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
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
This research trial studies genetic profiles in blood and tumor samples from patients with
 estrogen receptor positive and HER2 negative breast cancer that has spread to other places in
 the body who are receiving palbociclib and endocrine therapy. Examining the genetic changes
 associated with the cancer and comparing the genetic material from the cancer tissue with the
 genetic material found in the blood may help doctors to develop customized treatment for
 breast cancer.
PRIMARY OBJECTIVES:

 I. To identify novel genomic variants and pathways associated with baseline, as well as the
 change in serum thymidine kinase (TK1) levels (measured pre-registration, after two cycles,
 and at disease progression) among women with advanced hormone receptor (HR) positive breast
 cancer treated with palbociclib and endocrine therapy (ET).

 SECONDARY OBJECTIVES:

 I. To generate patient derived xenograft (PDX)s and organoids from tumor biopsies obtained at
 pre-registration, at 2 months, and at disease progression, to test novel endocrine therapy
 combinations. (PDX Aim) II. To test whether PDX engraftment is associated with progression
 free survival. (PDX Aim) Sequencing Aims III. to describe changes in the genomic landscape of
 HR-positive HER2-negative advanced breast cancer by comparing sequencing data
 (deoxyribonucleic acid [DNA] and ribonucleic acid [RNA]) from preregistration archival breast
 primary tumors (when available), with tumor biopsies obtained preregistration, after two
 months on study, and at disease progression on palbociclib and ET.

 IV. To evaluate whether genomic variants and pathways (measured using DNA and RNA sequencing
 at pre-registration and after two months of treatment) are associated with 1) PFS; 2)
 baseline and changes in serum TK1. (Sequencing Aim) V. To tabulate the number of patients who
 have targetable mutations found in the preregistration tumor biopsy and to record their
 subsequent treatment regimen following progression on palbociclib and ET. (Sequencing Aim)
 VI. To compare and contrast the actionable genomic alterations found in cfDNA or CTC derived
 DNA that are not found in tumor tissue. (Sequencing Aim) VII. To assess whether genetic
 alterations known to be associated with endocrine monotherapy resistance are seen in
 circulating tumor- DNA (ctDNA) and circulating tumor cell (CTC) derived DNA. (Sequencing Aim)
 VIII.To determine whether use of a 3D micro cancer model, combined with sequencing data from
 tumor biopsies, ctDNA and PDXs collected at the time of disease progression, can be used to
 personalize future treatment options for PROMISE participants. (Sequencing Aim) IX. To
 compare the changes in Ki67 levels (by immunohistochemistry [IHC]) and serum TK1 levels after
 2 months of treatment. (Proliferative biomarker aim) X. To assess whether the change in Ki67
 and serum TK1 levels after 2 months of treatment with palbociclib and ET is associated with
 progression free survival (PFS) outcomes. (Proliferative biomarker aim) XI. To assess whether
 high baseline serum TK1 levels (> 200 Du/L) are associated with PFS outcomes. (Proliferative
 biomarker aim) XII. To assess whether an increase in TK1 between 2 months and 12 months is
 associated with PFS. (Proliferative biomarker aim) XIII. To assess the change in EMT marker
 expression (e.g. Vimentin, SLUG and E-cadherin) and serum TK1 after two months of treatment
 with palbociclib and ET. (EMT aim) XIV. To determine the association between the expression
 of EMT markers and Ki67 levels after two months of treatment with palbociclib and ET. (EMT
 aim) XV. To determine the association between the expression of EMT markers after two months
 of treatment with palbociclib and ET, and PFS outcomes. (EMT aim) XVI. To assess whether
 there is a change in the level of tumor infiltrating lymphocytes (TILs) observed in archival
 tumor, at pre-registration, at 2 months, and at disease progression on palbociclib and ET.
 (Immune aim) XVII. To assess the change in TILs (including CD8, PD-L1, and FOXP3) after 2
 months of treatment with palbociclib and ET. (Immune aim) XVIII. To assess the association
 between TILs and serum TK1 levels at preregistration, at 2 months, and at disease progression
 on palbociclib and ET. (Immune aim) XIX. To characterize and evaluate changes in the immune
 landscape of HR+ HER2 -MBC using serial biopsies obtained pre-registration, at 2 months, and
 at disease progression (as well as archived primary tumor when available) using digital
 spatial profiling (DSP) (NanoString GeoMx platform) . (Immune aim) XX. To assess, by use of
 mass cytometry (CyTOF), whether i) peripheral blood immune markers obtained pretreatment are
 associated with either TK1 or PFS and ii) whether the changes in peripheral blood immune
 markers after 2 cycles of treatment are associated with changes in serum TK1 levels. (Immune
 aim) XXI. To discover putative mechanistic connections underlying bacteria-drug interactions
 in all patients. (Microbiome aim) XXII. To identify the biomolecular features within the gut
 (stool) microbiome and its association with the pharmacokinetics and pharmacodynamics of
 letrozole and palbociclib. (Microbiome aim) XXIII. To discover novel predictive biomarkers of
 resistance to CDK4/6i and ET and/or to find biomarkers that add additional predictive power
 to other promising biomarkers such as TK1 by performing the following: (Metabolic, proteomic
 and lipidomic aim) XXIV. A metabolomics analysis (>5,000 metabolites sampled through
 untargeted mass spectrometry at Metabolon) of paired serum samples obtained pre-registration
 and after 2 months on palbociclib and ET.

 XXIVa. An Olink-based cytokines panel (Explore panel of 1,536 proteins) of paired serum
 samples obtained pre-registration and after 2 months on palbociclib and ET.

 XXIVb. A lipidomics analysis (platform TBC) of paired serum samples obtained pre-registration
 and after 2 months on palbociclib and ET.

 XXV. To correlate the changes in the metabolites, cytokines and lipids to the preregistration
 genomic tumor characteristics, serial Ki67 levels and PFS outcomes. (Metabolic, proteomic and
 lipidomic aim) XXVI. To assess the change in serum TK1 levels after 2 months, and at disease
 progression, on palbociclib and ET, and its association with the preregistration
 CD44high/CD24/low/ERlow cancer stem cell-like phenotype, including the following: total and
 phosphorylated AURKA, breast cancer stemness biomarkers (CD44, CD24, ALDH1) EMT transcription
 factors (SMAD5, SOX2), cyclin E, cyclin A and phosphorylated Retinoblastoma (Rb). (Other aim)
 XXVII. To examine shifts in the populations of epithelial like CTCs and stem cell like CTCs
 during the course of endocrine therapy with palbociclib. (Other aim) XXVIII. To assess CTC
 expression of ER, HER2, and other markers of endocrine resistance. (Other aim)

 OUTLINE:

 Patents undergo collection of blood and stool samples at baseline, 7 days after letrozole
 monotherapy treatment, and at completion of each cycle, urine samples at baseline and
 completion of each cycle, and saliva samples at baseline. Patients also undergo collection of
 blood and urine samples at disease progression. Biopsy samples are analyzed for genetic
 profile via genome 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 every 6 months for 7 years.
Inclusion Criteria:

 -  PRE-REGISTRATION INCLUSION CRITERIA

 -  Women who have disease that is amenable to biopsy and agree to undergo a standard of
 care and /or research biopsy

 -  Note: If a standard of care biopsy was recently obtained =< 2 months of
 pre-registration, eligible patients should agree to a research biopsy of
 recurrent or metastatic breast cancer prior to the start of protocol treatment 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: The intention to begin palbociclib and letrozole as
 treatment for locally advanced or metastatic breast cancer

 -  Second line therapy setting only: The intention to begin palbociclib and fulvestrant
 as treatment for metastatic breast cancer (after progression on first line endocrine
 therapy)

 -  Note: Patients who are to receive second line endocrine therapy are allowed to
 remain on their most recent treatment (tamoxifen or an aromatase inhibitor during
 the pre-registration period as well as after registration while awaiting
 insurance approval for the use of palbociclib

 -  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 to lesions that will not be biopsied or used for assessing disease
 response (target lesions) is allowed during pre-registration

 -  No current evidence of visceral crisis

 -  History of central nervous system metastasis are allowed provided they have been
 treated (i.e., surgery, radiation, and/or radiosurgery) >= 12 weeks prior to
 pre-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 leutinizing hormone
 releasing hormone (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, blood, stool, and saliva and urine 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 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 (=< 14 days prior to registration)

 -  Platelet count >= 100,000/mm^3 (=< 14 days prior to registration)

 -  Hemoglobin >= 9.0 g/dL (=< 14 days prior to registration)

 -  Total bilirubin =< 1.5 x upper limit of normal (ULN), (=< 3 x ULN if Gilbert's
 disease) (=< 14 days prior to registration)

 -  Aspartate transaminase (AST) =< 3 x ULN (=< 5 x ULN if liver metastases present) (=<
 14 days prior to registration)

 -  Creatinine =< 1.5 x ULN (=< 14 days prior to registration)

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

 -  Toxicities related to all prior anticancer therapies must have resolved or stabilized,
 apart from alopecia and peripheral neuropathy; Note: Peripheral neuropathy which has
 resolved to =< grade 2 toxicity is acceptable

 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

 -  Note: Denosumab is exempt from this requirement and can be started at any
 time prior to initiation of palbociclib and letrozole/fulvestrant without
 the need to delay protocol therapy

 -  Radiation therapy =< 2 weeks

 -  Note: Palliative radiation therapy to lesions that will not be biopsied for
 this study or used for assessing disease response (target lesions) is
 permitted during the pre-registration period and does not count towards the
 2 week window

 -  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

 -  Women who have already commenced treatment with an aromatase inhibitor (first
 line setting) or fulvestrant (second line setting) prior to screening for this
 study or any prior palbociclib