Software for the complete characterization of antibody repertoires: from germline and mRNA sequence assembly to deep learning predictions of their protein structures and targets

每个人的B细胞群估计会产生1010种不同的抗体，统称为 抗体曲目。这种非同寻常的多样性对于应对 在一个人的一生中遇到的感染、疫苗接种和癌症。相反，监管方面的错误 该系统在一系列自身免疫性疾病中发挥着关键作用。抗体由两种蛋白质组成，一种是 重链和轻链，每个都包含一个可变区，VH和VL，它们一起赋予抗原结合 专一性。多样性是通过在编码基因座的三个V区进行差异重组而产生的 天真的曲目。一旦暴露于抗原，表达该抗原特异性抗体的B细胞就会经历 编码该基因的V区序列的克隆性扩展和集中体细胞超突变(SHM) 抗原识别结构域。这些克隆获得的B细胞(克隆型)各自表达不同的序列和 从而产生初始未突变抗体的结构变异。选择表达高亲和力变异体的细胞 因为在一个称为亲和力成熟的过程中。通过这种方式，成熟的曲目是从 那个人的抗原性接触。对这段历史的有效破译可能有助于改善 从更好的临床决策到改进的诊断和治疗，在许多方面促进了人类健康。 为了实现这一目标，DNA/RNA测序、蛋白质结构建模等方面正在取得的技术进步 软件和高性能可扩展计算机硬件正在制造虚拟谱系规模抗体 在不太遥远的将来可能实现的结构和抗原筛选。 在这个直接到第二阶段的应用程序中，我们建议构建一个软件套件来弥合 基因组学和结构生物学使抗体谱系能够被破译并以精致的细节挖掘。 为此，我们首先利用我们的高度可扩展的序列汇编程序XNG来产生单倍型阶段性和 可以模拟幼稚谱系的生殖系IG基因座的注释序列(目标1)。下一首, XNG用于汇编和注释产生线性VH和VL编码的批量BCR-SEQ数据 成熟剧目序列(目标2)。然后将翻译后的曲目序列用作我们的 蛋白质建模软件NovaFold-Ab和NovaFold-AI，其中高精度的3D抗体结构 预测(目标3)。然后在虚拟屏幕中使用这些抗体结构库来识别 使用我们的蛋白质相互作用建模程序NovaDock(Aim 4)与目标抗原结合。屏幕也可以是 提纯到感兴趣的特定表位，例如，那些已知能引发中和抗体的表位。如果实现了， 这些能力将为补充现有技术带来巨大的商业机会 改善临床护理和个性化医疗，并帮助开发更快、更高成本的产品 有效的诊断和治疗方法。

The B cell population in each individual produces an estimated 1010 different antibodies, collectively known as the antibody repertoire. This extraordinary diversity is essential for responding to the unique history of infections, vaccinations and cancer encountered over an individual’s lifetime. Conversely, regulatory errors in the system play a pivotal role in a host of auto-immune diseases. Antibodies are composed of two proteins, a heavy and light chain, each containing a variable region, VH and VL, which together confer antigen binding specificity. Diversity is initiated through differential recombination at the three V region encoding loci to produce the naïve repertoire. Upon antigen exposure, B cells expressing an antibody specific to that antigen undergo clonal expansion and concentrated somatic hypermutation (SHM) of V region sequences that code for the antigen recognition domain. Those clonally derived B cells (clonotypes) each express a different sequence and thereby structural variant of the initial unmutated antibody. Cells expressing higher affinity variants are selected for in a process known as affinity maturation. In this way, the mature repertoire is built from the history of antigenic encounters by that individual. Efficient deciphering of that history could contribute to improving human health in numerous ways from better clinical decision making to improved diagnostics and therapeutics. Toward that goal, ongoing technological advances in both DNA/RNA sequencing, protein structure modeling software and high-performance scalable computer hardware are making virtual repertoire scale antibody structure and antigen screening attainable in the not-too-distant future. In this Direct to Phase II application, we propose to build a software suite that bridges the gap between genomics and structural biology enabling antibody repertoires to be deciphered and mined in exquisite detail. To do so, we first leverage our highly extensible sequence assembler, XNG, to produce haplotype phased and annotated sequences of the germline IG loci from which the naïve repertoire can be simulated (Aim 1). Next, XNG is used to assemble and annotate bulk BCR-seq data producing the linear VH and VL encoding sequences of the mature repertoire (Aim 2). Translated repertoire sequences are then used as input for our protein modeling software, NovaFold-Ab and NovaFold-AI, where high accuracy 3D antibody structures are predicted (Aim 3). Those antibody structure libraries are then used in virtual screens to identify members that bind to a target antigen with our protein interaction modeling program, NovaDock (Aim 4). Screens can also be refined to specific epitopes of interest, for example, those known to elicit neutralizing antibodies. If realized, these capabilities will have significant commercial opportunities for complementing existing technology in improving clinical care and personalized medicine as well as aiding in the development of faster, more cost effective diagnostics and therapeutics.