Personalized Vaccine Immunotherapy in Combination With Checkpoint Inhibitor for Treatment of Triple Negative Breast Cancer

Inclusion Criteria:

• Written informed consent and Health Insurance Portability and Accountability Act (HIPAA) authorization for release of personal health information

• Must be age >= 18 years

• Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1 within 14days prior to tissue consent

• Absolute neutrophil count > 1500/mcL (obtained within 14 days prior to vaccineadministration)

• Absolute lymphocyte count >= 600 cells/µl (obtained within 14 days prior to vaccineadministration)

• Platelets > 100,000 mm (obtained within 14 days prior to vaccine administration)

• Hemoglobin > 9.0 g/dL (obtained within 14 days prior to vaccine administration) (NOTE: The use of transfusion or other intervention to achieve hemoglobin [Hgb] > 9.0g/dl is acceptable)

• Serum creatinine =< 1.5 x upper limit of normal (ULN) or calculated creatinineclearance >= 60 mL/min using Cockcroft-Gault equation for patients with creatininelevels > 1.5 x institutional ULN (obtained within 14 days prior to vaccineadministration)

• Total bilirubin =< 1.5 x ULN OR direct bilirubin =< 1 x ULN (obtained within 14 daysprior to vaccine administration)

• Aspartate aminotransferase (AST) and alanine aminotransferase (ALT) =< 2.5 x ULNunless liver metastases are present, in which case they must be =< 5 x ULN (obtainedwithin 14 days prior to vaccine administration)

• Bilirubin =< 1.5 X ULN (except in participants with documented Gilbert's disease,who must have a total bilirubin =< 3.0 mg/dL) (obtained within 14 days prior tovaccine administration)

• International normalized ratio (INR) or prothrombin time (PT) =< 1.5 x ULN unlesspatient is receiving anticoagulant therapy as long as PT or partial thromboplastintime (PTT) is within therapeutic range of intended use of anticoagulants (obtainedwithin 14 days prior to vaccine administration)

• Activated partial thromboplastin time (aPTT) =< 1.5 x ULN unless patient isreceiving anticoagulant therapy as long as PT or PTT is within therapeutic range ofintended use of anticoagulants (obtained within 14 days prior to vaccineadministration)

• TNBC as defined by estrogen receptor (ER)/progesterone receptor (PR) =< 10% ifAllred =< 3; Her2/neu negative as defined by scores of 0 or 1+ byimmunohistochemistry (IHC) or 2+ by IHC associated with a fluorescence in situhybridization (FISH) ratio of < 2.0 or < 6 Her2 copies per cell

• Patients with metastatic or inoperable locally advanced disease: Metastatic orinoperable locally advanced disease is defined as either histologically confirmedmetastatic breast cancer by biopsy; or locally advanced breast cancer that, in theopinion of the treating physician, is not amenable to curative intent surgicalresection; or, radiological or clinical evidence suggestive and supportive ofmetastatic disease

• Documented metastatic biopsy is not required provided the patient has a priordiagnosis of TNBC that otherwise meets the eligibility criteria

• Eligible patients must have =< 3 lines of chemotherapy in themetastatic/advanced disease setting. For patients who have relapsed within 6months of systemic therapy given within curative intent, that therapy willcount as a line of metastatic therapy. Last cycle of cytotoxic therapy must be >= 21 days prior to cycle (C)1 day (D)1 of vaccine. Last cycle of checkpointinhibitor therapy be >= 28 days prior to C1D1 of vaccine. Last dose ofradiotherapy must be >= 14 days prior to C1D1 of vaccine

• Prior checkpoint inhibitor is permitted. Patients who are known to have PD-L1positive with combined positive score (CPS) >= 10 will be required to have hadpembrolizumab therapy prior to enrollment

• Patients who are metastatic or inoperable, locally advanced will only beeligible for the Phase 1b combination cohort. They will not be eligible for thePhase 1a dose escalation cohort. Patients who have received prior anti-CTLA-4antibody will preferentially be enrolled to cohort B (combination of TMVvaccine with pembrolizumab). Patients who have received prior PD-L1 or PD-1antibody therapy will preferentially be enrolled to cohort C (combination ofTMV vaccine with ipilimumab). Patients with metastatic disease who havereceived no prior immune checkpoint inhibitor therapy will be assigned to atreatment arm based on available slots and discretion of treating physician

• Patients with early stage TNBC: Early stage TNBC is defined as clinical orpathologic Stage I-III TNBC

• After resection of disease in the breast and axilla, early stage patients areeligible for either the Phase 1a dose escalation of TMV vaccine monotherapyCohort A or the Phase 1b combination arm of the vaccine with immune checkpointinhibitor (ICI)

• Patients will be required to have completed adjuvant radiotherapy (ifindicated) >= 14 days prior to initiation of vaccine on trial

• Patients who have residual disease after completion neoadjuvant therapy thatproceed with adjuvant capecitabine can enroll >= 28 days after completion offinal dose of capecitabine. Patients electing to enroll onto the Phase 1aCohort A monotherapy arm can enroll prior to initiation of capecitabine,however must not initiate capecitabine prior to the Week 12 blood draw (measurement of immune biomarkers) on study

• Patients who have a germline BRCA 1/2 mutation that meet the Food and DrugAdministration (FDA) indication for use of adjuvant Olaparib can enroll >= 28days after completion of final dose of olaparib. Patients electing to enrollonto the Phase 1a Cohort A monotherapy arm can enroll prior to initiation ofolaparib, however must not initiate olaparib prior to the Week 12 blood draw (measurement of immune biomarkers) on study

• Patients who undergo upfront surgery: Patients may initiate injection ofvaccine >= 28 days after completion of final cycle of adjuvant chemotherapy

• Patients who have early stage breast cancer that have residual disease aftercompleting neoadjuvant chemotherapy with the KEYNOTE 522 regimen (pembrolizumabat a dose of 200 mg every 3 weeks plus weekly paclitaxel and carboplatin for 4cycles followed by pembrolizumab-doxorubicin-cyclophosphamide or ofpembrolizumab-epirubicin-cyclophosphamide every 3 weeks for 4 cycles):

• Patient enrolling onto Phase 1a Cohort A will initiate injection ofvaccine >= 28 days after completion of final cycle of standard of careadjuvant pembrolizumab

• Patient enrolling onto Phase 1b Cohort B or C will initiate injection ofvaccine >= 28 days surgical resection. Patients who have receivedpembrolizumab as part of the preoperative KEYNOTE 522 regimen willpreferentially be enrolled to cohort B (combination of TMV vaccine withpembrolizumab) and will receive up to 9 cycles of adjuvant pembrolizumabevery 3 weeks as per standard of care. Vaccine will be administered every 2 weeks for 3 doses prior to the first three ICI cycles

• Patients who have early stage breast cancer that have that have residualdisease after completing neoadjuvant chemotherapy with either dose-densedoxorubicin-cyclophosphamide followed by paclitaxel ordocetaxel-cyclophosphamide:

• Patient enrolling onto Phase 1a Cohort A will initiate injection ofvaccine >= 28 days surgical resection

• Patient enrolling onto Phase 1b Cohort B or C will initiate injection ofvaccine >= 28 days surgical resection. Patients will be assigned toreceive either pembrolizumab (Cohort B) every 3 weeks for 6 cycles oripilimumab (Cohort C) every 3 weeks for 4 cycles in combination with TMVvaccine based on available slots in each arm and discretion of treatingphysician. Vaccine will be administered every 2 weeks for 3 doses; the TMVvaccine will be administered prior to the ICI cycle if ICI is due.

• Weight of tumor tissue for production of vaccine must be at least 1 gram. Inmetastatic patients, preferentially, invasive tumor in breast or lymph node tissuewill be retrieved by excisional biopsy to ensure sufficient yield. In metastaticpatients who undergo initiation of first-line standard of care systemic therapy offstudy (i.e. pembrolizumab and chemotherapy in a PD-L1 positive patient), thenideally collection of tumor tissue will occur prior to treatment initiation ofstandard of care therapy to maximize cellularity. Metastatic patients who haveundergone mastectomy during curative treatment initially or have no invasive diseasein the breast, chest wall, or accessible regional lymph nodes, will be evaluated forimage-guided core biopsies of liver metastasis or video-assisted thorascopic wedgeresection of lung metastasis

• In patients with early stage TNBC undergoing upfront surgery, the tumor tissuewill be retrieved during lumpectomy/mastectomy. In early stage patients who areidentified as high risk of having residual disease after neoadjuvantchemotherapy or undergo upfront resection, tissue will be retrieved duringplanned lumpectomy or mastectomy

• Measurable disease is not required in metastatic patients but patients must havesufficient tumor to yield 1g on biopsy to enable production of personalized TMVvaccine product

• Patients will undergo germline testing to assess for a BRCA1/BRCA2 deleteriousmutation. Knowledge of germline status is not required to enroll on the study

• Able and willing to complete the entire study according to the study schedule

• Patients must give written informed consent. A copy of the signed informed consentform will be retained in the patient's chart

Exclusion Criteria:

• Weight of the tumor tissue is less 1 gram

• Clinically significant comorbid conditions such as cardiovascular disease orsignificant peripheral vascular (e.g., uncontrolled hypertension, myocardialinfarction, unstable angina) within 6 months of study entry, serious cardiacarrhythmia requiring medication, and uncontrolled infection

• No second malignancy except prior breast cancer or except non-melanomatous skincancer within the past 5 years

• Ongoing or planned systemic anti-cancer therapy or radiation therapy. Last cycle ofcytotoxic therapy must be >= 21 days prior to C1D1 of vaccine. Last cycle ofcheckpoint inhibitor therapy be >= 28 days prior to C1D1 of vaccine. Last dose ofradiotherapy must be >= 14 days prior to C1D1 of vaccine

• Pregnant or breastfeeding, or expecting to conceive or father children within theprojected duration of the study, starting with the pre-screening or screening visitthrough 120 days after the last dose of study treatment

• Has a known history of active tuberculosis (Bacillus Tuberculosis)

• History of allogeneic organ transplant

• Known active central nervous system (CNS) metastases and/or carcinomatousmeningitis. Patients with previously treated brain metastases may participateprovided they are stable (without evidence of progression by imaging for at least 4weeks prior to the first dose of study treatment and any neurologic symptoms havereturned to baseline), have no evidence of new or enlarging brain metastases, andare not using steroids for management of brain metastases for at least 7 days priorto study treatment. This exception does not include carcinomatous meningitis whichis excluded regardless of clinical stability

• Diagnosis of immunodeficiency or is receiving systemic steroid therapy or any otherform of immunosuppressive therapy within 7 days prior to the first dose of studytreatment, with the exceptions of intranasal and inhaled corticosteroids or systemiccorticosteroids at physiological doses, which are not to exceed 10 mg/day ofprednisone, or an equivalent corticosteroid

• Active autoimmune disease that has required systemic treatment in the past 2 years (i.e., with use of disease modifying agents, corticosteroids, or immunosuppressivedrugs). Replacement therapy (e.g., thyroxine, insulin, or physiologic corticosteroidreplacement therapy for adrenal or pituitary insufficiency) is not considered a formof systemic treatment

• Known history of non-infectious pneumonitis that required steroids or any evidenceof active pneumonitis

• Failure to recover from grade 3 or 4 toxicity from previous treatment

• For the combination cohort: prior grade 4 immune-related adverse events due toprevious ICI. Patients who experienced grade 2 or 3 toxicity with prior ICI therapymay enroll if toxicity reverted to =< grade 1