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Cigarette smoke and decreased DNA repair by Xeroderma Pigmentosum Group C use a double hit mechanism for epithelial cell lung carcinogenesis. 吸烟和着色性干皮病C组DNA修复减少是上皮细胞肺癌发生的双重打击机制。
Q2 Medicine Pub Date : 2025-05-20 DOI: 10.18632/oncotarget.28724
Nawar Al Nasrallah, Bowa Lee, Benjamin M Wiese, Marie N Karam, Elizabeth A Mickler, Huaxin Zhou, Nicki Paolelli, Robert S Stearman, Mark W Geraci, Catherine R Sears

Emerging evidence suggests a complex interplay of environmental and genetic factors in non-small cell lung cancer (NSCLC) development. Among these factors, compromised DNA repair plays a critical but incompletely understood role in lung tumorigenesis and concurrent lung diseases, such as chronic obstructive lung disease (COPD). In this study, we investigated the interplay between cigarette smoke, DNA damage and repair, focusing on the Nucleotide Excision Repair (NER) protein Xeroderma Pigmentosum Group C (XPC). We found decreased XPC mRNA expression in most NSCLCs compared to subject-matched, non-cancerous lung. In non-cancerous bronchial epithelial cells, cigarette smoke decreased NER, increased total DNA damage and resultant apoptosis, each exacerbated by XPC deficiency. In contrast, lung cancer cells exhibit greater resilience to cigarette smoke, requiring higher doses to induce comparable DNA damage and apoptosis, and are less reliant on XPC expression for survival. Importantly, XPC protects against chromosomal instability in benign bronchial epithelial cells, but not in lung cancer cells. Our findings support a "double hit" mechanism wherein early decreased XPC expression and resultant aberrant DNA repair, when combined with cigarette smoke exposure, may lead to loss of non-malignant epithelial cells (as observed in COPD), and contributes to early NSCLC transition through altered DNA damage response.

越来越多的证据表明,环境和遗传因素在非小细胞肺癌(NSCLC)的发展中具有复杂的相互作用。在这些因素中,受损的DNA修复在肺肿瘤发生和并发肺部疾病(如慢性阻塞性肺疾病(COPD))中起着关键但尚未完全了解的作用。在这项研究中,我们研究了香烟烟雾与DNA损伤和修复之间的相互作用,重点研究了核苷酸切除修复(NER)蛋白着色性干皮病C组(XPC)。我们发现,与受试者匹配的非癌性肺相比,大多数非小细胞肺癌的XPC mRNA表达降低。在非癌性支气管上皮细胞中,吸烟降低了NER,增加了总DNA损伤和由此导致的细胞凋亡,这些都因XPC缺乏而加剧。相比之下,肺癌细胞对香烟烟雾表现出更强的恢复能力,需要更高的剂量来诱导类似的DNA损伤和凋亡,并且不太依赖XPC表达来存活。重要的是,XPC在良性支气管上皮细胞中保护染色体不稳定,但在肺癌细胞中没有保护作用。我们的研究结果支持一种“双重打击”机制,即早期XPC表达下降和由此产生的DNA修复异常,当与香烟烟雾暴露相结合时,可能导致非恶性上皮细胞的损失(如在COPD中观察到的),并通过改变DNA损伤反应促进早期非小细胞肺癌的转变。
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引用次数: 0
Targeting PCNA/AR interaction inhibits AR-mediated signaling in castration resistant prostate cancer cells. 靶向PCNA/AR相互作用抑制AR介导的去势抵抗前列腺癌细胞信号传导
Q2 Medicine Pub Date : 2025-05-20 DOI: 10.18632/oncotarget.28722
Shan Lu, Zhongyun Dong

We previously showed that proliferating cell nuclear antigen (PCNA) interacts with androgen receptor (AR) through a PIP-box (PIP-box4) at the N-terminus of AR and regulates AR activity. In this study, we further investigated PCNA/AR interaction. We identified a second PIP-box (PIP-box592) in the DNA binding domain of AR and found that dihydrotestosterone enhances the binding of full-length AR (AR-FL) but not a constitutively active variant (AR-V7) to PCNA. Treatment with R9-AR-PIP, a PIP-box4-mimicking small peptide, inhibits the PCNA/AR interaction, AR occupancy at the androgen response element (ARE) in PSA and p21 genes, and expression of AR target genes, and induces cytotoxicity in AR-positive castration-resistant prostate cancer (CRPC) cells. R9-AR-PIP also significantly inhibits transcriptional activity of AR-FL upon dihydrotestosterone stimulation and the constitutive activity of AR-V7. Moreover, R9-AR-PIP and PCNA-I1S, a small molecule PCNA inhibitor, inhibit the ARE occupancy by AR-FL and AR-Vs in CCNA2 gene that encodes cyclin A2 and cyclin A2 expression. Finally, we found that cyclin A2 is overexpressed in all CRPC cells examined, suggesting that it may contribute to the development of CRPC. These data indicate that targeting PCNA/AR interaction inhibits both AR-FL- and AR-Vs-mediated signaling and implicates it could be a novel therapeutic strategy against CRPC.

我们之前的研究表明,增殖细胞核抗原(PCNA)通过雄激素受体(AR) n端PIP-box (PIP-box4)与AR相互作用并调节AR活性。在本研究中,我们进一步研究了PCNA/AR的相互作用。我们在AR的DNA结合域中发现了第二个PIP-box (PIP-box592),并发现双氢睾酮增强了全长AR (AR- fl)的结合,但没有组成型活性变体(AR- v7)与PCNA的结合。R9-AR-PIP是一种模拟pip box4的小肽,可抑制PCNA/AR相互作用、AR在PSA和p21基因中雄激素反应元件(ARE)的占据以及AR靶基因的表达,并诱导AR阳性去势抵抗性前列腺癌(CRPC)细胞的细胞毒性。R9-AR-PIP还显著抑制AR-FL在双氢睾酮刺激下的转录活性和AR-V7的组成活性。此外,R9-AR-PIP和小分子PCNA抑制剂PCNA- i1s可抑制AR-FL和AR-Vs在编码cyclin A2和cyclin A2表达的CCNA2基因上的ARE占用。最后,我们发现cyclin A2在所有检测的CRPC细胞中都过表达,这表明它可能有助于CRPC的发展。这些数据表明,靶向PCNA/AR相互作用可抑制AR- fl和AR- vs介导的信号传导,这可能是一种新的治疗CRPC的策略。
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引用次数: 0
Correction: Activation of PI3K/Akt/mTOR signaling in the tumor stroma drives endocrine therapy-dependent breast tumor regression. 更正:肿瘤基质中PI3K/Akt/mTOR信号的激活驱动内分泌治疗依赖性乳腺肿瘤消退。
Q2 Medicine Pub Date : 2025-05-20 DOI: 10.18632/oncotarget.28728
María Laura Polo, Marina Riggio, María May, María Jimena Rodríguez, María Cecilia Perrone, Melody Stallings-Mann, Diego Kaen, Marlene Frost, Matthew Goetz, Judy Boughey, Claudia Lanari, Derek Radisky, Virginia Novaro
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引用次数: 0
Retraction: RUNX2 promotes epithelial differentiation of ADSCs and burn wound healing via targeting E-cadherin. 收缩:RUNX2通过靶向E-cadherin促进ADSCs上皮分化和烧伤创面愈合。
Q2 Medicine Pub Date : 2025-05-20 DOI: 10.18632/oncotarget.28729
Qiang Li, Han Zhao, Sizhan Xia, Hanxiao Wei, Feifei Chen, Peisheng Jin
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引用次数: 0
Advancements in bladder cancer treatment: The synergy of radiation and immunotherapy. 膀胱癌治疗的进展:放射和免疫治疗的协同作用。
Q2 Medicine Pub Date : 2025-05-19 DOI: 10.18632/oncotarget.28723
Nazmul Hasan, Daniel Yang, Spencer Gibson, Barbod Khaleghi, Rozhan Ziari, Arash Rezazadeh Kalebasty

Different treatment strategies are required for the non-muscle-invasive, muscle-invasive, and metastatic stages of bladder cancer. Standard treatments include surgery, chemotherapy, and radiation; however, they have their limitations. New discoveries have shown that combining immunotherapy and radiation treatment may improve patient outcomes. Radiation therapy promotes immunogenic cell death, which leads to antigen release and immune cell activation, whereas immunotherapy enhances the immune system's ability to recognize and destroy cancer cells by targeting checkpoint pathways like PD-1/PD-L1 and CTLA-4. This review examines the synergistic mechanisms of diverse modalities, focusing on their capacity to alter the tumor microenvironment and elicit systemic anti-tumor responses, such as the abscopal effect. Key clinical trials, such as BTCRC-GU15-023 and ANZUP, have demonstrated the efficacy and safety of combining these medications. However, difficulties persist, such as overlapping toxicities, unpredictability in patient responses, and a lack of accurate patient selection markers. Large-scale randomized trials are needed in the future to fine-tune treatment procedures, minimize toxicity, and validate predictive biomarkers such as PD-L1 expression and tumor mutation burden. By addressing these hurdles, the combination of radiation treatment and immunotherapy has the potential to change the bladder cancer therapeutic landscape.

膀胱癌的非肌肉侵袭性、肌肉侵袭性和转移性阶段需要不同的治疗策略。标准治疗包括手术、化疗和放疗;然而,它们也有其局限性。新的发现表明,结合免疫治疗和放射治疗可能改善患者的预后。放射治疗促进免疫原性细胞死亡,导致抗原释放和免疫细胞活化,而免疫治疗通过靶向PD-1/PD-L1和CTLA-4等检查点途径增强免疫系统识别和摧毁癌细胞的能力。本文综述了多种模式的协同机制,重点关注它们改变肿瘤微环境和引发全身抗肿瘤反应的能力,如体外效应。关键的临床试验,如BTCRC-GU15-023和ANZUP,已经证明了这些药物联合使用的有效性和安全性。然而,困难仍然存在,例如重叠的毒性,患者反应的不可预测性,以及缺乏准确的患者选择标记。未来需要大规模的随机试验来调整治疗程序,最小化毒性,并验证预测性生物标志物,如PD-L1表达和肿瘤突变负担。通过解决这些障碍,放射治疗和免疫治疗的结合有可能改变膀胱癌的治疗前景。
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引用次数: 0
Retraction: RAB22A overexpression promotes the tumor growth of melanoma. 撤回:RAB22A过表达促进黑色素瘤的肿瘤生长。
Q2 Medicine Pub Date : 2025-05-19 DOI: 10.18632/oncotarget.28726
Feng Su, Yifei Chen, Shilin Zhu, Fangfang Li, Shuang Zhao, Lisa Wu, Xiang Chen, Juan Su
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引用次数: 0
Immune-mediated adverse events following atezolizumab and bevacizumab in a multinational Latin American cohort of unresectable hepatocellular carcinoma. 在一项拉丁美洲多国不可切除肝细胞癌队列中,阿特唑单抗和贝伐单抗后免疫介导的不良事件
Q2 Medicine Pub Date : 2025-05-19 DOI: 10.18632/oncotarget.28721
Leonardo Gomes da Fonseca, Federico Piñero, Margarita Anders, Carla Bermudez, Ezequiel Demirdjian, Adriana Varón, Daniela Perez, Jorge Rodriguez, Oscar Beltrán, Ezequiel Ridruejo, Pablo Caballini, Alexandre Araujo, Juan Diego Torres Florez, Juan Ignacio Marín, Marina Villa, Federico Orozco, Jaime Poniachik, Sebastián Marciano, Fernando Bessone, Manuel Mendizabal

Aims: Latin America has been underrepresented in trials evaluating immunotherapy for hepatocellular carcinoma (HCC). We aimed to describe the incidence of immune-related adverse events (irAEs) and their impact on outcomes in a Latin American cohort.

Methods: A multicenter prospective study was conducted in Argentina, Brazil, Chile, and Colombia, including patients who received atezolizumab plus bevacizumab. A time-covarite proportional hazard analysis evaluated the effect of irAEs.

Results: 99 patients were included. The median treatment duration was 6 months, with a median survival of 17.0 months (95% CI: 12.6-19.8). The irAE incidence rate was 2.1 cases per 100 persons-months (cumulative incidence 18.1% (95% CI: 11.1-27.2%)). Median time to irAE was 2.3 months (range 1.4-4.8), most frequently hepatitis (n = 6), thyroiditis (n = 5), and 8/18 required steroids. Follow-up, treatment duration, and overall survival were similar regardless of the occurrence of irAEs (HR = 1.71, 95% CI: 0.76-3.86; P = 0.19). Baseline alpha-feto protein ≥400 ng/ml (HR: 2.9 (95% CI: 1.1-7.6)) was independently associated with irAE.

Conclusion: The incidence of irAEs in this cohort is lower than reported in controlled trials, withouut impact on survival outcomes. Education and early recognition are crucial to ensure that these events are identified and addressed.

目的:拉丁美洲在评估肝细胞癌(HCC)免疫治疗的试验中代表性不足。我们的目的是描述拉丁美洲队列中免疫相关不良事件(irAEs)的发生率及其对结果的影响。方法:在阿根廷、巴西、智利和哥伦比亚进行了一项多中心前瞻性研究,包括接受atezolizumab加贝伐单抗治疗的患者。时间协变量比例风险分析评估了irae的效果。结果:纳入99例患者。中位治疗持续时间为6个月,中位生存期为17.0个月(95% CI: 12.6-19.8)。irAE发病率为每100人月2.1例(累积发病率18.1% (95% CI: 11.1-27.2%))。到irAE的中位时间为2.3个月(范围1.4-4.8),最常见的是肝炎(n = 6),甲状腺炎(n = 5), 8/18需要类固醇。无论是否发生irAEs,随访、治疗时间和总生存期相似(HR = 1.71, 95% CI: 0.76-3.86;P = 0.19)。基线α -胎蛋白≥400 ng/ml (HR: 2.9 (95% CI: 1.1-7.6))与irAE独立相关。结论:该队列中irae的发生率低于对照试验中报道的发生率,对生存结果没有影响。教育和早期认识对于确保发现和处理这些事件至关重要。
{"title":"Immune-mediated adverse events following atezolizumab and bevacizumab in a multinational Latin American cohort of unresectable hepatocellular carcinoma.","authors":"Leonardo Gomes da Fonseca, Federico Piñero, Margarita Anders, Carla Bermudez, Ezequiel Demirdjian, Adriana Varón, Daniela Perez, Jorge Rodriguez, Oscar Beltrán, Ezequiel Ridruejo, Pablo Caballini, Alexandre Araujo, Juan Diego Torres Florez, Juan Ignacio Marín, Marina Villa, Federico Orozco, Jaime Poniachik, Sebastián Marciano, Fernando Bessone, Manuel Mendizabal","doi":"10.18632/oncotarget.28721","DOIUrl":"10.18632/oncotarget.28721","url":null,"abstract":"<p><strong>Aims: </strong>Latin America has been underrepresented in trials evaluating immunotherapy for hepatocellular carcinoma (HCC). We aimed to describe the incidence of immune-related adverse events (irAEs) and their impact on outcomes in a Latin American cohort.</p><p><strong>Methods: </strong>A multicenter prospective study was conducted in Argentina, Brazil, Chile, and Colombia, including patients who received atezolizumab plus bevacizumab. A time-covarite proportional hazard analysis evaluated the effect of irAEs.</p><p><strong>Results: </strong>99 patients were included. The median treatment duration was 6 months, with a median survival of 17.0 months (95% CI: 12.6-19.8). The irAE incidence rate was 2.1 cases per 100 persons-months (cumulative incidence 18.1% (95% CI: 11.1-27.2%)). Median time to irAE was 2.3 months (range 1.4-4.8), most frequently hepatitis (<i>n</i> = 6), thyroiditis (<i>n</i> = 5), and 8/18 required steroids. Follow-up, treatment duration, and overall survival were similar regardless of the occurrence of irAEs (HR = 1.71, 95% CI: 0.76-3.86; <i>P</i> = 0.19). Baseline alpha-feto protein ≥400 ng/ml (HR: 2.9 (95% CI: 1.1-7.6)) was independently associated with irAE.</p><p><strong>Conclusion: </strong>The incidence of irAEs in this cohort is lower than reported in controlled trials, withouut impact on survival outcomes. Education and early recognition are crucial to ensure that these events are identified and addressed.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"16 ","pages":"348-360"},"PeriodicalIF":0.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12088043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PRDX1 protects ATM from arsenite-induced proteotoxicity and maintains its stability during DNA damage signaling. PRDX1保护ATM免受亚砷酸盐诱导的蛋白质毒性,并在DNA损伤信号传导过程中维持其稳定性。
Q2 Medicine Pub Date : 2025-05-19 DOI: 10.18632/oncotarget.28720
Reem Ali, Mashael Algethami, Amera Sheha, Shatha Alqahtani, Ahmad Altayyar, Ayat Lashen, Emad Rakha, Abdallah Alhaj Sulaiman, Srinivasan Madhusudan, Dindial Ramotar

Redox regulation and DNA repair coordination are essential for genomic stability. Peroxiredoxin 1 (PRDX1) is a thiol-dependent peroxidase and a chaperone that protects proteins from excessive oxidation. ATM kinase (Ataxia-Telangiectasia Mutated) and the MRN (MRE11-RAD50-NBS1) complex are DNA damage signaling and repair proteins. We previously showed that cells lacking PRDX1 are sensitive to arsenite, a toxic metal that induces DNA single- and double-strand breaks (DSBs). Herein, we showed that PRDX1 interacts with ATM. PRDX1-deleted cells have reduced ATM, MRE11, and RAD50 protein levels, but not NBS1. In control cells treated with arsenite, we observed γH2AX foci formation due to arsenite-induced DSBs, and not from PRDX1-deleted cells. Arsenite caused profound depletion of ATM in PRDX1-deleted cells, suggesting that PRDX1 protects and stabilizes ATM required to form γH2AX foci. Importantly, arsenite pretreatment of PRDX1-deleted cells caused hypersensitivity to chemotherapeutic agents that generate DSBs. Analysis of a clinical cohort of ovarian cancers treated with platinum chemotherapy revealed that tumours with high PRDX1/high ATM or high PRDX1/high MRE11 expression manifested aggressive phenotypes and poor patient survival. The data suggest that PRDX1 can predict responses to chemotherapy, and targeting PRDX1 could be a viable strategy to improve the efficacy of platinum chemotherapy.

氧化还原调控和DNA修复协调对基因组稳定至关重要。过氧还蛋白1 (PRDX1)是一种硫醇依赖性过氧化物酶和伴侣,保护蛋白质免受过度氧化。ATM激酶(ataxia -毛细血管扩张突变)和MRN (MRE11-RAD50-NBS1)复合物是DNA损伤信号和修复蛋白。我们之前的研究表明,缺乏PRDX1的细胞对亚砷酸盐敏感,亚砷酸盐是一种诱导DNA单链和双链断裂(dsb)的有毒金属。在这里,我们发现PRDX1与ATM相互作用。prdx1缺失细胞的ATM、MRE11和RAD50蛋白水平降低,但NBS1蛋白水平没有降低。在亚砷酸盐处理的对照细胞中,我们观察到γ - h2ax灶的形成是由亚砷酸盐诱导的dsb引起的,而不是来自prdx1缺失的细胞。亚砷酸盐导致PRDX1缺失的细胞中ATM的深度耗竭,表明PRDX1保护和稳定了形成γ - h2ax灶所需的ATM。重要的是,亚砷酸盐预处理prdx1缺失的细胞导致对产生dsb的化疗药物过敏。一项铂类化疗治疗的卵巢癌临床队列分析显示,PRDX1/ ATM高表达或PRDX1/ MRE11高表达的肿瘤表现出侵袭性表型,患者生存率较差。这些数据表明,PRDX1可以预测化疗反应,靶向PRDX1可能是提高铂化疗疗效的可行策略。
{"title":"PRDX1 protects ATM from arsenite-induced proteotoxicity and maintains its stability during DNA damage signaling.","authors":"Reem Ali, Mashael Algethami, Amera Sheha, Shatha Alqahtani, Ahmad Altayyar, Ayat Lashen, Emad Rakha, Abdallah Alhaj Sulaiman, Srinivasan Madhusudan, Dindial Ramotar","doi":"10.18632/oncotarget.28720","DOIUrl":"10.18632/oncotarget.28720","url":null,"abstract":"<p><p>Redox regulation and DNA repair coordination are essential for genomic stability. Peroxiredoxin 1 (PRDX1) is a thiol-dependent peroxidase and a chaperone that protects proteins from excessive oxidation. ATM kinase (Ataxia-Telangiectasia Mutated) and the MRN (MRE11-RAD50-NBS1) complex are DNA damage signaling and repair proteins. We previously showed that cells lacking PRDX1 are sensitive to arsenite, a toxic metal that induces DNA single- and double-strand breaks (DSBs). Herein, we showed that PRDX1 interacts with ATM. PRDX1-deleted cells have reduced ATM, MRE11, and RAD50 protein levels, but not NBS1. In control cells treated with arsenite, we observed γH2AX foci formation due to arsenite-induced DSBs, and not from PRDX1-deleted cells. Arsenite caused profound depletion of ATM in PRDX1-deleted cells, suggesting that PRDX1 protects and stabilizes ATM required to form γH2AX foci. Importantly, arsenite pretreatment of PRDX1-deleted cells caused hypersensitivity to chemotherapeutic agents that generate DSBs. Analysis of a clinical cohort of ovarian cancers treated with platinum chemotherapy revealed that tumours with high PRDX1/high ATM or high PRDX1/high MRE11 expression manifested aggressive phenotypes and poor patient survival. The data suggest that PRDX1 can predict responses to chemotherapy, and targeting PRDX1 could be a viable strategy to improve the efficacy of platinum chemotherapy.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"16 ","pages":"362-378"},"PeriodicalIF":0.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12088036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Retraction: Inhibition of protein phosphatase 2A with a small molecule LB100 radiosensitizes nasopharyngeal carcinoma xenografts by inducing mitotic catastrophe and blocking DNA damage repair. 小分子LB100抑制蛋白磷酸酶2A通过诱导有丝分裂突变和阻断DNA损伤修复使鼻咽癌异种移植物放射增敏。
Q2 Medicine Pub Date : 2025-05-19 DOI: 10.18632/oncotarget.28727
Peng Lv, Yue Wang, Jie Ma, Zheng Wang, Jing-Li Li, Christopher S Hong, Zhengping Zhuang, Yi-Xin Zeng
{"title":"Retraction: Inhibition of protein phosphatase 2A with a small molecule LB100 radiosensitizes nasopharyngeal carcinoma xenografts by inducing mitotic catastrophe and blocking DNA damage repair.","authors":"Peng Lv, Yue Wang, Jie Ma, Zheng Wang, Jing-Li Li, Christopher S Hong, Zhengping Zhuang, Yi-Xin Zeng","doi":"10.18632/oncotarget.28727","DOIUrl":"10.18632/oncotarget.28727","url":null,"abstract":"","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"16 ","pages":"361"},"PeriodicalIF":0.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12088030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analytical validation of a circulating tumor DNA assay using PhasED-Seq technology for detecting residual disease in B-cell malignancies. 利用PhasED-Seq技术检测b细胞恶性肿瘤残留疾病的循环肿瘤DNA分析验证
Q2 Medicine Pub Date : 2025-05-09 DOI: 10.18632/oncotarget.28719
Nina Klimova, Sandra Close, David M Kurtz, Richard D Hockett, Laura Hyland

Background: Circulating tumor DNA (ctDNA) can be used as a tool to detect minimal residual disease (MRD) which can provide important prognostic information in diffuse large B-cell lymphomas (DLBCL). Here, we present an ultra-sensitive MRD assay reliant on Phased Variant Enrichment and Detection Sequencing (PhasED-Seq), which leverages phased variants to detect ctDNA.

Methods: Blank plasma samples were used to assess assay specificity and a limiting dilution series with a DLBCL clinical-contrived sample was performed to assess assay sensitivity and precision. DLBCL plasma patient samples with MRD comparator assay results were tested with PhasED-Seq technology to assess assay accuracy.

Results: The assay's false positive rate was 0.24% and the background error rate was 1.95E-08. The limit of detection at 95% detection rate with 120 ng of input DNA was 0.7 parts in 1,000,000 and precision was >96%. Positive percent agreement for the MRD assay was 90.62% (95% CI 74.98%, 98.02%) and negative percent agreement was 77.78% (95% CI 52.73, 93.59) using a single nucleotide variant-based method as reference.

Conclusions: The PhasED-Seq-based MRD assay has strong analytical and clinical performance in B-cell malignancies. Improved ctDNA detection methods such as this may improve patient outcomes through detection of residual disease or early relapse.

背景:循环肿瘤DNA (ctDNA)可作为一种检测弥漫性大b细胞淋巴瘤(DLBCL)微小残留病变(MRD)的工具,为弥漫性大b细胞淋巴瘤(DLBCL)的预后提供重要信息。在这里,我们提出了一种依赖于相位变异富集和检测测序(Phased - seq)的超敏感MRD分析,它利用相位变异来检测ctDNA。方法:空白血浆样品用于评估检测的特异性,并使用临床人工制备的DLBCL样品进行极限稀释系列以评估检测的灵敏度和精度。采用phase - seq技术对具有MRD比较器检测结果的DLBCL血浆患者样本进行检测,以评估检测的准确性。结果:该方法的假阳性率为0.24%,背景误差率为1.95E-08。输入120 ng的DNA, 95%检出率下的检出限为0.7份/ 100万,精密度为0.96%。以单核苷酸变异为参考,MRD检测的阳性率为90.62% (95% CI 74.98%, 98.02%),阴性率为77.78% (95% CI 52.73, 93.59)。结论:基于phased - seq的MRD检测在b细胞恶性肿瘤中具有很强的分析和临床性能。改进的ctDNA检测方法可以通过检测残留疾病或早期复发来改善患者的预后。
{"title":"Analytical validation of a circulating tumor DNA assay using PhasED-Seq technology for detecting residual disease in B-cell malignancies.","authors":"Nina Klimova, Sandra Close, David M Kurtz, Richard D Hockett, Laura Hyland","doi":"10.18632/oncotarget.28719","DOIUrl":"https://doi.org/10.18632/oncotarget.28719","url":null,"abstract":"<p><strong>Background: </strong>Circulating tumor DNA (ctDNA) can be used as a tool to detect minimal residual disease (MRD) which can provide important prognostic information in diffuse large B-cell lymphomas (DLBCL). Here, we present an ultra-sensitive MRD assay reliant on Phased Variant Enrichment and Detection Sequencing (PhasED-Seq), which leverages phased variants to detect ctDNA.</p><p><strong>Methods: </strong>Blank plasma samples were used to assess assay specificity and a limiting dilution series with a DLBCL clinical-contrived sample was performed to assess assay sensitivity and precision. DLBCL plasma patient samples with MRD comparator assay results were tested with PhasED-Seq technology to assess assay accuracy.</p><p><strong>Results: </strong>The assay's false positive rate was 0.24% and the background error rate was 1.95E-08. The limit of detection at 95% detection rate with 120 ng of input DNA was 0.7 parts in 1,000,000 and precision was >96%. Positive percent agreement for the MRD assay was 90.62% (95% CI 74.98%, 98.02%) and negative percent agreement was 77.78% (95% CI 52.73, 93.59) using a single nucleotide variant-based method as reference.</p><p><strong>Conclusions: </strong>The PhasED-Seq-based MRD assay has strong analytical and clinical performance in B-cell malignancies. Improved ctDNA detection methods such as this may improve patient outcomes through detection of residual disease or early relapse.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"16 ","pages":"329-336"},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12068320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144023452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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