Pub Date : 2025-05-20DOI: 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.
{"title":"Cigarette smoke and decreased DNA repair by Xeroderma Pigmentosum Group C use a double hit mechanism for epithelial cell lung carcinogenesis.","authors":"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","doi":"10.18632/oncotarget.28724","DOIUrl":"10.18632/oncotarget.28724","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"16 ","pages":"396-409"},"PeriodicalIF":0.0,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12219255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111510","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}
Pub Date : 2025-05-20DOI: 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.
{"title":"Targeting PCNA/AR interaction inhibits AR-mediated signaling in castration resistant prostate cancer cells.","authors":"Shan Lu, Zhongyun Dong","doi":"10.18632/oncotarget.28722","DOIUrl":"10.18632/oncotarget.28722","url":null,"abstract":"<p><p>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 <i>PSA</i> and <i>p21</i> 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 <i>CCNA2</i> 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.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"16 ","pages":"383-395"},"PeriodicalIF":0.0,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12219270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111517","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}
Pub Date : 2025-05-20DOI: 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
{"title":"Correction: Activation of PI3K/Akt/mTOR signaling in the tumor stroma drives endocrine therapy-dependent breast tumor regression.","authors":"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","doi":"10.18632/oncotarget.28728","DOIUrl":"10.18632/oncotarget.28728","url":null,"abstract":"","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"16 ","pages":"379-381"},"PeriodicalIF":0.0,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12219265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111607","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}
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.
{"title":"Advancements in bladder cancer treatment: The synergy of radiation and immunotherapy.","authors":"Nazmul Hasan, Daniel Yang, Spencer Gibson, Barbod Khaleghi, Rozhan Ziari, Arash Rezazadeh Kalebasty","doi":"10.18632/oncotarget.28723","DOIUrl":"10.18632/oncotarget.28723","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"16 ","pages":"337-346"},"PeriodicalIF":0.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12088031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094482","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}
Pub Date : 2025-05-19DOI: 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.
{"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}
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.
{"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}
Pub Date : 2025-05-19DOI: 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}
Pub Date : 2025-05-09DOI: 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}