Gene Expression Profiles and Molecular Markers To Predict Recurrence of Dukes' B Colon Cancer

Wang, Yixin; Jatkoe, Tim; Zhang, Yi; Mutch, Matthew G.; Talantov, Dmitri; Jiang, Jian-Tang; McLeod, Howard L.; Atkins, David

doi:10.1200/jco.2004.08.186

Cited by 394 publications

(302 citation statements)

References 47 publications

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“…This would arguably eliminate two of our samples from analysis, which we were able to enrich to 490% purity. However, Wang et al (2004), who derived an expression profile predicting recurrence of Duke's B colorectal carcinoma, included only samples that were enriched to over 85% purity. We believe that in CRC samples, the stroma will contaminate the sample causing problems with patient classification, but that can be overcome with parenchymal purification.…”

Section: Discussionmentioning

confidence: 99%

Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification

et al. 2009

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Tumour stroma gene expression in biopsy specimens may obscure the expression of tumour parenchyma, hampering the predictive power of microarrays. We aimed to assess the utility of fluorescence-activated cell sorting (FACS) for generating cell populations for gene expression analysis and to compare the gene expression of FACS-purified tumour parenchyma to that of whole tumour biopsies. Single cell suspensions were generated from colorectal tumour biopsies and tumour parenchyma was separated using FACS. Fluorescence-activated cell sorting allowed reliable estimation and purification of cell populations, generating parenchymal purity above 90%. RNA from FACS-purified and corresponding whole tumour biopsies was hybridised to Affymetrix oligonucleotide microarrays. Whole tumour and parenchymal samples demonstrated differential gene expression, with 289 genes significantly overexpressed in the whole tumour, many of which were consistent with stromal gene expression (e.g., COL6A3, COL1A2, POSTN, TIMP2 ). Genes characteristic of colorectal carcinoma were overexpressed in the FACS-purified cells (e.g., HOX2D and RHOB ). We found FACS to be a robust method for generating samples for gene expression analysis, allowing simultaneous assessment of parenchymal and stromal compartments. Gross stromal contamination may affect the interpretation of cancer gene expression microarray experiments, with implications for hypotheses generation and the stability of expression signatures used for predicting clinical outcomes.

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Section: Discussionmentioning

confidence: 99%

Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification

et al. 2009

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“…Molecular testing to quantify mRNA expression of the BCR-ABL1 fusion gene in CML is an example of using molecular diagnostics to monitor response to therapy, monitor minimal residual disease (surveillance) and in some cases indicate specific changes in therapy 37 . 40,41 .…”

Section: Prognostic Molecular Diagnostics In Oncologymentioning

confidence: 99%

The Spectrum of Clinical Utilities in Molecular Pathology Testing Procedures for Inherited Conditions and Cancer

Joseph

Cankovic

Caughron³

et al. 2016

The Journal of Molecular Diagnostics

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“…Microarray gene expression analysis provides a fresh insight into the genetic basis of cancer initiation and progression (Luo et al, 2001;Hoek et al, 2004;Talantov et al, 2005) and -E-mail: gomez.luis@inia.es identification of genes that may be of prognostic value (Wang et al, 2004;Barrier et al, 2005) as well as genes that may be associated with aggressive tumor behavior (Bittner et al, 2000). In addition, microarray gene expression profiling has shown promise in evaluating the sensitivity of tumors to chemotherapy or other targeted approaches to therapy (Huang and Sadee, 2003;Mariadason et al, 2003;Alaoui-Jamali et al, 2004;Clarke et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Gene expression in Sinclair swine with malignant melanoma

Okomo-Adhiambo

Rink

Rauw

et al. 2012

Animal

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Sinclair swine develop an aggressive form of melanoma, which, in many cases, spontaneously regresses after a complete metastatic phase. We used Affymetrix GeneChip R Porcine Genome Arrays consisting of 24 123 probe sets to compare gene expression in white blood cells (WBCs) and various tissues including the liver, lungs, inguinal lymph nodes and spleen harvested from a Sinclair piglet afflicted by melanoma at birth and exhibiting metastatic lesions at weaning (6 weeks) with those from a full-sibling piglet that showed no incidence of melanoma at birth and weaning. The highest number (3489; ,14%) of significantly upregulated transcripts (fold change in gene expression >2.0 and t-test P-value r0.05) was observed in the liver, while the spleen exhibited the lowest number of upregulated transcripts (528; ,2%). Among significantly downregulated genes, the highest numbers were observed in the inguinal lymph nodes (3651; ,15%) and the least in WBCs (730; ,3%). Differentially expressed transcripts included genes involved in melanoma pathogenesis including SILV, TYR and RAB28. SILV was over-expressed 784-, 430-and 164-fold, while TYR was over-expressed 138-, 81-and 28-fold in the liver, lungs and inguinal lymph nodes, respectively. Quantitative real-time RT-PCR (qRT-PCR) confirmed the microarray data of 12 selected differentially expressed sequences. These results suggest that significant changes in gene expression occur during metastasis of malignant melanoma in the Sinclair swine model. In addition, qRT-PCR analysis of the above 12 differentially expressed sequences was carried out on liver samples collected from 22 pigs (12 of which had melanoma during the first 6 weeks of life), and an ANOVA test contrasting absolute RNA expression between pigs with regressing, progressing and without tumors was significant for TYR, TACSTD1, MATP, GPNMB and CYP4A22, with P-values of 0.034, 0.015, 0.007, 0.050 and 0.022, respectively.

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Gene Expression Profiles and Molecular Markers To Predict Recurrence of Dukes' B Colon Cancer

Cited by 394 publications

References 47 publications

Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification

Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification

The Spectrum of Clinical Utilities in Molecular Pathology Testing Procedures for Inherited Conditions and Cancer

Gene expression in Sinclair swine with malignant melanoma

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