Pub Date : 2024-09-15DOI: 10.1101/2024.09.10.612204
Laura Morano, Nadia Vie, Adam Aissanou, Tom Egger, Antoine Aze, Solene Fiachetti, Herve Seitz, Louis-Antoine Milazzo, Veronique GARAMBOIS, Nathalie Bonnefoy-Berard, Celine Gongora, Angelos Constantinou, Jihane Basbous
In cancer cells, ATR signaling is crucial to tolerate the intrinsically high damage levels that normally block replication fork progression. Assembly of TopBP1, a multifunctional scaffolding protein, into condensates is required to amplify ATR kinase activity to the levels needed to coordinate the DNA damage response and manage DNA replication stress. Many ATR inhibitors are tested for cancer treatment in clinical trials, but their overall effectiveness is often compromised by the emergence of resistance and toxicities. In this proof-of-concept study, we propose to disrupt the ATR pathway by targeting TopBP1 condensation. First, we screened a molecule-based library using a previously developed optogenetic approach and identified several TopBP1 condensation inhibitors. Amongst them, AZD2858 disrupted TopBP1 assembly induced by the clinically relevant topoisomerase I inhibitor SN-38, thereby inhibiting the ATR/Chk1 signaling pathway. We found that AZD2858 exerted its effects by disrupting TopBP1 self-interaction and binding to ATR in mammalian cells, and by increasing its chromatin recruitment in cell-free Xenopus laevis egg extracts. Moreover, AZD2858 prevented S-phase checkpoint induction by SN-38, leading to increased DNA damage and apoptosis in a colorectal cancer cell line. Lastly, AZD2858 showed synergistic effect in combination with the FOLFIRI chemotherapy regimen in a spheroid model of colorectal cancer.
在癌细胞中，ATR 信号对于耐受通常阻碍复制叉进展的内在高损伤水平至关重要。需要将多功能支架蛋白 TopBP1 组装成凝聚体，以将 ATR 激酶活性放大到协调 DNA 损伤反应和管理 DNA 复制压力所需的水平。在临床试验中，许多 ATR 抑制剂都被用于癌症治疗，但由于出现耐药性和毒性，它们的整体效果往往大打折扣。在这项概念验证研究中，我们建议通过靶向 TopBP1 缩合来破坏 ATR 通路。首先，我们利用之前开发的光遗传学方法筛选了一个分子库，并确定了几种 TopBP1 缩合抑制剂。在这些抑制剂中，AZD2858 破坏了由临床相关的拓扑异构酶 I 抑制剂 SN-38 诱导的 TopBP1 组装，从而抑制了 ATR/Chk1 信号通路。我们发现，在哺乳动物细胞中，AZD2858 通过破坏 TopBP1 的自身相互作用和与 ATR 的结合，以及在无细胞的爪蟾卵提取物中通过增加其染色质募集来发挥其作用。此外，AZD2858 还能阻止 SN-38 诱导的 S 期检查点，从而导致结直肠癌细胞系的 DNA 损伤和细胞凋亡增加。最后，在结直肠癌球形模型中，AZD2858 与 FOLFIRI 化疗方案联合使用显示出协同效应。
{"title":"TopBP1 biomolecular condensates: a new therapeutic target in advanced-stage colorectal cancer.","authors":"Laura Morano, Nadia Vie, Adam Aissanou, Tom Egger, Antoine Aze, Solene Fiachetti, Herve Seitz, Louis-Antoine Milazzo, Veronique GARAMBOIS, Nathalie Bonnefoy-Berard, Celine Gongora, Angelos Constantinou, Jihane Basbous","doi":"10.1101/2024.09.10.612204","DOIUrl":"https://doi.org/10.1101/2024.09.10.612204","url":null,"abstract":"In cancer cells, ATR signaling is crucial to tolerate the intrinsically high damage levels that normally block replication fork progression. Assembly of TopBP1, a multifunctional scaffolding protein, into condensates is required to amplify ATR kinase activity to the levels needed to coordinate the DNA damage response and manage DNA replication stress. Many ATR inhibitors are tested for cancer treatment in clinical trials, but their overall effectiveness is often compromised by the emergence of resistance and toxicities. In this proof-of-concept study, we propose to disrupt the ATR pathway by targeting TopBP1 condensation. First, we screened a molecule-based library using a previously developed optogenetic approach and identified several TopBP1 condensation inhibitors. Amongst them, AZD2858 disrupted TopBP1 assembly induced by the clinically relevant topoisomerase I inhibitor SN-38, thereby inhibiting the ATR/Chk1 signaling pathway. We found that AZD2858 exerted its effects by disrupting TopBP1 self-interaction and binding to ATR in mammalian cells, and by increasing its chromatin recruitment in cell-free Xenopus laevis egg extracts. Moreover, AZD2858 prevented S-phase checkpoint induction by SN-38, leading to increased DNA damage and apoptosis in a colorectal cancer cell line. Lastly, AZD2858 showed synergistic effect in combination with the FOLFIRI chemotherapy regimen in a spheroid model of colorectal cancer.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"125 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-15DOI: 10.1101/2024.09.11.612438
Khewoong Baek, Rebecca J Metivier, Shourya S Roy Burman, Jonathan W Bushman, Ryan J Lumpkin, Dinah M Abeja, Megha Lakshminarayan, Hong Yue, Samuel Ojeda, Alyssa L Verano, Nathanael Gray, Katherine A Donovan, Eric S Fischer
Targeted protein degradation and induced proximity refer to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of glues remains challenging, unbiased discovery methods are needed to unveil hidden chemical targets. Here we establish a high throughput affinity purification mass spectrometry workflow in cell lysates for the unbiased identification of molecular glue targets. By mapping the targets of 20 CRBN-binding molecular glues, we identify 298 protein targets and demonstrate the utility of enrichment methods for identifying novel targets overlooked using established methods. We use a computational workflow to estimate target confidence and perform a biochemical screen to identify a lead compound for the new non-ZF target PPIL4. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying new drug-induced protein interactions in cell lysates.
{"title":"Unveiling the hidden interactome of CRBN molecular glues with chemoproteomics","authors":"Khewoong Baek, Rebecca J Metivier, Shourya S Roy Burman, Jonathan W Bushman, Ryan J Lumpkin, Dinah M Abeja, Megha Lakshminarayan, Hong Yue, Samuel Ojeda, Alyssa L Verano, Nathanael Gray, Katherine A Donovan, Eric S Fischer","doi":"10.1101/2024.09.11.612438","DOIUrl":"https://doi.org/10.1101/2024.09.11.612438","url":null,"abstract":"Targeted protein degradation and induced proximity refer to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of glues remains challenging, unbiased discovery methods are needed to unveil hidden chemical targets. Here we establish a high throughput affinity purification mass spectrometry workflow in cell lysates for the unbiased identification of molecular glue targets. By mapping the targets of 20 CRBN-binding molecular glues, we identify 298 protein targets and demonstrate the utility of enrichment methods for identifying novel targets overlooked using established methods. We use a computational workflow to estimate target confidence and perform a biochemical screen to identify a lead compound for the new non-ZF target PPIL4. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying new drug-induced protein interactions in cell lysates.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.10.612209
Shamima Azma Ansari, Sibasish Mohanty, Pallavi Mohapatra, Rachna Rath, Dillip Muduli, Saroj Kumar Das Majumdar, Rajeeb K. Swain, Rupesh Dash
Docetaxel alone or in combination with other drugs is the most common chemotherapy regimen for several neoplasms including advanced OSCC. Unfortunately, chemoresistance leads to relapse and continued tumor growth. It is therefore important to explore the causative factors for docetaxel resistance. In this study, we performed a CRISPR-based kinome screening that identified Never In Mitosis Gene-A Related Kinase-9 (NEK9) as a major player of docetaxel resistance in OSCC, prostate, and pancreatic cancer lines. NEK9 expression was upregulated in tumor samples of chemotherapy non-responders compared to responder OSCC patients. Our validation data suggests selectively knocking out NEK9 sensitizes cancer cells to docetaxel. Mechanistically, we found that ablation of NEK9 induces DNA damage, activating ERK(p-T202/Y204) that leads to Gasdermin-E mediated Cancer Cell pyroptosis. The in-vitro kinase activity assay identified fostamatinib as a potent inhibitor of NEK9. The xenograft data suggest that fostamatinib restores docetaxel sensitivity and facilitates a significant reduction of tumor burden. Overall, our data suggests a novel combination of fostamatinib and docetaxel needs further clinical investigation in advanced OSCC.
多西他赛单独使用或与其他药物联合使用是包括晚期OSCC在内的多种肿瘤最常用的化疗方案。不幸的是，化疗耐药会导致复发和肿瘤继续生长。因此，探索多西他赛耐药的致病因素非常重要。在本研究中，我们进行了基于CRISPR的激酶组筛选，发现Never In Mitosis Gene-A Related Kinase-9（NEK9）是OSCC、前列腺癌和胰腺癌株中多西他赛耐药的主要参与者。与有耐药性的 OSCC 患者相比，NEK9 在化疗无应答者的肿瘤样本中表达上调。我们的验证数据表明，选择性敲除 NEK9 可使癌细胞对多西他赛敏感。从机理上讲，我们发现消减 NEK9 会诱导 DNA 损伤，激活 ERK(p-T202/Y204)，从而导致 Gasdermin-E 介导的癌细胞热休克。体外激酶活性测定发现，福斯塔替尼是NEK9的强效抑制剂。异种移植数据表明，福斯塔替尼能恢复多西他赛的敏感性，并能显著减轻肿瘤负荷。总之，我们的数据表明，在晚期OSCC中，需要进一步临床研究福斯塔替尼与多西他赛的新型组合。
{"title":"NEK9 ablation rewires docetaxel resistance through induction of ERK-mediated cancer cell pyroptosis","authors":"Shamima Azma Ansari, Sibasish Mohanty, Pallavi Mohapatra, Rachna Rath, Dillip Muduli, Saroj Kumar Das Majumdar, Rajeeb K. Swain, Rupesh Dash","doi":"10.1101/2024.09.10.612209","DOIUrl":"https://doi.org/10.1101/2024.09.10.612209","url":null,"abstract":"Docetaxel alone or in combination with other drugs is the most common chemotherapy regimen for several neoplasms including advanced OSCC. Unfortunately, chemoresistance leads to relapse and continued tumor growth. It is therefore important to explore the causative factors for docetaxel resistance. In this study, we performed a CRISPR-based kinome screening that identified Never In Mitosis Gene-A Related Kinase-9 (NEK9) as a major player of docetaxel resistance in OSCC, prostate, and pancreatic cancer lines. NEK9 expression was upregulated in tumor samples of chemotherapy non-responders compared to responder OSCC patients. Our validation data suggests selectively knocking out NEK9 sensitizes cancer cells to docetaxel. Mechanistically, we found that ablation of NEK9 induces DNA damage, activating ERK(p-T202/Y204) that leads to Gasdermin-E mediated Cancer Cell pyroptosis. The in-vitro kinase activity assay identified fostamatinib as a potent inhibitor of NEK9. The xenograft data suggest that fostamatinib restores docetaxel sensitivity and facilitates a significant reduction of tumor burden. Overall, our data suggests a novel combination of fostamatinib and docetaxel needs further clinical investigation in advanced OSCC.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.10.612298
Caitlin Bell, Richard Baylis, Nicolas Lopez, Wei Feng Ma, Hua Gao, Fudi Wang, Sharika Bamezai, Changhao Fu, Yoko Kojima, Shaunak Adkar, Lingfeng Luo, Clint Miller, Nicholas L Leeper
Background: Smooth muscle cell (SMC) plasticity and phenotypic switching play prominent roles in the pathogenesis of multiple diseases, but their role in tumorigenesis is unknown. We investigated whether and how SMC diversity and plasticity plays a role in tumor angiogenesis and the tumor microenvironment. Methods and Results: We use SMC-specific lineage-tracing mouse models and single cell RNA sequencing to observe the phenotypic diversity of SMCs participating in tumor vascularization. We find that a significant proportion of SMCs adopt a phenotype traditionally associated with macrophage-like cells. These cells are transcriptionally similar to resolution phase M2b macrophages, which have been described to have a role in inflammation resolution. Computationally predicted by the ligand-receptor algorithm CellChat, signaling from BST2 on the surface of tumor cells to PIRA2 on SMCs promote this phenotypic transition; in vitro SMC assays demonstrate upregulation of macrophage transcriptional programs, and increased proliferation, migration, and phagocytic ability when exposed to BST2. Knockdown of BST2 in the tumor significantly decreases the transition towards a macrophage-like phenotype, and cells that do transition have a comparatively higher inflammatory signal typically associated with anti-tumor effect. Conclusion: As BST2 is known to be a poor prognostic marker in multiple cancers where it is associated with an M2 macrophage-skewed TME, these studies suggest that phenotypically switched SMCs may have a previously unidentified role in this immunosuppressive milieu. Further translational work is needed to understand how this phenotypic switch could influence the response to anti-cancer agents and if targeted inhibition of SMC plasticity would be therapeutically beneficial.
{"title":"BST2 induces vascular smooth muscle cell plasticity and phenotype switching during cancer progression","authors":"Caitlin Bell, Richard Baylis, Nicolas Lopez, Wei Feng Ma, Hua Gao, Fudi Wang, Sharika Bamezai, Changhao Fu, Yoko Kojima, Shaunak Adkar, Lingfeng Luo, Clint Miller, Nicholas L Leeper","doi":"10.1101/2024.09.10.612298","DOIUrl":"https://doi.org/10.1101/2024.09.10.612298","url":null,"abstract":"Background: Smooth muscle cell (SMC) plasticity and phenotypic switching play prominent roles in the pathogenesis of multiple diseases, but their role in tumorigenesis is unknown. We investigated whether and how SMC diversity and plasticity plays a role in tumor angiogenesis and the tumor microenvironment. Methods and Results: We use SMC-specific lineage-tracing mouse models and single cell RNA sequencing to observe the phenotypic diversity of SMCs participating in tumor vascularization. We find that a significant proportion of SMCs adopt a phenotype traditionally associated with macrophage-like cells. These cells are transcriptionally similar to resolution phase M2b macrophages, which have been described to have a role in inflammation resolution. Computationally predicted by the ligand-receptor algorithm CellChat, signaling from BST2 on the surface of tumor cells to PIRA2 on SMCs promote this phenotypic transition; in vitro SMC assays demonstrate upregulation of macrophage transcriptional programs, and increased proliferation, migration, and phagocytic ability when exposed to BST2. Knockdown of BST2 in the tumor significantly decreases the transition towards a macrophage-like phenotype, and cells that do transition have a comparatively higher inflammatory signal typically associated with anti-tumor effect. Conclusion: As BST2 is known to be a poor prognostic marker in multiple cancers where it is associated with an M2 macrophage-skewed TME, these studies suggest that phenotypically switched SMCs may have a previously unidentified role in this immunosuppressive milieu. Further translational work is needed to understand how this phenotypic switch could influence the response to anti-cancer agents and if targeted inhibition of SMC plasticity would be therapeutically beneficial.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.10.612338
Yuri G. Vilela, Artur C. Fassoni, Armando G. M. Neves
Adaptive therapy is a promising paradigm for treating cancers, that exploits competitive interactions between drug-sensitive and drug-resistant cells, thereby avoiding or delaying treatment failure due to evolution of drug resistance within the tumor. Previous studies have shown the mathematical possibility of building cyclic schemes of drug administration which restore tumor composition to its exact initial value in deterministic models. However, algorithms for cycle design, the conditions on which such algorithms are certain to work, as well as conditions for cycle stability remain elusive. Here, we state biologically motivated hypotheses that guarantee existence of such cycles in two deterministic classes of mathematical models already considered in the literature: Lotka-Volterra and adjusted replicator dynamics. We stress that not only existence of cyclic schemes, but also stability of such cycles is a relevant feature for applications in real clinical scenarios. We also analyze stochastic versions of the above deterministic models, a necessary step if we want to take into account that real tumors are composed by a finite population of cells subject to randomness, a relevant feature in the context of low tumor burden. We argue that the stability of the deterministic cycles is also relevant for the stochastic version of the models. In fact, Dua, Ma and Newton [Cancers (2021)] and Park and Newton [Phys. Rev. E (2023)] observed breakdown of deterministic cycles in a stochastic model (Moran process) for a tumor. Our findings indicate that the breakdown phenomenon is not due to stochasticity itself, but to the deterministic instability inherent in the cycles of the referenced papers. We then illustrate how stable deterministic cycles avoid for very large times the breakdown of cyclic treatments in stochastic tumor models.
适应性疗法是治疗癌症的一种有前途的模式，它利用药物敏感细胞和耐药细胞之间的竞争性相互作用，从而避免或延缓因肿瘤内耐药性演变而导致的治疗失败。以往的研究表明，在数学上可以建立循环给药方案，在确定性模型中将肿瘤组成恢复到精确的初始值。然而，循环设计的算法、这种算法确定有效的条件以及循环稳定性的条件仍然难以确定。在此，我们提出了一些以生物学为动机的假设，以保证在文献中已考虑过的两类确定性数学模型中存在这种循环：洛特卡-伏特拉（Lotka-Volterra）和调整复制器动力学。我们强调，不仅存在循环方案，而且这种循环的稳定性也是实际临床应用的一个相关特征。我们还分析了上述确定性模型的随机版本，如果我们想考虑到真实肿瘤是由受随机性影响的有限细胞群组成，这是一个必要的步骤，这也是低肿瘤负荷背景下的一个相关特征。我们认为，确定性循环的稳定性也与随机模型有关。事实上，Dua、Ma 和 Newton [Cancers (2021)]以及 Park 和 Newton [Phys. Rev. E (2023)]在肿瘤的随机模型（莫伦过程）中观察到了确定性循环的崩溃。我们的研究结果表明，崩溃现象并不是由于随机性本身，而是由于参考文献中的周期所固有的确定性不稳定性。然后，我们说明了稳定的确定性循环如何在很大程度上避免了随机肿瘤模型中循环治疗的崩溃。
{"title":"On the design and stability of cancer adaptive therapy cycles: deterministic and stochastic models","authors":"Yuri G. Vilela, Artur C. Fassoni, Armando G. M. Neves","doi":"10.1101/2024.09.10.612338","DOIUrl":"https://doi.org/10.1101/2024.09.10.612338","url":null,"abstract":"Adaptive therapy is a promising paradigm for treating cancers, that exploits competitive interactions between drug-sensitive and drug-resistant cells, thereby avoiding or delaying treatment failure due to evolution of drug resistance within the tumor. Previous studies have shown the mathematical possibility of building cyclic schemes of drug administration which restore tumor composition to its exact initial value in deterministic models. However, algorithms for cycle design, the conditions on which such algorithms are certain to work, as well as conditions for cycle stability remain elusive. Here, we state biologically motivated hypotheses that guarantee existence of such cycles in two deterministic classes of mathematical models already considered in the literature: Lotka-Volterra and adjusted replicator dynamics. We stress that not only existence of cyclic schemes, but also stability of such cycles is a relevant feature for applications in real clinical scenarios. We also analyze stochastic versions of the above deterministic models, a necessary step if we want to take into account that real tumors are composed by a finite population of cells subject to randomness, a relevant feature in the context of low tumor burden. We argue that the stability of the deterministic cycles is also relevant for the stochastic version of the models. In fact, Dua, Ma and Newton [Cancers (2021)] and Park and Newton [Phys. Rev. E (2023)] observed breakdown of deterministic cycles in a stochastic model (Moran process) for a tumor. Our findings indicate that the breakdown phenomenon is not due to stochasticity itself, but to the deterministic instability inherent in the cycles of the referenced papers. We then illustrate how stable deterministic cycles avoid for very large times the breakdown of cyclic treatments in stochastic tumor models.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.07.611821
Kunwer S. Chhatwal, Hengrui Liu
BACKGROUND: RAD50 is one of the most critical genes in DNA double-strand break processing, which can lead to a single strand of DNA overhang and is potentially involved in forcing incomplete DNA repair. This research study aims to investigate the role of RAD50 in breast cancer diagnosis and prognosis. METHODS: Breast cancer mRNA expression data was collected from TCGA and the difference between cancer and non-cancer in gene expression of RAD50 was analyzed. The survival association of RAD50 was also analyzed. RESULTS: RAD50 expression is significantly lower in cancer than in normal tissue. High expression of RAD50 is associated with worse survival. Conclusion: RAD50 is a potential biomarker for breast cancer diagnosis and prognosis
{"title":"RAD50 is a potential biomarker for breast cancer diagnosis and prognosis","authors":"Kunwer S. Chhatwal, Hengrui Liu","doi":"10.1101/2024.09.07.611821","DOIUrl":"https://doi.org/10.1101/2024.09.07.611821","url":null,"abstract":"BACKGROUND: RAD50 is one of the most critical genes in DNA double-strand break processing, which can lead to a single strand of DNA overhang and is potentially involved in forcing incomplete DNA repair. This research study aims to investigate the role of RAD50 in breast cancer diagnosis and prognosis. METHODS: Breast cancer mRNA expression data was collected from TCGA and the difference between cancer and non-cancer in gene expression of RAD50 was analyzed. The survival association of RAD50 was also analyzed. RESULTS: RAD50 expression is significantly lower in cancer than in normal tissue. High expression of RAD50 is associated with worse survival. Conclusion: RAD50 is a potential biomarker for breast cancer diagnosis and prognosis","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"50 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.10.612212
Nicholas Allen Baclig Abad, Irina Glas, Chen Hong, Yoann Pageaud, Barbara Hutter, Benedikt Brors, Cindy Korner, Lars Feuerbach
Cancer is a heterogeneous disease that arises due to mutations that drive cancer progression. However, the identification of these functional mutations has typically focused only on protein-coding DNA. Among non-coding mutations, only a few have been clearly associated with cancer. We hypothesize that this gap in discovery is partly due to the limitations of current methods requiring high recurrence of mutations. To support candidate selection for experimental validation of lowly recurrent and singleton promoter mutations, new computational approaches for the integrated analysis of multi-omics data are required. To address this challenge, the REMIND-Cancer Pipeline leverages whole-genome sequencing and RNA-Seq data to extract and prioritize functional promoter mutations, regardless of their recurrence status. Subsequently, pSNV Hunter aggregates and visualizes comprehensive information for each candidate. We demonstrate the functionality of both tools by applying it to the PCAWG dataset. This workflow successfully identified and prioritized known highly-recurrent mutations, as well as, novel singletons and lowly recurrent candidates. Hence, the output of our workflow directly supports hypothesis generation for subsequent experimental validation to overcome limitations of recurrence-based approaches.
{"title":"Identifying, Prioritizing, and Visualizing Functional Promoter SNVs with the Recurrence-agnostic REMIND-Cancer Pipeline and pSNV Hunter","authors":"Nicholas Allen Baclig Abad, Irina Glas, Chen Hong, Yoann Pageaud, Barbara Hutter, Benedikt Brors, Cindy Korner, Lars Feuerbach","doi":"10.1101/2024.09.10.612212","DOIUrl":"https://doi.org/10.1101/2024.09.10.612212","url":null,"abstract":"Cancer is a heterogeneous disease that arises due to mutations that drive cancer progression. However, the identification of these functional mutations has typically focused only on protein-coding DNA. Among non-coding mutations, only a few have been clearly associated with cancer. We hypothesize that this gap in discovery is partly due to the limitations of current methods requiring high recurrence of mutations. To support candidate selection for experimental validation of lowly recurrent and singleton promoter mutations, new computational approaches for the integrated analysis of multi-omics data are required. To address this challenge, the REMIND-Cancer Pipeline leverages whole-genome sequencing and RNA-Seq data to extract and prioritize functional promoter mutations, regardless of their recurrence status. Subsequently, pSNV Hunter aggregates and visualizes comprehensive information for each candidate. We demonstrate the functionality of both tools by applying it to the PCAWG dataset. This workflow successfully identified and prioritized known highly-recurrent mutations, as well as, novel singletons and lowly recurrent candidates. Hence, the output of our workflow directly supports hypothesis generation for subsequent experimental validation to overcome limitations of recurrence-based approaches.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"47 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.13.612231
Caroline Hochheuser, Arjan Boltjes, Kaylee M Keller, Simon Tol, Marieke van de Mheen, Caroline Pita Barros, Zeinab van Gestel-Fadaie, André B.P. van Kuilenburg, Sander van Hooff, Carlijn Voermans, Jan J. Molenaar, Godelieve A.M. Tytgat, Ilse Timmerman
Bone marrow (BM) is a common site for solid tumor metastasis, often causing poor outcome. Here, we define the characteristics of BM-disseminated tumor cells (DTCs) using neuroblastoma as a model. We combined single-cell RNA-sequencing (scRNA-seq) and cell-surface protein analysis using 7 paired BM and primary tumor (PT) samples and found that DTCs contain a higher percentage of cycling cells and higher expression of neurodevelopmental genes compared to corresponding PT cells. In 6 patients, the copy number variation profile differed between PT cells and DTCs, indicating spatial heterogeneity. Within the BM, we detected dormant DTCs with potentially reduced chemosensitivity; this population contained cells expressing low levels of the immunotherapeutic antigen GD2 and increased NGFR expression. In conclusion, we characterized DTCs that are particularly challenging to target, offering new avenues for developing therapeutic strategies designed to target all subpopulations within the highly complex metastatic site, thereby preventing the development of drug-resistant clones.
{"title":"Metastatic tumor cells in bone marrow differ from paired neuroblastoma tumor and contain subsets with therapy-resistant characteristics","authors":"Caroline Hochheuser, Arjan Boltjes, Kaylee M Keller, Simon Tol, Marieke van de Mheen, Caroline Pita Barros, Zeinab van Gestel-Fadaie, André B.P. van Kuilenburg, Sander van Hooff, Carlijn Voermans, Jan J. Molenaar, Godelieve A.M. Tytgat, Ilse Timmerman","doi":"10.1101/2024.09.13.612231","DOIUrl":"https://doi.org/10.1101/2024.09.13.612231","url":null,"abstract":"Bone marrow (BM) is a common site for solid tumor metastasis, often causing poor outcome. Here, we define the characteristics of BM-disseminated tumor cells (DTCs) using neuroblastoma as a model. We combined single-cell RNA-sequencing (scRNA-seq) and cell-surface protein analysis using 7 paired BM and primary tumor (PT) samples and found that DTCs contain a higher percentage of cycling cells and higher expression of neurodevelopmental genes compared to corresponding PT cells. In 6 patients, the copy number variation profile differed between PT cells and DTCs, indicating spatial heterogeneity. Within the BM, we detected dormant DTCs with potentially reduced chemosensitivity; this population contained cells expressing low levels of the immunotherapeutic antigen GD2 and increased NGFR expression. In conclusion, we characterized DTCs that are particularly challenging to target, offering new avenues for developing therapeutic strategies designed to target all subpopulations within the highly complex metastatic site, thereby preventing the development of drug-resistant clones.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.10.612175
Camille Tessier, Jennifer Derrien, Aurore Dupuy, Thomas Pele, Martin Moquet, Julie Roul, Elise Douillard, Camille El Harrif, Xavier Pinson, Matthieu Le Gallo, Florence Godey, Patrick Tas, Roselyne Viel, Claude Prigent, Eric Letouze, Peggy Suzanne, Patrick Dallemagne, Mario Campone, Robert Weinberg, Jacqueline Lees, Philippe Juin, Vincent Guen
Tumor heterogeneity and plasticity, driven by Epithelial-Mesenchymal Transition (EMT), enable cancer therapeutic resistance. We previously showed that EMT promotes primary cilia formation, which enables stemness and tumorigenesis in triple-negative breast cancer (TNBC). Here, we establish a role for primary cilia in human TNBC chemotherapeutic resistance. We developed patient-derived organoids, and showed that these recapitulated the cellular heterogeneity of TNBC biopsies. Notably, one of the identified cell states bore a quasi-mesenchymal phenotype, primary cilia, and stemness signatures. We treated our TNBC organoids with chemotherapeutics and observed partial killing. The surviving cells with organoid-reconstituting capacity showed selective enrichment for the quasi-mesenchymal ciliated cell subpopulation. Genomic analyses argue that this enrichment reflects a combination of pre-existing cells and ones that arose through drug-induced cellular plasticity. We developed a family of small-molecule inhibitors of ciliogenesis and show that these, or genetic ablation of primary cilia, suppress chemoresistance. We conclude that primary cilia help TNBC to evade chemotherapy.
{"title":"Primary cilia promote EMT-induced triple-negative breast tumor heterogeneity and resistance to therapy","authors":"Camille Tessier, Jennifer Derrien, Aurore Dupuy, Thomas Pele, Martin Moquet, Julie Roul, Elise Douillard, Camille El Harrif, Xavier Pinson, Matthieu Le Gallo, Florence Godey, Patrick Tas, Roselyne Viel, Claude Prigent, Eric Letouze, Peggy Suzanne, Patrick Dallemagne, Mario Campone, Robert Weinberg, Jacqueline Lees, Philippe Juin, Vincent Guen","doi":"10.1101/2024.09.10.612175","DOIUrl":"https://doi.org/10.1101/2024.09.10.612175","url":null,"abstract":"Tumor heterogeneity and plasticity, driven by Epithelial-Mesenchymal Transition (EMT), enable cancer therapeutic resistance. We previously showed that EMT promotes primary cilia formation, which enables stemness and tumorigenesis in triple-negative breast cancer (TNBC). Here, we establish a role for primary cilia in human TNBC chemotherapeutic resistance. We developed patient-derived organoids, and showed that these recapitulated the cellular heterogeneity of TNBC biopsies. Notably, one of the identified cell states bore a quasi-mesenchymal phenotype, primary cilia, and stemness signatures. We treated our TNBC organoids with chemotherapeutics and observed partial killing. The surviving cells with organoid-reconstituting capacity showed selective enrichment for the quasi-mesenchymal ciliated cell subpopulation. Genomic analyses argue that this enrichment reflects a combination of pre-existing cells and ones that arose through drug-induced cellular plasticity. We developed a family of small-molecule inhibitors of ciliogenesis and show that these, or genetic ablation of primary cilia, suppress chemoresistance. We conclude that primary cilia help TNBC to evade chemotherapy.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.10.612261
Ryan C Graff, Adam Haimowitz, Jennifer Aguilan, Adriana Levine, Jinghang Zhang, Wenlin Yuan, Merone Roose-Girma, Somesekar Seshagiri, Steven A Porcelli, Matthew J Gamble, Simone Sidoli, Anne R Bresnick, Jonathan Backer
Platelets promote tumor metastasis by several mechanisms. Platelet-tumor cell interactions induce the release of platelet cytokines, chemokines, and other factors that promote tumor cell epithelial-mesenchymal transition and invasion, granulocyte recruitment to circulating tumor cells (CTCs), and adhesion of CTCs to the endothelium, assisting in their extravasation at metastatic sites. Previous studies have shown that platelet activation in the context of thrombus formation requires the Class IA PI 3-kinase PI3Kβ. We now define a role for platelet PI3Kβ in breast cancer metastasis. Platelet PI3Kβ is essential for platelet-stimulated tumor cell invasion through Matrigel. Consistent with this finding, in vitro platelet-tumor cell binding and tumor cell-stimulated platelet activation are reduced in platelets isolated from PI3Kβ mutant mice. RNAseq and proteomic analysis of human breast epithelial cells co-cultured with platelets revealed that platelet PI3Kβ regulates the expression of EMT and metastasis-associated genes in these cells. The EMT and metastasis-associated proteins PAI-1 and IL-8 were specifically downregulated in co-cultures with PI3Kβ mutant platelets. PI3Kβ mutant platelets are impaired in their ability to stimulate YAP and Smad2 signaling in tumor cells, two pathways regulating PAI-1 expression. Finally, we show that mice expressing mutant PI3Kβ show reduced spontaneous metastasis, and platelets isolated from these mice are less able to stimulate experimental metastasis in WT mice. Taken together, these data support a role for platelet PI3Kβ in promoting breast cancer metastasis and highlight platelet PI3Kβ as a potential therapeutic target.
{"title":"Platelet PI3Kβ regulates breast cancer metastasis","authors":"Ryan C Graff, Adam Haimowitz, Jennifer Aguilan, Adriana Levine, Jinghang Zhang, Wenlin Yuan, Merone Roose-Girma, Somesekar Seshagiri, Steven A Porcelli, Matthew J Gamble, Simone Sidoli, Anne R Bresnick, Jonathan Backer","doi":"10.1101/2024.09.10.612261","DOIUrl":"https://doi.org/10.1101/2024.09.10.612261","url":null,"abstract":"Platelets promote tumor metastasis by several mechanisms. Platelet-tumor cell interactions induce the release of platelet cytokines, chemokines, and other factors that promote tumor cell epithelial-mesenchymal transition and invasion, granulocyte recruitment to circulating tumor cells (CTCs), and adhesion of CTCs to the endothelium, assisting in their extravasation at metastatic sites. Previous studies have shown that platelet activation in the context of thrombus formation requires the Class IA PI 3-kinase PI3Kβ. We now define a role for platelet PI3Kβ in breast cancer metastasis. Platelet PI3Kβ is essential for platelet-stimulated tumor cell invasion through Matrigel. Consistent with this finding, in vitro platelet-tumor cell binding and tumor cell-stimulated platelet activation are reduced in platelets isolated from PI3Kβ mutant mice. RNAseq and proteomic analysis of human breast epithelial cells co-cultured with platelets revealed that platelet PI3Kβ regulates the expression of EMT and metastasis-associated genes in these cells. The EMT and metastasis-associated proteins PAI-1 and IL-8 were specifically downregulated in co-cultures with PI3Kβ mutant platelets. PI3Kβ mutant platelets are impaired in their ability to stimulate YAP and Smad2 signaling in tumor cells, two pathways regulating PAI-1 expression. Finally, we show that mice expressing mutant PI3Kβ show reduced spontaneous metastasis, and platelets isolated from these mice are less able to stimulate experimental metastasis in WT mice. Taken together, these data support a role for platelet PI3Kβ in promoting breast cancer metastasis and highlight platelet PI3Kβ as a potential therapeutic target.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"190 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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