Comprehensive validation and commercial readiness of SpliceIO, a software platform for neoantigen discovery using RNA-seq data

SpliceIO 的全面验证和商业准备，这是一个使用 RNA-seq 数据发现新抗原的软件平台

• 批准号: 10647773
• 负责人: MARTIN AKERMAN
• 金额: $ 98.03万
• 依托单位: ENVISAGENICS, INC.
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10647773
• 关键词: Alternative Splicing; Antigens; Automobile Driving; BRCA mutations; Benchmarking; Benign; Binding; Breast; Calibration; Case Study; Cell surface; Collaborations; Computer software; Coupled; Data; Development; Disease; Event; Fishes; Gene Expression Regulation; Generations; Genetic Transcription; Goals; High Prevalence; Immunooncology; Immunotherapeutic agent; Laboratories; Licensing; MHC antigen; Malignant Neoplasms; Malignant neoplasm of ovary; Mammary Gland Parenchyma; Mammary Neoplasms; Medical; Medically Underserved Area; Messenger RNA; Methods; Mutation; Non-Malignant; Organoids; Outcome; Pancreas; Patients; Pediatric Neoplasm; Performance; Phase; Population; Preventive; Process; Production; Prostate; Protein Isoforms; Proteins; Proteome; Proteomics; RNA; RNA Splicing; Readiness; Regulation; Research; Risk; Sampling; Small Business Innovation Research Grant; Source; Surface Antigens; Therapeutic; Tissues; Translations; Tumor Burden; Tumor stage; Universities; Validation; Woman; Work; brca gene; cancer immunotherapeutics; cancer therapy; candidate identification; candidate validation; clinical care; clinically actionable; commercialization; computational pipelines; deep sequencing; exome sequencing; malignant breast neoplasm; mammary; mutation carrier; neoantigens; novel; novel strategies; patient population; prospective; proteogenomics; tandem mass spectrometry; tool; transcriptome; transcriptome sequencing; tumor

PROJECT SUMMARY Accurate splicing is critical for the assembly of viable mRNA isoforms. Splicing errors, resulting in disease- causing mRNAs, occur frequently. In fact, ~50% of all cancer-driving synonymous mutations are predicted to cause splicing errors. Since the introduction of analytic software to quantify alternative splicing (AS) from RNA sequencing (RNAseq) data, evidence pointing to the importance of splicing regulation in cancer has mounted. Splicing errors are a major source of tumor-specific neoantigens, thus splicing research opens tremendous opportunities for the development of cancer immunotherapeutics and preventives. Envisagenics has developed SpliceIO, a software platform for neoantigen discovery using only RNAseq data. Most other methods for neoantigen prediction rely on whole-exome sequencing for the discovery of mutation-based neoantigens, a method that is not amenable to cancers with low tumor mutational burden (TMB), such as breast, prostate, pancreatic, pediatric tumors and other benign conditions. These cancers, however, are rich in splicing errors which can be detected with SpliceIO, making neoantigen discovery possible in this currently underserved area of medical need. Moreover, current methods predict neoantigens based on their ability to bind and be presented by MHC molecules which are downregulated in >60% of late-stage tumors. Since SpliceIO focuses on splicing errors it has the ability to predict both MHC-presented and MHC-independent antigens that are directly bound to the cell surface. The goal of this Direct-to-Phase II proposal is to build upon strong preliminary data and attain commercial readiness for SpliceIO. Envisagenics has been at the forefront of RNAseq-based target discovery since the development and commercialization of SpliceCore®, a software platform for the identification of druggable splicing isoforms. Envisagenics will utilize a proven commercialization strategy, which consists of comprehensive experimental validation to solidify a strong value proposition and commercial offering to prospective biopharma partners. In this proposal, we will develop a novel strategy for large-scale neoantigen validation using tandem mass spectrometry (MS/MS). In addition, we will scale identification of neoantigens using mammary organoids from BRCA1/2 mutation carriers. We present preliminary data equivalent to results from a Phase I SBIR and demonstrate the utility of splicing-derived target discovery for cancer therapeutics. To accomplish these goals and obtain commercial readiness for SpliceIO we will complete the following specific aims in this proposal: Aim 1: Develop a high-depth/high-sensitivity reference proteome for SpliceIO validation using MS/MS data. Aim 2: Neoantigen identification in BRCA1/2 mutation carriers using ultra-deep sequencing. Aim 3: Experimental validation of splicing-derived neoantigens. Completion of these aims will bring SpliceIO to a level of development proven to support successful commercialization and make a significant difference patient treatment and clinical care.

项目概要 准确的剪接对于可行的 mRNA 同种型的组装至关重要。剪接错误会导致疾病。 事实上，大约 50% 的癌症驱动同义突变预计会发生。 自从引入分析软件来量化 RNA 的选择性剪接 (AS) 以来，导致剪接错误。 随着测序（RNAseq）数据的不断增加，越来越多的证据表明剪接调控在癌症中的重要性。 剪接错误是肿瘤特异性新抗原的主要来源，因此剪接研究开启了巨大的大门 Envisagenics 的发展为癌症免疫治疗和预防提供了机遇。 SpliceIO，一个仅使用 RNAseq 数据发现新抗原的软件平台。 新抗原预测依赖于全外显子组测序来发现基于突变的新抗原， 不适用于低肿瘤突变负荷 (TMB) 的癌症，例如乳腺癌、前列腺癌、 然而，胰腺癌、儿童肿瘤和其他良性癌症却存在大量剪接错误。 可以使用 SpliceIO 进行检测，使得在目前服务不足的地区发现新抗原成为可能 此外，当前的方法根据新抗原的结合和呈递能力来预测它们。 由于 SpliceIO 专注于剪接，因此 MHC 分子在超过 60% 的晚期肿瘤中下调。 它能够预测直接结合的 MHC 呈递抗原和 MHC 独立抗原 细胞表面。 这项直接进入第二阶段提案的目标是建立在强有力的初步数据基础上并实现商业化 自成立以来，Envisagenics 一直处于基于 RNAseq 的靶标发现的前沿。 SpliceCore® 的开发和商业化，这是一个用于识别药物的软件平台 Envisagenics 将利用经过验证的商业化策略，其中包括全面的剪接异构体。 实验验证，为未来的生物制药公司巩固强大的价值主张和商业产品 在这项提案中，我们将开发一种使用串联进行大规模新抗原验证的新策略。 此外，我们将使用乳腺类器官对新抗原进行规模化鉴定。 我们提供了与 I 期 SBIR 结果相当的初步数据，以及 证明剪接衍生的靶标发现在癌症治疗中的实用性。 为了实现这些目标并为 SpliceIO 做好商业准备，我们将完成以下工作 该提案的具体目标： 目标 1：为 SpliceIO 开发高深度/高灵敏度参考蛋白质组 使用 MS/MS 数据进行验证 目标 2：使用超深深度鉴定 BRCA1/2 突变携带者的新抗原。 目标 3：剪接衍生新抗原的实验验证将实现这些目标。 SpliceIO 的开发水平已被证明能够支持成功的商业化并产生重大影响 不同的患者治疗和临床护理。