Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors

Background

Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive CNS tumors of infancy and early childhood. Hallmark is the surprisingly simple genome with inactivating mutations or deletions in the SMARCB1 gene as the oncogenic driver. Nevertheless, AT/RTs are infiltrated by immune cells and even clonally expanded T cells. However, it is unclear which epitopes T cells might recognize on AT/RT cells.

Methods

Here, we report a comprehensive mass spectrometry (MS)-based analysis of naturally presented human leukocyte antigen (HLA) class I and class II ligands on 23 AT/RTs. MS data were validated by matching with a human proteome dataset and exclusion of peptides that are part of the human benignome. Cryptic peptide ligands were identified using Peptide-PRISM.

Results

Comparative HLA ligandome analysis of the HLA ligandome revealed 55 class I and 139 class II tumor-exclusive peptides. No peptide originated from the SMARCB1 region. In addition, 61 HLA class I tumor-exclusive peptide sequences derived from non-canonically translated proteins. Combination of peptides from natural and cryptic class I and class II origin gave optimal representation of tumor cell compartments. Substantial overlap existed with the cryptic immunopeptidome of glioblastomas, but no concordance was found with extracranial tumors. More than 80% of AT/RT exclusive peptides were able to successfully prime CD8⁺ T cells, whereas naturally occurring memory responses in AT/RT patients could only be detected for class II epitopes. Interestingly, >50% of AT/RT exclusive class II ligands were also recognized by T cells from glioblastoma patients but not from healthy donors.

Conclusions

These findings highlight that AT/RTs, potentially paradigmatic for other pediatric tumors with a low mutational load, present a variety of highly immunogenic HLA class I and class II peptides from canonical as well as non-canonical protein sources. Inclusion of such cryptic peptides into therapeutic vaccines would enable an optimized mapping of the tumor cell surface, thereby reducing the likelihood of immune evasion.

Abstract P3-04-05: Identification of SAR439859, an orally bioavailable selective estrogen receptor degrader (SERD) that has strong antitumor activity in wild-type and mutant ER+ breast cancer models

Estrogen receptor positive (ER+) breast cancer accounts for 70% of all breast cancers and is primarily treated with endocrine therapy. Approximately 40% of patients on endocrine therapy will become resistant via a number of mechanisms. There is evidence that in many cases ER continues to play a central role, including mutations in ER leading to a constitutively active receptor. Estrogen receptor degraders like fulvestrant are effective in shutting down ER signaling; however, poor pharmaceutical properties limit fulvestrant clinical activity and prevent it from achieving maximum receptor blockade.

We describe the discovery of SAR439859, a novel, orally bioavailable SERD that is a potent antagonist and degrader of ER both in vitro and in vivo. SAR439859 has robust activity in multiple ER+ breast cancer cell lines including cells that are resistant to tamoxifen as well as cell lines harboring ER mutants. Across a large panel of ER+ cells, SAR439859 demonstrated broad and superior ER degradation activity than most SERDs undergoing clinical testing. This leads to a profound inhibition of ER signaling, better inhibition of cell growth and results in improved in vivo efficacy. SAR439859 demonstrated tumor regression in all ER+ BC models including MCF7-ESR1 mutant-Y537S model, as well as patient-derived xenograft model that is resistant to endocrine therapies. Furthermore, SAR439859 displays limited cross-resistance with other class of SERDs.

Taken together, these results suggest that SAR439859 would be of therapeutic benefit in metastatic BC setting for patients harboring wild type or mutant ER. SAR439859 is being advanced toward the clinic.

Citation Format: Shomali M, Cheng J, Koundinya M, Weinstein M, Malkova N, Sun F, Hebert A, Cindachao M, Hoffman D, McManus J, Levit M, Pollard J, Vincent S, Besret L, Adrian F, Winter C, El-Ahmad Y, Halley F, Hsu K, Lager J, Garcia-Echeverria C, Bouaboula M. Identification of SAR439859, an orally bioavailable selective estrogen receptor degrader (SERD) that has strong antitumor activity in wild-type and mutant ER+ breast cancer models [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-04-05.

P1-17-02: A Phase 1/2 Study of SAR245408 (S08) in Combination with Trastuzumab (T) or Paclitaxel (P) and T in Patients with HER2+ Metastatic Breast Cancer (MBC) Who Progressed on a Previous T-Based Regimen

BACKGROUND: Most HER2+ MBC patients (pts) treated with a combination of T+P progress within 1 year. Activation of downstream pathways through either deficiency in PTEN or mutations in the PI3K pathway has been implicated in the development of resistance to T. S08 is a potent, orally bioavailable, pan-PI3K inhibitor that inhibits phosphorylation of multiple downstream components of the PI3K/PTEN signaling pathway and has demonstrated activity as a single agent and in combination with other anticancer agents (Edelman G, et al., ASCO 2010; Traynor AM, et al. ASCO 2010).

PATIENTS and METHODS: This ongoing, open-label multicenter phase 1/2 study (NCT01042925) was designed to assess safety and tolerability of S08 in combination with either T or T+P. Eligible female pts were ≥18 yrs, ECOG PS 0–2, with adequate organ and marrow function and had advanced or recurrent HER2+ MBC disease refractory to T. Pts have received, and progressed on at least 1 prior T-containing regimen for metastatic disease. Pts were allocated to Arm 1 or Arm 2 and received different dose levels of S08 (starting dose 200 mg PO, daily) in combination with either T 8/6 mg/kg IV on Day (D) 1 q3w (Arm 1) or T 8/6 mg/kg IV on D1 + P 80 mg/m2 on D 1, 8, and 15 q3w (Arm 2). In phase 1, a standard ascending 3 + 3 dose escalation design was used in each arm to evaluate safety/tolerability of the combinations. Following establishment of preliminary maximal tolerated doses (MTDs) for each combination, subsequent pts will be accrued to the phase 2 portion. Approximately 25 additional pts will be enrolled in each arm to further evaluate the safety and estimate the overall response rate (ORR) in each arm.

RESULTS: As of June 1st 2011, 33 pts median age 55 yrs were enrolled; 18 to Arm 1 and 15 to Arm 2. Based on preliminary data of the study, in Arm 1, the most common treatment emergent adverse events (TEAEs) regardless of relationship include rash, diarrhea, fatigue, nausea, vomiting; in Arm 2 were neutropenia, diarrhea, fatigue, nausea, hyporexia, hypokalemia, peripheral neuropathy, rash and hyperglycemia. SAEs reported in Arm 1 (3 subjects) included Gr3 dehydration (2 cases), Gr3 epigastric pain and Gr2 dyspnea; those SAEs in Arm 2 (4 subjects) included Gr4 neutropenia, Gr3 anorexia, Gr3 dehydration, Gr3 epigastric pain, Gr3 thromboembolism, Gr2 nausea, Gr2 pneumonitis and Gr2 headache. A total of 4 DLTs were reported; 2 in Arm 1 [Gr3 skin rash (S08; 400 mg dose)] and 2 in Arm 2 [Gr4 neutropenia (S08; 200mg dose)] (table 1). With phase I nearly complete, the MTD for arm 1 is S08 300 mg PO daily and T 8/6 mg/kg D1 q3w. The data for Arm 2 (current dose level ongoing at the maximum allowed per protocol) will be completed in August 2011. Preliminary PK data did not show interactions between S08 and either T or T+P.

P1-17-09: A Phase 1/2 Dose-Escalation Study of SAR245408 (S08) or SAR245409 (S09) in Combination with Letrozole (L) in Subjects with Hormone Receptor-Positive and HER2−Negative (HR+/HER2−) Breast Cancer (BC) Refractory to a Nonsteroidal Aromatase Inhibitor (AI)

Background: Upregulation of PI3K activity is a common molecular mechanism involved in resistance to AIs. S08 is a potent, orally bioavailable, pan-PI3K inhibitor. S09 is a potent, orally bioavailable inhibitor of PI3K which also possesses mTOR inhibitory activity. Both compounds exhibit robust PI3K and ERK pathway inhibition in paired human tumor biopsy samples from phase 1 studies (Edelman G, et al. ASCO 2010; Brana I, et al. ASCO 2010).

Methods: This ongoing, open-label, multicenter, phase 1/2 study (NCT01082068) was designed to evaluate the safety and tolerability of L in combination with either S08 (Arm 1) or S09 (Arm 2). Eligible female patients (pts) were ≥18 yrs, ECOG PS 0–1, with advanced or recurrent HR+/HER2− BC whose disease is refractory to nonsteroidal AIs. Phase 1 used an ascending 3+3 dose-escalation design and pts were accrued to each arm until no more than 1/3 pts or ≥33% of 3–6 pts at a given dose level experienced a dose-limiting toxicity (DLT) during the first 28-day cycle. Pts were alternately assigned to Arm 1 or Arm 2 and received 2.5 mg L PO (qd) in combination with different dose levels of either S08 (Arm 1; starting dose 200 mg tablets, PO, qd) or S09 (Arm 2; starting dose of 30 mg capsules, PO, bid). After reaching a preliminary maximum tolerated dose (MTD) for each combination, pts will accrue to the phase 2 portion of the study. A two-stage design will be used evaluate the phase 2 co-primary endpoints of ORR and PFS. Each arm will be evaluated independently and no formal comparisons between arms are planned.

Results: As of June 1st 2011, 17 pts were enrolled to Arm 1 (8 pts) or Arm 2 (9 pts). Median age was 54 yrs. Based on preliminary data, the adverse event profile in both arms were similar to those reported in the single agent phase I studies for S08 and S09 respectively. SAEs reported in Arm 1 (2 subjects) included 2 cases of Gr1 pneumothorax and 1 Gr4 pneumonitis; in Arm 2 (2 subjects) included Gr4 lumbar pain and Gr4 elevation of ALT and AST. No DLTs were reported in Arm 1 while one DLT (Gr3 skin rash) was reported in Arm 2 at a dose level of S09 50 mg bid (table 1). Arm 1 dosing data from S08 400 mg qd + L 2.5 mg qd dose level (maximum dose level allowed per protocol) will be completed by August 2011. For Arm 2, the MTD was S09 50 mg bid + L 2.5 mg, qd.

An evaluation of the drug interaction potential of pazopanib, an oral vascular endothelial growth factor receptor tyrosine kinase inhibitor, using a modified Cooperstown 5+1 cocktail in patients with advanced solid tumors

Pazopanib, an oral inhibitor of vascular endothelial growth factor receptor, platelet-derived growth factor receptor, and c-kit kinases, inhibits multiple cytochrome P450 (CYP450) enzymes in vitro. This study in patients with advanced cancer evaluated the effect of pazopanib on CYP450 function by comparing the pharmacokinetics of CYP-specific probe drugs in the presence and absence of pazopanib. The probes used included midazolam (CYP3A specific), warfarin (CYP2C9 specific), omeprazole (CYP2C19 specific), caffeine (CYP1A2 specific), and dextromethorphan (CYP2D6 specific). The estimated ratios of the geometric means (90% confidence interval (CI)) for the area under the curve to the last measurable point (AUC(0-t)) for these probe drugs with/without pazopanib were as follows: midazolam, 1.35 (1.18-1.54); omeprazole, 0.81 (0.59-1.12); caffeine, 1.00 (0.77-1.30); and S-warfarin, 0.93 (0.84-1.03). The geometric least-squares (LS) mean ratio of urine dextromethorphan:dextrorphan ranged from 1.33 (0-4-h interval) to 1.64 (4-8-h interval). The data suggest that pazopanib is a weak inhibitor of CYP3A4 and CYP2D6 and has no effect on CYP1A2, CYP2C9, and CYP2C19 in patients with advanced cancer.

Preliminary results of a phase I study of bevacizumab (BV) in combination with everolimus (E) in patients with advanced solid tumors

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Background: BV is a potent inhibitor of vascular endothelial growth factor (VEGF) with broad clinical activity. E is an mTOR (mammalian target of rapamycin) inhibitor in development for cancer and solid organ transplant therapy. VEGF and mTOR inhibitors have anti-tumor and anti-angiogenesis effects alone and in combination in preclinical models. As a combination anti-angiogenesis therapy, we evaluated BV + E in a phase I, pharmacokinetic (PK), biomarker study. Methods: BV was dosed at 10mg/kg IV q14d. E was dosed at 5mg PO QD, escalating to 10mg QD. Cycle length was 28 days. DLT was defined as any grade 4 heme or grade 3/4 non-heme event in Cycle 1 related to treatment. Pts had advanced solid tumors, adequate organ function, and no increased risks for class-related toxicities. Serial blood samples were collected for PK studies of E. Dermal wound angiogenesis assays were performed pre and on treatment for phospho VEGFR2, AKT, mTOR, and S6K. Results: 14 pts have been enrolled (8 F, 6 M), 12 evaluable for toxicity, 14 for efficacy. Median age is 58y (range 29–73). At dose level 1 (BV 10mg/E 5mg) there were no DLT’s in 5 pts. At dose level 2 (BV 10mg/E 10mg), no DLT’s were noted in the initial 3 pts and the cohort was expanded to 9 pts. Side effects were primarily grade 1–2: pain (10/14), mucositis (9/14), anorexia (8/14), rash (7/14), bleeding (7/14), hyperlipidemia (6/14), fatigue (6/14), and HTN (4/14). 1 pt had a myocardial infarction at day 72 and one pt developed nephrotic syndrome at day 70. 7/14 pts had stable disease as best response (70–278d). Conclusions: BV + E is generally well-tolerated. Preliminary clinical activity and class-related side effects were noted. The recommended phase II dose is BV 10mg/kg IV q14d and E 10mg PO QD.

[Table: see text]

A case of infantile acute lymphoblastic leukemia presenting with rearrangement of MLL at 11q23 and apparent insertion or translocation at 10p12

We report the case of an 11-month-old patient with a clinical diagnosis of infantile acute lymphoblastic leukemia and an MLL (11q23) rearrangement in 69% of nuclei, revealed with interphase fluorescence in situ hybridization (FISH). Routine chromosome analysis of the bone marrow showed a very subtle rearrangement involving the short arm of chromosome 10 and the long arm of chromosome 11 in the abnormal cells. To clarify the nature of this rearrangement, we hybridized the MLL break-apart probe to previously G-banded slides. The rearrangement was interpreted as a small inversion within the band 11q23, separating the 5' MLL from the 3' MLL region. This segment on the long arm of chromosome 11 containing the rearranged MLL locus was either inserted in or translocated to the short arm of chromosome 10 at approximately band 10p12. The inversion affecting MLL may have followed insertion or preceded it. Molecular characterization of this rearrangement was not possible, due to limited sample material. There have been previous reports of rearrangements of MLL with the MLLT10 (alias AF10) gene locus at 10p12, including an interstitial inverted insertion of 11q13q23 in one case and insertion of 11q14q23 at 10p12 in another. These both resulted in a large derivative chromosome 10 and transcription of an MLL/MLLT10 fusion product. To our knowledge, the novel and cryptic rearrangement detected in our patient has not been described previously. A follow-up study of the patient's bone marrow at the end of induction therapy showed no morphologic evidence of residual leukemia and both FISH and chromosome analyses were normal.

Survival following Burkholderia cepacia sepsis in a patient with cystic fibrosis treated with corticosteroids

We describe an 11-year-old girl with cystic fibrosis (CF) who presented with respiratory failure and Burkholderia cepacia bacteremia (cepacia syndrome). She survived her illness after aggressive treatment with parenteral antibiotics and corticosteroids. We speculate that treatment with corticosteroids may decrease the influx of proinflammatory cytokines and neutrophil-induced inflammation, with resulting improvement in the outcome of cepacia syndrome in CF patients.