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Tumor microenvironment reprogramming improves nanomedicine-based chemo-immunotherapy in sarcomas. 肿瘤微环境重编程可改善肉瘤的纳米药物化疗免疫疗法。
IF 5.3 2区 医学 Q1 ONCOLOGY Pub Date : 2024-06-28 DOI: 10.1158/1535-7163.MCT-23-0772
Antonia Charalambous, Fotios Mpekris, Myrofora Panagi, Chrysovalantis Voutouri, Christina Michael, Alberto A Gabizon, Triantafyllos Stylianopoulos

Background/introduction: Sarcomas are a heterogenous group of rare cancers that originate in soft tissues or bones. Their complexity and tendency for metastases makes treatment challenging, highlighting the need for new therapeutic approaches to improve patient survival. The difficulties in treating these cancers primarily stem from abnormalities within the tumor microenvironment (TME), which lead to reduced blood flow and oxygen levels in tumors. Consequently, this hampers the effective delivery of drugs to tumors and diminishes treatment efficacy despite higher, toxic doses of chemotherapy. Here, we tested the mechanotherapeutic ketotifen combined with either pegylated-liposomal doxorubicin (PLD) or pegylated-liposomal co-encapsulated alendronate-doxorubicin (PLAD) plus anti-PD-1 antibody in mouse models of fibrosarcoma and osteosarcoma.

Results: We found that ketotifen successfully reprogrammed the TME by reducing tumor stiffness and increasing perfusion, proven by changes measured by shear-wave-elastography (SWE) and contrast-enhanced-ultrasound (CEUS) respectively, and enhanced the therapeutic efficacy of our nanomedicine-based chemo-immunotherapy protocols. An additional observation was a trend to improved antitumor response when nano-chemotherapy is given alongside anti-PD1 and when the immunomodulator alendronate was present in the treatment. We next investigated the mechanisms of action of this combination. Ketotifen combined with nanomedicine-based chemo-immunotherapy, increased T-cell infiltration, specifically cytotoxic CD8+ T cells and CD4+ T helper-cell and decreased the number of regulatory-T-cells. In addition, the combination also altered the polarization of tumor associated macrophages, favouring the M1 immune-supportive phenotype over the M2 immuno-suppressive phenotype.

Conclusion: Collectively, our findings provide evidence that ketotifen-induced TME reprograming can improve the efficacy of nanomedicine-based chemoimmunotherapy in sarcomas.

背景/简介:肉瘤是一类起源于软组织或骨骼的异质性罕见癌症。肉瘤的复杂性和转移倾向使治疗具有挑战性,因此需要新的治疗方法来提高患者的生存率。治疗这些癌症的困难主要源于肿瘤微环境(TME)的异常,这种异常会导致肿瘤内的血流和氧气水平降低。因此,这阻碍了药物向肿瘤的有效输送,并降低了治疗效果,尽管化疗剂量更高、毒性更强。在此,我们在纤维肉瘤和骨肉瘤小鼠模型中测试了机械治疗药物酮替芬与聚乙二醇化脂质体多柔比星(PLD)或聚乙二醇化脂质体共囊阿仑膦酸-多柔比星(PLAD)加抗-PD-1抗体的组合:结果:我们发现酮替芬通过降低肿瘤僵硬度和增加血流灌注成功地对TME进行了重编程(分别通过剪切波弹性成像(SWE)和对比增强超声(CEUS)测量到的变化证明了这一点),并增强了我们基于纳米药物的化疗免疫疗法方案的疗效。另一个观察结果是,当纳米化疗与抗PD1同时进行,并且治疗中含有免疫调节剂阿仑膦酸盐时,抗肿瘤反应有改善的趋势。我们接下来研究了这种组合的作用机制。酮替芬与基于纳米药物的化疗免疫疗法相结合,增加了T细胞浸润,特别是细胞毒性CD8+ T细胞和CD4+ T辅助细胞,并减少了调节性T细胞的数量。此外,联合疗法还改变了肿瘤相关巨噬细胞的极化,使M1免疫支持表型优于M2免疫抑制表型:总之,我们的研究结果提供了证据,证明酮替芬诱导的TME重编程可提高基于纳米药物的肉瘤化疗免疫疗法的疗效。
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引用次数: 0
The discovery of a potent PARP1 inhibitor Senaparib. 发现强效 PARP1 抑制剂 Senaparib。
IF 5.3 2区 医学 Q1 Medicine Pub Date : 2024-06-26 DOI: 10.1158/1535-7163.MCT-23-0625
Sui Xiong Cai, Ning Ma, Xiaozhu Wang, Mingchuan Guo, Yangzhen Jiang, Ye E Tian

Poly (ADP-ribose) polymerases 1 (PARP1) is a critical enzyme involved in DNA damage repair. It belongs to a super family of proteins and catalyzes poly (ADP-ribosyl)ation (PARylation). PARP1 inhibitors are effective to treat tumors that have homologous recombination deficiency (HRD) such as the ones with BRCA1/2 mutations. The PARP1 inhibitors that have been approved by FDA inhibit both PARP1 and PARP2. PARP2 has also been suggested to have similar function in DNA repair as PARP1. In addition to inhibiting PARP1 enzymatic activities, PARP1 inhibitors also cause PARP1 enzyme to be "trapped" on DNA which leads to DNA replication fork to stall and eventually double-strand DNA breaks and cell death. Here, we report a PARP1 inhibitor, Senaparib, which has a novel chemical structure and high potency inhibiting PARP1/2 enzymes. Senaparib was highly potent in cell viability tests against tumor cells with BRCA1/2 mutations. It was efficacious in CDX and PDX xenograft models in tumor harboring BRCA1/2 mutations. In combination studies, Senaparib used with temozolomide (TMZ) had shown strong synergistic cytotoxicity in both in vitro and in vivo experiments. Senaparib represents a novel class of PARP1 inhibitors that can be used for the treatment of cancer. A phase III clinical study of Senaparib for maintenance treatment following first-line chemotherapy in patients with advanced ovarian cancer has met its primary endpoint, and a new drug application of Senaparib has been accepted by National Medical Products Administration (NMPA) of China for review.

聚(ADP-核糖)聚合酶 1(PARP1)是一种参与 DNA 损伤修复的关键酶。它属于超级蛋白质家族,催化聚(ADP-核糖)合成(PARylation)。PARP1 抑制剂可有效治疗同源重组缺陷(HRD)肿瘤,如 BRCA1/2 基因突变的肿瘤。已获 FDA 批准的 PARP1 抑制剂可同时抑制 PARP1 和 PARP2。PARP2 也被认为在 DNA 修复中具有与 PARP1 相似的功能。除了抑制 PARP1 酶的活性外,PARP1 抑制剂还会导致 PARP1 酶被 "困住 "在 DNA 上,从而导致 DNA 复制叉停滞,最终导致双链 DNA 断裂和细胞死亡。在此,我们报告了一种 PARP1 抑制剂 Senaparib,它具有新颖的化学结构和抑制 PARP1/2 酶的高效力。在针对 BRCA1/2 基因突变的肿瘤细胞的细胞活力测试中,Senaparib 具有很高的效力。在 CDX 和 PDX 异种移植模型中,它对携带 BRCA1/2 突变的肿瘤具有疗效。在联合用药研究中,Senaparib 与替莫唑胺(TMZ)的体外和体内实验均显示出很强的协同细胞毒性。Senaparib 是一类可用于治疗癌症的新型 PARP1 抑制剂。Senaparib用于晚期卵巢癌患者一线化疗后的维持治疗的III期临床研究已达到主要终点,Senaparib的新药申请已被中国国家医药管理局受理审评。
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引用次数: 0
Discovery of Monovalent Direct Degraders of BRD4 That Act Via the Recruitment of DCAF11. 发现通过招募 DCAF11 起作用的 BRD4 单价直接降解剂
IF 5.3 2区 医学 Q1 Medicine Pub Date : 2024-06-22 DOI: 10.1158/1535-7163.MCT-24-0219
Gregory S Parker, Julia I Toth, Sarah Fish, Gabrielle A Blanco, Taylor Kampert, Xiaoming Li, Linette Yang, Craig R Stumpf, Kenneth Steadman, Aleksandar Jamborcic, Stephen Chien, Elizabeth Daniele, Alejandro Dearie, Geoffray Leriche, Simon Bailey, Peggy A Thompson

Targeted protein degradation (TPD) using the ubiquitin proteasome system (UPS) is a rapidly growing drug discovery modality to eliminate pathogenic proteins. Strategies for TPD have focused on heterobifunctional degraders that often suffer from poor drug-like properties, and molecular glues that rely on serendipitous discovery. Monovalent "direct" degraders represent an alternative approach, in which small molecules bind to a target protein and induce degradation of that protein through the recruitment of an E3 ligase complex. Using an ultra-high throughput cell-based screening platform, degraders of the bromodomain extra-terminal (BET) protein BRD4 were identified and optimized to yield a lead compound, PLX-3618. In this paper, we demonstrate that PLX-3618 elicited UPS-mediated selective degradation of BRD4, resulting in potent anti-tumor activity in vitro and in vivo. Characterization of the degradation mechanism identified DCAF11 as the E3 ligase required for PLX-3618-mediated degradation of BRD4. Protein-protein interaction studies verified a BRD4:PLX-3618:DCAF11 ternary complex, and mutational studies provided further insights into the DCAF11-mediated degradation mechanism. Collectively, these results demonstrate the discovery and characterization of a novel small molecule that selectively degrades BRD4 through the recruitment of the E3 substrate receptor, DCAF11, and promotes potent anti-tumor activity in vivo.

利用泛素蛋白酶体系统(UPS)进行靶向蛋白质降解(TPD)是一种快速发展的药物发现方式,可用于消除致病蛋白质。TPD的策略主要集中在异功能降解剂(通常具有较差的类药物特性)和依赖偶然发现的分子粘合剂上。单价 "直接 "降解剂代表了另一种方法,即小分子与目标蛋白质结合,通过招募 E3 连接酶复合物诱导该蛋白质降解。利用基于细胞的超高通量筛选平台,我们鉴定并优化了溴域末端外(BET)蛋白 BRD4 的降解剂,从而获得了先导化合物 PLX-3618。在本文中,我们证明了 PLX-3618 可诱导 UPS 介导的 BRD4 选择性降解,从而在体外和体内产生强效抗肿瘤活性。降解机制的表征确定了 DCAF11 是 PLX-3618 介导的 BRD4 降解所需的 E3 连接酶。蛋白-蛋白相互作用研究验证了BRD4:PLX-3618:DCAF11三元复合物,突变研究进一步揭示了DCAF11介导的降解机制。总之,这些研究结果表明发现并鉴定了一种新型小分子,它能通过招募 E3 底物受体 DCAF11 选择性地降解 BRD4,并在体内促进有效的抗肿瘤活性。
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引用次数: 0
Targeting Chemoresistance in Advanced Bladder Cancers with a Novel Adjuvant Strategy. 用新型辅助策略瞄准晚期膀胱癌的耐药性
IF 5.3 2区 医学 Q1 Medicine Pub Date : 2024-06-21 DOI: 10.1158/1535-7163.MCT-23-0806
Juliette R Seremak, Kunj Bihari Gupta, Sunilkanth Bonigala, Elise Liu, Brendan Marshall, Wenbo Zhi, Riham M Bokhtia, Siva S Panda, Vinata B Lokeshwar, Bal L Lokeshwar

Advanced urinary bladder cancer is characterized by rapid progression and development of therapy resistance. About 30% of the patients are diagnosed with high-grade tumors (grade > T2a). A typical nonsurgical treatment is systemic chemotherapy using cisplatin (C) and gemcitabine (G). However, treatment failure and subsequent disease progression are common in treated patients, and adjuvant therapies are not significantly effective. The therapeutic potential of a molecular hybrid of ursolic acid (UA), a pentacyclic-triterpene conjugated to N-methyl piperazine (UA4), was tested on both naïve (WT) and gemcitabine-resistant (GemR) variants of two human invasive bladder cancer cell lines, 5637 and T24. UA4 killed 5637 (4 µmol/L), T24 (4 µmol/L) WT, and GemR cells in vitro at equal potency. Pretreatment with UA4 followed by G synergistically killed WT and GemR cells by >50% compared with G followed by UA4. Oral gavage of UA4 (100 mg/kg) inhibited WT and GemR tumor growth in athymic mice. UA4 + G was more effective against GemR tumors than either drug alone. Studies revealed cytotoxic autophagy as a mechanism of UA4 cytotoxicity. UA4 induced moderate apoptosis in T24 but not in 5637 cells. Mitochondrial integrity and function were most affected by UA4 because of high levels of reactive oxygen species, disruption of mitochondrial membrane, and cell cycle arrest. These effects were enhanced in the UA4 + G combination. UA4 was well-tolerated in mice, and oral gavage led to a serum level >1 µmol/L with no systemic toxicity. These results show the potential of UA4 as a nontoxic alternative treatment for high-grade bladder cancer.

晚期膀胱癌的特点是病情进展迅速和出现耐药性。约 30% 的患者被诊断为高级别肿瘤(级别大于 T2a)。典型的非手术治疗方法是使用顺铂(C)和吉西他滨(G)进行全身化疗。然而,治疗失败和随后的疾病进展在接受治疗的患者中很常见,辅助疗法的效果也不明显。我们对熊果酸(UA)分子杂交体(一种与 N-甲基哌嗪共轭的五环三萜类化合物(UA4))的治疗潜力进行了测试,该杂交体适用于两种人类浸润性膀胱癌细胞系--5637 和 T24--的幼稚型(WT)和吉西他滨耐药型(GemR)变体。UA4 在体外杀死 5637(4 µmol/L)、T24(4 µmol/L)WT 和 GemR 细胞的效力相同。与先用 G 再用 UA4 的情况相比,先用 UA4 再用 G 的情况可协同杀死 WT 和 GemR 细胞 50%以上。口服 UA4(100 毫克/千克)可抑制 WT 和 GemR 肿瘤在无胸腺小鼠体内的生长。与单独使用两种药物相比,UA4 + G 对 GemR 肿瘤更有效。研究显示细胞毒性自噬是 UA4 细胞毒性的一种机制。UA4 可诱导 T24 细胞中度凋亡,但不能诱导 5637 细胞中度凋亡。线粒体的完整性和功能受 UA4 的影响最大,因为其中存在大量活性氧、线粒体膜破坏和细胞周期停滞。这些影响在 UA4 + G 组合中得到了加强。小鼠对 UA4 的耐受性良好,口服后血清中的 UA4 含量大于 1 µmol/L,且无全身毒性。这些结果表明,UA4 有可能成为治疗高级别膀胱癌的一种无毒替代疗法。
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引用次数: 0
Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation. 结合 EHMT 和 PARP 抑制:减少耐药卵巢癌肿瘤生长同时刺激免疫激活的策略
IF 5.7 2区 医学 Q1 Medicine Pub Date : 2024-06-12 DOI: 10.1158/1535-7163.MCT-23-0613
Lily L Nguyen, Zachary L Watson, Raquel Ortega, Elizabeth R Woodruff, Kimberly R Jordan, Ritsuko Iwanaga, Tomomi M Yamamoto, Courtney A Bailey, Francis To, Abigail D Jeong, Saketh R Guntupalli, Kian Behbakht, Veronica Gibaja, Nausica Arnoult, Alexis Cocozaki, Edward B Chuong, Benjamin G Bitler

Despite the success of poly-ADP-ribose polymerase inhibitors (PARPi) in the clinic, high rates of resistance to PARPi presents a challenge in the treatment of ovarian cancer, thus it is imperative to find therapeutic strategies to combat PARPi resistance. Here, we demonstrate that inhibition of epigenetic modifiers euchromatic histone lysine methyltransferases 1/2 (EHMT1/2) reduces the growth of multiple PARPi-resistant ovarian cancer cell lines and tumor growth in a PARPi-resistant mouse model of ovarian cancer. We found that combinatory EHMT and PARP inhibition increases immunostimulatory double-stranded RNA formation and elicits several immune signaling pathways in vitro. Using epigenomic profiling and transcriptomics, we found that EHMT2 is bound to transposable elements, and that EHMT inhibition leads to genome-wide epigenetic and transcriptional derepression of transposable elements. We validated EHMT-mediated activation of immune signaling and upregulation of transposable element transcripts in patient-derived, therapy-naïve, primary ovarian tumors, suggesting potential efficacy in PARPi-sensitive disease as well. Importantly, using multispectral immunohistochemistry, we discovered that combinatory therapy increased CD8 T-cell activity in the tumor microenvironment of the same patient-derived tissues. In a PARPi-resistant syngeneic murine model, EHMT and PARP inhibition combination inhibited tumor progression and increased Granzyme B+ cells in the tumor. Together, our results provide evidence that combinatory EHMT and PARP inhibition stimulates a cell autologous immune response in vitro, is an effective therapy to reduce PARPi-resistant ovarian tumor growth in vivo, and promotes antitumor immunity activity in the tumor microenvironment of patient-derived ex vivo tissues of ovarian cancer.

尽管多聚ADP核糖聚合酶抑制剂(PARPi)在临床上取得了成功,但PARPi的高耐药率给卵巢癌的治疗带来了挑战,因此寻找抗PARPi耐药的治疗策略势在必行。在这里,我们证明了抑制表观遗传修饰因子euchromatic组蛋白赖氨酸甲基转移酶1/2(EHMT1/2)可降低多种PARPi耐药卵巢癌细胞系的生长以及PARPi耐药卵巢癌小鼠模型的肿瘤生长。我们发现,联合抑制 EHMT 和 PARP 会增加免疫刺激性双链 RNA 的形成,并在体外激发多种免疫信号通路。利用表观基因组学分析和转录组学,我们发现 EHMT2 与转座元件结合,抑制 EHMT 会导致转座元件的全基因组表观遗传和转录抑制。我们在患者来源的、治疗无效的原发性卵巢肿瘤中验证了 EHMT 介导的免疫信号激活和转座元件转录物上调,这表明它对 PARPi 敏感的疾病也有潜在疗效。重要的是,通过使用多谱免疫组化技术,我们发现联合疗法提高了同一患者来源组织肿瘤微环境中 CD8 T 细胞的活性。在 PARPi 抗性合成小鼠模型中,EHMT 和 PARP 抑制联合疗法抑制了肿瘤的进展,并增加了肿瘤中 Granzyme B+ 细胞的数量。总之,我们的研究结果证明,EHMT和PARP抑制联合疗法能在体外激发细胞自体免疫反应,在体内是减少PARPi耐药卵巢肿瘤生长的有效疗法,并能促进卵巢癌患者来源体外组织肿瘤微环境中的抗肿瘤免疫活性。
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引用次数: 0
Abstract B004: An isogenic CRISPR screen identifies novel MYC-driven vulnerabilities 摘要 B004:异源CRISPR筛选发现新型MYC驱动的脆弱性
IF 5.7 2区 医学 Q1 Medicine Pub Date : 2024-06-10 DOI: 10.1158/1538-8514.synthleth24-b004
Peter Lin, Linda Penn
c-MYC (MYC) is a central regulatory protein that is dysregulated in >50% of all human cancers and is linked to aggressive disease. Developing MYC inhibitors would revolutionize cancer treatment; however, developing small molecules that directly target MYC is challenging. An alternative approach is to identify and inhibit critical MYC partner proteins to inactivate MYC and trigger cancer cell death. Inhibiting these targets therapeutically can result in synthetic lethality (MYC-SL), which can be exploited in MYC-dysregulated cancers. To identify MYC-SL targets, we performed a genome-wide CRISPR knock-out screen using an isogenic pair of normal and MYC-driven breast cancer cells. In contrast to other screens, this model is dependent on MYC and recapitulates human disease at both pathological and molecular levels in vivo. We identified high-priority hits to validate from the screen using two independent approaches: 1) a traditional gene-set enrichment analysis to identify highly represented biological pathways; and 2) analyzing the Cancer Dependency Map (DEPMAP) to select hits that are likely to be robust beyond the context of our screening conditions. Using a traditional gene-set enrichment analysis approach, we identified topoisomerase 1 (TOP1) as an actionable vulnerability that can be targeted with clinically approved inhibitors. Genetic and pharmacological inhibition of TOP1 resulted in MYC-driven cell death compared to that in control cells. Finally, drug response to TOP1 inhibitors significantly correlated with MYC levels and activity across panels of breast cancer cell lines and patient-derived organoids, highlighting TOP1 as a promising target for MYC-driven cancers. As a secondary approach to interpreting our CRISPR screen hits, we analyzed DEPMAP to identify MYC-SLs that are differentially essential in MYC-dependent cancer cells. Specifically, data from RNA interference screens in hundreds of cancer cell lines were used to describe the response of these cells to MYC knockdown. These data were used to define MYC-dependent and MYC-independent cell lines within the context of this analysis. These two groups were then investigated for their in silico response to the knockdown of each of our MYC-SL hits. MYC-SLs, which were also differentially essential in MYC-dependent cancer cells from DEPMAP, were prioritized for further investigation. Critical MYC cofactors that have been validated by us and others (e.g., CDK9) were identified, providing confidence in this approach, and rationalizing ongoing investigations. Together, this work features two successful strategies to prioritize hits from hundreds of synthetic-lethal genome-wide CRISPR screens to identify novel MYC-driven vulnerabilities in cancer. Citation Format: Peter Lin, Linda Penn. An isogenic CRISPR screen identifies novel MYC-driven vulnerabilities [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilitie
c-MYC(MYC)是一种中心调控蛋白,在50%以上的人类癌症中都会出现调控失调,并与侵袭性疾病有关。开发 MYC 抑制剂将彻底改变癌症治疗方法;然而,开发直接靶向 MYC 的小分子药物具有挑战性。另一种方法是识别并抑制关键的 MYC 伙伴蛋白,使 MYC 失活并引发癌细胞死亡。治疗性抑制这些靶点可导致合成致死(MYC-SL),MYC-SL 可用于 MYC 失调的癌症。为了鉴定 MYC-SL 靶点,我们使用一对正常和 MYC 驱动的乳腺癌细胞进行了全基因组 CRISPR 基因敲除筛选。与其他筛选不同的是,该模型依赖于 MYC,并在体内病理和分子水平上再现了人类疾病。我们通过两种独立的方法从筛选中确定了需要验证的高优先级基因:1) 传统的基因组富集分析,以确定高代表性的生物通路;以及 2) 分析癌症依赖性图谱 (DEPMAP),以选择在筛选条件之外可能具有稳健性的基因组。利用传统的基因组富集分析方法,我们发现拓扑异构酶 1(TOP1)是一个可操作的漏洞,可以用临床批准的抑制剂作为靶点。与对照细胞相比,基因和药物抑制 TOP1 会导致 MYC 驱动的细胞死亡。最后,对 TOP1 抑制剂的药物反应与乳腺癌细胞系和患者衍生的器官组织中的 MYC 水平和活性密切相关,这表明 TOP1 是治疗 MYC 驱动型癌症的理想靶点。作为解读 CRISPR 筛选结果的第二种方法,我们分析了 DEPMAP,以确定在 MYC 依赖性癌细胞中不同程度地必不可少的 MYC-SL。具体来说,数百种癌细胞系的 RNA 干扰筛选数据被用来描述这些细胞对 MYC 敲除的反应。这些数据被用来在分析中定义依赖 MYC 的细胞系和不依赖 MYC 的细胞系。然后研究了这两组细胞系对我们的 MYC-SL 基因敲除的反应。在 DEPMAP 的 MYC 依赖性癌细胞中,MYC-SL 也有不同程度的必需性,因此我们优先对其进行了进一步研究。我们和其他人已经验证的关键 MYC 辅助因子(如 CDK9)也被确定下来,从而为这种方法提供了信心,并使正在进行的研究更加合理。总之,这项工作采用了两种成功的策略,从数百个合成致死基因组范围的 CRISPR 筛选中优先选择命中的基因,以鉴定癌症中新的 MYC 驱动的脆弱性。引用格式:Peter Lin, Linda Penn.异源 CRISPR 筛选发现新型 MYC 驱动的脆弱性 [摘要].In:AACR 癌症研究特别会议论文集:扩展和转化癌症合成漏洞;2024 年 6 月 10-13 日;加拿大魁北克省蒙特利尔。费城(宾夕法尼亚州):AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B004.
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引用次数: 0
Abstract PR009: Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal cancers 摘要 PR009:胞苷二磷酸二酰甘油合成酶 2 是间充质癌症的合成致死靶点
IF 5.7 2区 医学 Q1 Medicine Pub Date : 2024-06-10 DOI: 10.1158/1538-8514.synthleth24-pr009
Tim Arnoldus, Alex van Vliet, Adriaan F.H. de Groot, Niek Blomberg, Onno B. Bleijerveld, Susan E. van Hal-van Veen, Anita E. Grootemaat, Rolf Harkes, N. N. van der Wel, Maarten Altelaar, Martin Giera, D. Peeper
Synthetic lethal interactions (SLIs) can provide a therapeutic index, as illustrated by PARP inhibition of BRCA-deficient cancers. This clinical success, and other examples, have spurred efforts to identify additional cancer-associated SLIs. Whereas additional SLIs based on genomic alterations in cancer have been identified, we set out to explore the SLI space as a function of differential RNA expression profiles in cancer and normal tissue, covering all ∼3.4e8 gene pairs. In our bioinformatic pipeline, synthetic lethality is scored by correlating DepMap dependency and expression data (n = 913 cancer cell lines), while cancer specificity is scored by comparing TCGA expression data for 9264 tumors and 741 healthy samples. Cancer specificity is confirmed by comparing also calibrated GTEx data for 17382 healthy tissue samples with calibrated DepMap expression data. With this pipeline we uncovered a frequent cancer-specific SLI between the paralogs cytidine diphosphate diacylglycerol synthase 1 (CDS1) and CDS2 (p<0.001 in all three analyses). Essentiality of CDS2 is observed in one third of cultured cancers (DepMap). Using CRISPR-Cas9 we confirm the CDS1-dependency for CDS2 essentiality in a panel of 12 cultured cancer cell lines, with lethality by CDS2 ablation reaching up to 98% in CDS1-negative cell lines. We also confirm the SLI using admixing experiments in tumor-bearing mice for two cell lines (6 mice per group, up to 95% synthetic lethality, p<0.001). The essentiality of CDS2 for cell survival is observed for mesenchymal-like cancers, which commonly express low levels of CDS1. To biochemically define the effects of CDS2 perturbation in CDS1-negative cancer cells, we performed multi-omic analyses in a panel of CDS1-negative cancer cell lines. The results show that mechanistically, the CDS1-2 SLI is accompanied by disruption of lipid homeostasis, including extensive accumulation of cholesterol esters and triglycerides. Additionally, quantitative western blotting for cleaved caspase-3 showed induction of apoptotic cell death (p<0.001 in 2 cell lines). To challenge the robustness of the SLI, we performed genome-wide CRISPR-Cas9 knockout screens in a panel of four CDS1-negative cancer cell lines. This failed to identify a common escape mechanism of death caused by CDS2 ablation. These findings suggest that no common escape to the combined loss of CDS1 and CDS2 is possible through loss-of-function. In conclusion, by computational, genetic, biochemical and functional analyses we demonstrate that CDS2 may serve as a target in mesenchymal cancers, meriting therapeutic exploration. Citation Format: Tim Arnoldus, Alex van Vliet, Adriaan F.H. de Groot, Niek Blomberg, Onno B. Bleijerveld, Susan E. van Hal-van Veen, Anita E. Grootemaat, Rolf Harkes, Nicole N. van der Wel, Maarten Altelaar, Martin Giera, Daniel S. Peeper. Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal cancers [abstract]. In: Proceedings of the A
合成致死相互作用(SLIs)可以提供一种治疗指标,如 PARP 对 BRCA 缺失型癌症的抑制作用。这一临床成功和其他例子促使人们努力找出更多与癌症相关的合成致死相互作用。尽管基于癌症基因组改变的其他 SLIs 已被确定,但我们仍着手探索作为癌症和正常组织中不同 RNA 表达谱函数的 SLI 空间,涵盖所有 3.4e8 对基因。在我们的生物信息学管道中,合成致死率是通过关联 DepMap 依赖性和表达数据(n = 913 个癌细胞系)来评分的,而癌症特异性则是通过比较 9264 个肿瘤和 741 个健康样本的 TCGA 表达数据来评分的。癌症特异性是通过比较 17382 个健康组织样本的校准 GTEx 数据和校准 DepMap 表达数据来确认的。通过这一管道,我们发现胞苷二磷酸二酰甘油合成酶 1(CDS1)和 CDS2 的旁系亲属之间经常存在癌症特异性 SLI(在所有三项分析中,P<0.001)。在三分之一的培养癌症(DepMap)中观察到了 CDS2 的本质。利用 CRISPR-Cas9,我们在 12 个培养癌细胞系中证实了 CDS2 的本质依赖于 CDS1,在 CDS1 阴性细胞系中,CDS2 消减的致死率高达 98%。我们还在肿瘤小鼠中对两种细胞系进行了混合实验,证实了SLI(每组6只小鼠,合成致死率高达95%,P<0.001)。在间充质样癌症中观察到 CDS2 对细胞存活的重要性,这些癌症通常表达低水平的 CDS1。为了从生化角度确定 CDS2 干扰对 CDS1 阴性癌细胞的影响,我们在一组 CDS1 阴性癌细胞系中进行了多组学分析。结果表明,从机理上讲,CDS1-2 SLI伴随着脂质平衡的破坏,包括胆固醇酯和甘油三酯的广泛积累。此外,对裂解的 caspase-3 进行定量 Western 印迹检测显示,细胞凋亡诱导(2 个细胞系的 p<0.001)。为了质疑 SLI 的稳健性,我们在四种 CDS1 阴性癌细胞系中进行了全基因组 CRISPR-Cas9 基因敲除筛选。这未能发现 CDS2 消减导致死亡的共同逃逸机制。这些发现表明,通过功能缺失,CDS1 和 CDS2 的联合缺失不可能导致共同的逃逸。总之,通过计算、遗传、生化和功能分析,我们证明 CDS2 可作为间充质癌症的靶点,值得进行治疗探索。引用格式:Tim Arnoldus, Alex van Vliet, Adriaan F.H. de Groot, Niek Blomberg, Onno B. Bleijerveld, Susan E. van Hal-van Veen, Anita E. Grootemaat, Rolf Harkes, Nicole N. van der Wel, Maarten Altelaar, Martin Giera, Daniel S. Peeper.胞苷二磷酸二酰甘油合成酶 2 是间充质癌症的合成致死靶点 [摘要]。In:AACR癌症研究特别会议论文集:扩展和转化癌症合成弱点;2024 年 6 月 10-13 日;加拿大魁北克省蒙特利尔。费城(宾夕法尼亚州):AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR009.
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引用次数: 0
Abstract B027: A pathway-informed framework to infer synthetic lethal relationships in pediatric cancer 摘要 B027:推断儿科癌症合成致死关系的路径信息框架
IF 5.7 2区 医学 Q1 Medicine Pub Date : 2024-06-10 DOI: 10.1158/1538-8514.synthleth24-b027
Anastasia Spinou, Richard Gremmen, Puck Veen, J. Drost, P. Kemmeren
Synthetic lethality, the combination of two mutated genes which results in cell death, has been greatly investigated due to its therapeutic potential in cancer. Despite the common practice of experimentally detecting synthetic lethality, here we extend a computational framework that employs co-occurrence of gene mutations to infer synthetic lethality by incorporating pathways. Pathways aggregate the mutated genes into a functional unit and give power to uncover relationships containing genes of low mutation frequency e.g. in pediatric cancer, which otherwise would not be observed by testing individual gene pairs. Our proposed framework is an alternative avenue to a more focused synthetic lethality search by exploiting mutation data & pathway knowledge. We infer potentially synthetic lethal relationships based on mutated gene co-occurrence. A less often than expected co-occurrence, or so-called mutual exclusivity (ME), indicates a potentially synthetic lethal relationship whereas one that occurs more often than expected (CO) indicates a potentially advantageous relationship. In this framework we use a selected set of biological pathways from Reactome to aggregate gene mutations per pathway for each individual tumor (SNVs and indels with high/moderate impact) within two public pediatric cancer datasets, TARGET and DKFZ. This results in mutated-pathway profiles per tumor which are tested for co-occurrence using rediscover. The test outputs significant co-occurring and mutually exclusive pathways from which we extract the underlying mutated gene pairs. The co-occurring and mutually exclusive gene pairs are then annotated for pathway epistasis, protein complexes and their presence in BioGRID and SynLethDB. Finally, the validity of the proposed gene pairs is examined in literature. The test detected 439 (ME: 369, CO:70) significant pathway pairs in TARGET and 49 (ME: 31, CO:18) in DKFZ across several cancer types. Out of these, 3185 gene pairs were extracted in TARGET (ME: 2671, CO: 514) and 331 (ME: 16, CO: 315) in DKFZ. These relationships are significantly more than the ones found when testing solely for gene pairs. Pathways aid in partially decreasing findings due to subtype or pathway epistasis. For example, FLT3-KRAS found in TARGET-B-ALL by the gene test is not detected by the pathway test. The test was, also, able to uncover mutually exclusive (ME) gene pairs in smaller datasets. The initially found ME genes TP53-DROSHA in Wilms tumors and KIT-NRAS in AML tumors in TARGET by the gene test, were detected in the corresponding cancer types’ DKFZ datasets. In addition to TP53-DROSHA, TP53-DGCR8 were found ME in Wilms tumors of DKFZ, indicating the microprocessor complex mutations ME to TP53 mutations. To sum up, we present a pathway-informed synthetic lethality inference framework for pediatric cancer to explore synthetic lethal relationships and other complex functional relationships between mutated genes by exploiting already existing data and
合成致死性是指两个突变基因的结合导致细胞死亡,由于其在癌症中的治疗潜力,合成致死性已被广泛研究。尽管实验检测合成致死率是常见的做法,但在这里,我们扩展了一个计算框架,利用基因突变的共生来推断合成致死率,并将路径纳入其中。通路将突变基因聚合成一个功能单元,能够揭示包含低突变频率基因(如儿科癌症中的基因)的关系,否则就无法通过检测单个基因对观察到这种关系。我们提出的框架是利用突变数据和通路知识进行更有针对性的合成致死性搜索的另一种途径。我们根据突变基因的共现推断潜在的合成致死关系。共同出现的频率低于预期,即所谓的互斥性(ME),表示潜在的合成致死关系,而出现频率高于预期(CO)则表示潜在的有利关系。在这一框架中,我们从 Reactome 中选择了一组生物通路,在两个公开的儿科癌症数据集 TARGET 和 DKFZ 中汇总了每个肿瘤的每个通路的基因突变(具有高/中度影响的 SNV 和嵌合体)。这样就得到了每个肿瘤的突变通路图谱,并使用 rediscover 对其共存性进行测试。测试会输出重要的共现和互斥通路,我们从中提取出潜在的突变基因对。然后,对共存和互斥基因对在 BioGRID 和 SynLethDB 中的通路外显性、蛋白质复合物及其存在进行注释。最后,在文献中检验了所提出的基因对的有效性。该测试在 TARGET 中检测到 439 个(ME:369,CO:70)重要的通路对,在 DKFZ 中检测到 49 个(ME:31,CO:18)重要的通路对,涉及多种癌症类型。其中,在 TARGET 中提取了 3185 个基因对(ME:2671,CO:514),在 DKFZ 中提取了 331 个基因对(ME:16,CO:315)。这些关系明显多于仅检测基因对时发现的关系。通路有助于部分减少亚型或通路表观性导致的结果。例如,基因检测在 TARGET-B-ALL 中发现的 FLT3-KRAS,在通路检测中却检测不到。该检验还能在较小的数据集中发现互斥(ME)基因对。在 TARGET 基因测试中最初发现的 Wilms 肿瘤中的 ME 基因 TP53-DROSHA 和 AML 肿瘤中的 KIT-NRAS 在相应癌症类型的 DKFZ 数据集中也被检测到。除TP53-DROSHA外,在DKFZ的Wilms肿瘤中还发现了TP53-DGCR8 ME,表明微处理器复合体突变ME与TP53突变有关。总之,我们提出了一个以通路为基础的儿科癌症合成致死推断框架,通过利用已有的数据和数据库信息,探索突变基因之间的合成致死关系和其他复杂的功能关系,作为后续实验的另一种途径。引用格式:Anastasia Spinou, Richard Gremmen, Puck Veen, Jarno Drost, Patrick Kemmeren.推断小儿癌症合成致死关系的路径信息框架[摘要]。In:AACR 癌症研究特别会议论文集:扩展和转化癌症合成脆弱性;2024 年 6 月 10-13 日;加拿大魁北克省蒙特利尔。费城(宾夕法尼亚州):AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B027.
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引用次数: 0
Abstract B012: Predicting targetable paralog synthetic lethalities and functional redundancies in cancer genomes 摘要 B012:预测癌症基因组中可靶向的旁系合成致死性和功能冗余
IF 5.7 2区 医学 Q1 Medicine Pub Date : 2024-06-10 DOI: 10.1158/1538-8514.synthleth24-b012
Rohan Dandage, Elena Kuzmin
Paralogs are prevalent in the human genome and are considered a rich source of synthetic lethality due to functional redundancy. For a cancer cell carrying a gene with Loss-Of-Function (LOF) mutation, inactivation of its paralog using gene editing can induce a selective decrease in viability, leaving normal cells that do not harbor the mutation unharmed. Previous studies have exploited this vulnerability of cancer genomes. However, the cancer-specificity of such synthetic lethality limits its application across different cancer types. Furthermore, the role of functional redundancy which can explain the cancer specificity has remained largely unexplored. In this study, we computationally predicted synthetic lethal paralogs along with mechanistically important functional redundancies between them in a cancer-specific manner. We applied our prediction method to publicly available data for an aggressive subtype of breast cancer called triple-negative breast cancer (TNBC), which lacks the expression key biomarkers and hence has the worst prognosis among other breast cancer subtypes. TNBC is characterized by the highest mutational load and the largest fraction of genome altered among the breast cancer subtypes providing a rich mutational landscape to identify LOF genes. Using the CRISPR inactivation screen data for cancer cell lines obtained from the Cancer Dependency Map (DepMap) project, we predicted sets of synthetic lethal paralogs that show a significantly greater viability decrease if a gene carries LOF and its paralog is inactivated, compared to the viability decrease due to the inactivation of only one of the paralogs. Consistent with previous findings of context-dependent synthetic lethality, we found that a relatively small fraction of TNBC-specific synthetic lethal paralogs overlapped with those found across other cancer types. To uncover the mechanistically important functional redundancies between paralogs, we analyzed the genomics and transcriptomics data from multiple sources: TNBC panel of primary tumors and patient-derived xenografts, Pan-Cancer Analysis of Whole Genomes (PCAWG), and the Cancer Cell Line Encyclopedia (CCLE). The functional redundancies varied across cancer types based on (1) mutual exclusivity of LOFs, (2) backup compensation of deleterious mutations, (3) backup upregulation, and (4) dosage balance. Overall, our findings show a strong context-dependency of synthetic lethal paralogs and estimates of functional redundancy, emphasizing the importance of such cancer-specific predictions in identifying targetable paralog synthetic lethalities. Collectively, the computational method and sets of targetable paralogs are a unique resource for developing precision oncology therapeutic strategies against TNBC and other cancers more broadly. Citation Format: Rohan Dandage, Elena Kuzmin. Predicting targetable paralog synthetic lethalities and functional redundancies in cancer genomes [abstract]. In: Proceedings of the AACR Speci
旁系亲属在人类基因组中非常普遍,由于功能冗余,被认为是合成致死率的丰富来源。对于携带功能缺失(LOF)突变基因的癌细胞来说,利用基因编辑技术使其旁系亲属失活,可以选择性地降低其存活率,而不携带突变基因的正常细胞则不会受到伤害。以往的研究已经利用了癌症基因组的这种脆弱性。然而,这种合成致死的癌症特异性限制了它在不同癌症类型中的应用。此外,能解释癌症特异性的功能冗余的作用在很大程度上仍未被探索。在本研究中,我们以癌症特异性的方式,通过计算预测了合成致死性旁系亲属以及它们之间重要的机理功能冗余。我们将我们的预测方法应用于一种侵袭性乳腺癌亚型--三阴性乳腺癌(TNBC)的公开数据,该亚型缺乏关键生物标志物的表达,因此在其他乳腺癌亚型中预后最差。在乳腺癌亚型中,TNBC的突变负荷最高,基因组改变的比例最大,这为鉴定LOF基因提供了丰富的突变图谱。利用从癌症依赖性图谱(DepMap)项目中获得的癌细胞系CRISPR失活筛选数据,我们预测了几组合成致死旁系亲属,如果一个基因携带LOF且其旁系亲属被失活,其存活率会显著下降,而如果仅有一个旁系亲属被失活,其存活率会显著下降。与之前关于上下文依赖性合成致死性的发现一致,我们发现 TNBC 特异性合成致死性旁系亲属中相对较小的一部分与其他癌症类型中发现的旁系亲属重叠。为了揭示旁系亲属之间在机理上重要的功能冗余,我们分析了多种来源的基因组学和转录组学数据:我们分析了多种来源的基因组学和转录组学数据:TNBC原发肿瘤和患者衍生异种移植物面板、泛癌全基因组分析(Pan-Cancer Analysis of Whole Genomes,PCAWG)和癌细胞系百科全书(Cancer Cell Line Encyclopedia,CCLE)。不同癌症类型的功能冗余各不相同,主要基于:(1)LOF 的互斥性;(2)有害突变的后备补偿;(3)后备上调;以及(4)剂量平衡。总之,我们的研究结果表明,合成致死旁系亲属和功能冗余估计值与具体情况密切相关,这强调了针对癌症的预测在确定可靶向的旁系亲属合成致死性方面的重要性。总而言之,计算方法和可靶向的旁系亲属集是开发针对 TNBC 和其他癌症的精准肿瘤治疗策略的独特资源。引用格式:Rohan Dandage, Elena Kuzmin.预测癌症基因组中的可靶向旁系合成致死性和功能冗余[摘要]。In:AACR 癌症研究特别会议论文集:扩展和转化癌症合成脆弱性;2024 年 6 月 10-13 日;加拿大魁北克省蒙特利尔。费城(宾夕法尼亚州):AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B012.
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引用次数: 0
Abstract IA017: Synthetic dependencies arising during tumor evolution 摘要 IA017:肿瘤进化过程中产生的合成依赖性
IF 5.7 2区 医学 Q1 Medicine Pub Date : 2024-06-10 DOI: 10.1158/1538-8514.synthleth24-ia017
Kris C. Wood
Our research focuses on defining tumor-selective survival dependencies and understanding how these dependencies change during tumor evolution. In this talk, I will provide an overview of our lab’s work, highlighting recent and ongoing studies uncovering mechanism-based synthetic lethalities arising in residual and fully drug resistant tumors whose therapeutic exploitation has the potential to select against the most aggressive forms of disease. Citation Format: Kris C. Wood. Synthetic dependencies arising during tumor evolution [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA017.
我们的研究重点是定义肿瘤选择性生存依赖性,并了解这些依赖性在肿瘤进化过程中如何变化。在本讲座中,我将概述我们实验室的工作,重点介绍最近和正在进行的研究,这些研究揭示了残留肿瘤和完全耐药肿瘤中出现的基于机制的合成致死性,利用这些机制进行治疗有可能选择性地对抗最具侵袭性的疾病。引用格式:克里斯-C-伍德肿瘤进化过程中产生的合成依赖性[摘要].In:AACR 癌症研究特别会议论文集:扩展和转化癌症合成脆弱性;2024 年 6 月 10-13 日;加拿大魁北克省蒙特利尔。费城(宾夕法尼亚州):AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA017.
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Molecular Cancer Therapeutics
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