Integrated analysis of diverse cancer types reveals a breast cancer-specific serum miRNA biomarker through relative expression orderings analysis.

PURPOSE: Serum microRNA (miRNA) holds great potential as a non-invasive biomarker for diagnosing breast cancer (BrC). However, most diagnostic models rely on the absolute expression levels of miRNAs, which are susceptible to batch effects and challenging for clinical transformation. Furthermore, current studies on liquid biopsy diagnostic biomarkers for BrC mainly focus on distinguishing BrC patients from healthy controls, needing more specificity assessment. METHODS: We collected a large number of miRNA expression data involving 8465 samples from GEO, including 13 different cancer types and non-cancer controls. Based on the relative expression orderings (REOs) of miRNAs within each sample, we applied the greedy, LASSO multiple linear regression, and random forest algorithms to identify a qualitative biomarker specific to BrC by comparing BrC samples to samples of other cancers as controls. RESULTS: We developed a BrC-specific biomarker called 7-miRPairs, consisting of seven miRNA pairs. It demonstrated comparable classification performance in our analyzed machine learning algorithms while requiring fewer miRNA pairs, accurately distinguishing BrC from 12 other cancer types. The diagnostic performance of 7-miRPairs was favorable in the training set (accuracy = 98.47%, specificity = 98.14%, sensitivity = 99.25%), and similar results were obtained in the test set (accuracy = 97.22%, specificity = 96.87%, sensitivity = 98.02%). KEGG pathway enrichment analysis of the 11 miRNAs within the 7-miRPairs revealed significant enrichment of target mRNAs in pathways associated with BrC. CONCLUSION: Our study provides evidence that utilizing serum miRNA pairs can offer significant advantages for BrC-specific diagnosis in clinical practice by directly comparing serum samples with BrC to other cancer types.

Screening prognostic markers for hepatocellular carcinoma based on pyroptosis-related lncRNA pairs.

BACKGROUND: Pyroptosis is closely related to cancer prognosis. In this study, we tried to construct an individualized prognostic risk model for hepatocellular carcinoma (HCC) based on within-sample relative expression orderings (REOs) of pyroptosis-related lncRNAs (PRlncRNAs). METHODS: RNA-seq data of 343 HCC samples derived from The Cancer Genome Atlas (TCGA) database were analyzed. PRlncRNAs were detected based on differentially expressed lncRNAs between sample groups clustered by 40 reported pyroptosis-related genes (PRGs). Univariate Cox regression was used to screen out prognosis-related PRlncRNA pairs. Then, based on REOs of prognosis-related PRlncRNA pairs, a risk model for HCC was constructed by combining LASSO and stepwise multivariate Cox regression analysis. Finally, a prognosis-related competing endogenous RNA (ceRNA) network was built based on information about lncRNA-miRNA-mRNA interactions derived from the miRNet and TargetScan databases. RESULTS: Hierarchical clustering of HCC patients according to the 40 PRGs identified two groups with a significant survival difference (Kaplan-Meier log-rank, p = 0.026). Between the two groups, 104 differentially expressed lncRNAs were identified (|log2(FC)|> 1 and FDR < 5%). Among them, 83 PRlncRNA pairs showed significant associations between their REOs within HCC samples and overall survival (Univariate Cox regression, p < 0.005). An optimal 11-PRlncRNA-pair prognostic risk model was constructed for HCC. The areas under the curves (AUCs) of time-dependent receiver operating characteristic (ROC) curves of the risk model for 1-, 3-, and 5-year survival were 0.737, 0.705, and 0.797 in the validation set, respectively. Gene Set Enrichment Analysis showed that inflammation-related interleukin signaling pathways were upregulated in the predicted high-risk group (p < 0.05). Tumor immune infiltration analysis revealed a higher abundance of regulatory T cells (Tregs) and M2 macrophages and a lower abundance of CD8 + T cells in the high-risk group, indicating that excessive pyroptosis might occur in high-risk patients. Finally, eleven lncRNA-miRNA-mRNA regulatory axes associated with pyroptosis were established. CONCLUSION: Our risk model allowed us to determine the robustness of the REO-based PRlncRNA prognostic biomarkers in the stratification of HCC patients at high and low risk. The model is also helpful for understanding the molecular mechanisms between pyroptosis and HCC prognosis. High-risk patients may have excessive pyroptosis and thus be less sensitive to immune therapy.

Construct of qualitative diagnostic biomarkers specific for glioma by pairing serum microRNAs.

BACKGROUND: Serum microRNAs (miRNAs) are promising non-invasive biomarkers for diagnosing glioma. However, most reported predictive models are constructed without a large enough sample size, and quantitative expression levels of their constituent serum miRNAs are susceptible to batch effects, decreasing their clinical applicability. METHODS: We propose a general method for detecting qualitative serum predictive biomarkers using a large cohort of miRNA-profiled serum samples (n = 15,460) based on the within-sample relative expression orderings of miRNAs. RESULTS: Two panels of miRNA pairs (miRPairs) were developed. The first was composed of five serum miRPairs (5-miRPairs), reaching 100% diagnostic accuracy in three validation sets for distinguishing glioma and non-cancer controls (n = 436: glioma = 236, non-cancers = 200). An additional validation set without glioma samples (non-cancers = 2611) showed a predictive accuracy of 95.9%. The second panel included 32 serum miRPairs (32-miRPairs), reaching 100% diagnostic performance in training set on specifically discriminating glioma from other cancer types (sensitivity = 100%, specificity = 100%, accuracy = 100%), which was reproducible in five validation datasets (n = 3387: glioma = 236, non-glioma cancers = 3151, sensitivity> 97.9%, specificity> 99.5%, accuracy> 95.7%). In other brain diseases, the 5-miRPairs classified all non-neoplastic samples as non-cancer, including stroke (n = 165), Alzheimer's disease (n = 973), and healthy samples (n = 1820), and all neoplastic samples as cancer, including meningioma (n = 16), and primary central nervous system lymphoma samples (n = 39). The 32-miRPairs predicted 82.2 and 92.3% of the two kinds of neoplastic samples as positive, respectively. Based on the Human miRNA tissue atlas database, the glioma-specific 32-miRPairs were significantly enriched in the spinal cord (p = 0.013) and brain (p = 0.015). CONCLUSIONS: The identified 5-miRPairs and 32-miRPairs provide potential population screening and cancer-specific biomarkers for glioma clinical practice.

A simple way to detect disease-associated cellular molecular alterations from mixed-cell blood samples.

Blood is a promising surrogate for solid tissue to investigate disease-associated molecular biomarkers. However, proportion changes of the constituent cells in the often-used peripheral whole blood (PWB) or peripheral blood mononuclear cell (PBMC) samples may influence the detection of cell-specific alterations under disease states. We propose a simple method, Ref-REO, to detect molecular alterations in leukocytes using the mixed-cell blood samples. The method is based on the predetermined within-sample relative expression orderings (REOs) of genes in purified leukocytes of healthy people. Both the simulated and real mixed-cell blood gene expression profiles were used to evaluate the method. Approximately 99% of the differentially expressed genes (DEGs) detected by Ref-REO in the simulated mixed-cell data are owing to the transcriptional alterations in leukocytes rather than the proportion changes of leukocytes. For the real mixed-cell data, the DEGs detected by Ref-REO in the PBMCs expression data for systemic lupus erythematosus (SLE) patients overlap significantly with the DEGs detected in the expression data of SLE CD4 + T cells and B cells and they are mainly enriched with mRNA editing and interferon-associated genes. The detected DEGs in the PWB data for lung carcinoma patients are significantly enriched with coagulation-associated functional categories that are closely associated with cancer progression. In conclusion, the proposed method is capable of detecting the disease-associated leukocyte-specific molecular alterations, using mixed-cell blood samples, which provides simple, transferable and easy-to-use candidates for disease biomarkers.

Identifying primary site of lung-limited Cancer of unknown primary based on relative gene expression orderings.

BACKGROUND: Precise diagnosis of the tissue origin for metastatic cancer of unknown primary (CUP) is essential for deciding the treatment scheme to improve patients' prognoses, since the treatment for the metastases is the same as their primary counterparts. The purpose of this study is to identify a robust gene signature that can predict the origin for CUPs. METHODS: The within-sample relative gene expression orderings (REOs) of gene pairs within individual samples, which are insensitive to experimental batch effects and data normalizations, were exploited for identifying the prediction signature. RESULTS: Using gene expression profiles of the lung-limited metastatic colorectal cancer (LmCRC), we firstly showed that the within-sample REOs in lung metastases of colorectal cancer (CRC) samples were concordant with the REOs in primary CRC samples rather than with the REOs in primary lung cancer. Based on this phenomenon, we selected five gene pairs with consistent REOs in 498 primary CRC and reversely consistent REOs in 509 lung cancer samples, which were used as a signature for predicting primary sites of metastatic CRC based on the majority voting rule. Applying the signature to 654 primary CRC and 204 primary lung cancer samples collected from multiple datasets, the prediction accuracy reached 99.36%. This signature was also applied to 24 LmCRC samples collected from three datasets produced by different laboratories and the accuracy reached 100%, suggesting that the within-sample REOs in the primary site could reveal the original tissue of metastatic cancers. CONCLUSIONS: The result demonstrated that the signature based on within-sample REOs of five gene pairs could exactly and robustly identify the primary sites of CUPs.

[Age-related DNA methylation changes in peripheral whole blood].

Aging is associated with many complex diseases such as cancer and neurodegenerative diseases. Recently, many age-related DNA methylation biomarkers in peripheral whole blood have been identified. These biomarkers may reflect DNA methylation changes derived from changes in the number of a specific leukocyte cell type during aging. To clarify the source of these age-related DNA methylation changes, we analysed DNA methylation profile of peripheral whole blood from three independent cohorts of healthy subjects and identified age-related DNA methylation CpG sites (arCpGs) using the Spearman's rank test with high reproducibility (Hypergeometric test, P=1.65 × 10⁻¹¹). Using a deconvolution algorithm, we found that the proportion of myeloid lineage cells was increased while that of lymphoid lineage cells was decreased in the peripheral whole blood with age (Spearman's rank correlation test, P<0.05, r ≤ 0.22). The CpG sites, whose methylation levels were significantly different in myeloid cells and lymphoid cells, were preferentially recognized as arCpGs in peripheral whole blood. Moreover, the arCpGs in CD4+ T cells significantly overlapped with that in peripheral whole blood (Hypergeometric test, P=6.14 × 10⁻¹²) and 99.1% of the overlapping arCpGs had consistent positive or negative correlations with age. Though the arCpGs in CD14+ monocytes did not significantly overlap with that in peripheral whole blood (Hypergeometric test, P=0.232), 90.1% of 51 overlapping arCpGs were correlated with age in CD14+ monocytes, peripheral whole blood, and CD4+ T cells consistently. In summary, most of the methylation changes in arCpGs identified in peripheral whole blood come from common or specific DNA methylation changes in leukocyte subtypes, while part of them reflect alterations in the number of specific cell types of leukocytes.

Personalized differential expression analysis in triple-negative breast cancer.

Identification of individual-level differentially expressed genes (DEGs) is a pre-step for the analysis of disease-specific biological mechanisms and precision medicine. Previous algorithms cannot balance accuracy and sufficient statistical power. Herein, RankCompV2, designed for identifying population-level DEGs based on relative expression orderings, was adjusted to identify individual-level DEGs. Furthermore, an optimized version of individual-level RankCompV2, named as RankCompV2.1, was designed based on the assumption that the rank positions of genes and relative rank differences of gene pairs would influence the identification of individual-level DEGs. In comparison to other individualized analysis algorithms, RankCompV2.1 performed better on statistical power, computational efficiency, and acquired coequal accuracy in both simulation and real paired cancer-normal data from ten cancer types. Besides, single sample GSEA and Gene Set Variation Analysis analysis showed that pathways enriched with up-regulated and down-regulated genes presented higher and lower enrichment scores, respectively. Furthermore, we identified 16 genes that were universally deregulated in 966 triple-negative breast cancer (TNBC) samples and interacted with Food and Drug Administration (FDA)-approved drugs or antineoplastic agents, indicating notable therapeutic targets for TNBC. In addition, we also identified genes with highly variable deregulation status and used these genes to cluster TNBC samples into three subgroups with different prognoses. The subgroup with the poorest outcome was characterized by down-regulated immune-regulated pathways, signal transduction pathways, and apoptosis-related pathways. Protein-protein interaction network analysis revealed that OAS family genes may be promising drug targets to activate tumor immunity in this subgroup. In conclusion, RankCompV2.1 is capable of identifying individual-level DEGs with high accuracy and statistical power, analyzing mechanisms of carcinogenesis and exploring therapeutic strategy.

Rank-based predictors for response and prognosis of neoadjuvant taxane-anthracycline-based chemotherapy in breast cancer.

For neoadjuvant taxane and anthracycline-based chemotherapy for breast cancer, patients with pathological complete response (pCR) have a favorable prognosis compared with patients with residual disease (RD). Although a number of pCR predictors based on microarray profiles have been proposed to guide neoadjuvant chemotherapy, most of these have not been independently validated in inter-laboratory datasets, possibly owing to the fact that microarray measurements are sensitive to experimental batch effects and inter-array data normalizations. In this study, we developed a rank-based method to tackle this difficulty. First, we extracted from two datasets a combination of gene pairs, each of which had opposing relative expression orders in patients with pCR and those with RD, and used these to build a pCR predictor. This pCR predictor was found to have sensitivities of 74 and 86 % and specificities of 71 and 68 % in another two independent datasets from multiple laboratories, and these results were better than the performances of three previously reported predictors. Considering that patients with minimal RD also tend to have a good prognosis, we then developed a prognosis predictor for RD as a complement to the pCR predictor, in order to identify a group of patients likely to have a good prognosis, taking into account both the RD level and the intrinsic risk factors. In the independent validation, there was a significant difference (P = 0.001) in distant relapse-free survival between the patients likely to and those not likely to have a good prognosis according to our prognosis predictor. In conclusion, the rank-based predictors for response and prognosis can accurately and robustly predict patients with improved prognosis who might benefit from neoadjuvant taxane and anthracycline-based chemotherapy.

Identification of differential DNA methylation alterations of ovarian cancer in peripheral whole blood based on within-sample relative methylation orderings.

Leukocyte cell proportion changes affect the detection of cancer-associated aberrant DNA methylation alterations in peripheral blood samples. We aimed to detect cellular DNA methylation changes in ovarian cancer (OVC) blood samples avoiding the above-mentioned cell-composition effects. Based on the within-sample relative methylation orderings (RMOs) of CpG loci in leukocyte subtypes, we developed the Ref-RMO method to detect aberrant methylation alterations from OVC blood samples. Stable CpG pairs with consistent RMOs in different leukocyte subtypes were determined, more than 99% of which retained their RMO patterns in peripheral whole blood (PWB) in independent datasets. Based on the stable CpG pairs, significantly reversed CpG pairs were detected from OVC PWB samples, which were relative to clinical information such as age, subtype, grade, stage, or CA125 level. Results showed 439 CpG loci were determined to be significant differential DNA methylations between OVC and healthy blood samples. They were mainly enriched in KEGG pathways, such as cytokine-cytokine receptor interaction, apoptosis, proteoglycans in cancer, and immune-associated Gene Ontology terms. STRING analysis showed that they tended to have functional interactions with cancer-associated genes recorded in the COSMIC database. Leukocyte cellular differential DNA methylations could be identified by the proposed RMO-based method from OVC PWB samples, which were cancer-associated aberrant signals against cell-composition effects.

An immuno-score signature of tumor immune microenvironment predicts clinical outcomes in locally advanced rectal cancer.

Background and purpose: Accumulating evidence indicates that neoadjuvant chemoradiotherapy(nCRT) success has an immune-associated constituent in locally advanced rectal cancer (LARC). The immune-associated configuration of the tumor microenvironment associated with responses to treatment was explored in LARC in this study. Material and methods: A novel analytic framework was developed based on within-sample relative expression orderings for identifying tumor immune-associated gene pairs and identified an immuno-score signature from bulk transcriptome profiling analysis of 200 LARC patients. And sequencing and microarray analysis of gene expression was conducted to investigate the association between the signature and response to nCRT, immunotherapy, and cell function of CD4 and CD8. The results were validated using 111 pretreated samples from publicly available datasets in multiple aspects and survival analyses. Results: The immuno-score signature of 18 immune-related gene pairs (referred to as IPS) was validated on bulk microarray and RNA-Seq data. According to the model's immune score, LARC patients were divided into high- and low-score groups. The patients with high-score were greater sensitivity to nCRT and immunotherapy, gaining a significantly improved prognosis. In addition, the immune-score gene pair signature was associated with type I anti-tumor T cell responses, positive regulators of T cell functions, and chromosomal instability while reflecting differences between CD8+ T cell subtypes. Conclusion: The immuno-score signature underlines a key role of tumor immune components in nCRT response, and predicts the prognosis of LARC patients as well.

Identification of an Individualized Prognostic Biomarker for Serous Ovarian Cancer: A Qualitative Model.

Serous ovarian cancer is the most common type of ovarian epithelial cancer and usually has a poor prognosis. The objective of this study was to construct an individualized prognostic model for predicting overall survival in serous ovarian cancer. Based on the relative expression orderings (Ea > Eb/Ea ≤ Eb) of gene pairs closely associated with serous ovarian prognosis, we tried constructing a potential individualized qualitative biomarker by the greedy algorithm and evaluated the performance in independent validation datasets. We constructed a prognostic biomarker consisting of 20 gene pairs (SOV-P20). The overall survival between high- and low-risk groups stratified by SOV-P20 was statistically significantly different in the training and independent validation datasets from other platforms (p < 0.05, Wilcoxon test). The average area under the curve (AUC) values of the training and three validation datasets were 0.756, 0.590, 0.630, and 0.680, respectively. The distribution of most immune cells between high- and low-risk groups was quite different (p < 0.001, Wilcoxon test). The low-risk patients tended to show significantly better tumor response to chemotherapy than the high-risk patients (p < 0.05, Fisher's exact test). SOV-P20 achieved the highest mean index of concordance (C-index) (0.624) compared with the other seven existing prognostic signatures (ranging from 0.511 to 0.619). SOV-P20 is a promising prognostic biomarker for serous ovarian cancer, which will be applicable for clinical predictive risk assessment.

Predict ovarian cancer by pairing serum miRNAs: Construct of single sample classifiers.

Objective: The accuracy of CA125 or clinical examination in ovarian cancer (OVC) screening is still facing challenges. Serum miRNAs have been considered as promising biomarkers for clinical applications. Here, we propose a single sample classifier (SSC) method based on within-sample relative expression orderings (REOs) of serum miRNAs for OVC diagnosis. Methods: Based on the stable REOs within 4,965 non-cancer serum samples, we developed the SSC for OVC in the training cohort (GSE106817: OVC = 200, non-cancer = 2,000) by focusing on highly reversed REOs within OVC. The best diagnosis is achieved using a combination of reversed miRNA pairs, considering the largest evaluation index and the lowest number of miRNA pairs possessed according to the voting rule. The SSC was then validated in internal data (GSE106817: OVC = 120, non-cancer = 759) and external data (GSE113486: OVC = 40, non-cancer = 100). Results: The obtained 13-miRPairs classifier showed high diagnostic accuracy on distinguishing OVC from non-cancer controls in the training set (sensitivity = 98.00%, specificity = 99.60%), which was reproducible in internal data (sensitivity = 98.33%, specificity = 99.21%) and external data (sensitivity = 97.50%, specificity = 100%). Compared with the published models, it stood out in terms of correct positive predictive value (PPV) and negative predictive value (NPV) (PPV = 96.08% and NPV=95.16% in training set, and both above 99% in validation set). In addition, 13-miRPairs demonstrated a classification accuracy of over 97.5% for stage I OVC samples. By integrating other non-OVC serum samples as a control, the obtained 17-miRPairs classifier could distinguish OVC from other cancers (AUC>92% in training and validation set). Conclusion: The REO-based SSCs performed well in predicting OVC (including early samples) and distinguishing OVC from other cancer types, proving that REOs of serum miRNAs represent a robust and non-invasive biomarker.

A 41-Gene Pair Signature for Predicting the Pathological Response of Locally Advanced Rectal Cancer to Neoadjuvant Chemoradiation.

Background and Purpose: Pathological response status is a standard reference for the early evaluation of the effect of neoadjuvant chemoradiation (nCRT) on locally advanced rectal cancer (LARC) patients. Various patients respond differently to nCRT, but identifying the pathological response of LARC to nCRT remains a challenge. Therefore, we aimed to identify a signature that can predict the response of LARC to nCRT. Material and Methods: The gene expression profiles of 111 LARC patients receiving fluorouracil-based nCRT were used to obtain gene pairs with within-sample relative expression orderings related to pathological response. These reversal gene pairs were ranked according to the mean decrease Gini index provided by the random forest algorithm to obtain the signature. This signature was verified in two public cohorts of 46 and 42 samples, and a cohort of 33 samples measured at our laboratory. In addition, the signature was used to predict disease-free survival benefits in a series of colorectal cancer datasets. Results: A 41-gene pair signature (41-GPS) was identified in the training cohort with an accuracy of 84.68% and an area under the receiver operating characteristic curve (AUC) of 0.94. In the two public test cohorts, the accuracy was 93.37 and 73.81%, with AUCs of 0.97 and 0.86, respectively. In our dataset, the AUC was 0.80. The results of the survival analysis show that 41-GPS plays an effective role in identifying patients who will respond to nCRT and have a better prognosis. Conclusion: The signature consisting of 41 gene pairs can robustly predict the clinical pathological response of LARC patients to nCRT.

A Qualitative Analysis Based on Relative Expression Orderings Identifies Transcriptional Subgroups for Alzheimer's Disease.

BACKGROUND: Alzheimer's disease (AD) is a heterogeneous neurodegenerative disease. However, few studies have investigated the heterogeneous gene expression patterns in AD. OBJECTIVE AND METHODS: We examined the gene expression patterns in four brain regions of AD based on the within-sample relative expression orderings (REOs). Gene pairs with significantly reversed REOs in AD samples compared to non-AD controls were identified for each brain region using Fisher's exact test, and filtered according to their transcriptional differences between AD samples. Subgroups of AD were classified by cluster analysis. RESULTS: REO-based gene expression profiling analyses revealed that transcriptional differences, as well as distinct disease subsets, existed within AD patients. For each brain region, two main subgroups were classified: one subgroup reported differentially expressed genes overlapped with the age-related genes, and the other was related to neuroinflammation. CONCLUSION: AD transcriptional subgroups might help understand the underlying pathogenesis of AD, and lend support to a personalized approach to AD management.

Identifying disease-associated pathways in one-phenotype data based on reversal gene expression orderings.

Due to the invasiveness nature of tissue biopsy, it is common that investigators cannot collect sufficient normal controls for comparison with diseased samples. We developed a pathway enrichment tool, DRFunc, to detect significantly disease-disrupted pathways by incorporating normal controls from other experiments. The method was validated using both microarray and RNA-seq expression data for different cancers. The high concordant differentially ranked (DR) gene pairs were identified between cases and controls from different independent datasets. The DR gene pairs were used in the DRFunc algorithm to detect significantly disrupted pathways in one-phenotype expression data by combing controls from other studies. The DRFunc algorithm was exemplified by the detection of significant pathways in glioblastoma samples. The algorithm can also be used to detect altered pathways in the datasets with weak expression signals, as shown by the analysis on the expression data of chemotherapy-treated breast cancer samples.

Identification of molecular alterations in leukocytes from gene expression profiles of peripheral whole blood of Alzheimer's disease.

Blood-based test has been considered as a promising way to diagnose and study Alzheimer's disease (AD). However, the changed proportions of the leukocytes under disease states could confound the aberrant expression signals observed in mixed-cell blood samples. We have previously proposed a method, Ref-REO, to detect the leukocyte specific expression alterations from mixed-cell blood samples. In this study, by applying Ref-REO, we detect 42 and 45 differentially expressed genes (DEGs) between AD and normal peripheral whole blood (PWB) samples in two datasets, respectively. These DEGs are mainly associated with AD-associated functions such as Wnt signaling pathways and mitochondrion dysfunctions. They are also reproducible in AD brain tissue, and tend to interact with the reported AD-associated biomarkers and overlap with targets of AD-associated PWB miRNAs. Moreover, they are closely associated with aging and have severer expression alterations in the younger adults with AD. Finally, diagnostic signatures are constructed from these leukocyte specific alterations, whose area under the curve (AUC) for predicting AD is higher than 0.73 in the two AD PWB datasets. In conclusion, gene expression alterations in leukocytes could be extracted from AD PWB samples, which are closely associated with AD progression, and used as a diagnostic signature of AD.

Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples.

Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that expression measurements of thousands of genes had at least two-fold change in FFPE samples compared with paired FF samples. Therefore, for a transcriptional signature based on risk scores summarized from the expression levels of the signature genes, the risk score thresholds trained from FFPE (or FF) samples could not be applied to FF (or FFPE) samples. On the other hand, we found that more than 90% of the relative expression orderings (REOs) of gene pairs in the FF samples were maintained in their paired FFPE samples and largely unaffected by the storage time. The result suggested that the REOs of gene pairs were highly robust against partial RNA degradation in FFPE samples. Finally, as a case study, we developed a REOs-based signature to distinguish liver cirrhosis from hepatocellular carcinoma (HCC) using FFPE samples. The signature was validated in four datasets of FFPE samples and eight datasets of FF samples. In conclusion, the valuable FFPE samples can be fully exploited to identify REOs-based diagnostic and prognostic signatures which could be robustly applicable to both FF samples and FFPE samples with degraded RNA.

Common DNA methylation alterations of Alzheimer's disease and aging in peripheral whole blood.

Alzheimer's disease (AD) is a common aging-related neurodegenerative illness. Recently, many studies have tried to identify AD- or aging-related DNA methylation (DNAm) biomarkers from peripheral whole blood (PWB). However, the origin of PWB biomarkers is still controversial. In this study, by analyzing 2565 DNAm profiles for PWB and brain tissue, we showed that aging-related DNAm CpGs (Age-CpGs) and AD-related DNAm CpGs (AD-CpGs) observable in PWB both mainly reflected DNAm alterations intrinsic in leukocyte subtypes rather than methylation differences introduced by the increased ratio of myeloid to lymphoid cells during aging or AD progression. The PWB Age-CpGs and AD-CpGs significantly overlapped 107 sites (P-value = 2.61×10-12) and 97 had significantly concordant methylation alterations in AD and aging (P-value < 2.2×10-16), which were significantly enriched in nervous system development, neuron differentiation and neurogenesis. More than 60.8% of these 97 concordant sites were found to be significantly correlated with age in normal peripheral CD4+ T cells and CD14+ monocytes as well as in four brain regions, and 44 sites were also significantly differentially methylated in different regions of AD brain tissue. Taken together, the PWB DNAm alterations related to both aging and AD could be exploited for identification of AD biomarkers.

Differential expression analysis for individual cancer samples based on robust within-sample relative gene expression orderings across multiple profiling platforms.

The highly stable within-sample relative expression orderings (REOs) of gene pairs in a particular type of human normal tissue are widely reversed in the cancer condition. Based on this finding, we have recently proposed an algorithm named RankComp to detect differentially expressed genes (DEGs) for individual disease samples measured by a particular platform. In this paper, with 461 normal lung tissue samples separately measured by four commonly used platforms, we demonstrated that tens of millions of gene pairs with significantly stable REOs in normal lung tissue can be consistently detected in samples measured by different platforms. However, about 20% of stable REOs commonly detected by two different platforms (e.g., Affymetrix and Illumina platforms) showed inconsistent REO patterns due to the differences in probe design principles. Based on the significantly stable REOs (FDR<0.01) for normal lung tissue consistently detected by the four platforms, which tended to have large rank differences, RankComp detected averagely 1184, 1335 and 1116 DEGs per sample with averagely 96.51%, 95.95% and 94.78% precisions in three evaluation datasets with 25, 57 and 58 paired lung cancer and normal samples, respectively. Individualized pathway analysis revealed some common and subtype-specific functional mechanisms of lung cancer. Similar results were observed for colorectal cancer. In conclusion, based on the cross-platform significantly stable REOs for a particular normal tissue, differentially expressed genes and pathways in any disease sample measured by any of the platforms can be readily and accurately detected, which could be further exploited for dissecting the heterogeneity of cancer.