses has occurred in the last 12
months prior to preregistration and both serum and follicle stimulating hormone
(FSH) levels are not in the laboratory?s reference range for postmenopausal
females

- Eastern Cooperative Oncology Group (ECOG) performance status: 0, 1, or 2

- Able to swallow oral formulation of drugs

- Signed and dated informed consent document for study participation

- Willing to submit tissue for required correlative research

- REGISTRATION INCLUSION CRITERIA

- Histologic confirmation from the pre-registration biopsy of either locally advanced or
metastatic breast cancer that is ER-positive and HER2 -negative

- Note: ER-positive disease is defined as >= 10% nuclear staining; HER2-negative
disease per 2013 American Society of Clinical Oncology/College of American
Pathologists (ASCO/CAP) guidelines, one of the following must apply:

- 0 or 1+ by immunohistochemistry (IHC) and not amplified by in situ
hybridization (ISH)

- 0 or 1+ by IHC and ISH not done

- 2+ by IHC and not amplified by ISH or

- IHC not done and not amplified by ISH

- Absolute neutrophil count (ANC) >= 1500/mm^3

- Platelet count >= 100,000/mm^3

- Hemoglobin >= 9.0 g/dL

- Total bilirubin =< 1.5 x upper limit of normal (ULN), (=< 3 x ULN if Gilbert?s
disease)

- Aspartate transaminase (AST) =< 3 x ULN (=< 5 x ULN if liver metastases present)

- Creatinine =< 1.5 x ULN

- Willing to return to enrolling institution for follow-up (during the active monitoring
phase of the study)

- Recovered from all toxicities from all prior anticancer therapies

Exclusion Criteria:

- PRE-REGISTRATION EXCLUSION CRITERIA

- History of metastatic ER negative or HER2 positive breast cancer

- Prior treatment in the metastatic setting with everolimus, or any agent whose
mechanism of action is to inhibit the PI3K-mTOR pathway

- Uncontrolled intercurrent illness including, but not limited to:

- Ongoing or active infection

- Symptomatic congestive heart failure

- Unstable angina pectoris

- Uncontrolled symptomatic cardiac arrhythmia

- Uncontrolled hypertension (defined as blood pressure > 160/90)

- Other active second malignancy other than non-melanoma skin cancers =< 3 years of
pre-registration; Note: a second malignancy is not considered active if all treatment
for that malignancy is completed and the patient has been disease-free for =< 3 years
prior to pre-registration

- Prior hematopoietic stem cell or bone marrow transplantation =< 3 years of
pre-registration

- Known hypersensitivity to palbociclib, letrozole, fulvestrant, goserelin (if
applicable) or to any of their excipients

- Known to be pregnant and planning to continue nursing

- REGISTRATION EXCLUSION CRITERIA

- No tumor identified on biopsy or insufficient tumor cells to obtain ER or HER2 status

- Any of the following therapies prior to registration:

- Chemotherapy =< 2 weeks

- Immunotherapy =< 2 weeks

- Biologic therapy =< 2 weeks

- Monoclonal antibodies =< 2 weeks

- Radiation therapy =< 2 weeks

- Anti HER2 or other ?targeted? therapy =< 2 weeks

- The following patients are not eligible

- Pregnant women

- Nursing women

- Women of childbearing potential who are unwilling to employ adequate
contraception