Prognostic significance of aberrant CpG islands methylation in human follicular and diffuse large B-cell lymphoma

Difuzni B-krupnoćelijski limfom (DBKL) i folikularni limfom (FL), predstavljaju najučestalije entitete nehočkinovih limfoma i zajedno čine oko 50 % svih B-ćelijskih neoplazija. To su klinički i biološki heterogena oboljenja, sa visoko varijabilnim odgovorom na terapiju i uprkos značajnom napretku u terapiji, u velikom broju slučajeva ostaju neizlečiva. Aktuelni terapijski pristupi su praćeni brojnim neželjenim efektima i dovode do dugotrajne remisije i preživljavanja kod svega 50 % bolesnika. Najznačajniji klinički prediktor ishoda bolesti do danas je internacionalni prognostički indeks (IPI za DBKL, odnosno, FLIPI za FL), koji obuhvata odgovarajuće kliničke prognostičke parametre. Uprkos tome, oboleli koji pripadaju istim IPI/FLIPI kategorijama ispoljavaju značajne razlike u odgovoru na terapiju i preživljavanju, što ukazuje na postojanje značajne biološke heterogenosti u okviru svake IPI/FLIPI kategorije. Zbog toga je neophodno pronalaženje novih prognostičkih molekularnih parametara, koji bi omogućili precizniju podelu obolelih u grupe različitog stepena rizika i izbor odgovarajuće terapije. Primenom PCR metode specifične za metilaciju (MSP), ispitivan je metilacioni status p16, p15, MGMT i DAPK gena kod obolelih od DBKL i FL, kao bi se utvrdio njihov potencijalni prognostički značaj. Kod obolelih od DBKL, metilacija nijednog gena nije pokazala prognostički značaj, mada je uočena tendencija ka akumulaciji metilacije p15 gena kod ispitanika sa povoljnijim kliničko-patološkim karakteristikama. Kod obolelih od FL metilacija p16, p15 i MGMT gena bi mogla da ima određeni prognostički značaj, ukoliko se kombinuje sa FLIPI, gradusom tumora, odnosno starosnim dobom obolelihi. Istovremena metilacija MGMT i DAPK gena bi mogla da ukaže na grupu obolelih potencijalno hemorezistentnih na primenjenu hemoterapiju i sklonu recidivima bolesti.Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) are the most comon subgroups of non-Hodgkin’s lymphoma and comprise approximately 50 % of all cases. They represents clinically and biologically heterogeneous diseases, characterized with highly variable response to the treatment, and remain incurable despite the significant advances in therapy. Actual therapy regimens are agressive, and long-term remission and survival are ashieved in only 50 % of patients. The strongest clinical predictor of outcome to date in DLBCL and FL patients is the International Prognostic Index (IPI for DLBCL and FLIPI for FL) which includes several clinico-pathological prognostic parameters. However, patients with identical IPI/FLIPI still exhibit marked variability in survival, suggesting the presence of significant biological heterogenity within the same risk category. So, it is important to investigate additional molecular markers in order to further stratify patients into diferent risk groups, choose appropriate treatement strategy and improve prognosis. In this study, methylation-specific polymerase chain reaction (MSP) was used to investigate the role and potential prognostic significance of the methylation status of p16, p15, MGMT and DAPK genes in patients with DLBCL and FL. No one of four examined genes showed prognostic significance in patients with DLBCL, though we observed a tendency toward accumulation of p15 methylation with favorable clinico-pathological parameters. However, in patients with FL, our results suggest that promoter methylation of p16, p15 and MGMT genes could have some prognostic value when used in combination with the FLIPI, tumor grade and patients age, respectively. Concurrent methylation of MGMT and DAPK genes could be the marker of tumor chemoresistance and disease recurrence

Prognostic significance of aberrant CpG islands methylation in human follicular and diffuse large B-cell lymphoma

Difuzni B-krupnoćelijski limfom (DBKL) i folikularni limfom (FL), predstavljaju najučestalije entitete nehočkinovih limfoma i zajedno čine oko 50 % svih B-ćelijskih neoplazija. To su klinički i biološki heterogena oboljenja, sa visoko varijabilnim odgovorom na terapiju i uprkos značajnom napretku u terapiji, u velikom broju slučajeva ostaju neizlečiva. Aktuelni terapijski pristupi su praćeni brojnim neželjenim efektima i dovode do dugotrajne remisije i preživljavanja kod svega 50 % bolesnika. Najznačajniji klinički prediktor ishoda bolesti do danas je internacionalni prognostički indeks (IPI za DBKL, odnosno, FLIPI za FL), koji obuhvata odgovarajuće kliničke prognostičke parametre. Uprkos tome, oboleli koji pripadaju istim IPI/FLIPI kategorijama ispoljavaju značajne razlike u odgovoru na terapiju i preživljavanju, što ukazuje na postojanje značajne biološke heterogenosti u okviru svake IPI/FLIPI kategorije. Zbog toga je neophodno pronalaženje novih prognostičkih molekularnih parametara, koji bi omogućili precizniju podelu obolelih u grupe različitog stepena rizika i izbor odgovarajuće terapije. Primenom PCR metode specifične za metilaciju (MSP), ispitivan je metilacioni status p16, p15, MGMT i DAPK gena kod obolelih od DBKL i FL, kao bi se utvrdio njihov potencijalni prognostički značaj. Kod obolelih od DBKL, metilacija nijednog gena nije pokazala prognostički značaj, mada je uočena tendencija ka akumulaciji metilacije p15 gena kod ispitanika sa povoljnijim kliničko-patološkim karakteristikama. Kod obolelih od FL metilacija p16, p15 i MGMT gena bi mogla da ima određeni prognostički značaj, ukoliko se kombinuje sa FLIPI, gradusom tumora, odnosno starosnim dobom obolelihi. Istovremena metilacija MGMT i DAPK gena bi mogla da ukaže na grupu obolelih potencijalno hemorezistentnih na primenjenu hemoterapiju i sklonu recidivima bolesti.Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) are the most comon subgroups of non-Hodgkin’s lymphoma and comprise approximately 50 % of all cases. They represents clinically and biologically heterogeneous diseases, characterized with highly variable response to the treatment, and remain incurable despite the significant advances in therapy. Actual therapy regimens are agressive, and long-term remission and survival are ashieved in only 50 % of patients. The strongest clinical predictor of outcome to date in DLBCL and FL patients is the International Prognostic Index (IPI for DLBCL and FLIPI for FL) which includes several clinico-pathological prognostic parameters. However, patients with identical IPI/FLIPI still exhibit marked variability in survival, suggesting the presence of significant biological heterogenity within the same risk category. So, it is important to investigate additional molecular markers in order to further stratify patients into diferent risk groups, choose appropriate treatement strategy and improve prognosis. In this study, methylation-specific polymerase chain reaction (MSP) was used to investigate the role and potential prognostic significance of the methylation status of p16, p15, MGMT and DAPK genes in patients with DLBCL and FL. No one of four examined genes showed prognostic significance in patients with DLBCL, though we observed a tendency toward accumulation of p15 methylation with favorable clinico-pathological parameters. However, in patients with FL, our results suggest that promoter methylation of p16, p15 and MGMT genes could have some prognostic value when used in combination with the FLIPI, tumor grade and patients age, respectively. Concurrent methylation of MGMT and DAPK genes could be the marker of tumor chemoresistance and disease recurrence

Multiple Roles of the RUNX Gene Family in Hepatocellular Carcinoma and Their Potential Clinical Implications

: Hepatocellular carcinoma (HCC) is one of the most frequent cancers in humans, characterised by a high resistance to conventional chemotherapy, late diagnosis, and a high mortality rate. It is necessary to elucidate the molecular mechanisms involved in hepatocarcinogenesis to improve diagnosis and treatment outcomes. The Runt-related (RUNX) family of transcription factors (RUNX1, RUNX2, and RUNX3) participates in cardinal biological processes and plays paramount roles in the pathogenesis of numerous human malignancies. Their role is often controversial as they can act as oncogenes or tumour suppressors and depends on cellular context. Evidence shows that deregulated RUNX genes may be involved in hepatocarcinogenesis from the earliest to the latest stages. In this review, we summarise the topical evidence on the roles of RUNX gene family members in HCC. We discuss their possible application as non-invasive molecular markers for early diagnosis, prognosis, and development of novel treatment strategies in HCC patients

Estrogen Receptor Beta: The Promising Biomarker and Potential Target in Metastases

The discovery of the Estrogen Receptor Beta (ERβ) in 1996 opened new perspectives in the diagnostics and therapy of different types of cancer. Here, we present a review of the present research knowledge about its role in endocrine-related cancers: breast, prostate, and thyroid, and colorectal cancers. We also discuss the reasons for the controversy of its role in carcinogenesis and why it is still not in use as a biomarker in clinical practice. Given that the diagnostics and therapy would benefit from the introduction of new biomarkers, we suggest ways to overcome the contradictions in elucidating the role of ERβ.Special Issue "Biomarkers in Hematological and Oncological Malignancies: Identification, Validation and Involvement in Molecular Pathways

Methylation-specific PCR: four steps in primer design

Methylation-specific PCR (MSP) is still the method of choice for a single gene methylation study. The proper design of the primer pairs is a prerequisite for obtaining reliable PCR results. Despite numerous protocols describing the rules for MSP primer design, none of them provide a comprehensive approach to the problem. Our aim was to depict a workflow for the primer design that is concise and easy to follow. In order to achieve this goal, adequate tools for promoter sequence retrieval, MSP primer design and subsequent in silico analysis are presented and discussed. Furthermore, a few instructive examples regarding a good versus a poor primer design are provided. Finally, primer design is demonstrated according to the proposed workflow. This article aims to provide researchers, interested in a single gene methylation studies, with useful information regarding successful primer design

RASSF1A and p16 promoter methylation and treatment response in chronic hepatitis C genotype 1b patients treated with pegylated interferon/ribavirin

Prevention of chronic hepatitis C (CHC) and its complications is based on antiviral therapy and early detection of reliable molecular markers in persons under risk. We investigated whether the methylation status of RASSF1A and p16 genes, alone or in combination with host and viral factors, affects the response to therapy with pegylated interferon/ribavirin (PEG-IFN/RBV). Methylation-specific polymerase chain reaction (MSP) was used to determine the methylation status of the target promoter sequences of RASSF1A and p16 in circulating-free DNA from the peripheral blood of 49 patients with CHC genotype 1b. The methylation status of the examined genes did not affect the response to therapy. However, the simultaneous presence of either RASSF1A or p16 methylation and the CC genotype of IL28B was significantly related to a sustained virologic response (P=0.009 and P=0.032, respectively). After Bonferroni correction, only the result concerning the RASSF1A gene remained significant (P<0.0125). Methylation of RASSF1A was associated with the CC genotype of the IL28B gene (P=0.024) and a higher viral load (≥400 000 IU/mL, P=0.009). Our results suggest that combined analysis of RASSF1A gene methylation and IL28B rs12979860 polymorphism could potentially help in the prediction of therapy response in CHC genotype 1b patients

Frequency of Aberrant Promoter Methylation of P15(Ink4b) and O-6-Methylguanine-Dna Methyltransferase Genes in B-Cell Non-Hodgkin Lymphoma: a Pilot Study

The methylation status of the target promoter sequences of p15(INK4B) (p15) and O-6-methylguanine-DNA methyltransferase (MGMT) genes was studied by methylation-specific PCR in 10 adult patients with de novo B-cell non-Hodgkin lymphoma (B-NHL). The aberrant hypermethylation of the p15 gene was more frequent (50%) compared to the hypermethylation of the MGMT gene (30%), and was detected in different types of B-NHL in both genes. Hypermethylation of the MGMT gene occurred exclusively in association with the hypermethylation of the p15 gene. All lymphoma patients with hypermethylation of the p15 and/or MGMT genes had a higher clinical stage of the disease (IV - V). We show the association of anemia and/or thrombocytopenia with the hypermethylation of the p15 gene, ascribing the p15 gene as a potential prognostic marker in B-NHL. Comethylation of MGMT with the p15 gene represents a novel finding and presents both genes as candidates for future studies of the hypermethylation profiles of B-NHL

Combined analysis of KRAS mutation and p16INK4a and p14ARF methylation status in locally advanced rectal carcinoma treated with preoperative chemoradiotherapy

Paper description:Patient responses to standard treatment of advanced stages of rectal carcinoma are variable, which emphasizes the need to define reliable predictive and prognostic molecular parameters.We propose a model of simultaneous analysis of KRAS gene mutation status and p16INK4a and p14ARF gene promoter methylation status in pre-treatment tumor biopsies.The simultaneous presence of p14ARF methylation and KRAS mutation was associated with more aggressive tumor behavior. The concurrent presence of alterations in all three examined genes was associated with shorter overall survival.Combined analysis of examined gene alterations revealed patient subgroups with a distinct pattern of tumor response and disease outcome.Abstract: Current management of locally advanced rectal carcinoma (LARC) involves preoperative chemoradiotherapy (preCRT) before surgery. Despite improved local control rate, the response to preCRT of individual patients is variable and may reflect heterogeneous biological properties among tumors of the same clinical stage. Identifying novel molecular parameters with predictive and/or prognostic value is of great clinical importance for a personalized therapeutic approach. In this study, KRAS mutation status was analyzed by direct sequencing, while methylation-specific polymerase chain reaction (MSP) was used to examine p16INK4a and p14ARF gene methylation status in pretreatment tumor biopsies of 60 patients with LARC. The examined molecular changes of KRAS, p16INK4a and p14ARF genes were mutually independent (p16INK4a/KRAS, P=0.272; p14ARF/KRAS, P=0.923; p16INK4a/p14ARF, P=0.715). However, the simultaneous presence of p14ARF methylation and KRAS mutation was associated with a more frequent appearance of local recurrences and distant metastasis (P=0.027). Moreover, patients with the simultaneous presence of p16INK4a and p14ARF methylation and KRAS mutation had significantly shorter overall survival (P=0.011). The obtained results strongly suggest that combined analyses of examined genetic and epigenetic molecular alterations could contribute to the identification of LARC patient subgroups with more aggressive tumor behavior and worse disease outcome

Micro Rna-21 Expression Levels in Invasive Breast Carcinoma with a Non-Invasive Component

Invasive ductal carcinomas with a non-invasive component (IDC-DCIS) are classified as a group of invasive breast carcinomas, together with pure invasive ductal carcinomas of the breast (IDC). MicroRNA-21 (miR-21) has been characterized as a factor of breast cancer invasiveness, however the difference in miR-21 expression levels between IDC-DCIS and pure IDC tumors and the correlations with standard diagnostic and prognostic parameters inside the IDC-DCIS group are unknown. Our aim was to determine if miR-21 had the ability to distinguish these two invasive breast cancer groups. Levels of miR-21 expression were measured by a stem-loop quantitative Real-Time PCR (RT-qPCR) method. Expression levels of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (Her-2) and proliferative index Ki-67 were evaluated by immunohistochemistry. IDC-DCIS tumors had significantly lower levels of miR-21 expression in grade 2 (P=0.003, Mann-Whitney U test), ER positive (P=0.025, Mann-Whitney U test) and PR positive tumors (P=0.024, Mann-Whitney U test) than pure IDCs. miR-21 levels showed a different pattern of expression in IDC-DCIS compared to IDC tumors, which is based on the difference in miR-21 expression between Her-2 negative and Her-2 positive IDC-DCIS tumors (P=0.030, Mann-Whitney U test) and high negative correlation of miR-21 levels with PR levels (rho=-0.886, P=0.006, Spearman correlation). According to our results, IDC-DCIS breast carcinomas act in a different manner in pure IDC tumors with regard to the relations between miR-21 expression levels and the standard diagnostic and prognostic parameters, such as Her-2 status, ER and PR status and protein levels

Hypermethylation of p15 Gene in Diffuse - Large B-Cell Lymphoma: Association with Less Aggressiveness of the Disease

In this study, methylation-specific polymerase chain reaction was used to investigate the potential prognostic significance of the methylation status of p15, p16, MGMT, and DAPK genes in 51 specimens of diffuse large B-cell lymphoma (DLBCL). Hypermethylation of p15 gene was significantly more prevalent in patients without relapse (p = 0.001) and there was a trend toward more frequent presence of p15 methylation in patients without death outcome within 5-year follow-up period (p = 0.086) Also, there was a trend toward accumulation of p15 methylation with favorable clinicopathological parameters including: age 60 years (p = 0.091), normal levels of lactate dehydrogenase (p = 0.090), Eastern Cooperative Oncology Group performance status LT 2 (p = 0.095), and low/intermediate low International Prognostic Index (p = 0.076). In the female group and group of the patients without bulky tumor mass, treated with chemotherapeutic regimens including rituximab, methylation of p15 was significantly related to longer overall survival (p = 0.036 and 0.027, respectively). Our results suggest that promoter methylation of p15 gene could have prognostic value in DLBCL patients treated with rituximab when used in combination with gender and tumor size