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Integrative analysis from multi-centre studies identifies a function-derived personalized multi-gene signature of outcome in colorectal cancer.

ABSTRACT: Colorectal cancer (CRC) is highly heterogeneous leading to variable prognosis and treatment responses. Therefore, it is necessary to explore novel personalized and reproducible prognostic signatures to aid clinical decision-making. The present study combined large-scale gene expression profiles and clinical data of 1828 patients with CRC from multi-centre studies and identified a personalized gene prognostic signature consisting of 46 unique genes (called function-derived personalized gene signature [FunPGS]) from an integrated statistics and function-derived perspective. In the meta-training and multiple independent validation cohorts, the FunPGS effectively discriminated patients with CRC with significantly different prognosis at the individual level and remained as an independent factor upon adjusting for clinical covariates in multivariate analysis. Furthermore, the FunPGS demonstrated superior performance for risk stratification with respect to other recently reported signatures and clinical factors. The complementary value of the molecular signature and clinical factors was further explored, and it was observed that the composite signature called IMCPS greatly improved the predictive performance of survival estimation relative to molecular signatures or clinical factors alone. With further prospective validation in clinical trials, the FunPGS may become a promising and powerful personalized prognostic tool for stratifying patients with CRC in order to achieve an optimal systemic therapy.

SUBMITTER: Sun J

PROVIDER: S-EPMC6653159 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Integrative analysis from multi-centre studies identifies a function-derived personalized multi-gene signature of outcome in colorectal cancer.

Sun Jie J Zhao Hengqiang H Lin Shuting S Bao Siqi S Zhang Yan Y Su Jianzhong J Zhou Meng M

Journal of cellular and molecular medicine 20190529 8

Colorectal cancer (CRC) is highly heterogeneous leading to variable prognosis and treatment responses. Therefore, it is necessary to explore novel personalized and reproducible prognostic signatures to aid clinical decision-making. The present study combined large-scale gene expression profiles and clinical data of 1828 patients with CRC from multi-centre studies and identified a personalized gene prognostic signature consisting of 46 unique genes (called function-derived personalized gene signa ...[more]

PMID: 31140730

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Project description:BackgroundLong non-coding RNAs (lncRNAs) have recently emerged as essential biomarkers of cancer progression. However, studies are limited regarding lncRNAs correlated with recurrence and fluorouracil-based adjuvant chemotherapy (ACT) in stage II/III colorectal cancer (CRC).Methods1640 stage II/III CRC patients were enrolled from 15 independent datasets and a clinical in-house cohort. 10 prevalent machine learning algorithms were collected and then combined into 76 combinations. 109 published transcriptome signatures were also retrieved. qRT-PCR assay was performed to verify our model.FindingsWe comprehensively identified 27 stably recurrence-related lncRNAs from multi-center cohorts. According to these lncRNAs, a consensus machine learning-derived lncRNA signature (CMDLncS) that exhibited best power for predicting recurrence risk was determined from 76 kinds of algorithm combinations. A high CMDLncS indicated unfavorable recurrence and mortality rates. CMDLncS not only could work independently of common clinical traits (e.g., AJCC stage) and molecular features (e.g., microsatellite state, KRAS mutation), but also presented dramatically better performance than these variables. qRT-PCR results from 173 patients further verified our in-silico findings and assessed its feasible in different centers. Comparisons of CMDLncS with 109 published transcriptome signatures further demonstrated its predictive superiority. Additionally, patients with high CMDLncS benefited more from fluorouracil-based ACT and were characterized by activation of stromal and epithelial-mesenchymal transition, while patients with low CMDLncS suggested the sensitivity to bevacizumab and displayed enhanced immune activation.InterpretationCMDLncS provides an attractive platform for identifying patient at high risk of recurrence and could optimize precision treatment to improve the clinical outcomes in stage II/III CRC.FundingThis study was supported by the National Natural Science Foundation of China (81,972,663); Henan Province Young and Middle-Aged Health Science and Technology Innovation Talent Project (YXKC2020037); and Henan Provincial Health Commission Joint Youth Project (SB201902014).

Project description:BackgroundDespite the extensive research approaches applied to characterise malignant melanoma, no specific molecular markers are available that are clearly related to the progression of this disease. In this study, our aims were to define a gene expression signature associated with the clinical outcome of melanoma patients and to provide an integrative interpretation of the gene expression -, copy number alterations -, and promoter methylation patterns that contribute to clinically relevant molecular functional alterations.MethodsGene expression profiles were determined using the Affymetrix U133 Plus2.0 array. The NimbleGen Human CGH Whole-Genome Tiling array was used to define CNAs, and the Illumina GoldenGate Methylation platform was applied to characterise the methylation patterns of overlapping genes.ResultsWE IDENTIFIED TWO SUBCLASSES OF PRIMARY MELANOMA: one representing patients with better prognoses and the other being characteristic of patients with unfavourable outcomes. We assigned 1,080 genes as being significantly correlated with ulceration, 987 genes were downregulated and significantly enriched in the p53, Nf-kappaB, and WNT/beta-catenin pathways. Through integrated genome analysis, we defined 150 downregulated genes whose expression correlated with copy number losses in ulcerated samples. These genes were significantly enriched on chromosome 6q and 10q, which contained a total of 36 genes. Ten of these genes were downregulated and involved in cell-cell and cell-matrix adhesion or apoptosis. The expression and methylation patterns of additional genes exhibited an inverse correlation, suggesting that transcriptional silencing of these genes is driven by epigenetic events.ConclusionUsing an integrative genomic approach, we were able to identify functionally relevant molecular hotspots characterised by copy number losses and promoter hypermethylation in distinct molecular subtypes of melanoma that contribute to specific transcriptomic silencing and might indicate a poor clinical outcome of melanoma.

Project description:Background and objectivesPatients with membranous nephropathy can have circulating autoantibodies against membrane-bound (phospholipase A2 receptor 1 [PLA2R1] and thrombospondin type-1 domain containing 7A [THSD7A]) and intracellular (aldose reductase, SOD2, and α-enolase) podocyte autoantigens. We studied their combined association with clinical outcomes.Design, setting, participants, & measurementsSerum levels of anti-PLA2R1, anti-THSD7A, anti-aldose reductase, anti-SOD2, and anti-α-enolase autoantibodies were determined in 285 patients at diagnosis and during follow-up using standardized and homemade assays. An eGFR>60 ml/min per 1.73 m2 and remission of proteinuria (<0.3/<3.5 g per d) after 12 months were the outcomes of interest.ResultsAt diagnosis, 182 (64%), eight (3%), and 95 (33%) patients were anti-PLA2R1+, anti-THSD7A+, and double negative, respectively. The prevalence of a detectable antibody to at least one intracellular antigen was similarly distributed in patients who were anti-PLA2R1+ (n=118, 65%) and double negative (n=64, 67%). Positivity for anti-PLA2R1, anti-SOD2, and anti-α-enolase antibodies and higher titers at diagnosis were associated with poor clinical outcome independently to each other. Combined positivity for anti-PLA2R1, anti-SOD2, and anti-α-enolase was associated with highest risk of poor outcome (odds ratio, 5.5; 95% confidence interval, 1.2 to 24; P=0.01). In Kaplan-Meier analysis, patients who were anti-PLA2R1+/anti-SOD2+ or anti-PLA2R1+/anti-α-enolase+ had lower eGFR at 12 months compared with patients who were anti-PLA2R1+/anti-SOD2- or anti-α-enolase-. Predictive tests (net reclassification index and area under the curve-receiver-operating characteristic analysis) showed that combined assessment of antibodies improved classification of outcome in 22%-34% of cases for partial remission of proteinuria and maintenance of normal eGFR. For patients with nephrotic syndrome at diagnosis, anti-SOD2 positivity and high anti-PLA2R1 titer were associated with a lack of complete remission. Patients who were anti-PLA2R1-/anti-intracellular antigens- had the lowest proteinuria and the highest eGFR at diagnosis and the lowest risk of lower eGFR at 12 months. Epitope spreading was present in 81% of patients who were anti-PLA2R1+ and was associated with increased positivity for intracellular antigens and poor eGFR at diagnosis and 12 months.ConclusionsCombined serological analysis of autoantibodies targeting membrane-bound and intracellular autoantigens identifies patients with poor clinical outcomes.

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Integrative analysis from multi-centre studies identifies a function-derived personalized multi-gene signature of outcome in colorectal cancer.

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Integrative analysis from multi-centre studies identifies a function-derived personalized multi-gene signature of outcome in colorectal cancer.

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