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Characterization of cis-regulatory elements and functional variants in colorectal cancer using epigenomics and CRISPRi screenings 使用表观基因组学和CRISPRi筛选鉴定结直肠癌顺式调控元件和功能变异。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-25 DOI: 10.1038/s43018-025-01031-z
Zequn Lu, Can Chen, Heng Zhang, Bin Li, Yizhuo Liu, Jiayi Guo, Runying Xu, Ke Shi, Qianying Ma, Ming Zhang, Yimin Cai, Jinyu Huang, Hui Geng, Linyun Fan, Caibo Ning, Yanmin Li, Shuoni Chen, Wen Tian, Kexin Hu, Haijie Li, Xiaojun Yang, Chaoqun Huang, Yongchang Wei, Xu Zhu, Xiangpan Li, Zhen Xiong, Ming Cai, Xiaoyang Wang, Shaokai Zhang, Hongda Chen, Min Dai, Kun Chen, Mingjuan Jin, Meng Jin, Ying Zhu, Jianbo Tian, Xiaoping Miao
Genetic variants associated with colorectal cancer (CRC) are primarily noncoding and reside in cis-regulatory elements (CREs), yet their underlying mechanisms remain elusive. Here we established a dynamic epigenetic atlas using multiomics data from 533 colorectal tissues spanning normal to advanced adenoma to cancer, identifying 7,492 differential CREs linked to 5,490 target genes. High-throughput CRISPR interference screening revealed 265 functional CREs involved in CRC cell proliferation. A polygenic risk score (PRS) based on functional CRE variants effectively predicted CRC and precancerous lesions among 476,770 individuals. Notably, the functional variant rs10871066 was significantly associated with increased risk of precancerous lesions and CRC (odds ratio = 1.27, P = 1.03 × 10−13). Mechanistically, rs10871066 triggers silencer-to-enhancer switching mediated by FOXP1 and TCF7L2, distally upregulating KLF5 to activate oncogenic pathways and PIBF1 to suppress natural killer cell cytotoxicity. Our study provides a comprehensive resource of dynamic epigenomic atlas, a functionally informed PRS for risk prediction and insights into epigenetic mechanisms underlying CRC development. Lu et al. characterize cis-regulatory element dynamics at different stages of colorectal cancer progression and identify a functional variant associated with increased colorectal cancer risk because of selective transcription factor binding.
与结直肠癌(CRC)相关的遗传变异主要是非编码的,存在于顺式调控元件(cre)中,但其潜在机制尚不清楚。在这里,我们利用533个从正常到晚期腺瘤到癌症的结直肠组织的多组学数据建立了一个动态表观遗传图谱,确定了7492个与5490个靶基因相关的差异cre。高通量CRISPR干扰筛选发现265个功能性CREs参与结直肠癌细胞增殖。基于功能性CRE变异的多基因风险评分(PRS)有效预测了476770例CRC和癌前病变。值得注意的是,功能变异rs10871066与癌前病变和CRC的风险增加显著相关(优势比= 1.27,P = 1.03 × 10-13)。机制上,rs10871066触发FOXP1和TCF7L2介导的沉默-增强转换,远端上调KLF5激活致癌途径和PIBF1抑制自然杀伤细胞的细胞毒性。我们的研究提供了一个全面的动态表观基因组图谱资源,一个用于风险预测的功能知情PRS,并深入了解CRC发展的表观遗传机制。
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引用次数: 0
Colorectal cancer cells hijack a brain–gut polysynaptic circuit from the lateral septum to enteric neurons to sustain tumor growth 结直肠癌细胞劫持从侧隔到肠神经元的脑-肠多突触回路以维持肿瘤生长。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-21 DOI: 10.1038/s43018-025-01033-x
Ying Li, Hao Yu, Zi-Ming Li, Kai-Wen Yin, Shi-Yang Jin, Chao-Chao Chen, Ming-Shi Tan, Chuan-Jie Zhang, Xun-Hua Liu, Wei-Peng Li, Jian-Ming Yang, Ai-Jun Zhou, Xiang Zhang, En-De Ni, Meng-Ling Wang, Hui Mo, Chao Qin, Jian Hu, Shu-Ji Li, Tian-Ming Gao, Jian-Ming Li
The bidirectional interaction between the brain and peripheral tumors is critical but poorly understood. Here we show GABAergic neurons in the lateral septum, a key brain region implicated in emotional regulation, connect via a polysynaptic circuit to enteric cholinergic neurons that send nerve fibers into the tumor microenvironment, which were then hijacked by colorectal cancer cells to sustain tumor growth in mice. Functionally, activation of this septo-enteric circuit induces GABA release from enteric cholinergic neurons, which in turn activates epsilon-subunit-containing GABAA receptors on tumor cells. Notably, chronic restraint stress potentiates activity within this circuit, exacerbating tumor progression. Clinically, patients with colorectal cancer exhibiting elevated neuronal activity in the septal region present with larger primary tumors. Collectively, our findings uncover a stress-sensitive septo-enteric polysynaptic pathway exploited by cancer cells to promote tumor growth, underscoring the previously unrecognized role of lateral septum-mediated neural circuitry and psychological stress in cancer progression. Li and colleagues report that a septo-enteric polysynaptic circuit that is activated by chronic stress links the brain to the tumor microenvironment to promote colorectal cancer growth.
大脑和周围肿瘤之间的双向相互作用至关重要,但人们对其了解甚少。在这里,我们展示了外侧隔膜中的gaba能神经元,一个涉及情绪调节的关键大脑区域,通过多突触回路与肠胆碱能神经元连接,后者将神经纤维发送到肿瘤微环境中,然后被结肠直肠癌细胞劫持以维持肿瘤生长。功能上,这种隔肠回路的激活诱导肠胆碱能神经元释放GABA,进而激活肿瘤细胞上含有epsilon亚单位的GABAA受体。值得注意的是,慢性约束应激增强了该回路的活性,加剧了肿瘤的进展。临床上,大肠癌患者中隔区神经元活动升高,原发肿瘤较大。总的来说,我们的研究结果揭示了癌细胞利用应激敏感的隔膜-肠多突触通路促进肿瘤生长,强调了以前未被认识到的外侧隔膜介导的神经回路和心理应激在癌症进展中的作用。
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引用次数: 0
A sphingolipid-derived paclitaxel nanovesicle enhances efficacy of combination therapies in triple-negative breast cancer and pancreatic cancer 鞘脂衍生的紫杉醇纳米囊泡提高了三阴性乳腺癌和胰腺癌联合治疗的疗效。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-21 DOI: 10.1038/s43018-025-01029-7
Zhiren Wang, Wenpan Li, Yanhao Jiang, Teng Ma, Mengwen Li, Shuang Wu, Tuyen Ba Tran, Leyla Estrella Cordova, Ethan Lin, Aaron James Scott, Jennifer Erdrich, Joyce Schroeder, Pavani Chalasani, Jianqin Lu
Taxol and Abraxane, the US Food and Drug Administration-approved paclitaxel (PTX) formulations, have revealed hypersensitivity due to excipients and mediocre efficacy due to insufficient tumor penetration, respectively. Here we developed a sphingolipid-derived PTX nanovesicle (paclitaxome) via covalently conjugating PTX to sphingomyelin, which improved pharmacokinetics and enhanced efficacy in metastatic triple-negative breast cancer and pancreatic cancer female mice and reduced myelosuppression. To bolster tumor penetration and reduce phagocytosis, we engineered a cationization-enabled transcytosis machinery by installing an ultra-pH-sensitive azepane (AZE) probe into paclitaxome and masked nanovesicle surface with a CD47 ‘self’ peptide (CD47p). The resulting CD47p/AZE–paclitaxome synchronized the co-delivery of gemcitabine or carboplatin to boost tumor inhibition and eradicate metastasis in late-stage KPC-Luc pancreatic cancer model and prevent tumor relapse and extend survival in postsurgical 4T1-Luc2 triple-negative breast cancer model in female mice. CD47p/AZE–paclitaxome also outperformed previous promising PTX nanoformulations. Finally, the series of nanoparticle modifications was applied to camptothecin, demonstrating its generalizability. Wang et al. designed sphingomyelin-derived vesicles that deliver paclitaxel to tumor site, improving its therapeutic efficacy and reducing associated toxicities, in mouse models of breast and pancreatic cancers.
美国食品和药物管理局(fda)批准的紫杉醇(PTX)制剂紫杉醇(Taxol)和Abraxane分别因赋形剂过敏和肿瘤渗透不足而疗效一般。本研究通过将PTX与鞘磷脂共价偶联,开发了鞘脂衍生的PTX纳米囊泡(紫杉醇组),改善了转移性三阴性乳腺癌和胰腺癌雌性小鼠的药代动力学,增强了疗效,并减少了骨髓抑制。为了促进肿瘤渗透和减少吞噬,我们设计了一种阳离子化激活的细胞吞噬机制,通过将超ph敏感的氮平(AZE)探针安装到紫杉醇组中,并用CD47“自身”肽(CD47p)掩盖纳米囊泡表面。在KPC-Luc晚期胰腺癌模型中,CD47p/AZE-paclitaxome与吉西他滨或卡铂同步共给药,增强肿瘤抑制和根除转移,在4T1-Luc2三阴性女性乳腺癌模型中,预防肿瘤复发和延长生存期。CD47p/AZE-paclitaxome也优于之前有前途的PTX纳米配方。最后,将一系列纳米粒子修饰应用于喜树碱,证明了其通用性。
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引用次数: 0
Evolutionary trajectories of IDH-mutant astrocytoma identify molecular grading markers related to cell cycling idh突变星形细胞瘤的进化轨迹确定了与细胞周期相关的分子分级标记。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-19 DOI: 10.1038/s43018-025-01023-z
Wies R. Vallentgoed, Youri Hoogstrate, Karin A. van Garderen, Levi van Hijfte, Erik van Dijk, Mathilde C. M. Kouwenhoven, Johanna M. Niers, Kaspar Draaisma, Ivonne Martin, Wendy W. J. de Leng, C. Mircea S. Tesileanu, Iris de Heer, Maud Diepeveen, Anna Lavrova, Paul P. Eijk, Marcel Bühler, Wolfgang Wick, Paul M. Clement, Marc Sanson, Enrico Franceschi, Thierry Gorlia, Vassilis Golfinopoulos, Michael Weller, Tobias Weiss, Pierre A. Robe, Johan M. Kros, Marion Smits, Mark van de Wiel, Bauke Ylstra, Roel G. W. Verhaak, Martin J. van den Bent, Bart A. Westerman, Pieter Wesseling, Pim J. French
The evolutionary processes that drive malignant progression of IDH-mutant astrocytomas remain unclear. Here, we performed multiomics on matched initial and recurrent tumor samples from a cohort of 105 patients and overlaid the data with detailed clinical annotation. We identified overlapping features associated with malignant progression that are derived from three molecular mechanisms: cell cycling, tumor cell (de)differentiation and remodeling of the extracellular matrix. Together, they provide a rationale of the underlying biology of tumor malignancy. DNA methylation levels decreased over time, predominantly in tumors with malignant transformation, and co-occurred with poor prognostic genetic events. We identified a DNA methylation-based signature strongly associated with survival, which allows objective, molecular-based grading of IDH-mutant astrocytomas to aid clinical decision making. Our findings were validated on large, independent cohorts of IDH-mutant astrocytoma samples. Lastly, in this retrospective study, we found little effect of radiotherapy or chemotherapy on the molecular features associated with malignant progression. Vallentgoed et al. integrate clinical and multiomic data from persons with matched initial and recurrent IDH-mutant astrocytomas to identify progression-associated mechanisms and report a DNA methylation-based signature associated with survival.
驱动idh突变星形细胞瘤恶性进展的进化过程尚不清楚。在这里,我们对105名患者的初始和复发肿瘤样本进行了多组学分析,并将数据与详细的临床注释叠加在一起。我们确定了与恶性进展相关的重叠特征,这些特征源于三种分子机制:细胞循环、肿瘤细胞(去)分化和细胞外基质的重塑。总之,它们为恶性肿瘤的潜在生物学提供了理论基础。DNA甲基化水平随着时间的推移而下降,主要发生在恶性转化的肿瘤中,并与预后不良的遗传事件共同发生。我们发现了一个与生存密切相关的DNA甲基化特征,这使得idh突变星形细胞瘤的客观、基于分子的分级能够帮助临床决策。我们的发现在idh突变星形细胞瘤样本的大型独立队列中得到了验证。最后,在这项回顾性研究中,我们发现放疗或化疗对与恶性进展相关的分子特征的影响很小。
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引用次数: 0
Prospects for ferroptosis therapies in cancer 铁下垂治疗癌症的前景。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-18 DOI: 10.1038/s43018-025-01037-7
Jessalyn M. Ubellacker, Scott J. Dixon
Ferroptosis is a nonapoptotic form of cell death characterized by lethal membrane lipid peroxidation. This mechanism was first characterized in cancer cells well over a decade ago, and there is much enthusiasm for the concept that certain cancers may be treated by inducing ferroptosis. However, therapies that engage ferroptosis have yet to enter clinical testing. In this Review, we highlight the gap between our rapidly expanding knowledge of the ferroptosis mechanism and its translation into cancer therapies. We discuss the known challenges that may be slowing ferroptosis therapies from reaching the clinic. Ubellacker and Dixon summarize the latest discoveries on ferroptosis in cancer, covering the molecular and cellular pathways underlying sensitivity and resistance to this type of cell death, as well as potential translational applications in cancer therapeutics.
铁下垂是一种以致死性膜脂过氧化为特征的非凋亡形式的细胞死亡。这种机制早在十多年前就在癌细胞中首次被发现,人们对某些癌症可能通过诱导铁下垂来治疗的概念非常感兴趣。然而,治疗铁下垂尚未进入临床试验。在这篇综述中,我们强调了我们快速扩展的铁下垂机制知识与其转化为癌症治疗之间的差距。我们讨论了已知的挑战,可能会减慢铁下垂疗法从达到临床。
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引用次数: 0
Innovative ways to target (K)RAS dependencies 针对(K)RAS依赖项的创新方法。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-13 DOI: 10.1038/s43018-025-01040-y
Heathcliff Dorado García
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引用次数: 0
SWIFT-seq enables comprehensive single-cell transcriptomic profiling of circulating tumor cells in multiple myeloma and its precursors SWIFT-seq能够对多发性骨髓瘤及其前体的循环肿瘤细胞进行全面的单细胞转录组学分析。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-08 DOI: 10.1038/s43018-025-01006-0
Elizabeth D. Lightbody, Romanos Sklavenitis-Pistofidis, Ting Wu, Junko Tsuji, Danielle T. Firer, Michael P. Agius, Ankit K. Dutta, Hadley Barr, Sungjae Kim, Jean-Baptiste Alberge, Sarah Nersesian, Tim Coorens, Nicholas J. Haradhvala, Nang Kham Su, Cody J. Boehner, Michelle P. Aranha, Mahshid Rahmat, Yoshinobu Konishi, Laura Hevenor, Katherine Towle, Erica Horowitz, Jacqueline Perry, Maya Davis, Kelly A. Walsh, Christian J. Cea-Curry, Grace Fleming, Michael E. Vinyard, Daniel Heilpern-Mallory, Habib El-Khoury, Annie Cowan, John E. Ready, Catherine R. Marinac, Gad Getz, Irene M. Ghobrial
Multiple myeloma is a bone marrow (BM) plasma cell malignancy preceded by precursor conditions. BM biopsies are conducted infrequently and can yield inconclusive results due to technical limitations. Profiling circulating tumor cells (CTCs) may enable noninvasive routine clinical assessments but remains challenging. Here, to address this, we describe a single-cell sequencing workflow to interrogate few tumor cells (SWIFT-seq), and employ single-cell RNA sequencing and B cell receptor sequencing on paired BM and CTCs from 101 patients and healthy donors. We establish a sequencing-based CTC enumeration strategy and develop a CTC classifier to infer cytogenetic abnormalities. Additionally, we leverage expression profiling to measure tumor proliferative index in CTCs, and demonstrate that clonal dynamics can be captured in CTCs. Last, we propose a circulatory dynamics model whereby tumor burden, proliferation, cytogenetics and a circulatory capacity signature influence CTC burden. Overall, SWIFT-seq may advance blood-based myeloma diagnostics, surveillance and prognostication, and reveal biological mechanisms of tumor dissemination. Lightbody et al. present SWIFT-seq, a single-cell RNA sequencing approach to profile circulating tumor cells from patients with multiple myeloma and its precursor conditions and leverage it to derive clinical and biological insights into the disease.
多发性骨髓瘤是一种骨髓浆细胞恶性肿瘤,有前体病变。脑脊髓瘤活检很少进行,由于技术限制,可能产生不确定的结果。循环肿瘤细胞(ctc)谱分析可以实现无创常规临床评估,但仍然具有挑战性。在这里,为了解决这个问题,我们描述了一个单细胞测序工作流程来询问少量肿瘤细胞(SWIFT-seq),并对来自101例患者和健康供体的配对BM和ctc使用单细胞RNA测序和B细胞受体测序。我们建立了基于序列的CTC枚举策略,并开发了CTC分类器来推断细胞遗传学异常。此外,我们利用表达谱来测量CTCs中的肿瘤增殖指数,并证明在CTCs中可以捕获克隆动态。最后,我们提出了一个循环动力学模型,其中肿瘤负荷、增殖、细胞遗传学和循环能力特征影响CTC负荷。总之,SWIFT-seq可能会促进基于血液的骨髓瘤诊断、监测和预后,并揭示肿瘤传播的生物学机制。
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引用次数: 0
Nanotechnology for immuno-oncology 纳米技术用于免疫肿瘤学。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-07 DOI: 10.1038/s43018-025-01025-x
Adam J. Grippin, DaeYong Lee, Eileen E. Parkes, Wen Jiang, Betty Y. S. Kim
Although the first generation of cancer immunotherapeutics produced unprecedented improvements in clinical outcomes for individuals with cancer, novel strategies to increase treatment specificity, delivery efficiency and pharmacokinetics are still needed. In this Review, we describe the potential advantages and current limitations of nanomaterials for cancer immunotherapy and highlight rational uses of nanosystems to generate potent and durable antitumor immune responses. We close with a review of the current state of clinical development of nanomedicine for cancer immunotherapy. Kim and colleagues provide an overview of the current state of the art of nanomaterials and their application in immuno-oncology, discussing preclinical development and the clinical landscape.
尽管第一代癌症免疫疗法对癌症患者的临床结果产生了前所未有的改善,但仍然需要新的策略来提高治疗特异性、递送效率和药代动力学。在这篇综述中,我们描述了纳米材料在癌症免疫治疗中的潜在优势和当前的局限性,并强调了纳米系统在产生有效和持久的抗肿瘤免疫反应方面的合理应用。最后,我们回顾了纳米药物用于癌症免疫治疗的临床发展现状。
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引用次数: 0
Author Correction: RIOK1 phase separation restricts PTEN translation via stress granules activating tumor growth in hepatocellular carcinoma 作者更正:RIOK1相分离通过应激颗粒激活肝癌肿瘤生长限制PTEN翻译。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-04 DOI: 10.1038/s43018-025-01043-9
Fanzheng Meng, Hairui Li, Yabin Huang, Chunxu Wang, Yufeng Liu, Chunting Zhang, Danlei Chen, Taofei Zeng, Shenyu Zhang, Yunyun Li, Bo Zhang, Chuandong Lang, Jie Xia, Wanxiang Xiong, Shixiang Pan, Xuedan Sun, Rick F. Thorne, Yao Liu, Jiabei Wang, Shugeng Zhang, Ruipeng Song, Jizhou Wang, Lianxin Liu
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引用次数: 0
Improved immune responses in lung cancer with radiotherapy and immune checkpoint inhibition 放疗和免疫检查点抑制改善肺癌的免疫应答。
IF 28.5 1区 医学 Q1 ONCOLOGY Pub Date : 2025-08-01 DOI: 10.1038/s43018-025-01019-9
In metastatic, immunologically ‘cold’ non-small cell lung cancer, the combination of radiation therapy and immune checkpoint inhibition (ICI) demonstrates heightened anti-tumor immune responses at non-irradiated sites and improved clinical responses compared with ICI alone. Radio-immunotherapy holds promise for patients with ICI-refractory lung cancer.
在转移性、免疫“冷”的非小细胞肺癌中,与单独使用免疫检查点抑制(ICI)相比,放射治疗和免疫检查点抑制(ICI)的联合治疗在非照射部位显示出更高的抗肿瘤免疫反应,并改善了临床反应。放射免疫疗法为ici难治性肺癌患者带来了希望。
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引用次数: 0
期刊
Nature cancer
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