Personalized NeoAntigen Cancer Vaccine w RT Plus Pembrolizumab for Patients With Newly Diagnosed GBM

I. Inclusion Criteria:

Participants must meet the following criteria on screening examination to be eligible to participate in the study (labs/tests/assessments within 14 days prior to initial study registration unless otherwise specified)

• Participant is willing and able to give written informed consent

• Pathologically confirmed WHO grade IV glioblastoma or variants (gliosarcoma,glioblastoma with oligodendroglial features, giant cell glioblastoma) with adequatetumor material for genomic sequencing. Participants will be eligible if the originaldiagnosis was a lower grade glioma and a subsequent histologic diagnosis ofglioblastoma or its variants was made, and patient received no prior therapy otherthan surgery

• Patients with a diagnosis of astrocytoma with molecular features ofglioblastoma will be considered eligible for trial.

• In addition, patients with IDH-mutated tumors will also continue to be eligiblefor trial, despite the release of updated WHO disease classifications in 2021.

• The tumor must be primarily supratentorial in location as determined by diagnosticimaging performed preoperatively

• Radiographic contrast enhancement attributable to residual tumor on post-operativeimaging performed within 72 hours of resection must not exceed 1 cm in maximaldiameter in biperpendicular plances (greater than 1 cm in one plane but less than 1cm in other planes will be allowed)

• CT or MRI within 14 days prior to start of study therapy (NOTE: This criterion doesnot apply to Cohort 1d participants who are registering after having initiatedstandard of care therapy.)

• Age ≥18 years

• Karnofsky performance status ≥ 70

• Participant is a candidate for, and agrees to receive conventional external beamradiotherapy. (Patients screening for Cohort 1d can be actively receiving - oralready completed - their first line conventional external beam radiotherapy.)

• No corticosteroid dosing within 5 days of radiation therapy initiation (Cohorts 1a, 1b, 1c, & 1d).

• Normal hematologic, renal and hepatic function as defined below:

• ANC: greater or equal to 1,000 /mcl

• Platelets: greater than or equal to 100,000 /mcl

• Hemoglobin: greater than or equal to 9 gm/dl or ≥5.6 mmol/L without transfusionor EPO dependency (within 7 days of assessment)

• International normalized ratio (INR) or prothrombin time: less than or equal to 1.5 times institutional ULN unless subject is receiving anticoagulant therapyas long as PT or PTT is within therapeutic range of intended use ofanticoagulants

• Activated partial thromboplatin time (aPTT): less than or equal to 1.5 Xinstitutional ULN unless subject is receiving anticoagulant therapy as long asPT or PTT is within therapeutic range of intended use of anticoagulants

• Serum creatinine: less than or equal to 1.5 X institutional ULN OR Measured orcalculated creatinine clearance ≥60 mL/min for subject with creatinine levels > 1.5 X institutional ULN

• Total bilirubin: less than or equal to 1.5 X institutional ULN (or less than orequal to 3.0 X institutional ULN for Gilbert's Syndrome) OR Direct bilirubin ≤institutional ULN for subjects with total bilirubin levels > 1.5 institutionalULN

• AST (SGOT) and ALT (SGPT): less than or equal to 2.5 X institutional ULN (orless than or equal to 5.0 X institutional ULN for Gilbert's Syndrome)

• MGMT promoter methylation status determined by an institutional CLIA-approvedlaboratory using a methylation specific PCR assay

• Adequate tumor content as determined by institutional pathologist for nucleic acidextraction and DNA sequence analysis

• Patients unable to undergo magnetic resonance (MR) imaging because of non-compatibledevices can be enrolled, provided CT scans are obtained and are of sufficientquality. Patients without non-compatible devices may not have CT scans performed tomeet this requirement

• An interval of at least 3 weeks between prior surgical resection to start of studytherapy (or one week for stereotactic biopsy to start of study treatment);

• Women of childbearing potential (WOCBP) must have a negative pregnancy test (minimumsensitivity 25 IU/L or equivalent of HCG) before entry onto the trial, because theeffects NeoVax on the developing human fetus are unknown

• Participants cannot be breast feeding;

• Female participants enrolled in the study, who are not free from menses for greaterthan or equal to 2 years, post hysterectomy/oophorectomy, or surgically sterilized,must be willing to use either 2 adequate barrier methods or a barrier method plus ahormonal method of contraception to prevent pregnancy or to abstain from sexualactivity throughout the study, starting with visit 1 through 120 days after the lastdose of the study therapy;

• Approved contraceptive methods include for example; intra uterine device, diaphragmwith spermicide, cervical cap with spermicide, male condoms, or female condom withspermicide. Spermicides alone are not an acceptable method of contraception;

• Male participants must agree to use an adequate method of contraception startingwith the first dose of radiation therapy through 120 days after the last dose ofstudy therapy.

II. Exclusion Criteria:

Participants who exhibit any of the following conditions at either screening timepoint will not be eligible for admission into or continuation on the study

• Stereotactic biopsy (without further resection);

• Tumor primarily localized in the infratentorial compartment or spinal cord - tumorswith limited infratentorial compartment or spinal cord involvement are eligible;

• Radiographic or cytologic evidence of diffuse leptomeningeal extension - tumors withlimited subependymal involvement are eligible;

• Participants who have received or plan to receive any additional treatment forglioblastoma aside from surgical resection and conventional radiotherapy (Cohort 1)and pembrolizumab (cohorts 1a, 1b and 1c) and temozolomide (cohort 1d), including -but not limited to - temozolomide (cohorts 1, 1a, 1b and 1c), stereotacticradiosurgery, placement of Gliadel (carmustine; BCNU) wafers, any other intratumoralor intracavitary treatment, brachytherapy, Novo-Tumor Treating Fields (Optune), orinvestigational therapeutic agents. (Cohort 1d participants may have alreadyinitiated or completed their RT with concomitant TMZ, and may have initiated theiradjuvant TMZ at the time of study entry as long as they do not have evidence ofprogressive disease and have undergone a leukopheresis or blood draw with adequatemononuclear cell collection.)

• Concomitant therapy with any anti-cancer agents, other investigational anti-cancertherapies, or immunosuppressive agents including but not limited to methotrexate,chloroquine, azathioprine, etc. within six months of study participation;

• History of severe allergic reactions attributed to any vaccine therapy for theprevention of infectious diseases;

• Active, known, or suspected autoimmune disease or immunosuppressive conditions thathas required systemic treatment in the past 2 years (i.e. with use of diseasemodifying agents, corticosteroids or immunosuppressive drugs) with the exception ofvitiligo, type 1 diabetes, residual autoimmune-related hypothyroidism requiringhormone replacement, or psoriasis not requiring systemic treatment. Replacementtherapy (eg., thyroxine, insulin, or physiologic corticosteroid replacement therapyfor adrenal or pituitary insufficiency, etc.) is not considered a form of systemictreatment.

• Known chronic infections with HIV, hepatitis B (HBV) or C (HCV), Hepatitis B virusDNA and testing for HCV RNA must be undetectable.

• Uncontrolled intercurrent illness including, but not limited to ongoing or activeinfection requiring treatment, symptomatic congestive heart failure, unstable anginapectoris, cardiac arrhythmia;

• Any underlying medical condition, psychiatric condition or social situation that inthe opinion of the investigator would compromise study administration as perprotocol or compromise the assessment of AEs;

• Planned major surgery;

• Pregnant women are excluded from this study because personalized neoantigen peptidesand poly-ICLC are agents with unknown risks to the developing fetus. Because thereis an unknown but potential risk of adverse events in nursing infants secondary totreatment of the mother with personalized neoantigen peptides and poly-ICLC, nursingwomen are excluded from this study;

• Individuals with a history of an invasive malignancy are ineligible except for thefollowing circumstances; a) individuals with a history of invasive malignancy areeligible if disease-free for at least 3 years and are deemed by the investigator tobe at low risk for recurrence of that malignancy; b) individuals with the followingcancers are eligible if diagnosed and treated - carcinoma in situ of the breast,oral cavity or cervix and basal cell or squamous cell carcinoma of the skin;

Coh 1a/1b/1c/1d Exclusions:

• Hypersensitivity to pembrolizumab or any of its excipients.

• Is currently participating and receiving study therapy or has participated in astudy of an investigational agent and received study therapy or used investigationaldevice within 4 weeks of the first dose of treatment. (NOTE: Participation in aclinical trial evaluating interventions for purposes other than GBM therapy is not abasis for exclusion, and may be permitted pending prospective approval of PrincipalInvestigator or designee.)

• Has had a prior anti-cancer monoclonal antibody (mAb) within 4 weeks prior to studyDay 1 or who has not recovered (i.e., less than or equal to Grade1 or at baseline)from adverse events due to agents administered more than 4 weeks earlier.

• Has had prior chemotherapy, targeted small molecule therapy, or radiation therapywithin 2 weeks prior to study Day 1 or who has not recovered (i.e., less than orequal to Grade 1 or at baseline) from adverse events due to a previouslyadministered agent.

• Note: Subjects with less than or equal to Grade 2 neuropathy are an exceptionto this criterion and may qualify for the study.

• Note: If subject received major surgery, subject must have recovered adequatelyfrom the toxicity and/or complications from the intervention prior to startingtherapy.

• Note: Cohort 1d participants may have already received their radiation therapywith concomitant temozolomide, and may have initiated their adjuvanttemozolomide, at the time of study entry as long as they do not have evidenceof progressive disease and have undergone a leukopheresis or blood draw withadequate mononuclear cell collection.

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

• Has known active central nervous system (CNS) metastases and/or carcinomatousmeningitis. Subjects with previously treated brain metastases may participate provedthe disease is stable (without evidence of progression by imaging for at least fourweeks prior to the first dose of trial treatment and any neurologic symptoms havereturned to baseline), have no evidence of new or enlarging brain metastases, andare not using steroids for at least 7 days prior to trial treatment. This exceptiondoes not include carcinomatous meningitis which is excluded regardless of clinicalstability;

• Has known history of non-infectious pneumonitis/ interstitial lung disease thatrequired steroids or has current pneumonitis/interstitial lung disease.

• Has received prior therapy with an anti-PD-1, anti-PD-L1, or anti-PD-L2 agent.

• Has received a live vaccine within 30 days of planned start of study therapy.Examples of live vaccines include, but are not limited to, the following: measles,mumps, rubella, varicella/zoster, yellow fever, rabies, BCG, and Typhoid vaccine.

• Note: Seasonal influenza vaccines for injection are generally inactivated fluvaccines and are allowed; however intranasal influenza vaccines (e.g.,Flu-Mist) are live attenuated vaccines, and are not allowed