Vlad Popovici

• Associate Professor
• Professor (Associate) at Masaryk University

Motivation: Whole genome expression profiling of large cohorts of different types of cancer led to the identification of distinct molecular subcategories (subtypes) that may partially explain the observed inter-tumoral heterogeneity. This is also the case of colorectal cancer (CRC) where several such categorizations have been proposed. Despite rece...

Background Genomics and proteomics are nowadays the dominant techniques for novel biomarker discovery. However, histopathology images contain a wealth of information related to the tumor histology, morphology and tumor-host interactions that is not accessible through these techniques. Thus, integrating the histopathology images in the biomarker dis...

A key requirement for precision medicine is the accurate identification of patients that would respond to a specific treatment or those that represent a high-risk group, and a plethora of molecular biomarkers have been proposed for this purpose during the last decade. Their application in clinical settings, however, is not always straightforward du...

As part of the MicroArray Quality Control (MAQC)-II project, this analysis examines how the choice of univariate feature-selection methods and classification algorithms may influence the performance of genomic predictors under varying degrees of prediction difficulty represented by three clinically relevant endpoints. We used gene-expression data f...

Our purpose was development and assessment of a BRAF-mutant gene expression signature for colon cancer (CC) and the study of its prognostic implications. A set of 668 stage II and III CC samples from the PETACC-3 (Pan-European Trails in Alimentary Tract Cancers) clinical trial were used to assess differential gene expression between c.1799T>A (p.V6...

Background Emerging evidence suggests that tumour morphological heterogeneity may influence mutational profiles relevant to therapy response. In this pilot study, we aimed to assess whether mutations identified within specific morphological patterns or at the invasion front correlate with shorter time to progression after anti‐EGFR therapy, as comp...

Colorectal cancer (CRC) is the third most common and lethal cancer type worldwide. Although CRC incidence in the older population has decreased in many countries, early-onset CRC cases (< 50 years age, EOCRC) have been rapidly increasing globally. The fecal microbiome has been reproducibly associated with CRC. However, microbiome differences accord...

Background Targeting RAS mutant (MT) colorectal cancer (CRC) remains a difficult challenge, mainly due to the pervasiveness of RAS/MEK-mediated feedback loops. Preclinical studies identified MET/STAT3 as an important mediator of resistance to KRAS-MEK1/2 blockade in RASMT CRC. This dose escalation/expansion study assessed safety and initial efficac...

Background Single-agent MEK1/2 inhibition has been disappointing in clinical trials targeting RAS mutant (MT) cancers, probably due to upstream receptor activation, resulting in resistance. We previously found that dual c-MET/MEK1/2 inhibition attenuated RAS MT colorectal cancer (CRC) xenograft growth. In this study, we assessed safety of MEK1/2 in...

Stage II colon cancer (CC) encompasses a heterogeneous group of patients with diverse survival experiences: 87% to 58% 5-year relative survival rates for stages IIA and IIC, respectively. While stage IIA patients are usually spared the adjuvant chemotherapy, some of them relapse and may benefit from it; thus, their timely identification is crucial....

Morphologic heterogeneity of colorectal adenocarcinoma (CRC) is poorly understood. Previously, we identified morphological patterns associated with CRC molecular subtypes, and showed that these patterns have distinct molecular motifs (Budinska et al., 2023). Here, we evaluated the heterogeneity of these patterns across CRC. Three pathologists evalu...

Heterogeneity of colorectal carcinoma (CRC) represents a major hurdle towards personalized medicine. Efforts based on whole tumor profiling demonstrated that the CRC molecular subtypes were associated with specific tumor morphological patterns representing tumor subregions. We hypothesize that whole-tumor molecular descriptors depend on the morphol...

Heterogeneity of colorectal carcinoma (CRC) represents a major hurdle towards personalized medicine. Efforts based on whole tumor profiling demonstrated that the CRC molecular subtypes were associated with specific tumor morphological patterns representing tumor subregions. We hypothesize that whole- tumor molecular descriptors depend on the morpho...

Heterogeneity of colorectal carcinoma (CRC) represents a major hurdle towards personalized medicine. Efforts based on whole tumor profiling demonstrated that the CRC molecular subtypes were associated with specific tumor morphological patterns representing tumor subregions. We hypothesize that whole-tumor molecular descriptors depend on the morphol...

Heterogeneity of colorectal carcinoma (CRC) represents a major hurdle towards personalized medicine. Efforts based on whole tumor profiling demonstrated that the CRC molecular subtypes were associated with specific tumor morphological patterns representing tumor subregions. We hypothesize that whole-tumor molecular descriptors depend on the morphol...

Integration of multi-omics data can provide a more complex view of the biological system consisting of different interconnected molecular components. We present a new comprehensive R/Bioconductor-package, IntOMICS, which implements a Bayesian framework for multi-omics data integration. IntOMICS adopts a Markov Chain Monte Carlo sampling scheme to s...

Heterogeneity of colorectal carcinoma (CRC) represents a major hurdle towards personalized medicine. Efforts based on whole tumor profiling demonstrated that the CRC molecular subtypes were associated with specific tumor morphological patterns representing tumor subregions. We hypothesize that molecular descriptors depend on morphological heterogen...

Background Integration of multi-omics data can provide a more complex view of the biological system consisting of different interconnected molecular components, the crucial aspect for developing novel personalised therapeutic strategies for complex diseases. Various tools have been developed to integrate multi-omics data. However, an efficient mult...

Background: Integration of multi-omics data can provide a more complex view of the biological system consisting of different interconnected molecular components, the crucial aspect for developing novel personalised therapeutic strategies for complex diseases. Various tools have been developed to integrate multi-omics data. However, an efficient mul...

Long-term dysbiosis of the gut microbiome has a significant impact on colorectal cancer (CRC) progression and explains part of the observed heterogeneity of the disease. Even though the shifts in gut microbiome in the normal-adenoma-carcinoma sequence were described, the landscape of the microbiome within CRC and its associations with clinical vari...

Featured Application The method described can be applied for stain-independent pathology image registration and content summarization. Abstract A novel deep autoencoder architecture is proposed for the analysis of histopathology images. Its purpose is to produce a disentangled latent representation in which the structure and colour information are...

Biomarker-guided treatment for patients with colon cancer is needed. We tested ABCG2 and topoisomerase 1 (TOP1) mRNA expression as predictive biomarkers for irinotecan benefit in the PETACC-3 patient cohort. The present study included 580 patients with mRNA expression data from Stage III colon cancer samples from the PETACC-3 study, which randomize...

Background: Breast cancer is a leading cause of cancer-related death in women worldwide. Despite extensive studies in all areas of basic, clinical and applied research, accurate prognosis remains elusive, thus leading to overtreatment of many patients. Diagnosis could be improved by introducing multigene molecular scores in standard clinical pract...

The dysfunction of the DNA mismatch repair system results in microsatellite instability (MSI). MSI plays a central role in the development of multiple human cancers. In colon cancer, despite being associated with resistance to 5-fluorouracil treatment, MSI is a favourable prognostic marker. In gastric and endometrial cancers, its prognostic value i...

Supplementary Figure S1: receiver operating characteristic curves of the proposed 25-gene expression signature and the published signatures trained exclusively on microarray data sets. Supplementary Figure S2: comparison of receiver operating characteristic curves of the proposed 25-gene expression signature in RNA-seq cohorts A1, C1, and D1 normal...

BRAFV600E mutations occur in 10% of colorectal cancer (CRC) cases, are associated with poor survival and have limited responses to BRAF/MEK inhibition with or without EGFR inhibition. There is an unmet need to understand the biology of poor prognostic BRAFMT CRC. We have used differential gene expression and pathway analyses of untreated stage II a...

One of the aims of high-throughput gene/protein profiling experiments is the identification of biological processes altered between two or more conditions. Pathway analysis is an umbrella term for a multitude of computational approaches used for this purpose. While in the beginning pathway analysis relied on enrichment-based approaches, a newer gen...

Details of the selected methods and used real data collection. (PDF)

Effect of the pathway size. (PDF)

Summarization of the Experiment 5. Heatmaps of the proportion of DEPs for all compared methods. (ZIP)

Effect of the number of DEGs. Proportion of DEPs depending on the number of DEGs for datasets from Disease-Control Data Collection. Each point represents one dataset. (PDF)

Distribution of p-values from Experiment 2. (PDF)

P-values and ranks of the target pathways—Disease-Control Data Collection details. Boxplots of p-values and rank of the estrogen receptor-containing pathways in Disease-Control Data Collection. Ranks are based on p-values. Pathway with the lowest p-value has rank 1. All pathways with the same p-value recieved same rank. The rank was incremented by...

Effect of individual genes in non-topological variants of the methods. (A) Proportion of differentially expressed pathways for different genes and the difference in expression induced between groups. (B) Dependence of the proportion of differentially expressed pathways on the difference in the gene position. In the non-topological variants of the m...

Effect of the number of Entrez IDs. Proportion of DEPs depending on the number of Entrez IDs for datasets from Breast Cancer Data Collection. Each point represents one dataset. (PDF)

Effect of the thresholds used for DEG detection. (PDF)

Summarization of the Experiment 3. Dependence of the proportion of DEPs on the difference in expression induced between groups, the gene mean expression and its postion. In SPIA, neutral interactions were drawn in grey. (PDF)

Effect of expression change in randomly selected multiple genes on the proportion of differentially expressed pathways. Sets of 2, 3, 4 and 5 genes were randomly selected from Non-small cell lung cancer pathway. Each circle represents one of those sets. Expression of genes in the set was modified with increments of 0.1 to 2 with step size 0.1 in 20...

P-values and ranks of the target pathways—Breast Cancer Data Collection details. Boxplots of p-values and rank of the estrogen receptor-containing pathways in Breast Cancer Data Collection. Ranks are based on p-values. Pathway with the lowest p-value has rank 1. All pathways with the same p-value recieved same rank. The rank was incremented by one...

P-values of the target pathways—Gene Overexpression Data Collection details. Heatmaps of p-values of the overexpressed oncogene-containing pathways in Gene Overexpression Data Collection. Pathways are ordered by the number of methods in which they are differentially expressed (p < 0.05). (PDF)

Accurate patient population stratification is a key requirement for a personalized medicine and more precise biomarkers are expected to be obtained by better exploiting the available data. We introduce a novel computational framework that exploits both the information from gene expression data and histopathology images for constructing a tissue-bas...

Introduction - MErCuRIC is a Phase Ib/II clinical trial study using a combined MEK1/2 - cMET inhibition in RAS MT and RAS WT (with aberrant c‐MET) colorectal cancer patients. As part of the discovery efforts on the cases enrolled in Phase I, we aimed to analyze the mutation status of 10 genes that could potentially be associated to the doublet MEK/...

Molecular subtypes have been recently derived for various types of cancer, in an attempt to characterize the inter- tumoral heterogeneity. In this work we explore the possibility of constructing predictors for molecular subtypes based on histopathology images. For this, we introduce a novel 2-level bag-of-features method and we apply it to a collec...

Accurate patient population stratification is a key requirement for a personalized medicine and more precise biomarkers are expected to be obtained by better exploiting the available data. We introduce a novel computational framework that exploits both the information from gene expression data and histopathology images for constructing a tissue-bas...

Histopathology imaging and gene expression profiling are two fundamental investigative techniques which allow the analysis of biological specimens from different perspectives. Given their apparent divergence in data representation, they are usually used separately, being connected only at the higher levels of data analysis. In this work we demonstr...

Scanned images of full histopathology slides of tumor tissue are usually highly heterogeneous, containing a wide variety of tissue compartments. Designing segmentation and image understanding methods that work globally is, therefore, a real challenge. However, if the context in which these methods are to be applied can be constrained, the quality o...

Background: RAS is mutated (RASMT) in ~55% of mCRC, and phase III studies have shown that patients harbouring RAS mutations do not benefit from anti-EGFR MoAbs. In addition, ~50% of RAS Wild Type (RASWT) will not benefit from the addition of an EGFR MoAb to standard chemotherapy. Hence, novel treatment strategies are urgently needed for RASMT and >...

Background: Prognosis prediction for resected primary colon cancer is based on the T-stage Node Metastasis (TNM) staging system. We investigated if four well-documented gene expression risk scores can improve patient stratification. Methods: Microarray-based versions of risk-scores were applied to a large independent cohort of 688 stage II/III t...

Background: Differences exist between the proximal and distal colon in terms of developmental origin, exposure to patterning genes, environmental mutagens, and gut flora. Little is known on how these differences may affect mechanisms of tumorigenesis, side-specific therapy response or prognosis. We explored systematic differences in pathway activa...

The EurOPDX Consortium is an initiative of translational and clinical researchers from 14 cancer centers and universities across 9 European countries, with the common goal of creating a network of clinically relevant models of human cancer, and in particular patient-derived xenograft (PDX) models. PDX models, which are generated by transplantation...

The mutation status of the BRAF and KRAS genes has been proposed as prognostic biomarker in colorectal cancer. Of them, only the BRAF V600E mutation has been validated independently as prognostic for overall survival and survival after relapse, while the prognostic value of KRAS mutation is still unclear. We investigated the prognostic value of BRA...

The recognition that colorectal cancer (CRC) is a heterogeneous disease in terms of clinical behaviour and response to therapy translates into an urgent need for robust molecular disease subclassifiers that can explain this heterogeneity beyond current parameters (MSI, KRAS, BRAF). Attempts to fill this gap are emerging. The Cancer Genome Atlas (TG...

Background Approximately 8-15% of colorectal (CRC) patients carry an activating mutation in BRAF. This CRC subtype is associated with poor outcome and with resistance, both to chemotherapeutic treatments and to tailored drugs. We recently showed that BRAF (V600E) colon cancers (CCs) have a characteristic gene expression signature (1, 2) which is fo...

In a robust and unsupervised analysis of 1113 stage II-III CRC gene expression profiles from PETACC3 and 4 public datasets we defined a set of five gene expression subtypes which were validated in an independent set of 720 samples. We tested these subtypes with common clinico-pathological features, copy number variations, mutations in key cancer as...

Distribution of β-catenin immunoreactivity of the invasion front counts between subtypes

Results of GSEA comparison of enrichment tested signatures in individual subtypes and normal samples

Graphs of joined distribution of dominant vsersus secondary patterns in each of the subtypes

(A) Heat map representing validation of gene expression patterns of subtypes. (B) Pairwise Fisher Z-transformed correlations of meta-genes in validation set. (C) Box plots representing medians of pairwise gene–gene Pearson correlations in the validation datasets

Expression of top five down- and top five up regulated genes from all pairwise comparisons between subtypes

(A) Other clinical and mutational markers tested and found non-significant between subtypes. (B) Clinical variables tested in the clusters of the validation test. (C) Distribution of significant clinical and mutational markers across subtypes. (D) Classification tree trained on clinical variables

Heat map of CNV profiles of 154 samples from the discovery set, randomly ordered inside each of the subtypes

Detailed results of pairwise comparisons of differentially expressed gene between subtypes

Detailed results of Cox proportional hazards models for RFS, OS and SAR for subtype, stage, MSI and BRAF and for meta-genes

Result of hypothesis testing of median log-scale copy number estimates of chromosome 20 of subtype B versus all other subtypes

e14544 Background: We identified CRC gene expression subtypes (ASCO 2012, #3511), which associate with established parameters of outcome as well as relevant biological motifs. We now substantiate their biological and potentially clinical significance by linking them with cell line data and drug sensitivity, primarily attempting to identify models f...

3522 Background: The BRAF and KRAS mutations have been proposed as prognostic markers in colorectal cancer (CRC). Of them, only the BRAF V600E mutation has been validated as prognostic for overall survival and survival after relapse, while the value of KRAS mutation is still unclear. Methods: In a cohort of 1423 stage II-III patients from the PETAC...

403 Background: Approximately 8-15% of colorectal (CRC) patients carry an activating mutation in BRAF. This CRC subtype is associated with poor outcome and with resistance, both to chemotherapeutic treatments and to tailored drugs. We recently showed that BRAF (V600E) colon cancers (CCs) have a characteristic gene expression signature (1, 2) which...

Background: The BRAF and KRAS mutations have been proposed as prognostic markers in colorectal cancer (CRC). Of them, only the BRAF V600E mutation has been validated as prognostic for overall survival and survival after relapse, while the value of KRAS mutation is still unclear. Methods: In a cohort of 1423 stage II-III patients from the PETACC-3 c...

Functional annotation: functional category analysis of the 64 genes by DAVID software

Genes in the MSI-64 gene signature

Microsatellite instability (MSI) occurs in 10-20% of colorectal tumours and is associated with good prognosis. Here we describe the development and validation of a genomic signature that identifies colorectal cancer patients with MSI caused by DNA mismatch repair deficiency with high accuracy. Microsatellite status for 276 stage II and III colorect...

To develop a comprehensive overview of copy number aberrations (CNAs) in stage-II/III colorectal cancer (CRC), we characterized 302 tumors from the PETACC-3 clinical trial. Microsatellite-stable (MSS) samples (n = 269) had 66 minimal common CNA regions, with frequent gains on 20 q (72.5%), 7 (41.8%), 8 q (33.1%) and 13 q (51.0%) and losses on 18 (5...

Affected genes in selected GISTIC amplicons. (XLS)

Boxplots for EGFR, ERBB2 and MYC’s mRNA expression grouped by CNA status. (PPT)

Kaplan-Meier curves demonstrate CNAs showing significant association with overall survival. (PPT)

Minimal common regions identified in 269 MSS stage-II/III colon cancer samples. (XLS)

GISTIC peaks identified in 269 MSS stage-II/III colon cancer samples. (XLS)

Characteristics of patients Included in the study. (XLS)

3511 Background: From a clinical perspective colorectal cancer (CRC) is a heterogeneous disease whose biological background is insufficiently understood. In order to adapt targeted treatment to biologically different categories of CRC patients, in depth understanding of the molecular mechanisms involved in CRC heterogeneity is urgently needed. Meth...

3575 Background: The activation of the MEK/ERK signaling cascade by KRAS or BRAF mutations has a high incidence in colorectal cancer (CRC). While these mutations are mutually exclusive, we have identified a highly conserved gene expression pattern, characteristic to BRAF mutants, that can also be observed in KRAS mutants (AACR 2011, JCO 2012), and...

3509 Background: Prognosis prediction for resected primary colon cancer is currently based on the tumor, nodes, metastasis (TNM) staging system. Gene expression based risk scores have been proposed, but need to be validated and integrated with clinical and TNM variables. We performed an independent assessment of the individual recurrence signatures...

Background: The activation of the MEK/ERK signaling cascade by KRAS or BRAF mutations has a high incidence in colorectal cancer (CRC). While these mutations are mutually exclusive, we have identified a highly conserved gene expression pattern, characteristic to BRAF mutants, that can also be observed in KRAS mutants (AACR 2011, JCO 2012), and which...

Background: We previously identified highly conserved gene expression patterns associated with BRAF V600E mutant MSS colon cancer (Tejpar et al, ASCO 2010). Since these tumors have very poor overall survival and are refractory to therapy, a better understanding of their molecular characteristics is relevant. In this study we explored if the observe...

A top scoring pair (TSP) classifier consists of a pair of variables whose relative ordering can be used for accurately predicting the class label of a sample. This classification rule has the advantage of being easily interpretable and more robust against technical variations in data, as those due to different microarray platforms. Here we describe...