Supporting data for ‘Enhancing MHC‑I–Mediated Immunity by ICMT Inhibition and Personalizing Chemotherapy with Patient‑Derived Organoids in Ovarian Cancer’

In this study, we performed a genome-wide CRISPR knockout screen to discover novel MHC-I–specific negative regulators in ovarian cancer. Isoprenylcysteine carboxylmethyltransferase (ICMT) emerged from this screen as a key MHC-I–specific negative regulator. Genetic knockdown and pharmacological inhibition of ICMT significantly increased surface MHC-I expression without inducing PD-L1, thereby enhancing CD8⁺ T cell–mediated killing of ovarian cancer cells <i>in vitro.</i> <i>In vivo</i>, ICMT inhibition sensitized tumours to anti–PD-L1 therapy by upregulating MHC-I expression and promoting CD8⁺ T-cell infiltration. Consistent with these findings, ICMT expression was negatively correlated with GZMB⁺CD8⁺ cytotoxic T cells in clinical ovarian cancer samples. Mechanistically, ICMT regulated surface MHC-I abundance through proteasome-dependent degradation.Patient-derived organoids (PDOs) were employed as a preclinical platform for drug testing and precision oncology. To test its feasibility to guide individualized therapy, we successfully established PDOs from 28 surgically resected primary ovarian tumours and 12 malignant ascites samples from patients with ovarian cancer. These PDOs recapitulated the histopathological features of their matched tumours. Drug testing revealed marked intra-patient heterogeneity in responses to chemotherapy and targeted agents. In PDOs derived from primary ovarian cancers, <i>in vitro</i> drug sensitivity correlated with patients’ progression‑free survival and CA‑125 normalization, and this association persisted even at clinical recurrence. In contrast, for PDOs derived from recurrent tumours, PDO drug responses did not correlate with clinical outcomes. Beyond clinically approved agents, we evaluated antibody–drug conjugates and observed substantial inter-patient heterogeneity in PDO responses, which was further validated in the patient-derived xenograft model. Additionally, we identified tumour stiffness and monocyte infiltration as factors associated with successful PDO establishment.

本研究开展了全基因组成簇规律间隔短回文重复序列（Clustered Regularly Interspaced Short Palindromic Repeats，CRISPR）基因敲除筛选，以发现卵巢癌中新型的主要组织相容性复合体I类（MHC-I）特异性负调控因子。经该筛选得到的异戊烯半胱氨酸羧基甲基转移酶（Isoprenylcysteine carboxylmethyltransferase，ICMT）被证实为关键的MHC-I特异性负调控因子。通过基因敲低与药物抑制ICMT，可显著提高卵巢癌细胞表面MHC-I的表达水平，且不会诱导程序性死亡受体配体1（Programmed Death-Ligand 1，PD-L1）的表达，进而增强CD8⁺ T细胞介导的卵巢癌细胞体外杀伤效应。体内实验中，通过上调MHC-I表达并促进CD8⁺ T细胞浸润，ICMT抑制可使肿瘤对抗PD-L1治疗产生敏感性。与上述研究结果一致，临床卵巢癌样本中ICMT的表达与颗粒酶B（Granzyme B，GZMB）阳性CD8⁺细胞毒性T细胞呈负相关。从机制层面来看，ICMT通过蛋白酶体依赖性降解途径调控细胞表面MHC-I的丰度。
患者来源类器官（Patient-derived organoids，PDOs）被用作药物测试与精准肿瘤学的临床前研究平台。为验证其指导个体化治疗的可行性，本研究成功从28例手术切除的原发性卵巢肿瘤样本以及12例卵巢癌患者的恶性腹水样本中构建了PDOs。所构建的PDOs可重现其匹配肿瘤的组织病理学特征。药物敏感性测试结果显示，同一患者体内的肿瘤对化疗药物及靶向药物的应答存在显著的异质性。在原发性卵巢癌来源的PDOs中，体外药物敏感性与患者的无进展生存期及癌抗原125（Cancer Antigen 125，CA-125）水平恢复正常显著相关，且该相关性在临床复发阶段依然成立。与之相对，复发肿瘤来源的PDOs的药物应答则与临床结局无显著关联。除临床获批药物外，本研究还评估了抗体药物偶联物（antibody–drug conjugates）的疗效，观察到PDOs对其的应答存在显著的患者间异质性，该结果在患者来源异种移植模型中得到了进一步验证。此外，本研究还明确肿瘤硬度与单核细胞浸润是影响PDOs成功构建的相关因素。