Aim:Resistance to fluoropyrimidine drugs(FPs)is a major cause of mortality in colorectal cancer(CRC).We assessed the potency advantage of the polymeric FP F10 relative to 5-fluorouracil(5-FU)in four human CRC cell lin...Aim:Resistance to fluoropyrimidine drugs(FPs)is a major cause of mortality in colorectal cancer(CRC).We assessed the potency advantage of the polymeric FP F10 relative to 5-fluorouracil(5-FU)in four human CRC cell lines that differ only in TP53 mutational status to determine how p53 mutations affect drug response and whether F10 is likely to improve outcomes.Methods:HCT-116 human CRC cells(p53^(+/+))and three isogenic variants(p53^(-/-),R248W/+,R248W/-)were assessed for drug response.Resistance factors were derived from cell viability data and used to establish the relative potency advantage for F10.Rescue studies with exogenous uridine/thymidine determined if cytotoxicity resulted from DNA-directed processes.Results:Significant resistance to 5-FU resulted from p53-loss or from gain-of-function(GOF)mutation(R248W)and was greatest when GOF mutation was coupled with loss of wild-type p53.F10 is much more potent than 5-FU(137-314-fold depending on TP53 mutational status).F10 and 5-FU induce apoptosis by DNA-and RNA-directed mechanisms,respectively,and only F10 shows a modest enhancement in cytotoxicity upon co-treatment with leucovorin.Conclusion:TP53 mutational status affects inherent sensitivity to FPs,with p53 GOF mutations most deleterious.F10 is much more effective than 5-FU regardless of TP53 mutations and has potential to be effective to CRC that is resistant to 5-FU due,in part,to TP53 mutations.展开更多
In gene expression profiling studies,including single-cell RNA sequencing(scRNA-seq)analyses,the identification and characterization of co-expressed genes provides critical information on cell identity and function.Ge...In gene expression profiling studies,including single-cell RNA sequencing(scRNA-seq)analyses,the identification and characterization of co-expressed genes provides critical information on cell identity and function.Gene co-expression clustering in scRNA-seq data presents certain challenges.We show that commonly used methods for single-cell data are not capable of identifying co-expressed genes accurately,and produce results that substantially limit biological expectations of co-expressed genes.Herein,we present single-cell Latent-variable Model(scLM),a gene coclustering algorithm tailored to single-cell data that performs well at detecting gene clusters with significant biologic context.Importantly,scLM can simultaneously cluster multiple single-cell datasets,i.e.,consensus clustering,enabling users to leverage single-cell data from multiple sources for novel comparative analysis.scLM takes raw count data as input and preserves biological variation without being influenced by batch effects from multiple datasets.Results from both simulation data and experimental data demonstrate that scLM outperforms the existing methods with considerably improved accuracy.To illustrate the biological insights of scLM,we apply it to our in-house and public experimental scRNA-seq datasets.scLM identifies novel functional gene modules and refines cell states,which facilitates mechanism discovery and understanding of complex biosystems such as cancers.A user-friendly R package with all the key features of the scLM method is available at https://github.com/QSong-github/scLM.展开更多
Topoisomerases are well-validated targets for cancer chemotherapy and DNA topoisomerase 1(Top1)is the sole target of the camptothecin(CPT)class of anticancer drugs.Over the last 20 years,multiple studies have shown To...Topoisomerases are well-validated targets for cancer chemotherapy and DNA topoisomerase 1(Top1)is the sole target of the camptothecin(CPT)class of anticancer drugs.Over the last 20 years,multiple studies have shown Top1 activity is modulated by non-native DNA structures and this can lead to trapping of Top1 cleavage complexes(Top1cc)and conversion to DNA double strand breaks.Among the perturbations to DNA structure that generate Top1cc are nucleoside analogs that are incorporated into genomic DNA during replication including cytarabine,gemcitabine,and 5-fluoro-2’-deoxyuridine(FdU).We review the literature summarizing the role of Top1cc in mediating the DNA damaging and cytotoxic activities of nucleoside analogs.We also summarize studies demonstrating distinct differences between Top1cc induced by nucleoside analogs and CPTs,particularly with regard to DNA repair.Collectively,these studies demonstrate that,while Top1 is a common target for both Top1 poisons such as CPT and nucleoside analogs such as FdU,these agents are not redundant.In recent years,studies have shown that Top1 poisons and nucleoside analogs together with other anti-cancer drugs such as cisplatin cause replication stress and the DNA repair pathways that modulate the cytotoxic activities of these compounds are being elucidated.We present an overview of this evolving literature,which has implications for how targeting of Top1 with nucleoside analogs can be used more effectively for cancer treatment.展开更多
Aggressive malignancies are characterized by relatively uncontrolled cell proliferation making them especially reliant on topoisomerase enzymes to enable high rates of DNA replication and transcription.DNA topoisomera...Aggressive malignancies are characterized by relatively uncontrolled cell proliferation making them especially reliant on topoisomerase enzymes to enable high rates of DNA replication and transcription.DNA topoisomerases resolve topological problems associated with DNA replication and other essential cellular processes involving DNA,such as transcription and recombination^([1]).As such,they are important targets for anti-cancer therapeutics.Further,understanding of topoisomerase biology is important for unraveling the mechanistic basis for resistance to many widely used anti-cancer drugs,such as doxorubicin,etoposide,and topotecan,for which DNA topoisomerases are established targets.Interestingly,several drugs that are not considered to directly target topoisomerase enzymes,such as the nucleoside analogs 5-FU and AraC,and those in development such as the polymeric fluoropyrimidine CF10^([2]),also affect the function of topoisomerases.展开更多
基金Studies were supported by the Comprehensive Cancer Center at Wake Forest University,Wake Innovations,North Carolina Biotechnology Center(Gmeiner W).Research reported in this publication was supported by the National Cancer Institute’s Cancer Center Support Grant award number P30CA012197 issued to the Wake Forest Baptist Comprehensive Cancer CenterAlso,Gmeiner W is supported by a NIH grant NIH-NCI R21 CA218933.
文摘Aim:Resistance to fluoropyrimidine drugs(FPs)is a major cause of mortality in colorectal cancer(CRC).We assessed the potency advantage of the polymeric FP F10 relative to 5-fluorouracil(5-FU)in four human CRC cell lines that differ only in TP53 mutational status to determine how p53 mutations affect drug response and whether F10 is likely to improve outcomes.Methods:HCT-116 human CRC cells(p53^(+/+))and three isogenic variants(p53^(-/-),R248W/+,R248W/-)were assessed for drug response.Resistance factors were derived from cell viability data and used to establish the relative potency advantage for F10.Rescue studies with exogenous uridine/thymidine determined if cytotoxicity resulted from DNA-directed processes.Results:Significant resistance to 5-FU resulted from p53-loss or from gain-of-function(GOF)mutation(R248W)and was greatest when GOF mutation was coupled with loss of wild-type p53.F10 is much more potent than 5-FU(137-314-fold depending on TP53 mutational status).F10 and 5-FU induce apoptosis by DNA-and RNA-directed mechanisms,respectively,and only F10 shows a modest enhancement in cytotoxicity upon co-treatment with leucovorin.Conclusion:TP53 mutational status affects inherent sensitivity to FPs,with p53 GOF mutations most deleterious.F10 is much more effective than 5-FU regardless of TP53 mutations and has potential to be effective to CRC that is resistant to 5-FU due,in part,to TP53 mutations.
基金the Cancer Genomics,Tumor Tissue Repository,and Bioinformatics Shared Resources under the NCI Cancer Center Support Grant to the Comprehensive Cancer Center of Wake Forest University Health Sciences,USA(Grant No.P30CA012197)。
文摘In gene expression profiling studies,including single-cell RNA sequencing(scRNA-seq)analyses,the identification and characterization of co-expressed genes provides critical information on cell identity and function.Gene co-expression clustering in scRNA-seq data presents certain challenges.We show that commonly used methods for single-cell data are not capable of identifying co-expressed genes accurately,and produce results that substantially limit biological expectations of co-expressed genes.Herein,we present single-cell Latent-variable Model(scLM),a gene coclustering algorithm tailored to single-cell data that performs well at detecting gene clusters with significant biologic context.Importantly,scLM can simultaneously cluster multiple single-cell datasets,i.e.,consensus clustering,enabling users to leverage single-cell data from multiple sources for novel comparative analysis.scLM takes raw count data as input and preserves biological variation without being influenced by batch effects from multiple datasets.Results from both simulation data and experimental data demonstrate that scLM outperforms the existing methods with considerably improved accuracy.To illustrate the biological insights of scLM,we apply it to our in-house and public experimental scRNA-seq datasets.scLM identifies novel functional gene modules and refines cell states,which facilitates mechanism discovery and understanding of complex biosystems such as cancers.A user-friendly R package with all the key features of the scLM method is available at https://github.com/QSong-github/scLM.
基金Research reported in this publication was supported by the National Cancer Institute’s Cancer Center Support Grant(P30CA012197)issued to the Wake Forest Baptist Comprehensive Cancer Center.Gmeiner WH is supported by NIH grant(NIH-NCI R21 CA218933).
文摘Topoisomerases are well-validated targets for cancer chemotherapy and DNA topoisomerase 1(Top1)is the sole target of the camptothecin(CPT)class of anticancer drugs.Over the last 20 years,multiple studies have shown Top1 activity is modulated by non-native DNA structures and this can lead to trapping of Top1 cleavage complexes(Top1cc)and conversion to DNA double strand breaks.Among the perturbations to DNA structure that generate Top1cc are nucleoside analogs that are incorporated into genomic DNA during replication including cytarabine,gemcitabine,and 5-fluoro-2’-deoxyuridine(FdU).We review the literature summarizing the role of Top1cc in mediating the DNA damaging and cytotoxic activities of nucleoside analogs.We also summarize studies demonstrating distinct differences between Top1cc induced by nucleoside analogs and CPTs,particularly with regard to DNA repair.Collectively,these studies demonstrate that,while Top1 is a common target for both Top1 poisons such as CPT and nucleoside analogs such as FdU,these agents are not redundant.In recent years,studies have shown that Top1 poisons and nucleoside analogs together with other anti-cancer drugs such as cisplatin cause replication stress and the DNA repair pathways that modulate the cytotoxic activities of these compounds are being elucidated.We present an overview of this evolving literature,which has implications for how targeting of Top1 with nucleoside analogs can be used more effectively for cancer treatment.
基金van Waardenburg RCAM in part funded by American Cancer Society UAB ACS-IRG Junior Faculty Development Grant(ACS-IRG-60-001-53)Department of Defense OCRP pilot award W81XWH-15-1-0198+2 种基金the National Institutes of Health Cancer Center Core Support Grant(P30CA013148)National Institutes of Health-National Institute of Disorders and Stroke(1R21NS116312-01A1)Gmeiner WH in part supported by the National Cancer Institute Cancer Center Support Grant(P30CA012197)issued to the Wake Forest Baptist Comprehensive Cancer Center and National Institutes of Health-National Cancer Institute R21 CA218933.
文摘Aggressive malignancies are characterized by relatively uncontrolled cell proliferation making them especially reliant on topoisomerase enzymes to enable high rates of DNA replication and transcription.DNA topoisomerases resolve topological problems associated with DNA replication and other essential cellular processes involving DNA,such as transcription and recombination^([1]).As such,they are important targets for anti-cancer therapeutics.Further,understanding of topoisomerase biology is important for unraveling the mechanistic basis for resistance to many widely used anti-cancer drugs,such as doxorubicin,etoposide,and topotecan,for which DNA topoisomerases are established targets.Interestingly,several drugs that are not considered to directly target topoisomerase enzymes,such as the nucleoside analogs 5-FU and AraC,and those in development such as the polymeric fluoropyrimidine CF10^([2]),also affect the function of topoisomerases.