Endogenous Retroviruses Research Articles

201 Clear Cell Meningioma Tumorigenesis Is Characterized by Expression of Human Endogenous Retroviruses

INTRODUCTION: Human endogenous retroviruses (HERVs) are transcriptionally silenced genetic remnants of ancient exogenous retroviruses in differentiated cells yet critical to early tissue development. We recently found that aberrant expression of HERV-K envelope protein, caused by SMARCB1 mutation, is critical for tumorigenesis in atypical teratoid rhabdoid tumor (AT/RT). Clear cell meningioma (CCM) demonstrates analogous altered chromatin remodeling via SMARCE1 loss of function and syncytial histopathologic features thereby indicating a putative role for HERV expression in CCM tumorigenesis. METHODS: Eight CCM samples were evaluated for SMARCE1 status. We then quantified expression of HERV-K envelope and OCT-4 protein, a marker of pluripotency, by immunohistochemistry and compared them using linear regression. Active HERV transcript production was evaluated by RNA in-situ hybridization. Finally, we induced SMARCE1 loss in neural stem cells (NSC’s) and assessed expression of multiple HERV transcripts. We further modeled SMARCE1 knock-down in vivo in a chicken embryo model to evaluate timing of aberrant HERV expression and CCM development. RESULTS: All CCM tumor samples demonstrated loss of SMARCE1 and expression of HERV-K-Env and OCT-4 proteins and HERV transcripts. Expression was more robust in syncytial tumor-initiating cells and surrounding extracellular vesicles. HERV-K-Env expression positively correlated with OCT-4 expression (Pearson’s R = 0.7461, p = 0.033). Finally, SMARCE1 knock-down in NSC's and chicken embryos resulted in expression of multiple HERVs, supporting SMARCE1 loss of function as the mechanism of increased HERV expression in our CCM cohort. CONCLUSIONS: As mediated by loss of SMARCE1 function, HERV transcription allows for pathogenic exportation of HERV proteins to surrounding cells to maintain pluripotency in both in vitro and in vivo models. Aberrant HERV expression may therefore represent a targetable anticancer pathway for CCM and similar CNS tumors.

383 Epigenetic Potentiation of Anti-tumor Immune Responses Using Viral Mimicry for Gliomas

INTRODUCTION: Human endogenous retroviruses (HERVs) account for approximately 8% of our genome and are evolutionary relics of a germline retroviral infection. Although normally silenced by a master epigenetic regulator, np220, HERVs may be re-expressed in cellular states with marked epigenetic dysregulation and induce innate anti-viral inflammatory responses. This viral mimicry immune response sensitizes tumors to immunotherapy by eliciting double-stranded RNAs (dsRNA)-mediated interferon signaling cascades. Hence, viral mimicry could serve as a predictor of clinical responses to immunotherapy. METHODS: We conducted a preclinical study on the role of np220 in GBM and mediating viral mimicry responses. RESULTS: Using a tailored bulk transcriptional dataset from 71 newly diagnosed high-grade GBMs, we demonstrated significantly negative correlations between np220 expression and 48 HERV superfamilies. Additionally, using a transcriptional deconvolution pipeline of low-and high-grade gliomas, we demonstrated that np220 is negatively correlated with innate antiviral immune response signatures (TLR3) (RTLR3 = -0.300, pTLR3 = 0.00006). Our in vitro studies have shown that NP220 knockdown induces intracellular HERV-mediated dsRNA-signaling cascades via RIG-1 and TLR3. NP220 knockdown exponentially increases PD-L1 expression (p-value: <0.001), and, increases cytoplasmic accumulation of cellular endogenous dsRNA in established human and mouse glioma cell lines which may induce the interferon-mediated response. This response was recapitulated in recurrent GBM samples with radiographic responses to checkpoint inhibition (anti-PD1) with widely increased expression of dsRNA, PD-L1 and perivascular CD8 cell infiltration, suggesting dsRNA-signaling may mediate response to immunotherapy. Furthermore, we showed np220 is linked to reduced immune cell infiltration (CD8, Dendritic Cells) in the glioma microenvironment through deconvolution of RNA-seq data from TCGA (RCD8 = -.202, RDC = -0.198) (pCD8 = 8.79E-06, pDC = 1.34E-05). CONCLUSIONS: Our findings suggest that np220 could serve as a target to potentiate glioma ICI for immune response.

HERV-E ƛ 4-1 activation in peripheral blood mononuclear cells of the recurrent depression patients under the influence of human recombinant IL-1β

IntroductionMental disorders represent complex phenotypes and are the leading causes of global disease burden. Human endogenous retroviruses (HERVs) are ancient retroviral DNA sequences established into germline. Their tight regulation is mainly achieved by epigenetic mechanisms, which can be altered by environmental factors - viral infections, inflammation, leading to HERV activation. The aberrant expression of HERVs associates with neurological diseases and mood disorders. We showed earlier that HERV-E ƛ 4-1 activation is associated with the recurrent depression stage of exacerbation and are accompanied by a pronounced increase in the proinflammatory activity of the peripheral blood mononuclear cells (PBMC).ObjectivesThe purpose of the study was to evaluate the activity of HERV-E ƛ 4-1 on PBMCs of patients with recurrent depression in remission, including under the influence of recombinant human IL-1β.MethodsThe study included 30 patients with an established diagnosis of recurrent depression (F 33.0) aged 26–45 years. PBMC were isolated using the Ficoll density gradient method and further cultured in the presence or absence of 1 mkg/ml of recombinant human IL-1β for 24 hours. HERV-E λ 4 – 1 env gene expression was determined by the PCR. Cells proliferative activity was determined by H3-thymidine incorporation. Cytokines content in culture supernatants was assessed by ELISA.ResultsIt was shown that in all samples of PBMC cultured without IL-1β the HERV-E λ 4 – 1 env expression was not determined. After the PBMC cocultivation with recombinant human IL-1β, HERV-E λ 4 – 1 env gene expression was determined in 86,7% of cases. The HERV-E ƛ 4-1 activation in PBMC after IL-1β influence was accompanied by increased cells proliferative activity and production of IL-1β, IL-6.ConclusionsOur data indicate that the HERV-E λ 4 – 1 env expression in PBMC of recurrent depression patients in the stage of remission induced by the influence of proinflammatory cytokines, such as IL-1β. This mechanism may be one of the possible regulators of HERV-E λ 4 – 1 activation in recurrent depression.Disclosure of InterestNone Declared

Pigs in Transplantation Research and Their Potential as Sources of Organs in Clinical Xenotransplantation.

The pig has long been used as a research animal and has now gained importance as a potential source of organs for clinical xenotransplantation. When an organ from a wild-type (i. e., genetically unmodified) pig is transplanted into an immunosuppressed nonhuman primate, a vigorous host immune response causes hyperacute rejection (within minutes or hours). This response has been largely overcome by 1) extensive gene editing of the organ-source pig and 2) the administration to the recipient of novel immunosuppressive therapy based on blockade of the CD40/CD154 T cell costimulation pathway. Gene editing has consisted of 1) deletion of expression of the 3 known carbohydrate xenoantigens against which humans have natural (preformed) antibodies and 2) the introduction of human 'protective' genes. The combination of gene editing and novel immunosuppressive therapy has extended life-supporting pig kidney graft survival to greater than 1 y and of pig heart survival to up to 9 mo. This review briefly describes the techniques of gene editing, the potential risks of transfer of porcine endogenous retroviruses with the organ, and the need for breeding and housing of donor pigs under biosecure conditions.

Ocrelizumab B cell depletion has no effect on HERV RNA expression in PBMC in MS patients

BackgroundEpstein barr virus (EBV) infection of B cells is now understood to be one of the triggering events for the development of Multiple Sclerosis (MS), a progressive immune-mediated disease of the central nervous system. EBV infection is also linked to expression of human endogenous retroviruses (HERVs) of the HERV-W group, a further risk factor for the development of MS. Ocrelizumab is a high-potency disease-modifying treatment (DMT) for MS, which depletes B cells by targeting CD20. ObjectivesWe studied the effects of ocrelizumab on gene expression in peripheral blood mononuclear cells (PBMC) from paired samples from 20 patients taken prior to and 6 months after beginning ocrelizumab therapy. We hypothesised that EBV and HERV-W loads would be lower in post-treatment samples. MethodsSamples were collected in Paxgene tubes, subject to RNA extraction and Illumina paired end short read mRNA sequencing with mapping of sequence reads to the human genome using Salmon and differential gene expression compared with DeSeq2. Mapping was also performed separately to the HERV-D database of HERV sequences and the EBV reference sequence. ResultsPatient samples were more strongly clustered by individual rather than disease type (relapsing/remitting or primary progressive), treatment (pre and post), age, or sex. Fourteen genes, all clearly linked to B cell function were significantly down regulated in the post treatment samples. Interestingly only one pre-treatment sample had detectable EBV RNA and there were no significant differences in HERV expression (of any group) between pre- and post-treatment samples. ConclusionsWhile EBV and HERV expression are clearly linked to triggering MS pathogenesis, it does not appear that high level expression of these viruses is a part of the ongoing disease process or that changes in virus load are associated with ocrelizumab treatment.

Retroelements in targeted antitumor therapy (review)

Background: Pathological expression of retroelements is determined in most malignant tumors, which reflects the pathogenesis of tumors, since activated retrotransposons cause genomic instability due to a cascade of mutual regulatory influence events between transposons, tumor suppressors and oncogenes. These relationships are reflected in the expression profiles of certain long non-coding RNAs and miRNAs in specific tumor tissues, since retroelements are key sources of non-coding RNAs. Since retroelements serve as drivers for the initiation and progression of carcinogenesis, it is promising to use drugs aimed at inhibiting their expression. The aim of the study: To determine the available methods of influencing retroelements in antitumor therapy, to evaluate the ways of their further improvement for the effective treatment of malignant neoplasms. Materials and methods: The databases Scopus, WoS, PubMed were used to analyze the role of retroelements in the development of tumors, methods of influencing them in the treatment of neoplasms. Results: Reverse transcriptase inhibitors have proven to be effective. Silencing of retrotransposons by acting on histone modifiers can lead to a weakening of the antitumor immune response; therefore, this approach requires RNA guides that direct the formation of heterochromatin in the area where strictly specific retroelements are located. A promising method is viral mimicry aimed at activating the interferon and T-cell response to artificially activated endogenous retroviruses. For this purpose, inhibitors of histone methyltransferases, DNA methyltransferases, and histone deacetylases are used. Their joint use is most effective, especially with PD-1 checkpoint blockers. The arrangement of retroelements in gene introns has become the basis for the development of spliceosomal targeted therapy, which also initiates an antitumor immune response to double-stranded RNA transcripts. We suggest the possibility of using antisense oligonucleotides targeting retroelements in anticancer therapy. Such approach is used to treat age-related macular degeneration, Fukuyama muscular dystrophy, amyotrophic lateral sclerosis. Antisense oligonucleotides targeting microRNAs, proto-oncogenes, and oncosuppressors are used in anticancer therapy and are closely related to retroelements, which could become promising targets for antisense oligonucleotides. Conclusion: In antitumor therapy, it is possible to use two diametrically opposed strategies for influencing retroelements: inhibition and activation. The most promising way is a combination of these methods with specific silencing of retrotransposons using guides (complementary RNAs) and stimulation of the expression of elements not involved in carcinogenesis, but activating the immune response.

VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.

Discovering disease causative pathogens, particularly viruses without reference genomes, poses a technical challenge as they are often unidentifiable through sequence alignment. Machine learning prediction of patient high-throughput sequences unmappable to human and pathogen genomes may reveal sequences originating from uncharacterized viruses. Currently, there is a lack of software specifically designed for accurately predicting such viral sequences in human data. We developed a fast XGBoost method and software VirusPredictor leveraging an in-house viral genome database. Our two-step XGBoost models first classify each query sequence into one of three groups: infectious virus, endogenous retrovirus (ERV) or non-ERV human. The prediction accuracies increased as the sequences became longer, i.e. 0.76, 0.93, and 0.98 for 150-350 (Illumina short reads), 850-950 (Sanger sequencing data), and 2000-5000 bp sequences, respectively. Then, sequences predicted to be from infectious viruses are further classified into one of six virus taxonomic subgroups, and the accuracies increased from 0.92 to >0.98 when query sequences increased from 150-350 to >850 bp. The results suggest that Illumina short reads should be de novo assembled into contigs (e.g. ∼1000 bp or longer) before prediction whenever possible. We applied VirusPredictor to multiple real genomic and metagenomic datasets and obtained high accuracies. VirusPredictor, a user-friendly open-source Python software, is useful for predicting the origins of patients' unmappable sequences. This study is the first to classify ERVs in infectious viral sequence prediction. This is also the first study combining virus sub-group predictions. www.dllab.org/software/VirusPredictor.html.

Activation of endogenous retroviruses and induction of viral mimicry by MEK1/2 inhibition in pancreatic cancer.

While pancreatic ductal adenocarcinomas (PDACs) are addicted to KRAS-activating mutations, inhibitors of downstream KRAS effectors, such as the MEK1/2 kinase inhibitor trametinib, are devoid of therapeutic effects. However, the extensive rewiring of regulatory circuits driven by the attenuation of the KRAS pathway may induce vulnerabilities of therapeutic relevance. An in-depth molecular analysis of the transcriptional and epigenomic alterations occurring in PDAC cells in the initial hours after MEK1/2 inhibition by trametinib unveiled the induction of endogenous retroviruses (ERVs) escaping epigenetic silencing, leading to the production of double-stranded RNAs and the increased expression of interferon (IFN) genes. We tracked ERV activation to the early induction of the transcription factor ELF3, which extensively bound and activated nonsilenced retroelements and synergized with IRF1 (interferon regulatory factor 1) in the activation of IFNs and IFN-stimulated genes. Trametinib-induced viral mimicry in PDAC may be exploited in the rational design of combination therapies in immuno-oncology.

Endogenous retroviral solo-LTRs in human genome.

Human endogenous retroviruses (HERVs) are derived from the infection and integration of exogenetic retroviruses. HERVs account for 8% of human genome, and the majority of HERVs are solitary LTRs (solo-LTRs) due to homologous recombination. Multiple findings have showed that solo-LTRs could provide an enormous reservoir of transcriptional regulatory sequences involved in diverse biological processes, especially carcinogenesis and cancer development. The link between solo-LTRs and human diseases still remains poorly understood. This review focuses on the regulatory modules of solo-LTRs, which contribute greatly to the diversification and evolution of human genes. More importantly, although inactivating mutations, insertions and deletions have been identified in solo-LTRs, the inherited regulatory elements of solo-LTRs initiate the expression of chimeric lncRNA transcripts, which have been reported to play crucial roles in human health and disease. These findings provide valuable insights into the evolutionary and functional mechanisms underlying the presence of HERVs in human genome. Taken together, in this review, we will present evidences showing the regulatory and encoding capacity of solo-LTRs as well as the significant impact on various aspects of human biology.

Different Host-Endogenous Retrovirus Relationships between Mammals and Birds Reflected in Genome-Wide Evolutionary Interaction Patterns.

Mammals and birds differ largely in their average endogenous retrovirus loads, namely the proportion of endogenous retrovirus in the genome. The host-endogenous retrovirus relationships, including conflict and co-option, have been hypothesized among the causes of this difference. However, there has not been studies about the genomic evolutionary signal of constant host-endogenous retrovirus interactions in a long-term scale and how such interactions could lead to the endogenous retrovirus load difference. Through a phylogeny-controlled correlation analysis on ∼5,000 genes between the dN/dS ratio of each gene and the load of endogenous retrovirus in 12 mammals and 21 birds, separately, we detected genes that may have evolved in association with endogenous retrovirus loads. Birds have a higher proportion of genes with strong correlation between dN/dS and the endogenous retrovirus load than mammals. Strong evidence of association is found between the dN/dS of the coding gene for leucine-rich repeat-containing protein 23 and endogenous retrovirus load in birds. Gene set enrichment analysis shows that gene silencing rather than immunity and DNA recombination may have a larger contribution to the association between dN/dS and the endogenous retrovirus load for both mammals and birds. The above results together showing different evolutionary patterns between bird and mammal genes can partially explain the apparently lower endogenous retrovirus loads of birds, while gene silencing may be a universal mechanism that plays a remarkable role in the evolutionary interaction between the host and endogenous retrovirus. In summary, our study presents signals that the host genes might have driven or responded to endogenous retrovirus load changes in long-term evolution.

Abstract 2721: FF01: a novel humanized heavy chain antibody targeting endogenous retroviruses with anti-lymphoma activity

Abstract Background: Human endogenous retroviruses (HERVs) are transposable elements (TE) derived from retrovirus infections that occurred millions of years ago. Despite constituting 8% of our genome, their biological role still needs to be explored. HERV-K (HML-2), a subgroup of HERVs, represents the most recent retroviruses integrated into the human germline DNA. Members of the HML-2 subgroup retain complete ORF with coding potential and have garnered the most attention in disease-related studies. HERVs exhibit physiological expression in embryonic stem cells but are heavily methylated and remain almost silent in normal adult tissues. Although the mechanisms underlying HERV-K contribution to tumor cell growth and survival remain poorly understood, aberrant expression of HERVs has been demonstrated in various human tumor tissues and lymphoma. These findings led us to explore HERV-K as a potential therapeutic target in B cell lymphomas .Methods: RNA data were analyzed with Telescope. Validations were performed by qPCR, Western blot, flow cytometry, and ELISA. Env structure was obtained with AlphaFold and peptides were purchased from GeneScript. Antibody-dependent cellular cytotoxicity (ADCC) was performed with the ADCC Reporter Bioassay (Promega). Internalization was assessed using the Incucyte Fabfluor-pH Antibody labeling reagents. Results: We assessed the TE expression in RNA-seq datasets of diffuse large B cell lymphoma (DLBCL) and B cells from healthy individuals. An MDS plot showed that TEs could separate neoplastic from healthy samples, demonstrating that tumoral and normal specimens have distinct TE and HERV expression profiles. Focusing on tumor samples, DLBCLs were divided into four clusters with different prognoses. Similar results were obtained in a 47 B-cell lymphoma cell line panel. Focusing on the HML-2 family in lymphoma patients, we identified many of them upregulated in tumors. We validated RNA and protein expression of the HML-2 envelope (env) in seventeen lymphoma cell lines, and in two of them, we also proved the protein surface expression. Env-specific siRNA reduced env expression determined a decrease in cell proliferation, suggesting a contribution to lymphoma cell growth. In silico examination of the env identified four linear regions with potential for antibody binding, and peptides covering them were synthesized. We screened 150 lymphoma patients' serum samples for IgG antibodies binding to the peptides, and all peptides showed positive hits. We used a phage display screen to obtain one nanobody, FF01, binding one peptide. FF01 induced ADCC in the cell line with high surface env expression and not in a negative one. FF01 was internalized in an expressing cell, proving the principle for using it as a component of an antibody-drug conjugate. Conclusions: Our data demonstrate that HERVs are in DLBCL patients and propose FF01 as a new candidate to target HERV Env+ lymphomas. Citation Format: Filippo Spriano, Luciano Cascione, Jacopo Sgrignani, Nikolai Bendik, Sara Napoli, Giulio Sartori, Eleonora Cannas, Tao Gongo, Alberto J. Arribas, Davide Rossi, Davide F. Robbiani, Andrea Cavalli, Francesco Bertoni. FF01: a novel humanized heavy chain antibody targeting endogenous retroviruses with anti-lymphoma activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2721.

Abstract 5673: Transposable element expression patterns in epigenetic mutational subtypes of clear cell renal cell carcinoma

Abstract Background: Clear cell renal cell carcinoma (ccRCC) is characterized by mutations in epigenetic modulators and by aberrant transposable element (TE) expression, each of which have been separately associated with immunotherapy (IO) benefit in specific clinical contexts. However, the relationship between mutations in epigenetic regulators and TE expression, and the potential effect of both somatic mutations and TE expression on clinical outcomes, has not been fully investigated. Methods: We utilized RNA sequencing from ccRCC patients’ tumors and cell lines to quantify TE subfamily expression with TEtranscripts (n=123 metastatic IO-treated; CheckMate-009, 010, 025, n=355 all stage TCGA untreated, n=8 CCLE). Locus-specific endogenous retrovirus (ERV) expression was quantified using hervQuant. Differential TE and ERV expression was determined using DESeq2. Samples were stratified by mutations in PBRM1, SETD2, BAP1 and KDM5C, four of the top five mutated genes in ccRCC. Multivariable CoxPH models and the log-rank test were used to compare overall (OS) and progression-free survival (PFS). Two validation metastatic ccRCC cohorts were employed: the everolimus arm of CheckMate-025 (n=78, CM025e) and IMmotion150 (n=146, IM150). Results: Global TE expression (LTR, LINE, SINE and DNA transposons) did not differ significantly across mutational and clinical subtypes. However, 29 of 795 TE subfamilies were differentially expressed in >1 mutational subtype across datasets, and 22 of 29 were ERVs. At locus-specific resolution, 52 of 3173 ERVs were differentially expressed in >1 mutational subtype across datasets. Additionally, 6 of the 52 ERVs nominally associated with PFS, and 4 nominally associated with OS, in the IO cohort. Among them, only ERVs 544 and 2014 associated with improved PFS (multivariable CoxPH p = 0.03 and 0.02, respectively) and were expressed across all datasets. Both ERVs also exhibited increased expression in PBRM1 mutant and decreased expression in BAP1 mutant vs. wildtype samples, in discovery (IO, TCGA, CCLE) and validation (CM025e, IM150) cohorts. Lastly, PBRM1 mutant patients with high ERV 544 or 2014 expression had improved PFS in the IO (log-rank p = 0.04 and 0.03, multivariable CoxPH p = 0.008 and 0.009, respectively, HR = 0.43 both), but not in the CM025e cohort, compared to other patients regardless of PBRM1 mutations. Conclusion: ERVs 544 and 2014 were upregulated in PBRM1 mutant and downregulated in BAP1 mutant samples. Coupled with PBRM1 inactivation, their expression served as a candidate biomarker of improved PFS in IO-treated ccRCC that may have additional biological relevance. Expanded functional and clinicogenomic studies of epigenetic mutational subtype-specific patterns of TE expression, and their relation to selective IO response, may guide additional discovery and therapeutic development strategies in ccRCC. Citation Format: Kevin Meli, Cora A. Ricker, Sabrina Y. Camp, Christof C. Smith, Chris Labaki, Eddy Saad, Hanna Soulati, Brendan Reardon, Jihye Park, Natalie I. Vokes, Benjamin G. Vincent, Toni K. Choueiri, David A. Braun, Eliezer M. Van Allen. Transposable element expression patterns in epigenetic mutational subtypes of clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5673.

Abstract 4095: Targeting alternative classes of tumor antigens to improve immunotherapy for microsatellite stable, mismatch repair-proficient colorectal cancer

Abstract Background: The clinical outcomes of immunotherapy for microsatellite stable (MSS) colorectal cancer (CRC) remains unsatisfactory. The development of more effective immunotherapies is hampered by limited knowledge of the appropriate target antigens, also considering the low burden of mutations generating neoantigens of these tumors. Alternative classes of MSS CRC antigens may provide actionable epitopes. Methods: We have characterized the immunopeptidome of 2 MSS CRC cell lines derived from the primary tumor (SW480) and a metastatic lymph node (SW620) of the same patient. Given the low mutational burden of MSS, we focused on peptides belonging to alternative sources of HLA-A*02 epitopes, such as proteasomal cis-spliced peptides derived from cancer testis antigens and linear epitopes derived from Human Endogenous Retroviruses (HERVs), which are frequently reactivated in CRC. Peptide immunogenicity was functionally validated based on their ability to expand HLA-A*02+ donor T cells (>3) specifically killing targets cells presenting the relevant peptides or HLA-matched CRC cell lines. In vivo epitope immunogenicity was verified by analyzing polyfunctional responses of human CD8+ T cells obtained from NSG-A2 mice humanized with A*02+ donor PBMCs and immunized with epitope-loaded nano-emulsions selectively targeting human Clec9A+ dendritic cells. Therapeutic exploitation of the novel epitopes was investigated by adoptive transfer of epitope-specific T cells in NSG-A2 mice injected with SW620 cells. Epitope-specific T cell responses were investigated in PBMCs from 10 MSS CRC patients and 7 donors. Results: Among >50,000 HLA-bound peptides identified by in depth immunopeptidomics analysis, 11 cis-spliced peptides and 5 HERV peptides were functionally validated as immunogenic. Epitope-specific T cells showed specific cytotoxic activity against SW480 and SW620 CRC cells. Globally, cis-spliced peptides were more immunogenic in vitro than HERV-derived peptides. The immunogenicity of both groups of peptides was confirmed in vivo in humanized mice. Adoptively transferred HERV or cis-spliced epitope specific T cells significantly inhibited the growth of SW620 cells in vivo, with cis-spliced epitope-specific T cells being more effective. Therapeutic efficacy of Clec9A-targeting vaccines exploiting these epitopes is currently under investigation. T cell responses specific for cis-spliced and HERV epitopes were detected in PBMCs from 3/4 MSS CRC HLA-A*02+ patients but in none of 4 HLA-A*02- MSS CRC patients or 7 healthy donors (4 HLA-A*02+ and 3 HLA-A*02-). Conclusions: We have identified and validated a new class of immunogenic HLA-A*02 epitopes derived from alternative classes of MSS CRC antigens. We also provide the proof of principle supporting their therapeutic exploitation to improve the management of these poorly immunogenic tumors. Citation Format: Riccardo Dolcetti, Bijun Zeng, Jingran Ye, Tima Shamekhi, Madeleine Harpur, Davide Moi, Sara Roth, Rob Ramsay, Divya Duscharla, Antony W. Purcell, Pouya Faridi, Roberta Mazzieri. Targeting alternative classes of tumor antigens to improve immunotherapy for microsatellite stable, mismatch repair-proficient colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4095.

Abstract 1244: Exploiting the pathogenesis of endogenous retrovirus to tackle squamous cancers

Abstract Retrotransposons are the evolution relic of ancestrally invaded retroviruses interspersed through our genome. Mostly domesticated as host regulome, retrotransposons shape lineage gene expressions or donate coding functions. A few rare evolutionarily young species remain virally active, leading to germline mutations and modulating immune functions. Aberrant retrotransposon activities have been widely observed in adult diseases, although the extent to which they ensue active viral form and function under those contexts is unclear. Their molecular trigger in adult pathophysiology is poorly defined. To address these questions, we use murine skin as our model, given its well-characterized, abundant and highly accessible adult stem cells, not only mediating postnatal remodeling and homeostatic regeneration, but also responding to stress by driving tissue repair and adaptations. By analyzing a genetic model lacking a known retrotransposon suppressor, histone methyltransferase Setdb1, which we found to be essential in the adult skin, we saw hair loss and hair follicle stem cell exhaustion phenotype, accompanied by a robust and selective surge of endogenous retroviruses (ERVs). When combined with squamous cell carcinoma drivers, Setdb1 loss significantly blocked tumor progression in vivo. Interestingly, compared to relatively mild or no induction of commonly observed evolutionarily young ERVs, the most induced species in our model is a class I ERV, murine leukemia virus (MuLV). We detected abundant retroviral peptides originated from its full-length copies through mass spectrometry and viral-like particles through transmission electron microscopy that are immunoreactive to a monoclonal MuLV env antibody. Similar viral-like particles were broadly evident across several epithelial tissues beyond skin, implicating its conserved function across squamous cancers. Epithelial originated ERVs elicit tissue wide inflammatory response, and can be ameliorated by pharmacological or genetic inhibition of retroviral activity. Physiologically, viral-coding ERVs arise as the epigenetic machinery declines in response to age-associated stress, and plummet when host safeguard prevails in UV induced skin hyperplasia. As an evolutionary conundrum, viral-coding ERVs pose a threat to host fitness and yet, they’ve resisted extinction persisting in the mammalian genome. Our findings suggest viral-coding ERVs wrestle with the host surveillance programs to regulate adult tissue physiology and pathology, thus providing a key target in eliciting innate immunity and tackling squamous cancers. Citation Format: Ying Lyu, Yejing Ge. Exploiting the pathogenesis of endogenous retrovirus to tackle squamous cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1244.

Pharmacological suppression of HHLA2 glycosylation restores anti-tumor immunity in colorectal cancer

Immunotherapy aimed at inhibiting the negative co-stimulatory molecule programmed cell death-ligand 1 (PD-L1) has limited effectiveness, with clinical response rates remaining below 10%–15%. Therefore, new immune checkpoints need to be explored. Our study focused on human endogenous retrovirus H long terminal repeat–associating protein 2 (HHLA2), a highly glycosylated member of the B7 family that is widely expressed in colorectal cancer. HHLA2 expression negatively correlates with the prognosis of colorectal cancer. Glycosylation of HHLA2, which is regulated by the glycosyltransferase STT3 oligosaccharyltransferase complex catalytic subunit A (STT3A), is crucial for protein stability and expression in cell membranes. Additionally, the binding of HHLA2 to the receptors killer cell immunoglobulin-like receptor, three immunoglobulin domains and long cytoplasmic tail 3 (KIR3DL3) and transmembrane and immunoglobulin (Ig) domain containing 2 (TMIGD2) is dependent on N-glycosylation. Moreover, N-glycosylation of HHLA2 promotes immune evasion in colorectal cancer by suppressing the immune response of NK cells. Notably, the STT3A inhibitor NGI-1 enhances the anti-tumor immune response of NK cells. Our findings provide new insights and a molecular basis for targeting HHLA2 in immunotherapy for colorectal cancer.

Abstract 8: Deep Immunomics pipeline for discovery and validation of novel cancer-specific T cell receptors

Abstract Background: T cell receptor-engineered T cell (TCR-T) therapy has been studied as a high potential approach for cancer treatment. Beyond cell-surface tumor antigens, TCR-Ts can recognize HLA-presented intracellular epitopes which allows them to address a wide range of cancer-specific targets. Existing TCR-T therapies focus on a limited number of epitopes, many of which are restricted to HLA allele HLA-A*02:01. Identification of novel anti-tumor TCRs covering a broad range of HLA alleles is necessary to address unmet clinical needs. Natural T cells undergo thymic selection and present a favorable safety profile for mining such anti-tumor TCRs for therapeutic development. However, discovery of natural anti-tumor TCRs has been challenging due to i) the absence of high-throughput methods for identifying tumor-reactive TCRs in limited quantity human samples and ii) lack of sensitivity in detecting low frequency, naturally occurring tumor-reactive T cells. Methods: We developed TargetScape® as a part of our Deep Immunomics platform for efficient discovery of natural tumor-specific TCRs in healthy donors and cancer patients. Cells from blood and tissue samples were stained with metal-barcoded peptide-MHC tetramers, containing 500+ tumor-specific antigens, alongside metal-conjugated antibodies, allowing rapid identification and high dimensional phenotypic analysis of CD8+ T cells at the millions of cells scale. Single-cell sequencing revealed paired TCR sequences. Selected TCRs were introduced into luminescent Jurkat reporter cells for validation screening with peptide-pulsed targets and the relevant HLA restriction. TCRs of interest were further integrated into primary T cells and evaluated for their effector function. Results: We utilize our sensitive, high-throughput TargetScape® platform to detect and characterize putative cancer-specific TCRs from blood and tissue samples in frequencies as low as ~0.003% of total CD8+ cells. We have functionally validated over 100 TargetScape® derived TCRs with luminescent Jurkat reporters. Validated TCRs cover high prevalence HLA alleles and target a broad range of cancer antigen classes, including tumor associated antigens (TAA), Human endogenous retroviruses (HERVs), shared splice variants, and frameshift mutations. Several natural TCRs demonstrate recognition of low concentrations of peptide, indicating high functional avidity. Further evaluations of specificity and activity of TCRs of interest transduced into primary T cells are currently in progress. Conclusions: Our Deep Immunomics platform allows us to identify and confirm activity of novel, naturally-derived TCR candidates against therapeutically relevant cancer antigens presented on six common HLA alleles. These findings validate our discovery workflow leading to a portfolio of potential clinically relevant candidates that are currently under preclinical development. Citation Format: Hannah Fields, Juliana Velez Lujan, Kan Xing Wu, Natalie Epstein, Nazihah Beevi, Florence Chioh, Nicholas Tan, Neeraja Kulkarni, Noella Mukobo, Srikanthi R, Yovita Purwanti, Evan Newell, Alessandra Nardin, Michael Fehlings, Katja Fink, Daniel MacLeod. Deep Immunomics pipeline for discovery and validation of novel cancer-specific T cell receptors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 8.

Abstract 6432: Co-expression of HERV-R, CCND1, BRAF, FOXA1, TMPRSS2, ATF4 and low expression of BAZ1B and KMT2D is associated with early detection and poor prognosis of prostate cancer in African Black men from Nigeria

Abstract Prostate cancer (CaP) is a heterogeneous disease characterized by features of non-aggressive, slow-growing disorders to fast-growing disease. Men of African ancestry have disproportionately higher incidence and mortality rates for CaP than men of European ancestry. While there is evidence for a higher genetic predisposition for incidence of CaP in men of African ancestry compared to men of European ancestry, there is paucity of molecular biology and transcriptomic studies on the role of Human endogenous retroviruses (HERVs) in relation to CaP-associated genes in CaP pathogenesis and prognosis. In this study, we performed bulk RNA sequencing (RNA-seq) on formalin-fixed paraffin-embeded (FFPE) CaP samples from Nigerian CaP patients to investigate the expression significance of HERV-R in relation to FOXA1, TMPRSS2, BAZ1B, KMT2D, ATF4 and BRAF genes. Based on this findings, we used immunohistochemistry (IHC), enzyme-linked immunosorbent assay (ELISA) and immunofluorescence (IF) to confirm the expression pattern of the HERV-R and FOXA1, TMPRSS2, BAZ1B, KMT2D, ATF4 and BRAF proteins on 45 FFPE CaP and blood plasma samples, and 5 CaP-free samples from patients in Zaria, Nigeria. Most of these patients were longitudinally followed from 2017 to date. The DESeq2 procedure was used for data processing, analysis, and differential expression analysis of the aforementioned genes. We found a significant expression of HERV-R in relation with FOXA1, TMPRSS2, BAZ1B, KMT2D, ATF4, CCND1 and BRAF in the CaP from rural Africans in Nigeria. HERV-R expression was found to be associated with increased PSA level, higher Gleason grade and poor prognosis of CaP. A CaP sample from an 80-year-old patient that was histologically diagnosed to have no malignancy seen despite high PSA level of >100 and poor disease outcomes shows a significant cytoplasmic expression of HERV-R, indicating that HERV-R may serve as an important biomarker for early detection. Unfortunately, we lost the 80-year-old patient to late detection before revisiting his case for proper histological diagnosis and management. In addition, some histologically diagnosed BPH samples that are apparently reported to be CaP-free show stromal cells expression of HERV-R and in some cases show expression of HERV-R in the prostatic glandular areas. In contrast, stromal cells of the CaP samples show no expression of HERV-R, but strong expression in the glandular areas. This may implicate a gradual transition from benign prostatic lesion to malignant prostatic disease. HERV-R expression in CaP may have a relationship with BRAF, CCND1, FOXA1, TMPRSS2 and ATF4 genes. These findings combined together, underscore the importance of the expanded concept of HERV-R expression and CaP associated genes in early detection of CaP and prognosis. Citation Format: Faruk Mohammed, Konrad Stawiski, Halimatu Sadiya Musa, Sani Kamarudeen Owolabi, Sani Abubakar, Solomon O. Rotimi, Adoke Kasimu Umar, Yawale Iliyasu, Ahmad Bello, Folakemi T. Odedina, Clayton C. Yates, Kevin Petrie, Franklin W. Huang, Sani Ibrahim. Co-expression of HERV-R, CCND1, BRAF, FOXA1, TMPRSS2, ATF4 and low expression of BAZ1B and KMT2D is associated with early detection and poor prognosis of prostate cancer in African Black men from Nigeria [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6432.

Abstract 1708: Transposable element derived enhancers in ovarian cancer

Abstract There is global epigenetic dysregulation during transformation from normal to cancerous cells. One of the many consequences of this global epigenetic dysregulation is the reactivation of transposable elements (TEs). TEs compose roughly half of the human genome and are normally repressed through epigenetic mechanisms such as DNA methylation and histone modifications. Endogenous retroviruses (ERVs) are a class of TEs that contain long terminal repeats (LTRs) with putative gene regulatory motifs. LTRs can be co-opted to be pro-tumorigenic by becoming non-canonical promotors for oncogenic genes. While several examples of TE-derived promotors have been reported in cancer, the potential significance of TE-derived enhancers remains largely unexplored. Here, we utilized publicly available multi-omics datasets (bulk and single-cell ATAC-seq, bulk and single-cell RNA-seq, and chromatin profiling) in the context of ovarian cancer to determine if there are tumor specific, TE-derived-enhancers that have gene regulatory function. We used CRISPRi technology to functionally validate a putative TE-derived enhancer and gene regulatory axis. We discovered that on the bulk tissue level, several TE families are enriched at open chromatin sites and sites marked by H3K27Ac (enhancer mark) of ovarian tumors, suggesting the presence of tumor specific, TE-derived enhancers. On the single-cell level, we discovered that ovarian cells have the highest expression of these TE transcripts compared to stromal and immune cells in the tumor microenvironment, suggesting that the increased TE-derived enhancer activity observed on the bulk level are specific to ovarian cells. Lastly, when we silenced a specific LTR18 locus upstream of a gene, TIPARP, TIPARP gene expression was also repressed, suggesting that these putative TE-derived enhancers have gene regulatory function. Determining the regulatory role of these TE-derived enhancers will provide novel insights into cancer-related transcriptomes. Citation Format: Lily L. Nguyen, Atma Ivancevic, Benjamin G. Bitler, Edward B. Chuong. Transposable element derived enhancers in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1708.

Abstract 2464: Defective NMD promotes aberrant intron retention in clear cell renal cell carcinoma

Abstract Clear cell renal cell carcinoma (ccRCC) is the 8th most common cancer in the United States, constituting 75% of all kidney cancer cases. Clear cell RCC (ccRCC) along with melanoma has traditionally been viewed as an immunotherapy responsive disease with a storied history of immunotherapy treatments including high dose interleukin 2 (IL2), interferon, and allogeneic stem cell transplant. Indeed, RCC was one of the first tumor types to garner FDA approval for PD1 immune checkpoint inhibition (ICI). However, unlike melanoma, most RCC tumors do not have a high tumor mutational burden (TMB) to potentially explain their immunotherapy responsiveness. We and others have sought to explain this unanswered question and have demonstrated that non-canonical tumor associated antigens like endogenous retroviruses (ERVs) may in part explain ICI response in RCC. We have noted that ccRCC tumors have the highest level of retained introns (RI) across all TCGA tumors, that RI levels are secondary to suppressed non-sense mediated decay (NMD) activity, and that one can subset ccRCC into RI-high and normal-like tumors. Moreover, we have found that mTOR signaling plays a key role in regulating NMD and intron retention and that mTOR inhibition can promote intron retention. We hypothesized that these aberrantly retained introns could serve as a rich source of highly foreign, tumor associated neoantigens and that of retained intron neoantigens, the ones not observed in normal tissue would be the most immunogenic. We derived a so called “Neo-RI-antigen burden” that represents the burden of retained intron neoantigens not found in normal tissues and demonstrate that the Neo-RI-antigen burden of complete responders is numerically higher than those with partial response or progressive disease in a dataset of immunotherapy treated melanoma patients. Our work suggests the possibility of using NMD-targeting drugs as a potential therapeutic in combination with ICI to enhance the overall treatment response. Citation Format: Mi Zhou, Gilbert Giri, William Y. Kim, Daniel Dominguez. Defective NMD promotes aberrant intron retention in clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2464.

Abstract 2838: ZNFX1 is a master regulator and tumor suppressor in epigenetically induced pathogen mimicry, mitochondrial dysfunction and STING-dependent signaling in cancer

Abstract Immunomodulatory agents are an important recent advance in cancer therapy, but utility is often limited by tumor immune evasion mechanisms. Strategic therapeutic activation of intracellular antiviral immune responses offers an opportunity to reverse immune evasion mechanisms and improve treatment outcomes. Anti-cancer agents such as, DNA methyltransferase inhibitors (DNMTis) induce re-expression of endogenous retroviruses (ERVs), leading to cytosolic double-stranded RNA (dsRNA) accumulation that activates interferon/inflammasome signaling. Moreover, poly (ADP ribose) polymerase inhibitors (PARPi) increase cytosolic dsDNA, activating stimulator of interferon (IFN) genes (STING). We reported that DNMTis in combination with PARPis induce STING-dependent signaling in a process termed pathogen mimicry response (PMR). Mitochondria (mt) are an important gateway for antiviral inflammasome signaling, but are not fully understood in cancer. Our studies of the little-known gene, NFX1-type zinc finger-containing 1 (ZNFX1), show that it acts as a master nucleic acid (dsRNA/DNA) sensor for mt gateway function. Bioinformatics analysis in primary ovarian tumors from TCGA and clinical trial RNAseq datasets, shows that increased ZNFX1 expression tracks with tumor stage and grade but inversely correlates with a mt dysfunction signature. In studies of high-grade and endometrial serous carcinoma (OC) cell lines (N=3), transfection of dsRNA/DNA mimics or DNMTi azacytidine (AZA) and PARPi (talazoparib [TAL]) treatments induce increased ZNFX1 expression and binding to mt antiviral protein (MAVs) localized on the mt outer membrane. Functional studies of mt dysfunction in OC cells, show that dsRNA/DNA as well as above viral mimicry drugs increase mt reactive oxygen species (ROS) as measured by mitosox flow cytometry. AZA and TAL treatments also increase fragmented mtDNA and oxidative mtDNA base damage, as measured by long range PCR and 8-oxoguanine (8-oxoG) ELISA assays. These drug treatments also increase release of mtDNA into the cytosol, resulting in STING-dependent inflammasome signaling and cytokine release. Notably, ZNFX1 knockout (KO) attenuates these dynamics, including in bioinformatics of RNA seq data, thus defining this gene as essential for IFN/inflammasome signaling induced by mtDNA damage. Further pathway analysis of ZNFX1 KO vs wild-type (WT) RNAseq data suggest increased proliferation and epithelial to mesenchymal transition (EMT) that was validated by in vitro and in vivo assays. Not only is ZNFX1 a master regular of the above mt dynamics, but it is a tumor suppressor in OC. Abrogating ZNFX1 expression in OC cells triggers increased cell proliferation, invasive capacity and, in-vivo, increased tumor growth. This work then suggests novel approaches to improve immune therapy responses in OC through manipulating ZNFX1. Citation Format: Lora Stojanovic, Rachel Abbotts, Kaushlendra Tripathi, Collin M. Coon, Sheng Liu, Jun Wan, Michael Topper, Stephen Baylin, Kenneth Nephew, Feyruz Rassool. ZNFX1 is a master regulator and tumor suppressor in epigenetically induced pathogen mimicry, mitochondrial dysfunction and STING-dependent signaling in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2838.