Weekly Digests
‹ Back to August

New neoantigen vaccine strategy aids checkpoint blockade in cold tumors

August 31, 2022

New neoantigen vaccine strategy aids checkpoint blockade in cold tumors

Given that checkpoint inhibition therapies have limited efficacy in tumors poorly infiltrated with T cells (immune cold tumors), combining these therapies with those attempting to increase antitumor T cell responses, such as vaccines, is warranted. Palmer et al. performed a phase 1/2 clinical trial assessing the safety and efficacy of an individualized neoantigen vaccine strategy combined with checkpoint inhibition in patients with various metastatic solid tumors. The interim results from this trial were recently published in Nature Medicine.

The heterologous prime-boost vaccine consisted of a chimpanzee adenovirus (ChAd68) and a fully synthetic Venezuelan equine encephalitis virus-based self-amplifying mRNA (samRNA) in a lipid nanoparticle. The researchers started out by assessing the potency and durability of immune responses obtained by this vaccine strategy in non-human primates (NHP). To do so, a model antigen cassette encoding six NHP-specific MAMU-A*01-restricted simian immunodeficiency virus (SIV) antigens was inserted into the vaccine platforms, and MAMU-A*01-positive rhesus macaques were injected intramuscularly (i.m.) with the ChAd68 prime, as well as samRNA boosts at 4, 12, and 20 weeks, with or without subcutaneous (s.c.) ipilimumab (anti-CTLA-4).

The ChAd68 prime induced immune responses against all six antigens, and these primed T cell responses were boosted by the samRNA, remaining detectable at 32 weeks. The addition of ipilimumab elevated T cell responses about 2-3 fold, which could be further elevated by readministration of ChAd68 at week 32. Antigen-specific effector memory T cells were generated and maintained over treatment. Six animals were studied for two years after prime vaccination alone using tetramer analysis of peripheral blood mononuclear cells (PBMCs). Antigen-specific central memory T cells were observed that had reactivity against four of the six antigens in these samples. Readministration of samRNA at this timepoint boosted antigen-specific T cell levels about 10-fold. Finally, CD8+ T cells from all six animals expressed cytotoxic activity against target cells.

The vaccine strategy was then assessed in a still ongoing phase 1/2 trial in patients with metastatic microsatellite-stable colorectal cancer (MSS-CRC, N=7)), non-small cell lung cancer (NSCLC, N=1), and gastroesophageal adenocarcinoma (GEA, N=6). Patients received i.m. injections of a single priming dose of ChAd68, followed by multiple i.m. boosts with escalating doses of the samRNA. The 20 highest-ranking mutations in the patient’s tumor tissue were selected for inclusion in a codon-optimized vaccine expression cassette; each mutation was encoded as a 25mer encompassing the mutation. Fourteen patients received the vaccination, as well as monthly intravenous (i.v.) nivolumab (anti-PD-1) beginning at the time of the first vaccine dose. Furthermore, patients treated at higher dose levels also received s.c. ipilimumab with each vaccination. There were no dose-limiting toxicities with this treatment. Treatment-related adverse events were consistent with vaccine-induced immune reactions and checkpoint inhibitor treatment.

The researchers assessed efficacy by analysis of neoantigen-specific T cells. For this, minimal epitope (8-11mer) peptide pools were designed for each patient with the 40 highest-ranked predicted neoepitopes (CD8 pool) and an additional pool with overlapping 15mers spanning each vaccine cassette (15mer pool). PBMC samples from 13 patients were stimulated with the peptide pools. This resulted in detectable IFNγ responses in all patients after the prime-boost, which was further enhanced in 67% of patients by a ChAd68 boost, which also elevated T cell levels. Long-lived T cell responses were maintained for over a year in three patients with available samples. Due to COVID-19 measures at the time of the study, some patients received the samRNA dosing at prolonged intervals. This, combined with the dose escalation study, revealed that lower doses and longer intervals between boosts may be beneficial for T cell responses, which is now being assessed in the ongoing phase 2 of this study.

To assess the breadth of the immune response to vaccination, four minipools covering the 20 patient-specific vaccine neoantigens were used to deconvolute T cell responses. All patients had detectable T cell responses to multiple mutations after treatment. Assessment against all 40 minimal epitopes included in the CD8 pool for three patients showed responses to over 50% of vaccine mutations in multiple HLA class I alleles for all three patients. Therefore, partial deconvolution via minipools (mixtures of 5 peptides) may underestimate the extent of the responses. Peptide HLA (pHLA) tetramer-positive CD8+ T cells were more commonly effector memory and less commonly naive when compared to total CD8+ T cells.

Secretion of various cytotoxic markers was detected in eight patients, and readministration of ChAd68 increased granzyme B secretion in response to CD8 pool stimulation in 4/6 patients. Stimulation of PBMCs with the CD8 pool induced expression of one or more of IFNγ, CD107α, TNFα, and/or IL-2 on CD8+ T cells. Additionally, co-culture of expanded neoantigen-specific T cells with single HLA allele-expressing target cells pulsed with cognate neoantigen peptides revealed T cell killing of target cells.

For two patients, baseline and on-treatment PBMCs were available for paired T cell receptor (TCR)seq and single-cell RNAseq. Increases in neoantigen-specific CD8+ T cells were detected after treatment, resulting in an enrichment of CD8+ T cells in treatment samples. Distinct TCR clonotypes were detected, and these T cells had increased expression of IFNG, GZMB, and/or TNFA transcripts. Putative neoantigen-specific T cells were detected in both the tumor and blood, suggesting vaccine-induced neoantigen-specific T cells infiltrated the tumor.

Finally, Palmer et al. assessed the clinical efficacy of this vaccination strategy. Patients with MSS-CRC and GEA had tumors with a low mutational burden, low PD-L1 expression, and limited infiltration of immune cells prior to treatment (immune cold tumors). One patient with GEA had a complete response and several patients in the study experienced stable disease (SD). The patients with MSS-CRC were further analyzed for overall survival (OS) and circulating tumor (ct)DNA. The 12-month OS rate was 42.9%, and patients with longer OS had lower post-treatment ctDNA levels. Patients with SD lasting <6 months had increased ctDNA concentrations, while 75% of patients with longer SD had lower levels of ctDNA, including two patients with complete ctDNA clearance, suggesting low ctDNA levels may be a biomarker for treatment efficacy.

In conclusion, these interim data suggest that this vaccine regimen is tolerable and may increase T cell immune responses in immune cold tumors. Further efficacy data will be obtained in the ongoing clinical trials with the determined dosing for this regimen.

Write-up by Maartje Wouters, image by Lauren Hitchings.


Palmer CD, Rappaport AR, Davis MJ, Hart MG, Scallan CD, Hong SJ, Gitlin L, Kraemer LD, Kounlavouth S, Yang A, Smith L, Schenk D, Skoberne M, Taquechel K, Marrali M, Jaroslavsky JR, Nganje CN, Maloney E, Zhou R, Navarro-Gomez D, Greene AC, Grotenbreg G, Greer R, Blair W, Cao MD, Chan S, Bae K, Spira AI, Roychowdhury S, Carbone DP, Henick BS, Drake CG, Solomon BJ, Ahn DH, Mahipal A, Maron SB, Johnson B, Rousseau R, Yelensky R, Liao CY, Catenacci DVT, Allen A, Ferguson AR, Jooss K. Individualized, heterologous chimpanzee adenovirus and self-amplifying mRNA neoantigen vaccine for advanced metastatic solid tumors: phase 1 trial interim results. Nat Med. 2022 Aug;28.

In the Spotlight...

Personalized neoantigen vaccine NEO-PV-01 with chemotherapy and anti-PD-1 as first-line treatment for non-squamous non-small cell lung cancer

Awad et al. demonstrated that a personalized neoantigen vaccine, NEO-PV-01, in combination with anti-PD-1 and chemo as first-line therapy for advanced non-squamous NSCLC was well tolerated, without any serious treatment-related adverse events. Pre-treatment T cell infiltration into the TME, HLA class-II gene expression, and TCR diversity correlated with clinical response. Post-vaccine tumor biopsies showed increase in CD4+ T cell infiltration with effector and cytotoxic phenotypes. NEO-PV-01 combination therapy induced neoepitope-specific, persistent, and cytotoxic T cell responses, along with non-vaccinated epitope spread to KRAS and other mutations.

Contributed by Shishir Pant

During early stages of cancer, neutrophils initiate anti-tumor immune responses in tumor-draining lymph nodes

Pylaeva et al. studied neutrophil function in tumor-draining lymph nodes (LNs) during head and neck cancer (HNC) progression. A murine HNC model and LNs from HNC patients revealed that neutrophils from metastasis-free, early stages (N0) transmigrated to LNs, accumulated in T cell-rich zones and activated T cells in an antigen-dependent fashion. In late (N1-3) metastatic HNC, GM-CSF released from LN mets triggered neutrophils to express PD-L1 and become immunosuppressive. Five-year HNC survival data revealed a similar dual role: high LN neutrophil numbers positively predicted survival in early stages (N0), but a worse outcome in late stages (N1-3).

Contributed by Katherine Turner

TCR-engineered iNKT cells induce robust antitumor response by dual targeting cancer and suppressive myeloid cells

Delfanti et al. transduced CD1d-restricted iNKT cells derived from a iVα14-Jα18 TCR Tg mouse with a second TCR specific for an MHC-I restricted surrogate TAA (OVA) and selected dual-reactive TCR-iNKT effectors. Tumor infiltration and antitumor activity of adoptively transferred TCR-iNKT cells in mice bearing tumors expressing the cognate antigen surpassed that of transferred non-transduced iNKT cells or CD8+ T cells engineered to express the same TCR. In the TME, TCR-iNKT cells modulated myeloid cells toward an inflammatory phenotype and killed tumor cells. Efficacy was boosted by microparticulate delivery of α-galactosyl ceramide agonist.

Contributed by Paula Hochman

Endocytic membrane repair by ESCRT-III controls antigen export to the cytosol during antigen cross-presentation

Gros et al. showed that in cross-presenting cDC1s, as compared to cDC2s, the efficient export of antigens to the cytosol was associated with a higher frequency of endolysosomal rupture and recruitment of endosomal sorting complex required for transport (ESCRT)-III, the major endocytic intracellular membrane repair system. shRNA silencing of ESCRT-III induced RIPK3/MLKL-dependent necroptotic processes and persistence of unrepaired, permeable endomembranes, which allowed unrestrained leakage/export of less degraded, large branched or folded antigens into the cytosol for enhanced antigen cross-presentation in vitro and in vivo.

Contributed by Paula Hochman

Signatures of recent activation identify a circulating T cell compartment containing tumor-specific antigen receptors with high avidity

Purcarea and Jarosch et al. showed that partial protection from a neoantigen+ tumor was provided by transfer of as few as 128 neoantigen-specific T cells into irradiated host mice. PD-1, TIM-3, and LAG-3 had concerted expression on transferred T cells, which was highest on exhausted TILs. TCR avidity of transferred cells correlated with tumor protective peripheral blood T cells expressing PD-1 levels lower than in TILs, reflecting recent activation, but not with abundance or phenotype of neoantigen-specific TILs. In two patients with melanoma, neoantigen-specific TCRs were enriched among T cells expressing RNA and protein signatures of recent T cell activation.

Contributed by Paula Hochman

Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade

Palmer and Webber et al. demonstrated that cytokine-induced SH2 protein (CISH) negatively regulated human T cell function and reactivity to neoantigens, and its genetic disruption improved the efficacy of adoptive TIL therapy. CISH KO in neoantigen-selected TILs enhanced cytokine polyfunctionality, cytolysis, and reactivity against identified neoantigens, and restored TIL reactivity against universal hot spot p53 mutations. CISH KO enhanced T cell proliferation, activation, and metabolism, but not maturation. The combination of CISH deletion in TILs and PD-1 blockade resulted in tumor regression and long-term survival in B16 melanoma-bearing mice.

Contributed by Shishir Pant

Everything New this Week In...

Close Modal

Small change for you. Big change for us!

This Thanksgiving season, show your support for cancer research by donating your change.

In less than a minute, link your credit card with our partner RoundUp App.

Every purchase you make with that card will be rounded up and the change will be donated to ACIR.

All transactions are securely made through Stripe.