LIG4

徐寒梅中国药科大学二级教授（博导），海洋药学专业负责人，江苏省合成多肽药物发现与评价工程研究中心主任，国家药典委员会委员，国家级高层次人才项目入选者。主编出版 3 部论著（《新药非临床研究与开发》《抗肿瘤药物药理学实验指南》《酶类药物学》），发表学术论文 213 篇（SCI 收录 81 篇）， 申请国内专利 32 项（获授权 24 项），培养研究生 160 名（博士 29 名）。主办“第十四届中国国际多肽学术会议暨第五届亚太国际多肽学术会议”，多次受邀参加国内外学术会议报告。研究领域涉及多肽药物研发、全新微肽发现及机制研究、长链非编码 RNA 与疾病关系的分子机制。主持课题包括国家自然科学基金、国家 “863”计划、国家重大专项和重大横向课题等项目 30 余项。先后获中国药科大学“十三五”科技突出贡献奖，联合国教科文组织和平中心“2020 跨文化科技大使”，教育部技术发明奖一等奖，中国产学研合作创新成果 奖二等奖，江苏医药科技进步奖一等奖、二等奖各 1 次，中国发明创业成果奖一等奖，江苏省科学技术奖一等奖，江苏省高校“青蓝工程”中青年学术带头人，内蒙古组织部 “草原英才”等奖励和荣誉。优化规律间隔成簇短回文重复序列相关核酸酶 9 敲入效率的研究进展 PPS 洪秀，李臣诚，徐寒梅 *（中国药科大学生命科学与技术学院，江苏 南京 210009）[ 摘要 ] 基因编辑技术可以通过在基因组 DNA 中精确插入、缺失或替换而人为地修饰靶位点的遗传物质。近年来，随着规律间隔成簇短回文重复序列及其相关核酸酶9（clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9, CRISPR/Cas9）系统的发展，研究人员对各种细胞基因组进行编辑的能力大大提高，但由于同源定向修复（homologous directed repair, HDR）效率低下，许多通过抑制非同源末端连接（non-homologous end joining, NHEJ）或增强 HDR 的方法，如化学调节、同步表达和同源臂优化等被开发出来用以提高基于 CRISPR/Cas9 系统的精确基因敲入效率，重点介绍这些方法如何优化 Cas9 敲入效率的最新进展。 基因编辑是针对靶基因进行插入、敲除和定点突变以完成精确修饰的基因工程技术 [1]，目前包括锌指核酸酶（zinc-finger nuclease，ZFN）技术、转录激活因子样效应核酸酶（transcription activator-like effector nuclease，TALEN）技术和规律间隔成簇短回文重复序列及其相关核酸酶9（clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9，CRISPR/Cas9）技术[2]。天然的CRISPR/Cas9 系统由Cas9，CRISPR 衍生 RNA（CRISPR-derived RNA，crRNA）和反式激活crRNA（trans-activating crRNA，tracrRNA）3 部分组成，crRNA 和 tracrRNA 通过局部碱基配对形成引导RNA（guide RNA，gRNA），与 Cas9 蛋白结合并引导其识别和切割目标 DNA 序列 [3]。CRISPR 介导的基因编辑使研究人员能够使用 Cas9 和适当的 gRNA 在基因组特定位置有效地引入双链断裂，并且通过非同源末端连接（nonhomologous end joining，NHEJ）和同源定向修复（homologous directed repair，HDR）2 种修复途径，实现突变或外源基因插入 [4]。NHEJ 修复方式通过在双链断裂处引入小的插入或缺失，造成基因移码突变；当外源模板存在时，可通过 HDR 实现基因的精准修复或片段插入 [5]。尽管 CRISPR/Cas9 可通过 HDR 介导基因敲入，但 HDR 仅在 G2 和 S 期细胞中活性较高，因此，对于神经元细胞等分裂缓慢或处于有丝分裂后期的细胞并不适用；此外，NHEJ途径是细胞中 DNA 修复的主要方式 [6]。因此，上述2 种因素导致 HDR 介导的基因修复效率较低，仅为0.1%~6.5%[7]。CRISPR 系统递送是实际应用的关键，目前它能通过 3 种形式被递送到细胞中，包括 DNA（质粒DNA）、信使 RNA（messenger RNA，mRNA）以及核糖核蛋白（ribonucleoprotein，RNP），不同的递送形式在病毒载体或非病毒载体的协助下进入细胞，从而完成靶标基因的编辑。第 1 种 DNA 递送需将 Cas9 蛋白、单向导 RNA（single guide RNA，sgRNA）的 DNA 序列构建于质粒载体中，再对质粒进行病毒包装（如慢病毒、腺相关病毒等），最终 Cas9 蛋白和 sgRNA 序列在病毒介导下进入细胞从而起始基因编辑。它操作简单且成本低，适用于基因功能的研究，但存在如下缺点：1）质粒载体过大，从而导致病毒包装效率和递送效率降低；2）DNA 序列需经转录、翻译形成 Cas9 蛋白、sgRNA 再起始编辑功能，降低了编辑效率；3）转染后的 Cas9 基因序列不易去除，导致 Cas9 蛋白长期存在细胞中，易引发更大的毒性和副作用 [8]。第2 种 mRNA 递送是将 Cas9 的 mRNA、sgRNA 序列在非病毒载体的介导下递送至靶细胞，起始基因编辑。这种递送形式的优点是由于 mRNA 无需转录，经翻译后即可启动基因编辑，使得编辑效率高于DNA 递送形式，且因 mRNA 不会长久维持在细胞中，从而降低了 CRISPR 系统的脱靶率。不过，由于 mRNA 的稳定性较差，对递送载体有较高要求。第 3 种 RNP 递送是将 Cas9 蛋 白、sgRNA 组装成RNP，然后通过非病毒载体直接递送于细胞中起始基因编辑，为目前最高效的 CRISPR/Cas9 基因编辑策略。该递送形式优势明显，递送至细胞后无需转录、翻译过程，直接起始基因编辑，从而能显著提高编辑效率，且 RNP 一般在细胞内 48 h 即可降解，不会在细胞中长期存在，从而降低了对细胞的毒性和不良影响，极大降低脱靶率，此外 RNP 递送不受细胞类型限制，使编辑更加精准、高效。但是 RNP转染的缺点是编辑时间较短，需在一段时间内提供足够的编辑工具，以便进行足够的编辑；并且，由于需要大量合成 Cas9 蛋白和 sgRNA，导致 RNP 转染的成本相对较高；在实验中选择RNP 转染还需要考虑 sgRNA 和 Cas9 蛋白的适配性。总之，CRISPR技术的快速发展提高了研究人员对细胞进行精确基因编辑的能力，但 CRISPR/Cas9 技术目前仍面临递送效率低、HDR 效率低、脱靶性，以及毒性和副作用等多种问题 [9]。鉴于 Cas9 诱导断裂的 HDR 效率相对较低，本文主要通过对供体模板及递送方式的优化，外源加入调控 NHEJ 或 HDR 相关信号通路、染色质开放或关闭状态、细胞周期的小分子化合物，构建敲除或过表达细胞系或利用小干扰 RNA（small interfering RNA，siRNA）调控细胞信号通路关键蛋白的表达，以及对 Cas9 系统的优化等方法来优化Cas9 敲入效率，从而提高编辑的特异性和减少脱靶效应，提升基因编辑的传递效率和导入能力，并实现更大片段的精准编辑，加速了基因编辑技术向临床转化，对于解决基因编辑面临的主要难点具有重要意义。1供体模板的优化策略常见供体模板有质粒、双链 DNA（double strand DNA，dsDNA）和单链 DNA（single-stranded DNA，ssDNA）3 种。质粒作为基因敲入模板，不仅制备周期长，且高浓度导入会造成较强的细胞毒性 [10]。因此，研究者常使用 dsDNA 或 ssDNA 作为供体模板。对于小片段的插入，通常选用 ssDNA 供体；对于荧光蛋白或基因表达盒等大片段插入，则一般选择dsDNA 和质粒供体。值得注意的是，左右同源臂一般以待敲入的目的细胞基因组为模板扩增，以避免不同细胞基因组差异导致左右同源臂不同源而降低 HDR 效率。由于通过同源重组修复途径敲入大于 2 000 bp 的长基因片段很难成功实现，因此，供体模板的设计是基因敲入实验所面临的主要挑战之一。下面将对模板选取及设计过程中可能遇到的问题进行归类分析，如根据敲入目标片段的长度和靶标的类型选择合适的模板的类型及设计最佳的同源臂大小来提高敲入效率（见表 1）。1.1供体模板的设计在基因编辑实验中，当插入目标片段长度小于 2 000 bp 时，ssDNA 在包含较短同源臂的情况下可以产生比 dsDNA 更高的 HDR 效率；无论使用 ssDNA 或 dsDNA 供体，使用非前间隔序列邻近基序（protospacer adjacent motif，PAM）链供体的HDR效率略高于PAM链供体，Liang等[11]研究表明，最优ssDNA的总长度约为200个碱基，30个碱基的3'端短同源臂和 40 个碱基的 5' 端长同源臂组成的不对称同源臂供体 DNA 在诱导性多能干细胞（induced pluripotent stem cell，iPSC）中可实现 45% 的敲入效率。此外，当 sgRNA 的切割位点位于敲入位点上游 5 bp 或下游 3 bp 时，基因的敲入效率最佳。值得注意的是，为了避免二次切割，可将对应 sgRNA 的PAM 或邻近 PAM 的序列进行同义突变。当目标片段长度大于 2 000 bp 时，选择同源臂长度为 600 ~ 2 000 bp 的质粒或 dsDNA 更加合适。然而哺乳动物细胞中对于长片段 DNA 的精准插入效率非常低，Gao 等 [12] 开发了简单的基因组编辑方法，称为转录偶联 Cas9 介导的编辑（transcription-coupled Cas9-mediated editing，TEd）， 当 插 入 大DNA 片段时它可以实现比传统 Cas9 介导的编辑更高的效率。首先研究者发现处于转录耦合状态的供体 DNA 能够显著提高绿色荧光蛋白（gene fluorescent protein，GFP）的精准插入效率，随后基于上述发现设计开发了一系列优化的 TEd 基因编辑系统，通过在同源供体 DNA 上引入启动子以形成 TC-donor（transcription-coupled HR-donor）， 并在其转录产物 TC-RNA 的 3' 端添加多个 MS2 茎环结构（MS2 binding loops）以及在 Cas9 上融合 MS2适配体的结合结构域，该团队发现优化后的 TEd 系统对于 GFP 的精准插入效率可以达到传统方法的 10倍左右，并在高达 10 000 bp 的 DNA 片段敲入方面也获得了很好的效果。总之，在 Cas9 实验中，当插入片段长度小于2 000 bp 时，ssDNA 供体可提供更短的同源臂，获得比 dsDNA 形式的模板更高的插入效率；当目标片段长度大于 2 000 bp 时，应选择同源臂长度为 600 ~2 000 bp 的质粒或 dsDNA。与相同长度的 ssDNA 供体相比，长 dsDNA 供体更有可能产生细胞毒性：供体越长，细胞毒性就越明显，且增加较长 dsDNA 供体的浓度也会导致毒性的产生。dsDNA 供体的另一问题是它们更倾向于插入整个供体序列，包括同源组。此外，在设计 HDR 供体 DNA 的时候，还应该注意以下 2 点：1）如果在 HDR 实验中使用 Cas9 核酸酶，最好使用与目标 DNA 的 2 条链匹配的同源序列检测 ssDNA 供体；2）当使用 Cas9 系统时，要避免在 HDR 修复后重新产生 PAM 位点。设计 ssDNA供体序列，应在 PAM 位点引入同义突变，这样 RNP就不能识别修复后的序列。否则，Cas 核酸酶可能会重新切割修复后的 DNA，除了所需的 HDR 突变外，还会形成 NHEJ 介导的插入缺失。因此，设计 HDR供体模板时，要注意区分短型插入和长型插入。对于较短或中等长度插入，建议使用 ssDNA 作为 HDR 供体模板。根据敲入目标片段的大小选择合适的供体类型及最佳长度的左右同源臂，并对 PAM 位点引入同义突变，同时，也要考虑敲入不同靶标的难易程度，从而不断提高 HDR 介导的敲入效率。1.2 供体模板的修饰对供体模板进行化学修饰或组蛋白修饰将提高其稳定性及基因编辑效率。考虑到 dsDNA 在细胞内极易被降解、敲入效率低，Akhmetzyanova 等 [13] 研究发现，双链模板的末端修饰能提高供体的稳定性，他们采用体外合成 Cas9-RNP 和 5' 端修饰的短同源臂dsDNA 供体进行结合，选择了 13 种化学基团对双链模板进行修饰，并选用 HCT116 细胞进行筛选和效率测试，结果发现所有修饰均能在不同程度上提高编辑效率，其中利用化学基团 C6-聚乙二醇 5' 端修饰的dsDNA 模板能够将敲入效率提高为未修饰模板的 5~6 倍，并且在 293T 细胞中将长度为 700 bp DNA 片段的敲入效率提高到 65%。此外，在短的 ssDNA 模板的5'端或3'端添加硫代磷酸二酯键能提高其稳定性，减少核酸外切酶的影响，从而提高在 iPSC 和 Jurkat细胞等核酸酶水平高的细胞中的编辑效率。另外，在基于 HDR 的基因编辑中，通常以纯化或“裸露”的 DNA 为供体模板。但细胞中的DNA 是被组蛋白包裹成染色质的天然形式存在的，而组蛋白 H3K36 三甲基化（H3K36me3）是人类细胞HDR 至关重要的修饰，Cruz-Becerra 等 [14] 发现，与裸 DNA 供体模板相比，组蛋白修饰的染色质供体模板能够更有效地发生同源链配对，其基因编辑效率是裸 DNA 供体模板的 2.3~7.4 倍。综上，利用 5' 端化学修饰的 dsDNA 作为模板，结合高稳定和低脱靶性的 Cas9-RNP 递送，能够实现比未修饰情况下高出 5 倍的敲入效率，并且在人类胚胎肾脏细胞中对长度为 700 bp 的 DNA 片段实现了效率达 65% 的敲入。通过用更稳定的硫代磷酸二酯键替代磷酸键，对 ssDNA 供体进行末端修饰，可以增强其稳定性。该策略不仅大幅度地提高了敲入效率，也极大地缩短了制备周期，给未来的基因编辑实验和基因治疗手段提供了更大的可能性。另一方面，H3K36me3 和 H3K4me3 甲基化修饰介导人类细胞中的同源重组与 Cas9 融合，使得 HDR 效率提高了 3 倍，且减少了脱靶效应，证明了组蛋白修饰提高了 CRISPR/Cas9 介导的 HDR 修复效率。1.3 供体模板与 Cas9 的递送形式目前有以下几种方法可将 CRISPR/Cas9 及其组分递送到目标细胞，包括 Cas9-RNP，Cas9-mRNA和 Cas9 质粒形式以及病毒、非病毒等载体。1.3.1 Cas9-RNP Cas9-RNP 复合物由 Cas9 蛋白和sgRNA 组成，该形式递送 Cas9 蛋白和 sgRNA 是最直接简便的方法，无需转录和翻译过程，能直接快速启动基因编辑过程，脱靶率低且毒性小。但由于Cas9-RNP 复合物尺寸较大不易包封，该形式递送存在一定的难点 [15]。Chandrasekaran等[15]通过电转将 Cas9/sgRNA导入原代 T 细胞，成功实现了近 40% 的基因编辑效率；进一步引入 HDR 模板，产生了 20% 的基因敲入效率。Kim等[16] 通过电转的方式将 Cas9/sgRNA 递呈至人红白血病细胞系（K562），通过改变 sgRNA靶向不同的位点，分别获得 16%~72% 的编辑效率，平均效率为 44%。在其他方式难以转染的人成纤维细胞和多能干细胞中，通过电转也能分别得到 19%和 23% 的基因编辑效率。1.3.2 Cas9-mRNA RNA 水平递送编码 Cas9 蛋白的mRNA 和 sgRNA，mRNA 能较快启动基因编辑，但该递送方法的局限性在于 mRNA 本身稳定性差且在体内外都容易受到 RNA 酶的降解，限制了基因编辑的持续时间，降低了基因编辑效果 [17]。Liu 等 [18] 发现结合了二硫键的脂质纳米颗粒BAMEA-O16B可以高效地将 Cas9 mRNA 和 sgRNA传递到细胞中。研究表明，使用BAMEA-O16B同时递送 Cas9 mRNA 和 sgRNA 可以抑制 293T 细胞的 GFP 表达，基因编辑效率高达 90%。 1.3.3 Cas9 质粒 由于稳定性高、操作简单、成本低等优点，从 DNA 水平递送编码 Cas9 蛋白和sgRNA 的质粒成为常用的递送形式。然而递送质粒会降低基因编辑效率，延长 Cas9 切割时间从而增加脱靶率 [18-19]。Liu 等 [18] 设计了基于聚合物/无机杂化纳米粒子的双重靶向递送系统，将 CRISPR/Cas9 质粒递送至人乳腺癌细胞 MCF-7 细胞核中，基因编辑效率高达90%。Zhang 等 [19] 研发了基于聚乙二醇-b-聚乳酸-羟基乙酸二嵌段共聚物 [poly (ethylene glycol)-b-poly (lactic-co-glycolic acid)，PEG-b-PLGA] 纳米颗粒的递送系统，其能够将 CRISPR/Cas9 质粒 DNA 递送至多个器官的血管系统中，并实现了 80% 的基因编辑效率。1.3.4 病毒和非病毒载体 病毒载体是 CRISPR/Cas9系统最常用的递送载体，但病毒载体可能会导致宿主产生有害的免疫原性和突变，限制了其应用；非病毒载体具有免疫原性低、无内源病毒重组的优点，因而纳米粒子制剂载体受到广泛的关注 [20]。基于阳离子脂质体的纳米颗粒常用于递送CRISPR/Cas9 系统，Zhang 等 [21] 合成了新型聚乙二醇磷脂修饰的阳离子脂质纳米粒子递送系统，从而使体外 A375 细胞的转染效率达 47.7%，且含有酯基的可生物降解的脂质样化合物在体内外均表现出有效的 Cas9 mRNA 递送。壳聚糖也是良好的聚合物载体，Qiao 等 [22] 将红色荧光蛋白包封在壳聚糖中形成带正电荷的纳米颗粒，将 Cas9-RNP 和 ssDNA 供体同时递送到细胞质中，具有很高的基因组编辑效率且无细胞毒性。目前，基因编辑体内递送相关的免疫原性问题仍需进行全面分析，体内已存在的与递送载体相关的中和抗体有可能对基因编辑形成干扰，对 Cas9 或其他基因编辑元件的细胞免疫反应可导致转染细胞被清除，基因编辑在转染细胞中长期持续的表达也可能激活适应性免疫反应。与长期表达的递送方式相比，瞬时递送的优势就在于能够降低脱靶的概率，这在体内基因编辑中尤其重要，因为即使非常低频的脱靶在长期表达时也可能导致癌变。Cas9-mRNA 为快速、稳定性差且在体内外都易受到降解的递送形式，适用于周期短的实验研究；Cas9 质粒稳定性高、操作简单、成本低，是常用的体外递送形式，但由于各类转染试剂存在细胞毒性，并且切割时间长，容易引起脱靶效应；与以 DNA/RNA 为基础的递送技术相比，RNP 体系直接在体外将 Cas9 蛋白和 gRNA 组装形成 RNP 复合物，通过电转法等方式导入靶细胞，实现 Cas9 的瞬时表达。该递送形式使细胞毒性更低，半衰期更短，同时采用其进行基因编辑可带来更低的脱靶效应。由于 RNP 在血液中易被蛋白酶降解，RNP 介导的CRISPR 基因编辑更多用于体外实验 [23]。目前病毒载体仍然是临床试验的常用载体。病毒载体可实现高转染效率，但是存在包装外源片段长度有限、免疫原性强和具有潜在脱靶效应等局限性。其中，慢病毒宿主范围广，基因容量大，感染效率高，能整合基因到宿主细胞，实现长期稳定表达，常构建稳定株；腺相关病毒免疫原性低，具有多种血清型，体内扩散能力强，常用于体内研究；腺病毒携带外源基因片段大，感染效率高，主要用于体外难感染的细胞。非病毒载体的原理是采用人工合成的载体材料的物理化学性质来介导基因的转移，包括脂质纳米颗粒、电穿孔、细胞穿透肽等作为递送方式。与病毒载体相比较，非病毒载体具有安全性高、包装尺寸大、免疫原性弱、靶向性可控的优点，但实验耗材成本高，存在细胞毒性，部分细胞类型递送效率低 [24-25]。因此，研究人员可根据实验需求选取合适的递送方式，例如 Cas9-RNP，Cas9-mRNA，Cas9 质粒以及通过病毒和非病毒载体包装的递送系统，包括阳离子脂质体的纳米颗粒、壳聚糖等，从而能在体内外有效提高基因编辑效率。2 调控 DNA 双链断裂修复的小分子化合物 如前所述，自然界中 HDR 的频率非常低，哺乳动物细胞通过多种机制优先使用 NHEJ 进行 DNA 双链断裂（double-strand break，DSB）修复，除了有丝分裂外，NHEJ 在整个细胞周期中都是活跃的，而 HDR 仅限于 S 期和 G2 期活跃。研究表明，NHEJ小分子抑制剂、HDR 激活剂和细胞周期抑制剂可影响 DSB 修复的不同方面，使 DSB 修复平衡转向HDR，有利于提高 CRISPR/Cas9 系统的基因敲入效率（见图 1），如细胞周期抑制剂可通过延长细胞周期的 S 期和 G2 期的长度以提高 HDR 的效率 [26]。目前开发的小分子化合物已被用于提高 HEK 293细胞、人类 iPSCs、小鼠胚胎干细胞（embryonic stem cells，ESCs）和小鼠胚胎中的 HDR 效率（见表 2）。2.1 调控 HDR 与 NHEJ 相关信号通路的小分子 参与双链断裂 DNA 修复途径的某些小分子通过作用于 DNA 修复过程中的关键蛋白以有效提高敲入效率（见图 1）。DNA 修复途径包括 HDR和 NHEJ。HDR 激活剂或 NHEJ 抑制剂可有效提高 HDR 敲 入 效 率。 其 中 HDR 激活剂有 RS-1 和brefeldinA；NHEJ 抑制剂包括 SCR7，L755507，NU7026，白藜芦醇，NU7441 和 KU-0060648。RAD51 是有丝分裂细胞中催化 DNA 同源重组修复过程中同源配对的唯一蛋白，其通过介导 DNA链配对和交换而参与 DNA 同源重组修复。Song 等[27]研究表明，RS-1 可激活 RAD51 蛋白，使 RAD51 蛋白与 DNA 的结合更稳定，从而将 HDR 修复效率提高 3 倍，值得注意的是，高浓度 RS-1 具有较强的细胞毒性。胞内蛋白运输抑制剂能抑制物质从内质网向高尔基体的运输，Hong 等 [28] 研究发现，使用胞内蛋白运输抑制剂 brefeldinA，可将 HDR 效率提高 2 倍。DNA 连接酶Ⅳ（DNA ligase IV，LIG4）是 NHEJ途径的关键酶，Ray 等[29] 发现 SCR7 是 LIG4 的抑制剂，能抑制 NHEJ 活性，在 A549 细胞中，相较于未处理的对照组，SCR7 使靶位点的插入效率提高约 3 倍。β3-肾上腺素能受体是一类 G 蛋白偶联受体，Murakami等 [30] 研究发现 L755507 和 NU7026 是β3-肾上腺素能受体激动剂，可增强 CRISPR 介导的HDR 效率，最佳使用剂量为 5 μmol·L-1，并且在 24 h以内效果最佳，可将敲入效率提高 3 倍。为了研究DNA 依赖性蛋白激酶催化亚单位（DNA-dependent protein kinase catalytic subunit，DNA-PKcs）对 DSB的 NHEJ 修复途径的影响，Sak 等 [31] 评估了 DNAPKcs 特异性抑制剂 NU7441 对不同状态的非小细胞肺癌细胞株 DSB 修复的细胞周期特异性作用，结果显示 NU7441 以细胞周期依赖性的方式抑制 NHEJ的效率。Robert 等 [32] 研究显示，DNA 蛋白激酶抑制剂 NU7441 和 KU-0060648 能抑制 NEHJ 活性，将 HDR 效率提高 3 倍。Li 等 [33] 研究发现，白藜芦醇可抑制 LIG4 的表达，使猪胎儿成纤维细胞的 HDR 效率提高 2~3 倍。此外，他们还发现白藜芦醇以剂量依赖性的方式抑制 S 期猪胎儿成纤维细胞，而 HDR 相关基因如RAD51 和 RAD52 的表达与白藜芦醇呈剂量依赖性增加。因此，白藜芦醇通过与多个 DNA 损伤相关蛋白相互作用，增加了 CRISPR/Cas9 介导的 HDR 效率。综上，为了提高 CRISPR/Cas9 介导的 HDR 效率，研究人员可选择性使用小分子化合物，如 HDR 激活剂 RS-1 和 brefeldinA 分别作用于靶标 RAD51 和高尔基体，将敲入效率提高 2~ 3 倍；NHEJ 抑制剂包括SCR7，L755507，NU7026，NU7441，KU-0060648和白藜芦醇等，通过作用于不同的靶标，主要有LIG4，DNA 蛋白激酶和 β3-肾上腺素能受体，抑制NHEJ 修复途径，从而使 HDR 修复效率提高 2~5 倍。2.2 调控染色质开放或关闭状态的小分子靶向 DSB 的可及性主要取决于染色质状态，并且 DNA 有效修复的第一步是允许修复途径相关的蛋白质结合，HDR 与 NHEJ 的修复平衡与染色质结构的状态相关。染色质结构的开放或关闭状态主要由组蛋白乙酰化和去乙酰化的平衡控制，而组蛋白乙酰化由组蛋白乙酰化酶（histone acetylase，HAT）和组蛋白去乙酰化酶（histone deacetylase，HDAC）严格调控。乙酰化导致开放活跃的染色质状态，HDAC 使组蛋白去乙酰化，实现染色质致密卷曲。HDAC 抑制剂可通过提高染色质特定区域组蛋白乙酰化水平，促进开放染色质位点，从而调控CRISPR/Cas9 的基因编辑效率 [34]。HDAC 抑制剂能抑制 NHEJ 关键因子的去乙酰化，显著增加 G2/M 期的细胞百分比，并相应减少了 G1/S 期的细胞数量，从而促进HDR 修复途径。Li 等 [35] 通过评估组蛋白修饰剂如 HDAC 抑制剂和HAT（靶点包括 p300/CBP，Tip60 和 MOZ）抑制剂对 CRISPR/Cas9 介导的基因编辑效率的影响，证明了抑制 HDAC1 和 HDAC2 的活性，能够增强 HDR介导的基因敲入效率；相反，抑制 HDAC3 会降低基因编辑效率。因此，HDAC 抑制剂作为内源性途径调控因子，能抑制 NHEJ 修复途径，提高 HDR 修复效率，为细胞自身修复途径的基因编辑提供有力条件。2.3 调控细胞周期的小分子由于 HDR 发生在细胞周期的 S 期和 G2 期，所以一些研究将细胞周期抑制剂与基因编辑相配对，使细胞周期同步化并将靶细胞阻滞或延迟在 S 期或G2 期从而提高 HDR 效率（见图 2）。细胞周期抑制剂通过抑制微管聚合来使细胞停滞在 G2/M 期。Lin 等 [36] 对 6 种可逆化学细胞周期抑制剂进行了评估，包括 4 种 G1/S 阻滞剂（阿菲迪霉素、羟基脲、含羞草素和胸腺嘧啶），1 种 G2/M阻滞剂（诺考达唑）和 1 种 M/G1 阻滞剂（洛伐他汀），该研究发现诺考达唑和另一 G2/M 阻滞剂（ABT-751）可通过作用于 β 微管蛋白来增强 CRISPR/Cas9 活性，将 HDR 修复效率提高 3~6 倍。周期蛋白依赖性激酶（cyclin-dependent kinase，CDK）是调节细胞周期进程的异二聚丝氨酸/苏氨酸蛋白激酶，在 S 期阶段该酶的活性增加激活了 HDR修复通路的关键标志，如激活 DNA 末端切除过程。Smirnikhina 等 [37] 利用 CDK 抑制剂靛红素，通过在S 期或 G2 期阻滞靶细胞，提高了 CRISPR/Cas9 介导的 HDR 修复效率。细胞分裂周期7 相关蛋白激酶（cell division cycle seven associated protein kinase，CDC7）属于丝氨酸-苏氨酸激酶，可被 Dbf4 依赖性激酶（Dbf4-dependent kinase，DDK）激活，是细胞进入 S 期的必要因子，抑制 CDC7 蛋白可导致细胞周期停滞在 G1/S 期。CDC7/DDK 复合体使微小染色体维持蛋白（minichromosome mantenance protein，MCM） 维 持 磷 酸 化， 从 而 启动 G1/S 期的过渡。Wienert 等 [38] 研究发现 XL413 为CDC7 抑制剂，能够可逆地阻断 MCM 的磷酸化，并在 S 期早期阻滞细胞。在 K562 细胞中，XL413将增强型蓝色荧光蛋白（enhanced blue fluorescence protein，EBFP）和增强绿色荧光蛋白（enhanced green fluorescent protein，EGFP）的基因编辑效率分别提高了1.4 和 1.8 倍。此外，敲低蛋白 CDC7 能在可逆的 S 期减缓过程中激活 HDR 途径，使许多情况下（包括原代 T 细胞）的 HDR 修复效率提高 3.5 倍。综上，使用不同细胞周期蛋白抑制剂将靶细胞阻滞或延迟在 S 期或 G2 期可针对性地提高 HDR 修复效率。不过，细胞周期抑制剂可能引起部分细胞凋亡，研究者需要进行预实验探索最适浓度。3调控 DNA 双链断裂修复的关键蛋白表达 除了 NHEJ 抑制剂或 HDR 激活剂，还可通过构建敲除细胞系或利用 siRNA/ 短发夹 RNA（short hairpin RNA，shRNA）敲低或过表达修复通路关键蛋白来提高 CRISPR/Cas9 诱导的 HDR 效率，如敲低 Ku70，Ku80，DNA-PKcs，p53 结合蛋白 1（p53-binding protein 1，53BP1），以及过表达 RAD51 和RAD52（见表 3[39-48]），具体作用机制如图 3 所示。Chu 等 [39] 发现，在 HEK293/TLR 细胞中，Ad4蛋白处理能降低 LIG4 的表达，显著抑制了 NHEJ的效率。该研究还发现利用 siRNA 降低 LIG4 的表达可使 HDR 效率提高 2.8 倍。Li 等 [40] 利用 siRNA减少 NHEJ 通路中关键因子 Ku70 和 Ku80 的表达，增加了多个 HDR 效率，包括同源重组、单链退火和单链寡核苷酸介导的 DNA 修复。DNA-PKcs 是磷脂酰肌醇 3-激酶相关激酶（phosphoinositide 3-kinase-related kinase，PIKK）家族的成员，该家族包括具有高度同源的催化结构域的蛋白质，如 PI3K，毛细血管扩张性共济失调突变蛋白（ataxia-telangiectasia mutated protein，ATM），ATR（ATM and Rad3 related）和哺乳动物雷帕霉素靶蛋白（mammalian target of rapamycin，mTOR）[41]。DNA-PKcs 的激酶活性在 NHEJ 启动步骤中起着重要作用，Liu 等 [41] 研究表明 DNA-PKcs表达下调可使 HDR 效率增加 2.8 倍。53BP1 是真核细胞中 DSB 修复途径选择的关键调控因子，通过抑制末端切除导致 NHEJ 优先于HDR，使得 HDR 启动受限。Canny 等 [42] 通过阻断53BP1 在 DNA 损伤位点的积累，发现53BP1 抑制剂可以提高人类和小鼠细胞中 HDR 依赖基因组编辑的效率，最高可提高 5.6 倍，并提高了基因靶向性和与 dsDNA 或 ssDNA 供体的染色体基因转换。RAD51 和 RAD52 是 HDR 过程中的关键蛋白，Kurihara 等 [43] 研究发现在神经元细胞中共转染过表达 RAD51，敲入效率提高了 2.5 倍。Shao 等 [44] 研究显示，RAD52 在 293T 细胞中的过表达，使 HDR修复效率增加 3 倍。该课题组还发现 RAD52 和SCR7 的联合使用将 HDR 效率提高约 40%。CtBP相互作用蛋白（CtBP-interacting protein，CtIP） 是 同 源 重 组 早 期 步 骤 的 关 键 蛋 白， 主 要作为辅因子诱导减数分裂重组蛋白 11（meiotic recombination 11，MRE11）核酸内切酶对 DNA 末端切割，激活 HDR 途径 [45]。Charpentier 等 [46] 研究发现，CtIP 最小的 N 端片段可激活 HDR 修复，从而提高了靶位点的基因编辑效率。Engeland 等 [47] 研究显示，P21 蛋白与许多转录因子相互作用，P21 蛋白能抑制 CDK4 的活性，使周期抑制蛋白 Rb 不能发生磷酸化，细胞周期相关转录因子 E2F 不能释放，进而使细胞周期停滞在 S/G1 期，从而增加 HDR 效率。Gutshner 等 [48] 试图通过直接同步 Cas9 的表达与细胞周期进展来激活 HDR 修复活性，结果发现将人 Geminin 蛋白的 N 端区域与 Cas9 融合，诱导Cas9 在 G1 期降解，使目标 DNA 切割限制在 S/G2 期，HDR 效率增加至 87%。综上，干扰或过表达 DSB 修复途径关键蛋白的策略有利于生成精确基因修饰的细胞系和生物体，研究者可通过 siRNA 减 少 Ku70，Ku80，LIG4，DNA-PKcs，53BP1，CDK，CtIP 等表达或对蛋白RAD51 和 RAD52 过表达从而提高 HDR 修复效率，抑制 NHEJ 修复活性。除了通过调控 DSB 修复的关键蛋白表达的策略之外，Ye 等[49] 开发了新的方法，用 CRISPR 激活（CRISPRa） 或 CRISPR 沉 默（CRISPRi）来调节NHEJ 和 HDR 通 路，CRISPRi 或 CRISPRa 复合物能抑制 NHEJ 修复途径并激活 HDR 修复，显著提高CRISPR 介导的基因编辑的 HDR 效率。4优化 Cas9 系统从 Cas9 蛋白的性质出发，如表面电荷、末端残基及拓扑结构，可以对其进行修饰或改造，使其更适配于不同载体系统的体内递送，促进 Cas9-RNP的基因编辑。具体包括如下方法：1）Cas9 核酸酶的末端修饰，如添加标签蛋白或融合蛋白结构域；2）基于 Cas9 蛋白的结构特点和催化原理对其进行工程化改造，从而筛选出优异的 Cas9 突变体；3）对 Cas9 拓扑结构进行调整，如与特定蛋白功能域融合，或同时表达多个 sgRNAs 或 Cas9 实现 CRISPR/Cas9 系统的多重编辑及调控 [50]。4.1 Cas9 的修饰 CRISPR/Cas9 介导的同源重组修复是由 Cas9在 gRNA 介导的双链断裂后，在切割位点利用供体DNA 进行的修复途径。供体 DNA 在切割位点的富集程度将决定同源重组能否发生，供体 DNA 在切割区域的低浓度是同源重组的限速步骤。基于此问题，Ling 等 [51] 采用非天然氨基酸偶联技术实现 Cas9 蛋白与供体 DNA 的直接或间接偶联，将其共递送进入体内，实现切割区域供体 DNA 的有效富集，在细胞水平实现同源重组水平大幅提升10~20 倍。此外，使用含叠氮基的氨基酸对 Cas9 蛋白进行化学修饰，通过加成反应缀合供体 ssDNA 或DNA 衔接子，从而将修饰的或未修饰的供体 DNA模板募集到 RNP 复合物中，结果显示用 G1367-AeF（苯丙氨酸突变位点 G1367）RNP 和二苄基环辛炔（dibenzocyclooctyne，DBCO）修饰的 ssDNA 共转染细胞的 HDR 效率增加了1.6 倍。Huang 等[52] 开发了 Cas9 ProSNA-sgRNA 核糖核蛋白递送系统，通过在 Cas9 蛋白 N 端修饰 3 个连续的 GALA 肽促进核递送效率。结果显示 Cas9 ProSNA RNP 在 4 种不同的细胞中的基因编辑效率为 32%~47%。4.2 Cas9 突变体 CRISPR/Cas9 推动了基因编辑技术的发展，但PAM 要求限制了精确基因编辑方法的适用性，使目标编辑发生在 PAM 的特定距离或特定范围内 [53]。不过，随着人们对 Cas9 蛋白三维结构和作用机制的深入认识，通过对 Cas9 蛋白进行工程化改造就逐渐成为优化提升 CRISPR/Cas9 系统的有力手段。该方法以 Cas9 蛋白的结构特点和催化原理为指引，对Cas9 蛋白相应的结构域进行设计改造，来筛选性能更为优异的 Cas9 突变体。Huang 等 [54] 研究发现通过定向进化生成的 4 种Cas9 突变体能够共同靶向人类基因组中大多数富含嘧啶的 PAM 序列。结果显示 Nme2Cas9 突变体成功突破了传统 PAM 的限制，并实现高效的基因编辑。Wang 等 [55] 研究发现将微生物单链退火蛋白（single chain annealing protein，SSAP）与催化失活的 dCas9结合形成无切割的基因编辑器 dCas9-SSAP 具有较低的目标误差和最小的脱靶效应，可有效插入千碱基的序列，效率约达 20%。4.3 Cas9 蛋白与特定功能蛋白融合目前通过将特定蛋白或功能域与 Cas9 融合，可以有效提高 HDR 敲入效率。单碱基编辑和引导编辑器（prime editor，PE）编辑可实现精准的碱基替换和片段的插入而无需 DSB过程。该系统通过对靶位点的“搜索”和“替换”，可实现 4 种碱基之间的任意替换及小片段的精准插入和删除，克服了 CRISPR/Cas9 系统介导的 HDR 效率低和碱基编辑系统不能实现碱基颠换的困难 [56]。 Peterka 等[57]将逆转录酶和野生型 SpCas9 进行融合构建了 PEn 蛋白，利用常规的先导编辑向导RNA（prime editing guide RNA，pegRNA），PEn可通过同源依赖性 DSB 修复机制实现小 DNA 插入，效率达 50%。Jiang 等 [58] 将具有双链切割活性的 Cas9 与逆转录酶融合，并结合 2 条靶向互补 DNA链 pegRNA，开发出了 PEDAR 系统，它可以高效地诱导 20 ~ 700 bp 片段的缺失和 30 bp 片段的插入。Adikusuma 等 [59] 同样利用野生型 SpCas9 构建了新的PE 系统，并且将蛋白、pegRNA 和 nicking sgRNA 整合在同一质粒中进行表达，该系统在 293T 细胞中平均编辑效率可达 67%。此外，将该系统注射小鼠胚胎，在新生小鼠中最高可以实现 100% 的编辑效率。Aird等[60]将HUH核酸内切酶与Cas9融合表达，实现了稳定的共价 RNP-ssDNA 复合体，结果显示通过 HUH-Cas9 融合蛋白与 ssDNA 共价结合可使HDR 效率增强 30 倍。Ma 等 [61] 将最小基元 Brex27与 spCas9 融合构建成 miCas9，研究发现以 Cas9-mRNA 形式递送时，miCas9 的编辑效率提高了 2.5倍；此外，Ma 等 [62] 将 Cas9 与全长睡美人（sleeping beauty，SB）转座子（Cas9- SB）、SB 的 RED 结构域（Cas9-N123） 和 SB 的 PAI 结 构 域（Cas9-N57）融合，经流式细胞术（flow cytometry，FCM）分析显示，Cas9-N57 融合蛋白将 HDR 编辑效率提高了 1.5 倍。由于 HDR 增强子（HDR-enhancer，HE）是同源重组早期阶段的关键蛋白 CtIP 发挥活性所必需的最小 N 末端多聚化结构域，因此 HE 可通过增强HDR 提高Cas9 基因敲入效率。Charpentier 等 [63] 将HE 与 Cas9 融合，结果显示 Cas9-HE 融合物在包括人类细胞系、iPSCs 和大鼠受精卵中获得的基因编辑效率为仅用 Cas9 的 2 倍或更高。如前所述，Cas9-HE 融合物允许在若干实验系统中获得更高的转基因整合效率。此外，使用 Cas9-HE 非常简单且不需要使用基因修饰的细胞或药理学试剂，极大地提高了基因编辑应用的靶向范围，从而有利于提高 HDR 效率。HDR 和 NHEJ 之间的平衡与位点特异性的染色质状态相关。研究发现 CRISPR/Cas9 诱导 DSB的 NHEJ 修复效率在常染色区域较高，而微同源末端连接（microhomology-mediated end joining，MMEJ）和 HDR 偏向异染色质 [64]。因此可通过染色质重塑因子来调控染色质状态，使平衡偏向 HDR。Chen 等 [65] 将染色质重塑因子 PRDM9 与 Cas9 融合，将 HDR 效率提高了 3 倍，且未增加脱靶效应。 综上所述，将 Cas9 蛋白与特定功能蛋白，包括逆转录酶、内切酶、同源重组关键蛋白以及染色质重塑因子，融合表达的策略具有较高的基因组特异性，是未来基因组工程应用的有效工具。4.4 gRNA 优化和表达策略多重编辑CRISPR/Cas9系统与 TALEN 和 ZFN等核酸酶相比具有很大优势，其意味着多个 sgRNAs或 Cas9 能够同时表达从而极大地提高了 CRISPR/Cas9 系统进行基因编辑或转录调控的效率和靶向范围，多重编辑性使该系统在生物工程领域得到极大应用和发展。Hsieh-Feng 等 [66] 研究表明，高效表达多个 sgRNAs 在实现优化或多重基因组编辑中起着关键作用，研究发现各种 CRISPR/Cas9 的表达盒配置、转录本处理过程和传递策略都优化 sgRNA 的表达。此外，通过修饰或改变 sgRNA 识别区长度，可实现 CRISPR 系统的多重编辑或调控。CRISPR/Cas9 系统的特异性主要体现在 sgRNA对 Cas9 切割位点的特异性识别与结合，增强细胞内sgRNAs 的稳定性和特异性有助于提高基因组编辑效率，减少脱靶效应。基于 sgRNA 的骨架结构，可在特定位点进行修饰或改造，例如截短或延长 sgRNA 的 5'端或 3' 端来增减其长度；引入 2' 核糖化学修饰 sgRNA的骨架。此外，sgRNA 含有保守的核酸序列，可合理设计与之碱基互补配对的序列，复合成双链连接到载体上，从而提高递送效率 [67]。Wang 等 [68] 针对 sgRNA种子区核糖 2'-OH 与 Cas9 蛋白之间的相互作用位点，发现可利用特定位点的化学修饰来调节Cas9蛋白活性，通过在这些特定的位点引入 1 个发光性基团，实现了Cas9 活性的光学控制，从而间接调控基因编辑效率。综 上， 研 究 人 员 通 过 工 程 化 Cas9 蛋白或sgRNA 等方式，使 CRISPR/Cas9 系统的靶向范围、靶向特异性和保真性均得到了拓展和提高。当然，无论是通过针对 Cas 蛋白自身结构的优化改造，还是采用优化设计 sgRNA 等方式，均能在一定程度上提升 CRISPR/Cas9 系统的应用性能。5总结与展望CRISPR/Cas9 诱导的 HDR 是精确可控的基因组 DNA 编辑工具 [69]。然而，由于哺乳动物细胞对NHEJ 的偏好性大于 HDR，基于 HDR 的精准基因敲入效率很低，因此，综合考虑细胞周期和 DSB 修复的关系对于提高基因敲入效率至关重要。目前，可采用在 ssDNA 或 dsDNA 供体末端引入化学修饰以增强供体稳定性，供体共价连接到CRISPR/Cas9 系统上提高切割位点局部浓度的方法提高基因敲入效率。但这些方法存在操作困难、成本高等问题。因此，需要进一步优化供体模板，以促进 CRISPR/Cas9 介导的基因敲入在临床治疗中的应用。此外，该系统还受限于 PAM 序列的依赖性和脱靶效应，应用在人类疾病基因治疗时需要提高其保真性、安全性等因素。例如通过优化 Cas9 蛋白或gRNA 从而拓宽 PAM 序列识别范围并提高靶向特异性，通过融合效应结构域或进行转录调控。CRISPR/Cas9 系统在临床试验中的递送主要依赖于物理途径和病毒载体，这受到细胞损伤和安全性问题的严重阻碍。非病毒纳米载体的开发将有助于拓展 CRISPR/Cas9 系统的医学应用。有效和安全的递送策略仍然是 CRISPR/Cas9 系统临床应用的主要挑战。研究人员需根据每种 CRISPR/Cas9 模式的作用机制和理化性质，合理设计载体，使基因组编辑效率最大化，脱靶风险最小化。尽管研究人员已对 CRISPR/Cas9 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A G-quadruplex motif at the 3' end of sgRNAs improves CRISPR-Cas9 based genome editing efficiency [J]. Chem Commun, 2018, 54(19): 2377-2380.[68] Wang Y, Liu Y, Xie F, et al. Photocontrol of CRISPR/Cas9 function by site-specific chemical modification of guide RNA [J]. Chem Sci, 2020, 11(42): 11478-11484.[69] Zhang F, Wen Y, Guo X. CRISPR/Cas9 for genome editing: progress, implications and challenges [J/OL]. Hum Mol Genet, 2014, 23(R1): R40-6[2023-06-27]. https://pubmed.ncbi.nlm.nih.gov/24651067/. DOI: 10.1093/hmg/ddu125.免责声明“药渡”公众号所转载该篇文章来源于其他公众号平台，主要目的在于分享行业相关知识，传递当前最新资讯。图片、文章版权均属于原作者所有，如有侵权，请及时告知，我们会在24小时内删除相关信息。微信公众号的推送规则又双叒叕改啦，如果您不点个“在看”或者没设为"星标"，我们可能就消散在茫茫文海之中~点这里，千万不要错过药渡的最新消息哦！

Anticipate 2024 Product Revenue Growth of at Least 10% vs. 2023 Excluding Enzyme Sales Related to PAXLOVID™ Recently Announced Debt Financing Reinforces Strong Financial Position with Projected Runway Through Expected Positive Cash-flow Around End of 2026 2024 to Focus on Securing Early Access Customers for ECO Synthesis™ Manufacturing Platform, Launch of Double-stranded RNA Ligase and Return to Growth for Pharmaceutical Manufacturing REDWOOD CITY, Calif., Feb. 28, 2024 (GLOBE NEWSWIRE) -- Codexis, Inc., (NASDAQ: CDXS), a leading enzyme engineering company, today announced financial results for the fourth quarter and fiscal year ended December 31, 2023, and provided a business update. “We are thrilled with how we closed out 2023, and it’s quite clear that the strategic decisions we made last year are translating into real momentum as we kick off 2024. We recently executed asset purchases for our lead biotherapeutics asset, CDX-7108, with Nestlé Health Science, and our newly engineered dsDNA ligase with Roche. We also completed an out-licensing deal with Aldevron for our Codex® HiCap RNA Polymerase to extend our commercial reach into the growing mRNA-based therapeutics market. Finally, we have made impressive technical progress with our ECO Synthesis™ manufacturing platform since unveiling the technology last spring, culminating in the demonstration of gram-scale synthesis in December. In alignment with our prioritized strategy, we’re driving value from non-core assets by putting them in the hands of capable partners while we focus on unlocking the vast potential of the ECO Synthesis™ manufacturing platform and returning our foundational, revenue-generating Pharmaceutical Manufacturing business to double-digit growth this year,” said Stephen Dilly, MBBS, PhD, Chief Executive Officer of Codexis. “Our recently announced non-dilutive financing with Innovatus further strengthens our financial position by both buffering our cash runway and providing capital to fund our planned ECO Synthesis™ Innovation Lab to further test the ECO Synthesis™ manufacturing platform in a non-GMP setting. We look forward to several upcoming milestones, including an important technical update at the TIDES USA annual meeting in May, as well as initiating early access customer testing of the ECO Synthesis™ manufacturing platform and launching our dsRNA ligase program in the second half of this year.” Fourth Quarter and Recent Business Highlights In November 2023 at the TIDES Europe annual meeting, Codexis presented a technical update for its Enzyme-Catalyzed Oligonucleotide (ECO) Synthesis™ manufacturing platform, which is in development to enable the commercial-scale production of ribonucleic acid interference (RNAi) therapeutics using an enzymatic route of synthesis. The presentation focused on the Company’s broader enzyme evolution and process development efforts for both the iterative nucleotide addition and the supply of critical nucleotide reagents. Driving for high volumetric productivity, data highlighted multiple, consecutive additions of 2’-modified RNA nucleotides to a growing oligonucleotide sequence, achieving significant coupling efficiencies with immobilized enzymes. Additionally, proof-of-concept was presented for an enzymatic “one-pot, two-step” phosphorylation cascade to manufacture nucleotide reagents for supply with the ECO Synthesis™ manufacturing platform. In November 2023, Codexis announced the formation of its Strategic Advisory Board (SAB) to guide the Company’s strategic direction and offer valuable insights to inform the continued development of the ECO Synthesis™ manufacturing platform. John Maraganore, PhD, founder and former Chief Executive Officer of Alnylam Pharmaceuticals, joined the SAB as its inaugural external member. In February 2024, the Company announced the addition of Masad Damha, PhD, and Jim Lalonde, PhD, to the SAB. Dr. Damha is the Distinguished James McGill Professor at McGill University and his research has been instrumental in the development of new therapeutic drugs based on RNA targeting and gene editing. Dr. Lalonde is a consultant focused on enzyme engineering and biotechnology companies and the former Senior Vice President of Research and Development at Codexis, where he oversaw the development of more than 50 enzymes for biotherapeutics, drug manufacturing, nutrition and molecular diagnostics applications. In December 2023, David Butler, PhD, Chief Technology Officer at Hongene Biotech Corporation, joined Dr. Maraganore and Codexis leadership for a virtual key opinion leader event focused on the ECO Synthesis™ technology platform. Drs. Maraganore and Butler discussed the growth of RNAi therapeutics as a modality, the manufacturing landscape and the potential role of an enzymatic route of synthesis to enable the commercial-scale production of these therapeutics. A replay of the virtual event is accessible on the Investor Relations section of the Company’s website, located here. In December 2023, Codexis achieved gram-scale synthesis with its ECO Synthesis™ technology platform, demonstrating the preparative-scale manufacture of an oligonucleotide, composed of the modified nucleotide building blocks typically used in ribonucleic acid (RNA) therapeutics, under process-like conditions. Successful completion of this technical milestone enables Codexis engineers to initiate a comprehensive assessment of the purity pro small interference RNA (siRNA) developed with the ECO Synthesis™ manufacturing platform. Separately, data collected on process-related parameters provides foundational information for early models of the siRNA manufacturing process and allows the Company to open conversations with early access customers on their RNAi therapeutics manufacturing processes. In December 2023, the Company entered into an agreement with Aldevron, a global leader in the custom development and manufacture of plasmid DNA, RNA and proteins for the biotech industry, for the global exclusive license to Codexis’ Codex® HiCap RNA Polymerase. Under the terms of the deal, Aldevron will receive global manufacturing and commercialization rights to the Codex® HiCap RNA Polymerase and Codexis will receive payments for near-term technical milestones, along with commercial milestones and sales-based royalties. In December 2023, Codexis and Nestlé Health Science entered into a purchase agreement for CDX-7108, an investigational therapy for the potential treatment of exocrine pancreatic insufficiency (EPI). Under the terms of the agreement, Codexis will receive up to $45 million in potential milestone payments, including a $5 million upfront payment received in January 2024, as well as high single-digit net-sales-based royalties. Codexis will receive up to an additional $5 million if Nestlé Health Science exercises an option to purchase two additional early-stage enzymes being developed for EPI. In February 2024, Codexis announced it had entered into a loan facility agreement with an affiliate of Innovatus Capital Partners, LLC, for up to $40 million. The non-dilutive capital reinforces the strength of Codexis’ cash position, provides additional buffer on the Company’s projected cash runway and enables the accelerated development of certain elements of the ECO Synthesis™ manufacturing platform, including the planned build-out of an ECO Synthesis™ Innovation Lab. In February 2024, the Company announced it had entered into an exclusive, global license agreement with Roche for Codexis’ newly engineered dsDNA ligase. Under the terms of the agreement, Codexis is eligible to receive upfront and technical milestone payments. This deal supersedes the prior exclusive license on the evolved T4 DNA ligase. Upcoming Milestones Codexis plans to present a technical update on the ECO Synthesis™ manufacturing platform at the TIDES USA annual meeting in May 2024. During the event, the Company expects to highlight ECO Synthesis™ platform data demonstrating the linear synthesis of a full-length oligonucleotide strand composed of modified nucleotides and representative of double-stranded siRNA therapeutics. Early access customer testing of the ECO Synthesis™ manufacturing platform remains on track to initiate in the second half of 2024. Feedback from this program will provide valuable insights and could lead to initial commercial licensing opportunities in 2025, ahead of an anticipated full commercial launch of the platform in 2026. The Company anticipates making its newly engineered, double-stranded RNA (dsRNA) ligase, or ecoRNA™ ligase, program widely available for customers in the second half of 2024. As part of Codexis’ initial market entry into the RNAi therapeutics space, the ecoRNA™ ligase program is designed to augment and improve traditional phosphoramidite chemistry by stitching together small, manufactured strands of RNA. In addition to enabling the more efficient use of existing facilities, the ecoRNA™ ligase program provides an opportunity to educate potential customers on the benefits of incorporating enzymatic solutions as a complement to their current manufacturing processes. Fiscal Year2023 Financial Highlights Total revenues, excluding enzyme sales related to PAXLOVID™, decreased by 2% to $62.0 million for fiscal year 2023 compared to $63.2 million for fiscal year 2022. Including enzyme sales related to PAXLOVID™, total revenues were $70.1 million for fiscal year 2023 compared to $138.6 million for fiscal year 2022. Product revenues, excluding enzyme sales related to PAXLOVID™, decreased by 16% to $34.8 million for fiscal year 2023 compared to $41.3 million for fiscal year 2022. Including enzyme sales related to PAXLOVID™, product revenues were $42.9 million for fiscal year 2023 compared to $116.7 million for fiscal year 2022. R&D revenues for fiscal year 2023 were $27.2 million compared to $21.9 million for fiscal year 2022; the increase was primarily due to higher license fees from Pfizer and Nestlé, offset by lower R&D fees from existing collaboration agreements. Product gross margin, excluding enzyme sales related to PAXLOVID™, was 63% for fiscal year 2023 compared to 52% for fiscal year 2022. The increase was largely due to deferred product revenue with no related costs in 2023 that was recognized due to the planned termination of an enzyme supply agreement with a food and feed customer, partially offset by variability in the product mix. Including enzyme sales related to PAXLOVID™, product gross margin for fiscal year 2023 was 70% compared to 67% for fiscal year 2022. R&D expenses for fiscal year 2023 were $58.9 million compared to $80.1 million for fiscal year 2022; the decrease was primarily driven by a decrease in costs associated with lower headcount, a decrease in outside services related to manufacturing and regulatory expense, lower lab supplies expense, and a decrease in lease costs due to assignment of the San Carlos facility lease. Selling, General & Administrative expenses for fiscal year 2023 were $53.3 million compared to $52.2 million for fiscal year 2022; the increase was primarily due to higher payroll-based expenses and higher fees for outside services, partially offset by lower stock-based compensation costs. The net loss for fiscal year 2023 was $76.2 million, or $1.12 per share, compared to a net loss of $33.6 million, or $0.51 per share, for the fiscal year 2022. Excluding enzyme sales related to PAXLOVID™, net loss for the fiscal year 2023 would have been $84.4 million, or $1.24 per share. Further excluding all charges related to the restructuring and non-cash impairment charges, net loss for fiscal year 2023 was $50.8 million, or $0.74 per share. As of December 31, 2023, the Company had pro forma cash and cash equivalents of $70.1 million, including cash and cash equivalents of approximately $65.1 million as of December 31, 2023, and a $5.0 million upfront payment received in January 2024 related to the recent Nestlé transaction. In addition, the Company retained approximately $29.2 million in net proceeds from a previously announced debt financing in February 2024. Fourth Quarter2023 Financial Highlights Total revenues, excluding enzyme sales related to PAXLOVID™, increased by 42% to $18.4 million for fourth quarter 2023 compared to $13.0 million in fourth quarter 2022. Including enzyme sales related to PAXLOVID™, total revenues were $26.6 million in fourth quarter 2023 compared to $30.4 million in fourth quarter 2022. Product revenues, excluding enzyme sales related to PAXLOVID™, increased by 69% to $9.9 million for fourth quarter 2023 compared to $5.9 million in fourth quarter 2022. Including enzyme sales related to PAXLOVID™, product revenues were $18.1 million in fourth quarter 2023 compared to $23.3 million in fourth quarter 2022. R&D revenues for fourth quarter 2023 were $8.5 million compared to $7.1 million in fourth quarter 2022; the increase was primarily due to higher license fees, offset by lower R&D fees from existing collaboration agreements. Product gross margin, excluding enzyme sales related to PAXLOVID™, was 71% for fourth quarter 2023 compared to 44% in fourth quarter 2022. The increase was largely due to increased sales of higher margin products. Including enzyme sales related to PAXLOVID™, product gross margin for fourth quarter 2023 was 84% compared to 64% in fourth quarter 2022. R&D expenses for fourth quarter 2023 were $11.2 million compared to $19.7 million in fourth quarter 2022; the decrease was primarily driven by a decrease in costs associated with lower headcount, a decrease in outside services related to manufacturing and regulatory expenses and lower lab supply. Selling, General & Administrative expenses for fourth quarter 2023 were $12.2 million compared to $12.3 million in fourth quarter 2022; the decrease was primarily due to lower payroll-based expenses and stock-based compensation costs. The net loss for fourth quarter 2023 was $7.2 million, or $0.10 per share, compared to a net loss of $12.6 million, or $0.19 per share, for fourth quarter 2022. Excluding enzyme sales related to PAXLOVID™, net loss for fourth quarter 2023 would have been $15.3 million, or $0.22 per share. Excluding all non-cash impairment charges, net income for fourth quarter 2023 was $1.1 million, or $0.02 per share. 2024 Financial Guidance Codexis is introducing financial guidance for 2024, as follows: Product revenues are expected to be in the range of $38 million to $42 million, excluding revenue related to PAXLOVID™. R&D revenues are expected to be in the range of $18 million to $22 million. Gross margin on product revenue is expected to be in the range of 58% to 63%, excluding revenue related to PAXLOVID™. In addition, Codexis expects that its existing cash and cash equivalents will be sufficient to fund its planned operations through positive cash flow, expected around the end of 2026. Conference Call and Webcast Codexis will hold a conference call and webcast today beginning at 4:30 p.m. ET. A live webcast and slide presentation to accompany the conference call will be available on the Investors section of the Company website at . The conference call dial-in numbers are 877-705-2976 for domestic callers and 201- 689-8798 for international callers. A telephone recording of the call will be available for 48 hours beginning approximately two hours after the completion of the call by dialing 877-660-6853 for domestic callers or 201-612-7415 for international callers. Please use the passcode 13726635 to access the recording. A webcast replay will be available on the Investors section of the Company website for 90 days, beginning approximately two hours after the completion of the call. About Codexis Codexis is a leading enzyme engineering company leveraging its proprietary CodeEvolver® technology platform to discover, develop and enhance novel, high-performance enzymes and other classes of proteins. Codexis enzymes solve for real-world challenges associated with small molecule pharmaceuticals manufacturing and nucleic acid synthesis. The Company is currently developing its proprietary ECO Synthesis™ manufacturing platform to enable the scaled manufacture of RNAi therapeutics through an enzymatic route. Codexis’ unique enzymes can drive improvements such as higher yields, reduced energy usage and waste generation, improved efficiency in manufacturing and greater sensitivity in genomic and diagnostic applications. For more information, visit . Forward-Looking Statements This press release contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended. In some cases, you can identify forward-looking statements by terminology such as “aim,” “anticipate,” “assume,” “believe,” “contemplate,” “continue,” “could,” “design,” “due,” “estimate,” “expect,” “goal,” “intend,” “may,” “objective,” “plan,” “positioned,” “potential,” “predict,” “seek,” “should,” “suggest,” “target,” “on track,” “will,” “would” and other similar expressions that are predictions of or indicate future events and future trends, or the negative of these terms or other comparable terminology. To the extent that statements contained in this press release are not descriptions of historical facts, they are forward-looking statements reflecting the current beliefs and expectations of management, including but not limited to statements regarding anticipated milestones, including product launches, technical milestones, data releases and public announcements related thereto; whether Codexis will be able to, and the timing of it entering pre-commercial testing of its ECO Synthesis™ manufacturing platform with select customers in 2024, entering into initial commercial licensing opportunities in 2025 and the subsequent expected commercial launch in 2026; Codexis’ expectations regarding 2024 product revenues, R&D revenues and gross margin on product revenue, as well as its ability to fund planned operations through the end of 2026; Codexis’ ability to achieve positive cash flow around the end of 2026; Codexis’ expectation that its newly engineered double-stranded ecoRNA™ ligase program will be widely available for customers in 2024 and the potential of its ecoRNA™ ligase program to, among other things, improve traditional phosphoramidite chemistry and enable more efficient use of existing manufacturing infrastructure; Codexis’ expectation that its Pharmaceutical Manufacturing business will return to growth in 2024; the anticipated use of proceeds under Codexis’ new loan facility with Innovatus, including the planned ECO Synthesis™ Innovation Lab; the potential of the ECO Synthesis™ manufacturing platform, including its ability to be broadly utilized and to enable commercial-scale manufacture of RNAi therapeutics through an enzymatic route; and expectations regarding future demand for siRNA and dsRNA. You should not place undue reliance on these forward-looking statements because they involve known and unknown risks, uncertainties and other factors that are, in some cases, beyond Codexis’ control and that could materially affect actual results. Factors that could materially affect actual results include, among others: Codexis’ dependence on its licensees and collaborators; if any of its collaborators terminate their development programs under their respective license agreements with Codexis; Codexis may need additional capital in the future in order to expand its business; if Codexis is unable to successfully develop new technology such as its ECO Synthesis™ manufacturing platform and dsRNA; Codexis’ dependence on a limited number of products and customers, and potential adverse effects to Codexis’ business if its customers’ products are not received well in the markets; if Codexis is unable to develop and commercialize new products for its target markets; if competitors and potential competitors who have greater resources and experience than Codexis develop products and technologies that make Codexis’ products and technologies obsolete; Codexis’ ability to comply with debt covenants under its loan facility; if Codexis is unable to accurately forecast financial and operational performance; and market and economic conditions may negatively impact Codexis business, financial condition and share price. Additional information about factors that could materially affect actual results can be found in Codexis’ Annual Report on Form 10-K that will be filed with the Securities and Exchange Commission (SEC) on or about the date hereof, including under the caption “Risk Factors,” and in Codexis’ other periodic reports filed with the SEC. Codexis expressly disclaims any intent or obligation to update these forward-looking statements, except as required by law. Codexis’ results for the quarter and year ended December 31, 2023, are not necessarily indicative of our operating results for any future periods. For More Information Investor Contact Carrie McKim (336) 608-9706 ir@codexis.com Media Contact Lauren Musto (650) 421-8205 media@codexis.com Codexis, Inc. Condensed Consolidated Statements of Operations (unaudited) (In Thousands, Except Per Share Amounts) Three Months Ended December 31, Year Ended December 31, 2023 2022 2023 2022 Revenues: Product revenue $ 18,099 $ 23,300 $ 42,906 $ 116,676 Research and development revenue 8,462 7,075 27,237 21,914 Total revenues 26,561 30,375 70,143 138,590 Costs and operating expenses: Cost of product revenue 2,861 8,456 12,809 38,033 Research and development 11,234 19,689 58,885 80,099 Selling, general and administrative 12,184 12,314 53,250 52,172 Restructuring charges — 3,167 3,284 3,167 Asset impairment and other charges — — 9,984 — Total costs and operating expenses 26,279 43,626 138,212 173,471 Loss from operations 282 (13,251 ) (68,069 ) (34,881 ) Interest income 906 823 4,172 1,441 Other income (expense), net (8,345 ) (26 ) (12,274 ) 124 Loss before income taxes (7,157 ) (12,454 ) (76,171 ) (33,316 ) Provision for income taxes 35 151 69 276 Net loss $ (7,192 ) $ (12,605 ) $ (76,240 ) $ (33,592 ) Net loss per share, basic and diluted $ (0.10 ) $ (0.19 ) $ (1.12 ) $ (0.51 ) Weighted average common stock shares used in computing net loss per share, basic and diluted 69,500 65,558 68,131 65,344 Codexis, Inc. Condensed Consolidated Balance Sheets (unaudited) (In Thousands) December 31, 2023 2022 Assets Current assets: Cash and cash equivalents $ 65,116 $ 113,984 Restricted cash, current 519 521 Financial assets: Accounts receivable 10,036 31,904 Contract assets 815 2,116 Unbilled receivables 9,142 7,016 Total financial assets 19,993 41,036 Less: allowances (65 ) (163 ) Total financial assets, net 19,928 40,873 Inventories 2,685 2,029 Prepaid expenses and other current assets 5,218 5,487 Total current assets 93,466 162,894 Restricted cash 1,062 1,521 Investment in non-marketable equity securities 9,700 20,510 Right-of-use assets - Operating leases, net 13,137 39,263 Property and equipment, net 15,487 22,614 Goodwill 2,463 3,241 Other non-current assets 1,246 350 Total assets $ 136,561 $ 250,393 Liabilities and Stockholders’ Equity Current liabilities: Accounts payable $ 5,947 $ 3,246 Accrued compensation 11,246 11,453 Other accrued liabilities 4,735 15,279 Current portion of lease obligations - Operating leases 3,781 5,360 Deferred revenue 10,121 13,728 Total current liabilities 35,830 49,066 Deferred revenue, net of current portion 640 16,881 Long-term lease obligations - Operating leases 12,243 38,278 Other long-term liabilities 1,233 1,371 Total liabilities 49,946 105,596 Stockholders’ equity: Common stock 7 6 Additional paid-in capital 584,138 566,081 Accumulated deficit (497,530 ) (421,290 ) Total stockholders’ equity 86,615 144,797 Total liabilities and stockholders’ equity $ 136,561 $ 250,393

1DNA双链断裂（DSB）修复途径合成致死性是诱导细胞死亡的生物过程，其基于同时抑制在细胞存活所需的过程中的两种途径并行作用，仅抑制一种途径会导致细胞存活。合成致死策略已在抗癌治疗中得到广泛应用。由于一种途径可能由于转化相关变化而在癌细胞中失活，因此靶向另一种途径触发细胞死亡，同时保留健康细胞1。癌细胞的关键特征之一是由DNA损伤的积累，包括DNA双链断裂（DSB），这是细胞中最致命的DNA损伤之一。然而，癌细胞能够通过调节其DNA修复途径存活和增殖，这可能与正常细胞中的DNA修复途径不同1。DSB可以通过两种主要机制进行修复：BRCA1/2介导的同源重组（HR）和典型 DNA-PKcs介导的非同源末端连接（c-NHEJ）（图1）1。HR被认为是一种准确的DSB修复途径，因为它依赖于细胞周期S/G2期细胞的姐妹染色单体作为DNA合成和DSB修复的模板。因此，HR能够修复DSB，主要在增殖细胞中1。HR修复途径由两个经典的肿瘤抑制基因BRCA1和BRCA2编码的蛋白质进行全面调节，然后募集RAD51及其旁系同源物（包括RAD51B，RAD51C，RAD51D，XRCC2和XRCC3）和RAD54以识别同源DNA模板并进行链侵袭以修复DSBs。另一方面，NHEJ是一种容易出错的DSB修复机制。NHEJ可以是分为c-NHEJ和a-NHEJ（也称为MMEJ或TMEJ）两种途径1。图1. DNA双链断裂（DSB）修复途径包括同源重组（HR），规范非同源末端连接（c-NHEJ）和替代非同源末端连接（a-NHEJ）/微同源介导的末端连接（MMEJ）/DNA聚合酶θ（Polθ）介导的末端连接（TMEJ）2PARPi在造血恶性肿瘤中的治疗潜力最近的很多研究表明，即使在白血病中很少检测到BRCA1/2突变，PARP抑制剂（PARPi）诱导的合成致死性也可以有效地在 BRCA1/2 缺陷造血恶性细胞中起作用。此外，诱导造血恶性肿瘤的遗传改变，例如驱动骨髓和淋巴恶性肿瘤的癌基因，包括 AML1-ETO（也称为 RUNX1-RUNX1T1）、BCR-ABL1、PML-RARa、TCF3-HLF、IDH1/2mut和IGH-MYC以及肿瘤抑制基因（例如TET2、WT1）的功能缺失突变可导致HR和/或c-NHEJ活性失调，从而使细胞容易受到PARPi引发的合成致死效应的影响（图2和图3）1。图2. PARP抑制剂在造血恶性肿瘤和其他显示癌基因/突变（A）和酪氨酸激酶抑制剂（B）诱导的HR/c-NHEJ缺乏症的肿瘤中的应用此外，Bac等人描述了那些恶性造血细胞表达致癌酪氨酸激酶 （OTK）（例如 BCR-ABL1、FLT3（ITD）、JAK2（V617F））由于ROS产量增加自发积累高水平的氧化DNA损伤和DSB 1。然而，OTK阳性细胞能够逃逸来自 DSB 的细胞毒性作用，这是由于增强/调节的 DSB 修复。FDA批准的特异性酪氨酸激酶抑制剂（TKi）（JAK1/2抑制剂鲁索利替尼，FLT3抑制剂奎扎替尼，ABL1抑制剂伊马替尼）对这些OTK的抑制导致急性HR / c-NHEJ缺乏症（由于BRCA1，BRCA2，RAD51和/或LIG4的下调）和对PARPi的敏感性（图2-4）。因此，TKi和PARPi的联合使用能够根除增殖和静止的恶性造血干细胞和祖细胞1。图3. 诱发HR / c-NHEJ缺乏症的癌基因/突变图4. 诱导HR/c-NHEJ缺乏的治疗药物3对PARPi的获得性耐药机制尽管 PARPi 在 DSB 修复缺陷的癌细胞中具有很强的效力，但在BRCA1/2 缺陷和 HRD 中已经报道了对 PARPi 诱导的合成致死性的抵抗力肿瘤细胞（图5）。PARPi的耐药性的主要原因是BRCA1/2突变癌细胞HR修复活性的恢复2。详细地说，BRCA1/2中的继发突变与原始突变导致的链终止子/移码的废除有关，导致全长 BRCA1/2 开放阅读框的恢复。因此，活性BRCA1/BRCA2蛋白表达被恢复，从而重新启动功能齐全的HR途径3,4。除了BRCA1/2中其他突变介导的耐药性外，还提出了BRCA1启动子甲基化的减少/丧失，从而恢复了BRCA1的表达而导致对PARPi的耐药性5。图5. 对PARPi的获得性耐药机制BRCA1-BRCA2-RAD51轴对于同源重组修复（HRR）至关重要。EMI1调节三阴性乳腺癌（TNBC）细胞中的 PARPi 敏感性。EMI1的F盒结构域组装一个SCF泛素连接酶复合物，该复合物靶向RAD51进行降解。在一部分对PARPi难治的BRCA1缺陷三阴性乳腺癌细胞中，EMI1表达的降低会损害EMI依赖性RAD51的降解，从而恢复HR修复活性导致对PARPi的耐药性（图6）6。图6. KEAP1的增加导致EMI1表达的降低导致对PARPi的耐药机制EMSY是I型干扰素反应的负调节因子，也抵消了HR修复途径，KEAP1靶向EMSY进行泛素介导的降解。因此，KEAP1的过表达破坏了EMSY的稳定性，导致HR恢复和对PARPi的抵抗。相反，由于基因突变引起的KEAP1失活导致EMSY的稳定和HR缺乏而使得非小细胞肺癌对PARPi变得敏感（图7）7。图7. EMI1表达的降低导致EMSY的减少，从而对PARPi的耐药机制PARP1的下调或者突变都可能导致BRCA1/2缺陷肿瘤细胞中的PARPi耐药性（图5）。通过53BP1-RIF1的复合物，53BP1介导的DSB末端切除术抑制导致c-NHEJ活性增强，减少对PARP1依赖性a-NHEJ的依赖性，从而引起PARPi耐药性8.因此，53BP1在BRCA1-null小鼠胚胎干细胞中的抑制促进DSB末端切除以限制c-NHEJ，从而使细胞对PARPi致敏。在BRCA1突变的乳腺癌细胞中，由于HR修复活性的部分恢复，53BP1的体细胞丢失导致奥拉帕尼耐药，从而降低BRCA1缺陷小鼠乳腺肿瘤对该抑制剂的反应（图5）。53BP1定位于DSB的阻断也有助于BRCA1缺陷肿瘤中PARPi的失活，这是由TIRR表达增加介导的9。SHLD1/2/3复合物的失活以及DSB末端切除术中其他蛋白（包括RIF1和REV7）的表达降低，恢复了HR的功能活性，降低了PARPi的疗效（图8）10。以相同的机制方式，TRIP13是SHLD1 /2 /3复合物的负调节因子，通过解离REV7-SHLD1/2/3去促进HR。因此，TRIP13的扩增诱导BRCA1/2突变癌症对PARPi的耐药11。图8. SHLD1/2的敲除在BRCA1敲除细胞中导致对PARPi的耐药机制除了在HR通路中起作用外，据报道，BRCA1和BRCA2在维持复制分叉的完整性方面发挥作用12。在BRCA1和BRCA2缺陷细胞中对PARPi获得性耐药可能是由于EZH2缺失导致MRE1和MUS81核酸酶表达降低，导致对复制叉的保护性反应（图9）12,13。图9. MRE1、MUS81和EZH2的下调导致对PARPi的耐药机制除了基于恢复HR或复制叉保护的获得性PARPi抗性机制之外，最近的一项研究报告称，通过恢复Okazaki片段处理（OFP）减少/丢失DNA复制间隙可以诱导抗性。基本上，据报道，复制间隙是BRCA1/2缺陷细胞中PARPi反应的主要决定因素。一般来说，BRCA1/2的缺乏会扩大复制间隙，导致细胞的PARPi敏感性1。然而，在同时敲除BRCA1和53BP1的细胞模型中，通过恢复XRCC1-LIG3恢复OFP，导致减少/耗尽复制差距，并最终对PARPi产生抵抗力。相反，双倍敲除53BP1和LIG3使BRCA1突变细胞对PARPi重新敏感（图10）14。图10. XRCC1-LIG3的增加恢复OFP对PARPi产生耐药性4预先存在的 PARPi 耐药性机制HR和/或c-NHEJ缺陷的血液系统恶性肿瘤在模拟外周血微环境（PBM） 的条件下对PARPi介导的合成致死性敏感，在模拟骨髓微环境（BMM）的条件对 PARPi 产生抗性。Bac等人表明转化生长因子β1（TGF-1）由骨髓基质细胞产生的激活缺氧诱导的TGF-受体（TGF R）激酶-SMAD2/3在白血病细胞中的规范途径以促进DSB的修复（图11）1。TGFβR激酶抑制剂没有改变白血病细胞对PBM中PARPi的敏感性，表明DSB修复活动中TGFβR-SMAD3信号传导的调节在BMM中是排他性的。在机制上，TGFβR激酶信号通过BRCA1/2、ATM，DNA-PKcs和LIG4的上调刺激BMM中白血病细胞中DSB的修复。这一发现表明TGFβR激酶抑制剂在PARPi介导的造血恶性肿瘤干预中的潜在临床应用。事实上，TGFβR激酶的抑制剂galunisertib已经在临床上几种癌症的试验得到应用 15,16，恢复了BMM中白血病细胞的PARPi敏感性。因此，Bac等人假设在PARPi治疗中加入galunisertib应该改善治疗效果1。图11. 通过在缺氧骨髓微环境中激活TGF-β1—TGFβR—SMAD2/3信号传导，恢复HR/c-NHEJ缺陷白血病中的HR/c-NHEJ的PARP抑制剂耐药的预先存在机制除此之外，还有一些其它预先存在的对PARPi的耐药机制，比如DNMT3A的突变导致功能丧失，FLT3激酶与ITD融合突变导致FLT3激酶激活，JAK2的V617K突变导致JAK2激酶的激活，c-KIT的N822K突变导致c-KIT激酶的激活，EGFR的激活和IGF-1R的激酶等都可能导致预先存在的PARPi抑制剂的耐药（图12）1。图12. 预先存在的 PARPi 耐药性机制5小结鉴于负责PARPi耐药性的机制途径列表不断增加，必须实现对预先存在和获得的PARPi耐药的药理学抑制，以提高PARPi介导的合成的治疗效率杀伤力。例如，白血病细胞中预先存在的PARPi耐药性可以通过联合PARP和TGFβR激酶抑制剂（使BMM中的白血病细胞再敏化）、PARP和TET2双加氧酶抑制剂（使携带DNMT3A突变的白血病重新致敏）以及PARP和OTK抑制剂（FLT3（ITD）、JAK2（V617F）、c-KIT（N822K）、EGFR、IGF-1R）解决。获得性 PARPi 抗性可通过以下方式预防，如更具侵略性的“双重合成致死”方法（同时靶向PARP1和RAD52），可在更短的时间内消除更多的肿瘤细胞，从而减少抗性克隆出现的时间依赖性的机会。此外，如果 PARPi出现耐药性，这些克隆可以通过抑制另一种DNA修复机制来消除，例如Pol介导的TMEJ 17。参考文献：1.Bac Viet Le, Paulina Podszywałow-Bartnicka, Katarzyna Piwocka, and Tomasz Skorski, Pre-Existing and Acquired Resistance to PARP Inhibitor-Induced Synthetic Lethality, Cancers 2022, 14, 5795.2.Quigley, D.; Alumkal, J.J.; Wyatt, A.W.; Kothari, V.; Foye, A.; Lloyd, P.; Aggarwal, R.; Kim, W.; Lu, E.; Schwartzman, J.; et al. 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