Human endogenous retroviruses (HERV) form a substantial part of the human genome, but mostly remain transcriptionally silent under strict epigenetic regulation, yet can potentially be reactivated by ...malignant transformation or epigenetic therapies. Here, we evaluate the potential for T cell recognition of HERV elements in myeloid malignancies by mapping transcribed HERV genes and generating a library of 1169 potential antigenic HERV-derived peptides predicted for presentation by 4 HLA class I molecules. Using DNA barcode-labeled MHC-I multimers, we find CD8
T cell populations recognizing 29 HERV-derived peptides representing 18 different HERV loci, of which HERVH-5, HERVW-1, and HERVE-3 have more profound responses; such HERV-specific T cells are present in 17 of the 34 patients, but less frequently in healthy donors. Transcriptomic analyses reveal enhanced transcription of the HERVs in patients; meanwhile DNA-demethylating therapy causes a small and heterogeneous enhancement in HERV transcription without altering T cell recognition. Our study thus uncovers T cell recognition of HERVs in myeloid malignancies, thereby implicating HERVs as potential targets for immunotherapeutic therapies.
Background
Standard care for patients with high-risk myelodysplastic syndrome (MDS) is hypomethylating agents such as azacitidine (AZA), which can induce expression of methylated tumor-associated ...antigens and therefore potentiate immunotherapeutic targeting.
Method
In this phase 1 trial, we combined AZA with a therapeutic peptide vaccine targeting antigens encoded from
NY-ESO-1, MAGE-A3, PRAME,
and
WT-1
, which have previously been demonstrated to be upregulated by AZA treatment.
Result
Five patients who had responded to AZA monotherapy were included in the study and treated with the vaccine. The combination therapy showed only few adverse events during the study period, whereof none classified as serious. However, no specific immune responses could be detected using intracellular cytokine staining or ELISpot assays. Minor changes in the phenotypic composition of immune cells and their expression of stimulatory and inhibitory markers were detected. All patients progressed to AML with a mean time to progression from inclusion (TTP) of 5.2 months (range 2.8 to 7.6). Mean survival was 18.1 months (range 10.9 to 30.6) from MDS diagnosis and 11.3 months (range 4.3 to 22.2) from inclusion. Sequencing of bone marrow showed clonal expansion of malignant cells, as well as appearance of novel mutations.
Conclusion
The patients progressed to AML with an average time of only five months after initiating the combination therapy. This may be unrelated to the experimental treatment, but the trial was terminated early as there was no sign of clinical benefit or immunological response.
Why the manuscript is especially interesting
This study is the first to exploit the potential synergistic effects of combining a multi-peptide cancer vaccine with epigenetic therapy in MDS. Although our results are negative, they emphasize challenges to induce immune reactivity in patients with high-risk MDS.
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EMUNI, FZAB, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NUK, OILJ, PNG, SAZU, SBCE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Background: Standard care for patients with high risk myelodysplastic syndrome (MDS) is hypomethylating agents, such as azacitidine (AZA). AZA can induce expression of silenced genes, including ...methylated tumor associated antigens. Such tumor associated antigens may be recognized by T cells, and therefore exploited for immunotherapeutic targeting. To our knowledge, this is the first clinical study that combine hypomethylating agents with a multi-peptide therapeutic cancer vaccine in a hematological malignancy.
Method: In this open label phase 1 trial (ClinicalTrials.gov NCT02750995), we combine AZA with a peptide vaccine targeting antigens encoded from NY-ESO-1, MAGE-A3, PRAME and WT-1, which have previously been demonstrated to be upregulated by AZA treatment. Four long synthetic peptides containing previously described class I and class II epitopes for a variety HLA types was emulsified in Incomplete Freund's Adjuvant for subcutaneous injection. Patients were included following verified treatment response to six courses of AZA monotherapy.
Result: Five patients were included in the study and treated with the vaccine. The combination therapy showed only few adverse events during the study period, whereof none classified as serious. There was one instance of grade 4 toxicity; a case of neutrophil count decrease, requiring administration of prophylactic antibiotics, and two instances of grade 3 toxicity; platelet count decrease and neutrophil count decrease. No vaccine-specific immune response could be detected using intracellular cytokine staining or ELISpot assays, however changes in the phenotypic composition of immune cells and their expression of stimulatory and inhibitory markers were identified in individual patients. All patients progressed to AML with a mean time to progression from inclusion (TTP) of 4.9 months (range 2.8 to 7.6). Survival was 17 months (range 10.9 to 30.6) from MDS diagnosis. Sequencing of bone marrow showed clonal evolution of malignant cells, as well as appearance of novel mutations.
Conclusion: The patients progressed to AML with an average time of only five months after initiating the combination therapy. This may be unrelated to the experimental treatment, but the trial was terminated early as there was no sign of clinical benefit or immunological response.
Figure 1. (a) Trial design. All participants received six courses of AZA prior to inclusion and were evaluated with bone marrow biopsy for treatment response. Vaccination was given together with the next three courses of AZA. (b) Vaccine composition. Synthetic long peptides from NY-ESO-1, PRAME, MAGE-A3 and WT-1 were emulsified in adjuvant Montanide ISA 51.
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No relevant conflicts of interest to declare.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract
Human endogenous retroviruses (HERVs) form a substantial part of the human genome. However, most elements remain transcriptionally silent. Malignant transformation and epigenetic therapies ...may induce transcription of HERV elements. Such HERV elements could potentially trigger adaptive immune responses and provide targets for immunotherapy applications. Here, we evaluate the potential for T cell recognition of HERV elements in myeloid malignancies. We studied 66 HERV genes reported to retain transcriptional activity and generated a library of 1,169 potential antigenic HERV-derived peptides predicted for presentation by 4 HLA class I molecules. Through the use of DNA barcode-labeled MHC-I multimers, we identified CD8+ T cell populations recognizing 29 HERV-derived peptides, represented by 18 different HERVs. T cell recognition of HERVs was detected in half of the 34 patients analyzed and was significantly enhanced in patients compared to healthy donors. Patients with HERV-derived T cell reactivity demonstrated improved viral-antigen recognition following treatment, indicating that HERV-derived T cell recognition may contribute to the therapy-induced clinical improvement and immune reconstitution. In line with the T cell data, transcriptomic analyses revealed a significantly enhanced transcription of the HERVs in patients compared to healthy donors. DNA-demethylating therapy did not result in additional transcriptional enhancement of the HERVs evaluated for T cell recognition. Our study demonstrates substantial T cell recognition of HERVs in myeloid malignancies. These HERVs could serve as a reservoir of antigens potentially exploited as immunotherapeutic targets in malignancies with low mutational burden.
Multicolor flow cytometry is an essential tool for studying the immune system in health and disease, allowing users to extract longitudinal multiparametric data from patient samples. The process is ...complicated by substantial variation in performance between each flow cytometry instrument, and analytical errors are therefore common. Here, we present an approach to overcome such limitations by applying a systematic workflow for pairing colors to markers optimized for the equipment intended to run the experiments. The workflow is exemplified by the design of four comprehensive flow cytometry panels for patients with hematological cancer. Methods for quality control, titration of antibodies, compensation, and staining of cells for obtaining optimal results are also addressed. Finally, to handle the large amounts of data generated by multicolor flow cytometry, unsupervised clustering techniques are used to identify significant subpopulations not detected by conventional sequential gating.
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•Multicolor flow cytometry is a powerful tool for analyzing patient samples in clinical and translational research. However, since flow cytometers' performance, avoidance of unsatisfactory loss of data resolution due to spectral overlap when using multiple colors can be challenging.•We outline a systematic workflow for panel design by using a Spillover Spread Matrix, recorded on the machine intended to run the experiments. The workflow ensures that poorly expressed antigens are coupled with the brightest fluorochromes and that fluorochromes with significant spectral overlap do not bind to the same cell type, which is essential for obtaining reliable results.•Furthermore, we address state-of-the-art methods for compensation, quality control, staining of cells, and data analysis using conventional gating and unsupervised clustering.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
We hypothesized that resistance to hypomethylating agents (HMA) among patients with myelodysplastic syndrome (MDS) and chronic myelomonocytic leukemia (CMML) would be overcome by combining a ...programmed death-ligand 1 antibody with an HMA.
We conducted a Phase I/II, multicenter clinical trial for patients with MDS not achieving an International Working Group response after at least 4 cycles of an HMA ("refractory") or progressing after a response ("relapsed") with 3+ or higher risk MDS by the revised International Prognostic Scoring System (IPSS-R) and CMML-1 or -2. Phase I consisted of a 3+3 dose-escalation design beginning with guadecitabine at 30 mg/m2 and escalating to 60 mg/m2 Days 1 to 5 with fixed-dose atezolizumab: 840 mg intravenously Days 8 and 22 of a 28-day cycle. Primary endpoints were safety and tolerability; secondary endpoints were overall response rate (ORR) and survival.
Thirty-three patients, median age 73 (range 54-85), were treated. Thirty patients had MDS and 3 had CMML, with 30% relapsed and 70% refractory. No dose-limiting toxicities were observed in Phase I. There were 3 (9%) deaths in ≤ 30 days. Five patients (16%) came off study for drug-related toxicity. Immune-related adverse events (IRAE) occurred in 12 (36%) patients (4 grade 3, 3 grade 2, and 5 grade1). ORR was 33% 95% confidence interval (CI), 19%-52% with 2 complete remission (CR), 3 hematologic improvement, 5 marrow CR, and 1 partial remission. Median overall survival was 15.1 (95% CI, 8.5-25.3) months.
Guadecitabine with atezolizumab has modest efficacy with manageable IRAEs and typical cytopenia-related safety concerns for patients with relapsed or refractory MDS and CMML.
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