Vaccine Therapy, Radiation Therapy, Pembrolizumab, and Temozolomide in Treating Patients with Newly Diagnosed Glioblastoma or Personalized Neoantigen Vaccine for Progressive/Recurrent Low-Grade Glioma

Inclusion Criteria

• STUDY ELIGIBILITY CRITERIA FOR REGISTRATION FOR COHORTS 1A, 1B, 1C, 1D and 1E:
• Participant is willing and able to give written informed consent
• COHORTS 1A, 1B, 1C, AND 1D): Pathologically confirmed World Health Organization (WHO) grade 4 glioblastoma or variants (gliosarcoma, glioblastoma with oligodendroglial features, giant cell glioblastoma) with adequate tumor material for genomic sequencing; participants will be eligible if the original diagnosis was a lower grade glioma and a subsequent histologic diagnosis of glioblastoma or its variants was made, and they received no prior therapy other than surgery * Patients with a diagnosis of astrocytoma with molecular features of glioblastoma will be considered eligible for trial * In addition, patients with IDH-mutated tumors will also continue to be eligible for trial, despite the release of updated WHO disease classifications in 2021 * Cohort 1e: Pathologically confirmed WHO grade 2 glioma with adequate material for genomic sequencing. Patients with molecular genetic features of glioblastoma (including any of the following: EGFR amplification; TERT promoter mutation; monosomy 10; 2 copy loss/inactivation of CDKN2A/B or 9p21.3) are not eligible, however patients who do not have sufficient tumor material for examination of these abnormalities may be eligible for study participation
• The tumor must be primarily supratentorial in location as determined by diagnostic imaging performed preoperatively
• COHORTS 1A, 1B, 1C, AND 1D: Radiographic contrast enhancement attributable to residual tumor on post-operative imaging performed within 72 hours of resection must not exceed 1 cm in maximal diameter in bi-perpendicular planes (> 1 cm in one plane but < 1 cm in other planes will be allowed)
• Patients screening for Cohort 1e must have either: * Significant residual tumor (defined as > 1 cm x 1 cm in perpendicular plane) following most recent surgical resection * OR evidence of tumor progression within one year of study enrollment
• COHORTS 1A, 1B, 1C AND 1D: Computed tomography (CT) or magnetic resonance imaging (MRI) within 14 days prior to start of study therapy (radiation therapy [RT], temozolomide [TMZ], and/or pembrolizumab). CT or MRI within 14 days prior to registration for Cohort 1e * NOTE: This criterion does not apply to Cohort 1d participants who are registering after having initiated standard of care therapy
• Age >= 18 years
• Karnofsky performance status >= 70
• COHORTS 1A, 1B, 1C AND 1D): Participant is a candidate for, and agrees to receive conventional external beam radiotherapy (patients screening for cohort 1d can be actively receiving - or already completed - their first line conventional external beam radiotherapy)
• No corticosteroid dosing within 5 days of radiation therapy initiation (cohorts 1a, 1b, 1c, & 1d) or within 5 days of study registration (cohort 1e)
• Absolute neutrophil count >= 1,500/mcL
• Platelets >= 100,000/mcL
• Hemoglobin >= 9 g/dL or >= 5.6 mmol/L without transfusion or erythropoietin (EPO) dependency (within 7 days of assessment)
• Serum creatinine =< 1.5 x institutional upper limit of normal (ULN) OR measured or calculated creatinine clearance (glomerular filtration rate [GFR] can also be used in place of creatinine or creatinine clearance [CrCl]) >= 60 mL/min for subject with creatinine levels > 1.5 x institutional ULN * Creatinine clearance should be calculated per institutional standard
• Serum total bilirubin =< 1.5 x institutional ULN (=< 3 x institutional ULN for Gilbert’s syndrome) OR direct bilirubin =< institutional ULN for subjects with total bilirubin levels > 1.5 institutional ULN
• Aspartate aminotransferase (AST) (serum glutamic oxaloacetic transaminase [SGOT])/alanine aminotransferase (ALT) (serum glutamate pyruvate transaminase [SGPT]) =< 2.5 x institutional ULN OR =< 5 x institutional ULN for subjects with Gilbert's syndrome
• International normalized ratio (INR) or prothrombin time (PT) =< 1.5 X institutional ULN unless subject is receiving anticoagulant therapy as long as PT or partial thromboplastin time (PTT) is within therapeutic range of intended use of anticoagulants
• Activated partial thromboplastin time (aPTT) =< 1.5 x institutional ULN unless subject is receiving anticoagulant therapy as long as PT or PTT is within therapeutic range of intended use of anticoagulants
• (COHORTS 1A, 1B, 1C AND 1D): MGMT promoter methylation testing will be performed by an institutional Clinical Laboratory Improvement Amendments (CLIA)-approved laboratory using a methylation specific polymerase chain reaction (PCR) assay to detect deoxyribonucleic acid (DNA) methylation within the promoter region of the MGMT gene * Participants with an MGMT promoter that is unmethylated will be enrolled to cohort 1a, 1b and 1c * Participants with tumor MGMT promoter that is methylated or partially methylated will be enrolled to cohort 1d
• Adequate tumor content as determined by institutional pathologist for nucleic acid extraction and DNA sequence analysis
• Patients unable to undergo MR imaging because of non-compatible devices can be enrolled, provided CT scans are obtained and are of sufficient quality; patients without non-compatible devices may not have CT scans performed to meet this requirement
• For participants who may be randomized to Cohort 1a or 1c: An interval of at least 3 weeks between prior surgical resection (or one week for stereotactic biopsy) to initiation of first dose of pembrolizumab
• Women of childbearing potential (WOCBP) must have a negative pregnancy test (minimum sensitivity 25 IU/L or equivalent of human chorionic gonadotropin [HCG]) before entry onto the trial
• Participants cannot be breast feeding
• Female participants enrolled in the study, who are not free from menses for > 2 years, post hysterectomy/oophorectomy, or surgically sterilized, must be willing to use either 2 adequate barrier methods or a barrier method plus a hormonal method of contraception to prevent pregnancy or to abstain from sexual activity throughout the study, starting with visit 1 through 120 days after the last dose of study therapy; approved contraceptive methods include for example; intra uterine device, diaphragm with spermicide, cervical cap with spermicide, male condoms, or female condom with spermicide; spermicides alone are not an acceptable method of contraception
• Male participants must agree to use an adequate method of contraception starting with the first dose of radiation therapy through 120 days after the last dose of study therapy

Exclusion Criteria

• Tumors primarily localized in the infratentorial compartment or spinal cord – tumors with limited infratentorial compartment or spinal cord involvement are eligible
• Radiographic or cytologic evidence of diffuse leptomeningeal extension - tumors with limited subependymal involvement are eligible
• Concomitant therapy with any anti-cancer agents, other investigational anti-cancer therapies, or immunosuppressive agents including but not limited to methotrexate, chloroquine, azathioprine, etc. within six months of study participation * NOTE: IDH1-inhibitor therapy (vorasidenib) IS permissible for COH 1E participants
• History of severe allergic reactions attributed to any vaccine therapy for the prevention of infectious diseases
• Active, known, or suspected autoimmune disease or immunosuppressive conditions that has required systemic treatment in the past 2 years (i.e. with use of disease modifying agents, corticosteroids or immunosuppressive drugs) with the exception of vitiligo, type 1 diabetes, residual autoimmune-related hypothyroidism requiring hormone replacement, or psoriasis not requiring systemic treatment. Replacement therapy (eg., thyroxine, insulin, or physiologic corticosteroid replacement therapy for adrenal or pituitary insufficiency, etc.) is not considered a form of systemic treatment
• Known chronic infections with HIV, hepatitis B (HBV) or C (HCV). Hepatitis B virus deoxyribonucleic acid (DNA) and testing for HCV ribonucleic acid (RNA) must be undetectable
• Uncontrolled intercurrent illness including, but not limited to ongoing or active infection requiring treatment, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia
• Any underlying medical condition, psychiatric condition or social situation that in the opinion of the investigator would compromise study administration as per protocol or compromise the assessment of adverse events (AEs)
• Planned major surgery
• Pregnant women are excluded from this study because personalized neoantigen peptides and poly-ICLC are agents with unknown risks to the developing fetus. Because there is an unknown but potential risk of adverse events in nursing infants secondary to treatment of the mother with personalized neoantigen peptides and poly-ICLC, nursing women are excluded from this study
• Individuals with a history of an invasive malignancy are ineligible except for the following circumstances: a) individuals with a history of invasive malignancy are eligible if they have been disease-free for at least 3 years and are deemed by the investigator to be at low risk for recurrence of that malignancy; b) individuals with the following cancers 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
• Is currently participating and receiving study therapy or has participated in a study of an investigational agent and received study therapy or used an investigational device within 4 weeks of the first dose of treatment. * NOTE: Participation in a clinical trial evaluating interventions for purposes other than GBM or LGG therapy is not a basis for exclusion, and may be permitted pending prospective approval of principal investigator or designee
• Has had a prior anti-cancer monoclonal antibody (mAb) within 4 weeks prior to study day 1 or who has not recovered (i.e., ≤ grade 1 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 therapy within 2 weeks prior to study day 1 or who has not recovered (i.e., ≤ grade 1 or at baseline) from adverse events due to a previously administered agent. * Note: Subjects with ≤ grade 2 neuropathy are an exception to this criterion and may qualify for the study. * Note: If subject received major surgery, they must have recovered adequately from the toxicity and/or complications from the intervention prior to starting therapy. * Note: Cohort 1d participants may have already received their radiation therapy with concomitant temozolomide, and may have initiated their adjuvant temozolomide, at the time of study entry as long as they do not have evidence of progressive disease and have undergone a leukapheresis with adequate mononuclear cell collection. * Cohort 1e participants who are receiving IDH1 inhibitor therapy with at least stable disease and lack of unacceptable toxicity (defined as grade ≥ 3 related adverse event) may be considered for study participation
• Has a known history of active TB (Bacillus Tuberculosis)
• Has known active central nervous system (CNS) metastases and/or carcinomatous meningitis. Subjects with previously treated brain metastases may participate provided they are stable (without evidence of progression by imaging for at least four weeks prior to the first dose of trial treatment and any neurologic symptoms have returned to baseline), have no evidence of new or enlarging brain metastases, and are not using steroids for at least 7 days prior to trial treatment. This exception does not include carcinomatous meningitis which is excluded regardless of clinical stability
• Has known history of non-infectious pneumonitis/interstitial lung disease that required 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, Bacillus Calmette-Guerin (BCG), and typhoid vaccine. * Note: Seasonal influenza vaccines for injection are generally inactivated flu vaccines and are allowed; however intranasal influenza vaccines (e.g., Flu-Mist®) are live attenuated vaccines, and are not allowed
• The following will exclude participants for cohorts 1a, 1b, 1c and 1d: * Planned day 1 of XRT > 6 weeks after date of surgery; * Participants must initiate XRT within 6 weeks of surgery (ideally within 4 weeks); * Stereotactic biopsy (without further resection); * Patients with significant tumor progression before start of RT will be excluded unless granted prior documented approval from the study’s overall principal investigator (PI); * Participants who have received or plan to receive any additional treatment for glioblastoma 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), stereotactic radiosurgery, placement of Gliadel® (carmustine; BCNU) wafers, any other intratumoral or intracavitary treatment, brachytherapy, Novo-Tumor Treating Fields (Optune®), or investigational therapeutic agents; ** Cohort 1d participants may have already initiated or completed their radiation therapy with concomitant temozolomide, and may have initiated their adjuvant temozolomide, at the time of study entry as long as they do not have evidence of progressive disease and have undergone a leukapheresis or blood draw with adequate mononuclear cell collection. * Hypersensitivity to pembrolizumab or any of its excipients.
• The following will exclude participants for cohort 1e: * Evidence of most recent tumor progression > 1 year from study registration * Molecular genetic features consistent with high-grade glioma including any of the following: EGFR amplification; TERT promoter mutation; monosomy 10; 2 copy loss/inactivation of CDKN2A/B or 9p21.3