[CHEK1 expression and inhibitors in TP53 mutant cancer]

The most frequently mutated gene in human tumors is TP53 and its mutation significantly deteriorates patients' survival. However, to date no targeted therapy is established for TP53 mutated tumors. Here, our aim was to identify druggable kinases with higher expression in TP53 mutated tumors, as well as relate these to altered prognosis. We also aimed to validate a target gene in TP53 wild type and mutant isogenic cell lines using a specific kinase inhibitor. Gene expression and mutation data were collected from 994 lung tumor samples. Samples were separated based on TP53 mutation status, and differential gene expression was compared using Mann-Whitney test between patient cohorts. Prognostic value of identified genes was validated in an array-based lung cancer dataset (n=1926). Survival analysis was performed using Cox proportional hazards regression and Kaplan-Meier survival plots. Effect of TP53 mutations on CHEK1 expression was validated in the A549 isogenic lung cancer cell line. The cell line was also treated using Chk1 protein specific kinase inhibitor to monitor cell functions. Expression of CHEK1 was elevated significantly among targetable kinases and higher expression of CHEK1 related to worse prognosis. Our results confirm the higher expression of CHEK1 kinase associated to TP53 mutations and to shorter survival.

[Subgroup-specific genomic alterations and potential prognostic biomarkers in childhood medulloblastomas]

Despite continuing advances in therapeutic strategies, survival of childhood medulloblastoma (MB) patients has reached a plateau in the past decade. Current clinical approaches divide patients into average- and high-risk treatment categories, although this categorization does not take patient heterogeneity into account. Advanced genomics has initiated an exciting transition that lead to a consensus of four distinct molecular entities within MBs (WNT-activated, SHH-activated, Group 3 MB, and Group 4 MB), each with distinct origins, demographics, molecular alterations and clinical outcomes. Within each of the four primary subgroups additional subtypes started to emerge with distinct biological backgrounds and clinical outcomes. Here we summarize subgroup-specific genomic alterations, affected signaling pathways and potential prognostic biomarkers. The poor prognosis associated with recurrent disease is responsible for the stagnant survival rates. Nevertheless, the mortality is unlikely to change without new biomarkers linked to different mechanisms of pathway activation.

[Genome engineering using the CRISPR-Cas9 system and applications in cancer research]

Today, we have to investigate the effects of selected mutations and molecular alterations - this is made possible by the new genome editing technologies. In these, either a section of the DNA is deleted or moved, or a targeted mutation is introduced into the cell. Here, we describe in detail the CRISPR-Cas9 genome editing method. The technology is based on a feature used by bacteria to combat recurrent viral infections. At present, commencing a set of modifications, the method is functional and can be applied in eukaryotic cells as well. The method has three major steps: first, the system has to be carefully designed and constructed, then the construct has to be introduced into the target cells by transfection, and finally, the achieved effect has to be functionally validated. The reliability of the method enables multiple applications in oncology, including the detailed and efficient investigation of oncogenes, tumor suppressor genes, chromosomal translocations and other molecular changes. At the moment, available CRISPR-Cas9 protocols enable both in vitro and in vivo application. All these already made CRISPR-Cas9 one of the basic methods required for future-proof oncology research.

[Internet-based opportunities in breast cancer diagnostics and research]

A new generation of internet-based diagnostic and research tools have arrived in the last decade. The most extensive group of these includes programs predicting the expected survival mainly by utilizing clinical data of the patient. This includes Adjuvant! Online, the MSKCC and MD Anderson nomograms and the UK-based PREDICT algorithm. A common feature of all these is the comparison of the given patient to previously treated breast cancer samples, and evaluating the clinical outcome of these previous patients. New diagnostic biomarkers can be gene expression or mutation based. Of these, large transcriptomic databases lay the basis for the KMplot.com analysis platform which is capable to assess the prognostic value of a selected gene or gene set. The link between a given mutation and survival is the focus of the cBioportal and the G-2-O software. Diagnosis is based on a transcriptome-level data derived using gene chips in the RecurrenceOnline algorithm. A risk of breast cancer development is assessed by a polygenic model in BOADICEA. In our review we target oncologists, pathologists and breast cancer researchers and provide a comprehensive summary of these and other analysis platforms.

[HER2-positive breast cancer: available targeted agents and biomarkers for therapy response]

In the last decade, the targeted therapy of breast cancer became part of routine clinical protocols all over the globe. Options in today's targeted therapy include hormonal therapy and the modulation of the EGFR/HER-pathway. Of the four HER receptors, HER2 is the target of currently used treatment strategies. HER2 activates multiple intracellular pathways via RAS, RAF and PI3K. We give a comprehensive summary of approved monoclonal antibodies and tyrosine kinase inhibitors acting over HER2, including trastuzumab, lapatinib and pertuzumab. We elaborate on their mechanism of action and on clinical trials behind their approval. Agents in third phase clinical studies (neratinib, afatinib) are also described. We give a brief overview of agents currently in phase I and phase II studies; these are acting over the PI3K pathway, over IGFR1 and over HSP90. Furthermore, currently validated negative biomarkers (markers predicting lack of response) in clinical use are also summarized. Finally, the major bottlenecks of clinical application including tumor heterogeneity and the high diversity of clinical studies are discussed. For a breakthrough we will need to identify new positive biomarkers of therapy response.

[Prognostic and predictive markers of malignant melanoma]

Malignant melanoma biologically can be divided into non-metastatic and metastatic forms which cannot be predicted precisely using classical clinicopathological parameters, therefore studies on novel genetic or protein markers are abundant in the literature. These studies did not result in clinically useful markers because mostly ignored the results of studies on the genetic basis of metastatic potential of malignant melanoma. Accordingly, the list of promising novel markers is short (BCL2, CDK2, MART-1, OPN). Similar to other solid malignancies, introduction of targeted therapy into clinical practice of melanoma turned the attention toward the genetic basis of resistance to chemo- and targeted therapies. These novel data could lead to the development of molecular diagnostics which can help in designing more effective therapeutic strategies of malignant melanoma.

Helicobacter pylori and antrum erosion-specific gene expression patterns: the discriminative role of CXCL13 and VCAM1 transcripts

BACKGROUND AND AIMS

Chronic Helicobacter pylori infection affects approximately half of the world, leads to chronic gastritis and peptic ulceration, and is linked to gastric carcinoma. Our aims were to compare the gene expression profile (GEP) of H. pylori-positive and H. pylori-negative gastric erosions and adjacent mucosa to explain the possible role and response to H. pylori infection and to get erosion-related mRNA expression patterns.

METHODS

Total RNA was extracted, amplified, and biotinylated from gastric biopsies of patients with H. pylori-positive and H. pylori-negative antrum erosions (ER) (8/8) and adjacent macroscopically normal mucosae (8/8). The GEP was evaluated using HGU133plus2.0 microarrays. Two independent normalizations (MAS5.0, RMA), PAM feature selection, hierarchical cluster analysis, and discriminant analysis were done. The expression of 14 genes was also measured by real-time-polymerase chain reaction. VCAM-1 and CXCL13 immunohistochemistry (IHC) was done.

RESULTS

In H. pylori infection, significant overexpression of MHC class II antigen-presenting genes, interleukin-7 receptor, ubiquitin-D, CXCR4, lactoferrin immune response-related genes, CXCL-2 and -13, CCL18 chemokine ligand, and VCAM-1 genes were established. In erosive gastritis, increased proliferation (MET) and transport (UCP2, SCFD1, KPNA4) were found, while genes associated with adhesion (SIGLEC11), transcription regulation (ESRRG), and electron and ion transport (ACADM, CLIC6) were down-regulated. Discriminant analysis successfully classified all samples into four groups (HP+ER-, HP+ER+, HP-ER+, HP-ER-) using a reduced gene set (20). Significant overexpression of VCAM-1 and CXC13 protein was detected by IHC in HP+ samples (p < .05).

CONCLUSIONS

Whole genomic microarray analysis yielded new H. pylori infection and erosion-related gene expression changes. Discriminative genes can be used in mRNA-based diagnostic classification of gastric biopsies.

Use of Routinely Collected Amniotic Fluid for Whole-Genome Expression Analysis of Polygenic Disorders

Background: Neural tube defects related to polygenic disorders are the second most common birth defects in the world, but no molecular biologic tests are available to analyze the genes involved in the pathomechanism of these disorders. We explored the use of routinely collected amniotic fluid to characterize the differential gene expression profiles of polygenic disorders.

Methods: We used oligonucleotide microarrays to analyze amniotic fluid samples obtained from pregnant women carrying fetuses with neural tube defects diagnosed during ultrasound examination. The control samples were obtained from pregnant women who underwent routine genetic amniocentesis because of advanced maternal age (&gt;35 years). We also investigated specific folate-related genes because maternal periconceptional folic acid supplementation has been found to have a protective effect with respect to neural tube defects.

Results: Fetal mRNA from amniocytes was successfully isolated, amplified, labeled, and hybridized to whole-genome transcript arrays. We detected differential gene expression profiles between cases and controls. Highlighted genes such as SLA, LST1, and BENE might be important in the development of neural tube defects. None of the specific folate-related genes were in the top 100 associated transcripts.

Conclusions: This pilot study demonstrated that a routinely collected amount of amniotic fluid (as small as 6 mL) can provide sufficient RNA to successfully hybridize to expression arrays. Analysis of the differences in fetal gene expressions might help us decipher the complex genetic background of polygenic disorders.