Alternative splicing of pre-mRNA transcripts is an important regulatory mechanism that increases the diversity of gene products in eukaryotes.Various studies have linked specific transcript isoforms to altered drug re...Alternative splicing of pre-mRNA transcripts is an important regulatory mechanism that increases the diversity of gene products in eukaryotes.Various studies have linked specific transcript isoforms to altered drug response in cancer;however,few algorithms have incorporated splicing information into drug response prediction.In this study,we evaluated whether basal-level splicing information could be used to predict drug sensitivity by constructing doxorubicin-sensitivity classification models with splicing and expression data.We detailed splicing differences between sensitive and resistant cell lines by implementing quasi-binomial generalized linear modeling(QBGLM)and found altered inclusion of 277 skipped exons.We additionally conducted RNA-binding protein(RBP)binding motif enrichment and differential ex-pression analysis to characterize cis-and trans-acting elements that potentially influence doxorubicin response-mediating splicing alterations.Our results showed that a classification model built with skipped exon data exhibited strong predictive power.We discovered an association between differentially spliced events and epithelial-mesenchymal transition(EMT)and observed motif enrichment,as well as differential expression of RBFOX and ELAVL RBP family members.Our work demonstrates the potential of incorporating splicing data into drug response algorithms and the utility of a QBGLM approach for fast,scalable identification of relevant splicing differences between large groups of samples.展开更多
Acid–base homeostasis is a fundamental property of living cells,and its persistent disruption in human cells can lead to a wide range of diseases.In this study,we conducted a computational modeling analysis of transc...Acid–base homeostasis is a fundamental property of living cells,and its persistent disruption in human cells can lead to a wide range of diseases.In this study,we conducted a computational modeling analysis of transcriptomic data of 4750 human tissue samples of 9 cancer types in The Cancer Genome Atlas(TCGA)database.Built on our previous study,we quantitatively estimated the average production rate of OHby cytosolic Fenton reactions,which continuously disrupt the intracellular pH(pHi)homeostasis.Our predictions indicate that all or at least a subset of 43 reprogrammed metabolisms(RMs)are induced to produce net protons(H+)at comparable rates of Fenton reactions to keep the pHi stable.We then discovered that a number of wellknown phenotypes of cancers,including increased growth rate,metastasis rate,and local immune cell composition,can be naturally explained in terms of the Fenton reaction level and the induced RMs.This study strongly suggests the possibility to have a unified framework for studies of cancerinducing stressors,adaptive metabolic reprogramming,and cancerous behaviors.In addition,strong evidence is provided to demonstrate that a popular view that Na+/H+exchangers along with lactic acid exporters and carbonic anhydrases are responsible for the intracellular alkalization and extracellular acidification in cancer may not be justified.展开更多
Purpose:This study aimed to examine the effect of radiation esophagitis(RE)and the dynamics of RE on subse-quent survival in non-small cell lung cancer(NSCLC)patients who underwent radiotherapy.Experimental Design:Pat...Purpose:This study aimed to examine the effect of radiation esophagitis(RE)and the dynamics of RE on subse-quent survival in non-small cell lung cancer(NSCLC)patients who underwent radiotherapy.Experimental Design:Patients with NSCLC treated with fractionated thoracic radiotherapy enrolled in prospective trials were eligible.RE was graded prospectively according to Common Terminology Criteria for Adverse Events(CTCAE)v3.0 per protocol requirement weekly during-RT and 1 month after RT.This study applied conditional survival assessment which has advantage over traditional survival analysis as it assesses the survival from the event instead of from the baseline.P-value less than 0.05 was considered to be significant.The primary endpoint is overall survival.Results:A total of 177 patients were eligible,with a median follow-up of 5 years.The presence of RE,the maximum RE grade,the evolution of RE and the onset timing of RE events were all correlated with subsequent survival.At all conditional time points,patients first presented with RE grade1(initial RE1)had significant inferior subsequent survival(multivariable HRs median:1.63,all P-values<0.05);meanwhile those with RE progressed had significant inferior subsequent survival than those never develop RE(multivariable HRs median:2.08,all P-values<0.05).Multivariable Cox proportional-hazards analysis showed significantly higher C-indexes for models with inclusion of RE events than those without(all P-values<0.05).Conclusion:This study comprehensively evaluated the impact of RE with conditional survival assessment and demonstrated that RE is associated with inferior survival in NSCLC patients treated with RT.展开更多
基金supported by the National Institutes of Health,USA(Grant No.R01CA213466)awarded to YL.the Precision Health Initiative at Indiana University.
文摘Alternative splicing of pre-mRNA transcripts is an important regulatory mechanism that increases the diversity of gene products in eukaryotes.Various studies have linked specific transcript isoforms to altered drug response in cancer;however,few algorithms have incorporated splicing information into drug response prediction.In this study,we evaluated whether basal-level splicing information could be used to predict drug sensitivity by constructing doxorubicin-sensitivity classification models with splicing and expression data.We detailed splicing differences between sensitive and resistant cell lines by implementing quasi-binomial generalized linear modeling(QBGLM)and found altered inclusion of 277 skipped exons.We additionally conducted RNA-binding protein(RBP)binding motif enrichment and differential ex-pression analysis to characterize cis-and trans-acting elements that potentially influence doxorubicin response-mediating splicing alterations.Our results showed that a classification model built with skipped exon data exhibited strong predictive power.We discovered an association between differentially spliced events and epithelial-mesenchymal transition(EMT)and observed motif enrichment,as well as differential expression of RBFOX and ELAVL RBP family members.Our work demonstrates the potential of incorporating splicing data into drug response algorithms and the utility of a QBGLM approach for fast,scalable identification of relevant splicing differences between large groups of samples.
基金supported by the National Science Foundation of USA(Grant No.2047631)and partially by Georgia Research Alliance,USA。
文摘Acid–base homeostasis is a fundamental property of living cells,and its persistent disruption in human cells can lead to a wide range of diseases.In this study,we conducted a computational modeling analysis of transcriptomic data of 4750 human tissue samples of 9 cancer types in The Cancer Genome Atlas(TCGA)database.Built on our previous study,we quantitatively estimated the average production rate of OHby cytosolic Fenton reactions,which continuously disrupt the intracellular pH(pHi)homeostasis.Our predictions indicate that all or at least a subset of 43 reprogrammed metabolisms(RMs)are induced to produce net protons(H+)at comparable rates of Fenton reactions to keep the pHi stable.We then discovered that a number of wellknown phenotypes of cancers,including increased growth rate,metastasis rate,and local immune cell composition,can be naturally explained in terms of the Fenton reaction level and the induced RMs.This study strongly suggests the possibility to have a unified framework for studies of cancerinducing stressors,adaptive metabolic reprogramming,and cancerous behaviors.In addition,strong evidence is provided to demonstrate that a popular view that Na+/H+exchangers along with lactic acid exporters and carbonic anhydrases are responsible for the intracellular alkalization and extracellular acidification in cancer may not be justified.
基金supported by Shenzhen Fundamental Research Program(JCYJ2020109150427184)Shenzhen Science and Technology Program(KQTD20180411185028798)Shenzhen Fun-damental Research Program(JCYJ20180508153249223).
文摘Purpose:This study aimed to examine the effect of radiation esophagitis(RE)and the dynamics of RE on subse-quent survival in non-small cell lung cancer(NSCLC)patients who underwent radiotherapy.Experimental Design:Patients with NSCLC treated with fractionated thoracic radiotherapy enrolled in prospective trials were eligible.RE was graded prospectively according to Common Terminology Criteria for Adverse Events(CTCAE)v3.0 per protocol requirement weekly during-RT and 1 month after RT.This study applied conditional survival assessment which has advantage over traditional survival analysis as it assesses the survival from the event instead of from the baseline.P-value less than 0.05 was considered to be significant.The primary endpoint is overall survival.Results:A total of 177 patients were eligible,with a median follow-up of 5 years.The presence of RE,the maximum RE grade,the evolution of RE and the onset timing of RE events were all correlated with subsequent survival.At all conditional time points,patients first presented with RE grade1(initial RE1)had significant inferior subsequent survival(multivariable HRs median:1.63,all P-values<0.05);meanwhile those with RE progressed had significant inferior subsequent survival than those never develop RE(multivariable HRs median:2.08,all P-values<0.05).Multivariable Cox proportional-hazards analysis showed significantly higher C-indexes for models with inclusion of RE events than those without(all P-values<0.05).Conclusion:This study comprehensively evaluated the impact of RE with conditional survival assessment and demonstrated that RE is associated with inferior survival in NSCLC patients treated with RT.
