scholarly journals Gene networks and expression quantitative trait loci associated with adjuvant chemotherapy response in high-grade serous ovarian cancer

BMC Cancer ◽  
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jihoon Choi ◽  
Danai G. Topouza ◽  
Anastasiya Tarnouskaya ◽  
Sean Nesdoly ◽  
Madhuri Koti ◽  
...  
2020 ◽  
Author(s):  
Jihoon Choi ◽  
Anastasiya Tarnouskaya ◽  
Sean Nesdoly ◽  
Danai G. Topouza ◽  
Madhuri Koti ◽  
...  

Abstract Background A major impediment in the treatment of ovarian cancer is the relapse of platinum-resistant tumors, which occurs in approximately 25% of patients. A better understanding of the biological mechanisms underlying platinum-based response will improve treatment efficacy through genetic testing and novel therapies.Methods Using data from high-grade serous ovarian carcinoma (HGSOC) patients in the Cancer Genome Atlas (TCGA), we classified those who remained progression-free for 12 months following platinum-based chemotherapy as “chemo-sensitive” (N=160) and those who had recurrence within six months as “chemo-resistant” (N=110). Univariate and multivariate analysis of expression microarrays identified differentially expressed genes and co-expression gene networks associated with chemotherapy response. Moreover, we integrated genomics data to determine expression quantitative trait loci (eQTL).Results Differential expression of the Valosin-containing protein (VCP) gene and five co-expression gene networks were associated with chemotherapy response in HGSOC. VCP and the gene networks contribute to protein processing in the endoplasmic reticulum, which has been implicated in chemotherapy response. These findings were successfully replicated using independent replication cohort. Furthermore, 192 QTLs were associated with these gene networks and BRCA2 expression.Conclusion This study implicates both known and novel genes as well as biological networks underlying response to platinum-based chemotherapy among HGSOC patients.


2019 ◽  
Author(s):  
Jihoon Choi ◽  
Anastasiya Tarnouskaya ◽  
Sean Nesdoly ◽  
Danai G. Topouza ◽  
Madhuri Koti ◽  
...  

AbstractBackgroundA major impediment in the treatment of ovarian cancer is the relapse of platinum-resistant tumors, which occurs in approximately 25% of patients. A better understanding of the biological mechanisms underlying platinum-based response will improve treatment efficacy through genetic testing and novel therapies.MethodsUsing data from high-grade serous ovarian carcinoma (HGSOC) patients in the Cancer Genome Atlas (TCGA), we classified those who remained progression-free for 12 months following platinum-based chemotherapy as “chemo-sensitive” (N=160) and those who had recurrence within six months as “chemo-resistant” (N=110). Univariate and multivariate analysis of expression microarrays identified differentially expressed genes and co-expression gene networks associated with chemotherapy response. Moreover, we integrated genomics data to determine expression quantitative trait loci (eQTL).ResultsDifferential expression of the Valosin-containing protein (VCP) gene and five co-expression gene networks were associated with chemotherapy response in HGSOC. VCP and the gene networks contribute to protein processing in the endoplasmic reticulum, which has been implicated in chemotherapy response. These findings were successfully replicated using independent replication cohort. Furthermore, 192 QTLs were associated with these gene networks and BRCA2 expression.ConclusionThis study implicates both known and novel genes as well as biological networks underlying response to platinum-based chemotherapy among HGSOC patients.


2020 ◽  
Author(s):  
Jihoon Choi ◽  
Danai G. Topouza ◽  
Anastasiya Tarnouskaya ◽  
Sean Nesdoly ◽  
Madhuri Koti ◽  
...  

Abstract Background A major impediment in the treatment of ovarian cancer is the relapse of platinum-resistant tumors, which occurs in approximately 25% of patients. A better understanding of the biological mechanisms underlying platinum-based chemotherapy response will improve treatment efficacy through genetic testing and novel therapies. Methods Using data from high-grade serous ovarian carcinoma (HGSOC) patients in the Cancer Genome Atlas (TCGA), we classified those who remained progression-free for 12 months following platinum-based chemotherapy as “chemo-sensitive” (N=160) and those who had recurrence within six months as “chemo-resistant” (N=110). Univariate and multivariate analysis of expression microarrays identified a differentially expressed gene and co-expression gene networks associated with chemotherapy response. Moreover, we integrated genomics data to determine expression quantitative trait loci (eQTL). Results Differential expression of the Valosin-containing protein ( VCP ) gene and five co-expression gene networks were significantly associated with chemotherapy response in HGSOC. VCP and the most significant co-expression network module contribute to protein processing in the endoplasmic reticulum, which has been implicated in chemotherapy response. Both univariate and multivariate findings were successfully replicated in an independent ovarian cancer cohort. Furthermore, we identified 192 cis-eQTLs associated with the expression of genes in the co-expression networks and 4 cis-eQTLs associated with BRCA2 expression. Conclusion This study implicates both known and novel genes as well as biological processes underlying response to platinum-based chemotherapy among HGSOC patients.


2017 ◽  
Vol 136 (11-12) ◽  
pp. 1477-1487 ◽  
Author(s):  
Elena Grassi ◽  
Elisa Mariella ◽  
Mattia Forneris ◽  
Federico Marotta ◽  
Marika Catapano ◽  
...  

2007 ◽  
Vol 36 (suppl) ◽  
pp. 211-218 ◽  
Author(s):  
Guilherme Jordão de Magalhães Rosa

Genética genômica é um termo utilizado para representar o estudo de processos genéticos controladores de caracteres fenotípicos de herança complexa, a partir da análise conjunta de informação relativa a fenótipos, estruturas de parentesco, marcadores moleculares e expressão gênica. Estudos de genética genômica são utilizados, por exemplo, para a estimação da herdabilidade de níveis de transcrição, para o mapeamento de locos controladores da expressao gênica (eQTL, do inglês expression Quantitative Trait Loci), e para o estudo de redes regulatórias. Genética genômica geralmente envolve experimentos com microarrays, os quais são ainda bastante caros e trabalhosos, limitando o tamanho amostral e conseqüentemente o poder estatístico de tais estudos. Desta maneira, é essencial que tais experimentos sejam otimizados do ponto de vista do delineamento, a partir de criteriosa escolha das amostras (indivíduos) a serem utilizadas, e do controle rigoroso dos vários fatores que podem afetar as variáveis-resposta de interesse. Outro ponto fundamental na condução de tais experimentos refere-se à marcação das amostras de mRNA com os fluoróforos e ao pareamento das mesmas em cada lâmina de microarray, os quais devem ser cuidadosamente planejados para que não haja confundimento entre estes efeitos e os fatores biológicos de interesse. Nesta apresentação serão discutidas algumas estratégias para o planejamento de estudos de genética genômica, incluindo a seleção de indivíduos objetivando-se a maximização da dissimilaridade genética ou do número de eventos de recombinação, bem como a condução eficiente dos ensaios com microarrays para diferentes objetivos experimentais.


2005 ◽  
Vol 5 (4) ◽  
pp. 254-259 ◽  
Author(s):  
Pawan Kulwal ◽  
Neeraj Kumar ◽  
Ajay Kumar ◽  
Raj Kumar Gupta ◽  
Harindra Singh Balyan ◽  
...  

2012 ◽  
Vol 2 (2) ◽  
pp. 213-221 ◽  
Author(s):  
Daniel Bottomly ◽  
Martin T. Ferris ◽  
Lauri D. Aicher ◽  
Elizabeth Rosenzweig ◽  
Alan Whitmore ◽  
...  

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