Laura Vizkeleti - Academia.edu (original) (raw)
Papers by Laura Vizkeleti
pm PTEN) and no KIT mutations or mutations in the NRAS gene alone, and 2.) melanomas on CSD skin ... more pm PTEN) and no KIT mutations or mutations in the NRAS gene alone, and 2.) melanomas on CSD skin with infrequent BRAF mutations and KIT mutations in approximately 20%. Melanomas developing on glabrous skin or under the nails were considered as acral melanomas based on the genetic features such as oncogene amplifications and mutations or amplification of KIT in 40% of cases. Finally, mucosal melanomas were proposed as separate entity based on the patterns of chromosomal aberrations. administered, including immune-related enterocolitis, hepatitis, and dermatitis. There are many other targeted therapies (e.g. imatinib, lapatinib, anti-VEGF treatments or the improvement of immunotreatments) in clinical trials which may have an impact in the future melanoma treatment, perhaps in combination with molecular targeted therapies. However,
PubMed, Sep 1, 2015
Metastatic process accounts for the vast majority of melanoma associated mortality, and also resu... more Metastatic process accounts for the vast majority of melanoma associated mortality, and also results in difficulties in the effective treatment. Therefore, identification of novel biomarkers could contribute to melanoma prognosis, and may also provide new opportunities for efficient cancer treatment. Several signaling pathways have been identified as key regulators in melanoma progression, including the frequent activation of Ras/MAPK signaling pathway through the mutant BRAF or NRAS genes. Besides, alterations of CCND1 may also be of great importance. The oncogene plays a significant role in the G1/S phase transition of the cell cycle, and its transcriptional activation is primarily carried out by the Ras/MAPK cascade. One of our aims was to determine the genetic and gene expression alterations of CCND1 during melanoma progression, considering the mutation status of BRAF and NRAS genes. Analysis of CCND1 copy number alterations revealed significant association with poor clinical outcome in primary melanomas, which was influenced by the mutation status of BRAF or NRAS in the term of sun exposure. Regarding gene expression, CCND1 mRNA level decreased in lesions with multiple metastases and were correlated with both the mRNA levels and mutation status of BRAF and NRAS. CCND1 protein expression was associated with Breslow thickness, metastasis formation and shorter survival time. However, the proportion of cells expressing the protein showed a heterogeneous distribution, influencing the association with clinical-pathological parameters. Therefore melanoma cell lines with different biological behavior were also analyzed for protein expression. These experiments revealed an increasing CCND1 protein level throughout primary cancer progression, which then decreased in the metastasis. The other purpose of our study was to determine the role of 7q31 region in melanoma progression, which was found frequently altered using array comparative genomic hybridization (aCGH). 7q31 is a gene dense locus, including the FRA7G fragile site, which serves as a mutation hot spot. In its close vicinity TES (focal adhesions) and CAV1 (lipid rafts) genes are located. Using interphase FISH, significant associations were found between 7q31 copy number alterations and poor clinical outcome. Both mRNA and protein levels of CAV1 decreased in thick lesions whereas primary melanomas forming multiple metastases were featured by decreased TES mRNA level.
Melanoma Research, Apr 1, 2016
The Cancer Genome Atlas (TCGA) data analysis aCGH data of melanoma samples deposited into the Ski... more The Cancer Genome Atlas (TCGA) data analysis aCGH data of melanoma samples deposited into the Skin Cutaneous Melanoma dataset (TCGA, Provisional) were analyzed. The results shown are in whole based upon data generated by the TCGA Research Network (http://cancergenome.nih.gov). Dataset includes GISTIC-CNA data of 366 melanoma samples. Data mining was performed using cBioPortal (http://www.cbioportal.org/) [1, 2]. All searches were done according to the cBioPortal's instructions. In agreement with the Reviewer's suggestion we performed additional analyses to validate candidate genes that were identified in our study. We performed real-time PCR experiments to examine gene expression levels of 14 genes (GDNF,
Melanoma Research, Aug 1, 2019
Selective inhibition of the mutant BRAF protein is a highly promising therapeutic approach for me... more Selective inhibition of the mutant BRAF protein is a highly promising therapeutic approach for melanoma patients carrying the BRAF V600E mutation. Despite the remarkable clinical response, most patients develop resistance and experience tumour regrowth. To clarify the molecular background of BRAF inhibitor resistance, we generated four drug-resistant melanoma cell lines from paired primary/metastatic cell lines using a vemurafenib analogue PLX4720. Three of the resistant cell lines showed decreased proliferation after drug withdrawal, but the proliferation of one cell line (WM278 RES) increased notably. Furthermore, we observed opposite phenomena in which a 'drug holiday' could not only be beneficial but also contribute to tumour progression. Using genomic and proteomic approaches, we found significantly different alterations between the sensitive and resistant cell lines, some of which have not been reported previously. In addition to several other changes, copy number gains were observed in all resistant cell lines on 8q24.11-q24.12 and 8q21.2. Gene expression analysis showed that most genes upregulated in the resistant cell lines were associated with cell motility and angiogenesis. Increased expression of six proteins (ANGPLT4, EGFR, Endoglin, FGF2, SerpinE1 and VCAM-1) and decreased expression of two proteins (osteopontin and survivin) were observed consistently in all resistant cell lines. In summary, we identified new genomic alterations and characterized the protein expression patterns associated with the resistant phenotype. Although several proteins have been shown to be associated with BRAF resistance, our study is the first to describe the association of VCAM-1 and osteopontin with BRAF resistance. Melanoma Res 29:390-400
Cancer and Metastasis Reviews, Mar 1, 2016
Malignant melanoma of the skin is the most aggressive human cancer given that a primary tumor a f... more Malignant melanoma of the skin is the most aggressive human cancer given that a primary tumor a few millimeters in diameter frequently has full metastatic competence. In view of that, revealing the genetic background of this potential may also help to better understand tumor dissemination in general. Genomic analyses have established the molecular classification of melanoma based on the most frequent driver oncogenic mutations (BRAF, NRAS, KIT) and have also revealed a long list of rare events, including mutations and amplifications as well as genetic microheterogeneity. At the moment, it is unclear whether any of these rare events have role in the metastasis initiation process since the major drivers do not have such a role. During lymphatic and hematogenous dissemination, the clonal selection process is evidently reflected by differences in oncogenic drivers in the metastases versus the primary tumor. Clonal selection is also evident during lymphatic progression, though the genetic background of this immunoselection is less clear. Genomic analyses of metastases identified further genetic alterations, some of which may correspond to metastasis maintenance genes. The natural genetic progression of melanoma can be modified by targeted (BRAF or MEK inhibitor) or immunotherapies. Some of the rare events in primary tumors may result in primary resistance, while further new genetic lesions develop during the acquired resistance to both targeted and immunotherapies. Only a few genetic lesions of the primary tumor are constant during natural or therapy-modulated progression. EGFR4 and NMDAR2 mutations, MITF and MET amplifications and PTEN loss can be considered as metastasis drivers. Furthermore, BRAF and MITF amplifications as well as PTEN loss are also responsible for resistance to targeted therapies, whereas NRAS mutation is the only founder genetic lesion showing any association with sensitivity to immunotherapies. Unfortunately, there are hardly any data on the possible organ-specific metastatic drivers in melanoma. These observations suggest that clinical management of melanoma patients must rely on the genetic analysis of the metastatic lesions to be able to monitor progression-associated changes and to personalize therapies.
Magyar onkologia, May 18, 2021
Target-specific inhibition of the BRAFV600E mutant protein has been a major breakthrough in the t... more Target-specific inhibition of the BRAFV600E mutant protein has been a major breakthrough in the treatment of metastatic cutaneous melanoma. However, the success of therapies is significantly overshadowed by the development of resistance. Understanding the molecular mechanisms associated with acquired resistance is an important step to increase the effectiveness of melanoma treatment. Our aim was to elucidate the molecular differences underlying the development of drug resistance using a mutant BRAF protein inhibitor (vemurafenib analogue: PLX4720) in BRAFV600E mutant melanoma cell lines. We developed four BRAF inhibitor-resistant cell lines and examined the effect of BRAF inhibitor "withdrawal" on cell division. ArrayCGH was used to define genetic, and Affymetrix HumanGene 1.0 microarray to monitor gene expression alterations between the sensitive and resistant cell lines. Protein expression was determined using Proteome Profiler Human XL Oncology Array. We found that withdrawal of the inhibitor reduces cell proliferation in the resistant cells. The invasive potential of the resistant cells increased. Using genomic and proteomic methods we described new molecular alterations associated with acquired resistance.
Journal of Clinical Oncology, May 20, 2018
e21528Background: Metastatic drivers in melanomas are in focus of translational research. Methods... more e21528Background: Metastatic drivers in melanomas are in focus of translational research. Methods: 50 patients were collected with primary skin melanomas and 139 corresponding visceral metastases a...
International Journal of Molecular Sciences, Feb 28, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cells
MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcriptio... more MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcription factor, MYC plays a diverse regulatory role in many cellular processes, including cell cycle and metabolism, both in physiological and pathological conditions. The relentless growth and proliferation of tumor cells lead to an insatiable demand for energy and nutrients, which requires the rewiring of cellular metabolism. As MYC can orchestrate all aspects of cellular metabolism, its altered regulation plays a central role in these processes, such as the Warburg effect, and is a well-established hallmark of cancer development. However, our current knowledge of MYC suggests that its spatial- and concentration-dependent contribution to tumorigenesis depends more on changes in the global or relative expression of target genes. As the direct targeting of MYC is proven to be challenging due to its relatively high toxicity, understanding its underlying regulatory mechanisms is essential for th...
Aberrant stem cell-like activity and impaired differentiation are central to the development of c... more Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation respectively in pooled CRISPR screening formats. We then constructed a dual reporter system that simultaneously monitors aberrant stem cell-like and differentiation activity in the same CRC cell line, improving our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the SWI/SNF BAF complex as a negative regulator of differenti...
International Journal of Molecular Sciences, 2022
We developed a human melanoma model using the HT168-M1 cell line to induce IFN-α2 resistance in v... more We developed a human melanoma model using the HT168-M1 cell line to induce IFN-α2 resistance in vitro (HT168-M1res), which was proven to be maintained in vivo in SCID mice. Comparing the mRNA profile of in vitro cultured HT168-M1res cells to its sensitive counterpart, we found 79 differentially expressed genes (DEGs). We found that only a 13-gene core of the DEGs was stable in vitro and only a 4-gene core was stable in vivo. Using an in silico cohort of IFN-treated melanoma tissues, we validated a differentially expressed 9-gene core of the DEGs. Furthermore, using an in silico cohort of immune checkpoint inhibitor (ICI)-treated melanoma tissues, we tested the predictive power of the DEGs for the response rate. Analysis of the top four upregulated and top four downregulated genes of the DEGs identified WFDC1, EFNA3, DDX10, and PTBP1 as predictive genes, and analysis of the “stable” genes of DEGs for predictive potential of ICI response revealed another 13 genes, out of which CDCA4, ...
Magyar onkologia, 2021
Negative predictive markers of the anti-EGFR antibody therapies are RAS or BRAF mutations, while ... more Negative predictive markers of the anti-EGFR antibody therapies are RAS or BRAF mutations, while left sidedness can be considered as a positive predictor. Here we analyzed 97 wild type RAS metastatic colorectal cancers looking for the prognostic and predictive roles of EGFR protein expression. We found that right-sided colorectal cancers are characterized by significantly higher EGFR protein expression as compared to left-sided ones, irrespective of the primary or metastatic tissue analysis. Furthermore, tumors with multiple organ involvement are characterized by significantly higher EGFR protein expression as compared to single organ ones. In the homogenous cetuximab treated cohort (n=90) we have found that lower than the applied EGFR protein expression cut-off was associated with favorable survival. In the multivariate analysis only sidedness proved to be a strong independent predictor, however sidedness is an EGFR-dependent predictor of anti-EGFR therapy.
Experimental Dermatology, 2019
Tumor cell invasion is one of the key processes during cancer progression, leading to life‐threat... more Tumor cell invasion is one of the key processes during cancer progression, leading to life‐threatening metastatic lesions in melanoma. As methylation of cancer‐related genes plays a fundamental role during tumorigenesis and may lead to cellular plasticity which promotes invasion, our aim was to identify novel epigenetic markers on selected invasive melanoma cells. Using Illumina BeadChip assays and Affymetrix Human Gene 1.0 microarrays, we explored the DNA methylation landscape of selected invasive melanoma cells and examined the impact of DNA methylation on gene expression patterns. Our data revealed predominantly hypermethylated genes in the invasive cells affecting the neural crest differentiation pathway and regulation of the actin cytoskeleton. Integrative analysis of the methylation and gene expression profiles resulted in a cohort of hypermethylated genes (IL12RB2, LYPD6B, CHL1, SLC9A3, BAALC, FAM213A, SORCS1, GPR158, FBN1 and ADORA2B) with decreased expression. On the other ...
Pathology & Oncology Research, 2019
Right-and left-sided colorectal cancers (RSCRC and LSCRC, respectively) are different development... more Right-and left-sided colorectal cancers (RSCRC and LSCRC, respectively) are different developmentally, genetically and prognostically. Clinical data also indicate that they respond differently to anti-EGFR therapies. The role of EGFR protein expression in KRAS wild type colorectal cancer is also controversial. Here we have used a cohort of anti-EGFR antibody treated KRAS-wild type colorectal cancer patients (n = 97) to analyse the prognostic role of EGFR protein expression in relation to sidedness. In our cohort EGFR copy number, determined by FISH, was not associated with the level of EGFR protein, assessed by immunohistochemistry and measured by H-scoring. There was a significantly higher EGFR H-score detected in RSCRC as compared to LSCRC in primary tumors (p = 0.04). Furthermore, in a proportion of cases (n = 31) metastatic tissues were also available and their analysis also found a significantly higher EGFR H-score in metastases of RSCRC compared to LSCRC (p = 0.018). Kaplan Meyer survival analysis demonstrated that anti-EGFR antibody therapies were more effective in case of LSCRC compared to RSCRC. Although in case of progression-free survival data just indicated a trend (p = 0.065), in case of overall survival the difference was significant favouring LSCRC (p = 0.047). These data demonstrated for the first time that the EGFR protein expression is significantly higher in KRAS wild type RSLCL as compared to LSCRC. Meanwhile it is somewhat unexpected that the lower EGFR protein expression was found to be associated with better efficacy of anti-EGFR antibody therapies of colorectal cancer, the finding of which must be further validated.
Acta Oncologica, 2019
Background: Chemotherapeutic agents are often mutagenic. Induction of mutation associated neo-epi... more Background: Chemotherapeutic agents are often mutagenic. Induction of mutation associated neo-epitopes is one of the mechanisms by which chemotherapy is thought to increase the number of tumor-infiltrating lymphocytes, but the clinical relevance of this triggered immune response is not known. We decided to investigate, whether treatment with various chemotherapeutic agents with significantly different mutagenic capacity induce a significantly different number of stromal tumor-infiltrating lymphocytes (StrTIL) in the clinical setting. Methods: 112 breast carcinoma cases treated with pre-operative chemotherapy were selected for the study. According to chemotherapy regimen 28/112 patients received platinum-based, 42/112 cyclophosphamide-based and 42/112 anthracycline-based chemotherapy. The percentage of stromal tumor-infiltrating lymphocytes (StrTIL) was evaluated on hematoxylineosin stained slides of pre-treatment core biopsy (pre-StrTIL) and post-treatment surgical tumor samples (post-StrTIL), according to the most recent recommendation of International TILs Working Group. In survival analyses, TIL changes (∆StrTIL) were calculated from the difference between post-StrTIL and pre-StrTIL. Results: Of the 112 cases, 58.0% (n=65) were hormone receptor (HR) positive and 42.0% (n=47) were HR negative. There was a trend of higher post-StrTIL compared to pre-StrTIL (median 6.25% vs. 3.00%; p<0.001). When analyzing the pre-StrTIL and post-StrTIL among the three treatment groups, we experienced significant StrTIL increase independently of the treatment applied. Based on the results of survival analyses both post-StrTIL and ∆StrTIL was found to be independent prognostic factor in HR negative cases. Each 1% increase in post-StrTIL reduced the hazard of distant metastases development by 2.6% (hazard ratio: 0.974; this material for any purpose without crediting the original authors.
Cancers, 2021
Malignant melanoma is one of the most aggressive skin cancers with high potential of visceral dis... more Malignant melanoma is one of the most aggressive skin cancers with high potential of visceral dissemination. Since the information about melanoma genomics is mainly based on primary tumors and lymphatic or skin metastases, an autopsy-based visceral metastasis biobank was established. We used copy number variation arrays (N = 38 samples) to reveal organ specific alterations. Results were partly completed by proteomic analysis. A significant increase of high-copy number gains was found in an organ-specific manner, whereas copy number losses were predominant in brain metastases, including the loss of numerous DNA damage response genes. Amplification of many immune genes was also observed, several of them are novel in melanoma, suggesting that their ectopic expression is possibly underestimated. This “immunogenic mimicry” was exclusive for lung metastasis. We also provided evidence for the possible autocrine activation of c-MET, especially in brain and lung metastases. Furthermore, freq...
Cancers, Mar 10, 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
bioRxiv (Cold Spring Harbor Laboratory), Feb 3, 2023
Despite advancements in early cancer detection and prevention methods, colorectal cancer (CRC) re... more Despite advancements in early cancer detection and prevention methods, colorectal cancer (CRC) remains a significant global health problem. It is the third most common cancer and the second leading cause of cancer-related deaths worldwide. Additionally, there has been a marked increase of incidence in young adults, and the reasons for this tendency are not fully understood. Therefore, the need for more effective diagnostic methods of assessing disease risk at early stage is crucial.
PurposeDue to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (cc... more PurposeDue to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (ccRCC) has not benefitted from targeted synthetic lethality-based therapies. We investigated whether nucleotide excision repair (NER) deficiency is present in an identifiable subset of ccRCC cases that would render those tumors sensitive to therapy targeting this specific DNA repair pathway aberration.Experimental DesignWe used functional assays that detect UV-induced 6-4 pyrimidine-pyrimidone photoproducts to quantify NER deficiency in ccRCC cell lines. We also measured sensitivity to irofulven, an experimental cancer therapeutic agent that specifically targets cells with inactivated transcription-coupled nucleotide excision repair (TC-NER). In order to detect NER deficiency in clinical biopsies, we assessed whole exome sequencing data for the presence of an NER deficiency associated mutational signature previously identified in ERCC2 mutant bladder cancer.ResultsFunctional assays showed ...
pm PTEN) and no KIT mutations or mutations in the NRAS gene alone, and 2.) melanomas on CSD skin ... more pm PTEN) and no KIT mutations or mutations in the NRAS gene alone, and 2.) melanomas on CSD skin with infrequent BRAF mutations and KIT mutations in approximately 20%. Melanomas developing on glabrous skin or under the nails were considered as acral melanomas based on the genetic features such as oncogene amplifications and mutations or amplification of KIT in 40% of cases. Finally, mucosal melanomas were proposed as separate entity based on the patterns of chromosomal aberrations. administered, including immune-related enterocolitis, hepatitis, and dermatitis. There are many other targeted therapies (e.g. imatinib, lapatinib, anti-VEGF treatments or the improvement of immunotreatments) in clinical trials which may have an impact in the future melanoma treatment, perhaps in combination with molecular targeted therapies. However,
PubMed, Sep 1, 2015
Metastatic process accounts for the vast majority of melanoma associated mortality, and also resu... more Metastatic process accounts for the vast majority of melanoma associated mortality, and also results in difficulties in the effective treatment. Therefore, identification of novel biomarkers could contribute to melanoma prognosis, and may also provide new opportunities for efficient cancer treatment. Several signaling pathways have been identified as key regulators in melanoma progression, including the frequent activation of Ras/MAPK signaling pathway through the mutant BRAF or NRAS genes. Besides, alterations of CCND1 may also be of great importance. The oncogene plays a significant role in the G1/S phase transition of the cell cycle, and its transcriptional activation is primarily carried out by the Ras/MAPK cascade. One of our aims was to determine the genetic and gene expression alterations of CCND1 during melanoma progression, considering the mutation status of BRAF and NRAS genes. Analysis of CCND1 copy number alterations revealed significant association with poor clinical outcome in primary melanomas, which was influenced by the mutation status of BRAF or NRAS in the term of sun exposure. Regarding gene expression, CCND1 mRNA level decreased in lesions with multiple metastases and were correlated with both the mRNA levels and mutation status of BRAF and NRAS. CCND1 protein expression was associated with Breslow thickness, metastasis formation and shorter survival time. However, the proportion of cells expressing the protein showed a heterogeneous distribution, influencing the association with clinical-pathological parameters. Therefore melanoma cell lines with different biological behavior were also analyzed for protein expression. These experiments revealed an increasing CCND1 protein level throughout primary cancer progression, which then decreased in the metastasis. The other purpose of our study was to determine the role of 7q31 region in melanoma progression, which was found frequently altered using array comparative genomic hybridization (aCGH). 7q31 is a gene dense locus, including the FRA7G fragile site, which serves as a mutation hot spot. In its close vicinity TES (focal adhesions) and CAV1 (lipid rafts) genes are located. Using interphase FISH, significant associations were found between 7q31 copy number alterations and poor clinical outcome. Both mRNA and protein levels of CAV1 decreased in thick lesions whereas primary melanomas forming multiple metastases were featured by decreased TES mRNA level.
Melanoma Research, Apr 1, 2016
The Cancer Genome Atlas (TCGA) data analysis aCGH data of melanoma samples deposited into the Ski... more The Cancer Genome Atlas (TCGA) data analysis aCGH data of melanoma samples deposited into the Skin Cutaneous Melanoma dataset (TCGA, Provisional) were analyzed. The results shown are in whole based upon data generated by the TCGA Research Network (http://cancergenome.nih.gov). Dataset includes GISTIC-CNA data of 366 melanoma samples. Data mining was performed using cBioPortal (http://www.cbioportal.org/) [1, 2]. All searches were done according to the cBioPortal's instructions. In agreement with the Reviewer's suggestion we performed additional analyses to validate candidate genes that were identified in our study. We performed real-time PCR experiments to examine gene expression levels of 14 genes (GDNF,
Melanoma Research, Aug 1, 2019
Selective inhibition of the mutant BRAF protein is a highly promising therapeutic approach for me... more Selective inhibition of the mutant BRAF protein is a highly promising therapeutic approach for melanoma patients carrying the BRAF V600E mutation. Despite the remarkable clinical response, most patients develop resistance and experience tumour regrowth. To clarify the molecular background of BRAF inhibitor resistance, we generated four drug-resistant melanoma cell lines from paired primary/metastatic cell lines using a vemurafenib analogue PLX4720. Three of the resistant cell lines showed decreased proliferation after drug withdrawal, but the proliferation of one cell line (WM278 RES) increased notably. Furthermore, we observed opposite phenomena in which a 'drug holiday' could not only be beneficial but also contribute to tumour progression. Using genomic and proteomic approaches, we found significantly different alterations between the sensitive and resistant cell lines, some of which have not been reported previously. In addition to several other changes, copy number gains were observed in all resistant cell lines on 8q24.11-q24.12 and 8q21.2. Gene expression analysis showed that most genes upregulated in the resistant cell lines were associated with cell motility and angiogenesis. Increased expression of six proteins (ANGPLT4, EGFR, Endoglin, FGF2, SerpinE1 and VCAM-1) and decreased expression of two proteins (osteopontin and survivin) were observed consistently in all resistant cell lines. In summary, we identified new genomic alterations and characterized the protein expression patterns associated with the resistant phenotype. Although several proteins have been shown to be associated with BRAF resistance, our study is the first to describe the association of VCAM-1 and osteopontin with BRAF resistance. Melanoma Res 29:390-400
Cancer and Metastasis Reviews, Mar 1, 2016
Malignant melanoma of the skin is the most aggressive human cancer given that a primary tumor a f... more Malignant melanoma of the skin is the most aggressive human cancer given that a primary tumor a few millimeters in diameter frequently has full metastatic competence. In view of that, revealing the genetic background of this potential may also help to better understand tumor dissemination in general. Genomic analyses have established the molecular classification of melanoma based on the most frequent driver oncogenic mutations (BRAF, NRAS, KIT) and have also revealed a long list of rare events, including mutations and amplifications as well as genetic microheterogeneity. At the moment, it is unclear whether any of these rare events have role in the metastasis initiation process since the major drivers do not have such a role. During lymphatic and hematogenous dissemination, the clonal selection process is evidently reflected by differences in oncogenic drivers in the metastases versus the primary tumor. Clonal selection is also evident during lymphatic progression, though the genetic background of this immunoselection is less clear. Genomic analyses of metastases identified further genetic alterations, some of which may correspond to metastasis maintenance genes. The natural genetic progression of melanoma can be modified by targeted (BRAF or MEK inhibitor) or immunotherapies. Some of the rare events in primary tumors may result in primary resistance, while further new genetic lesions develop during the acquired resistance to both targeted and immunotherapies. Only a few genetic lesions of the primary tumor are constant during natural or therapy-modulated progression. EGFR4 and NMDAR2 mutations, MITF and MET amplifications and PTEN loss can be considered as metastasis drivers. Furthermore, BRAF and MITF amplifications as well as PTEN loss are also responsible for resistance to targeted therapies, whereas NRAS mutation is the only founder genetic lesion showing any association with sensitivity to immunotherapies. Unfortunately, there are hardly any data on the possible organ-specific metastatic drivers in melanoma. These observations suggest that clinical management of melanoma patients must rely on the genetic analysis of the metastatic lesions to be able to monitor progression-associated changes and to personalize therapies.
Magyar onkologia, May 18, 2021
Target-specific inhibition of the BRAFV600E mutant protein has been a major breakthrough in the t... more Target-specific inhibition of the BRAFV600E mutant protein has been a major breakthrough in the treatment of metastatic cutaneous melanoma. However, the success of therapies is significantly overshadowed by the development of resistance. Understanding the molecular mechanisms associated with acquired resistance is an important step to increase the effectiveness of melanoma treatment. Our aim was to elucidate the molecular differences underlying the development of drug resistance using a mutant BRAF protein inhibitor (vemurafenib analogue: PLX4720) in BRAFV600E mutant melanoma cell lines. We developed four BRAF inhibitor-resistant cell lines and examined the effect of BRAF inhibitor "withdrawal" on cell division. ArrayCGH was used to define genetic, and Affymetrix HumanGene 1.0 microarray to monitor gene expression alterations between the sensitive and resistant cell lines. Protein expression was determined using Proteome Profiler Human XL Oncology Array. We found that withdrawal of the inhibitor reduces cell proliferation in the resistant cells. The invasive potential of the resistant cells increased. Using genomic and proteomic methods we described new molecular alterations associated with acquired resistance.
Journal of Clinical Oncology, May 20, 2018
e21528Background: Metastatic drivers in melanomas are in focus of translational research. Methods... more e21528Background: Metastatic drivers in melanomas are in focus of translational research. Methods: 50 patients were collected with primary skin melanomas and 139 corresponding visceral metastases a...
International Journal of Molecular Sciences, Feb 28, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cells
MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcriptio... more MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcription factor, MYC plays a diverse regulatory role in many cellular processes, including cell cycle and metabolism, both in physiological and pathological conditions. The relentless growth and proliferation of tumor cells lead to an insatiable demand for energy and nutrients, which requires the rewiring of cellular metabolism. As MYC can orchestrate all aspects of cellular metabolism, its altered regulation plays a central role in these processes, such as the Warburg effect, and is a well-established hallmark of cancer development. However, our current knowledge of MYC suggests that its spatial- and concentration-dependent contribution to tumorigenesis depends more on changes in the global or relative expression of target genes. As the direct targeting of MYC is proven to be challenging due to its relatively high toxicity, understanding its underlying regulatory mechanisms is essential for th...
Aberrant stem cell-like activity and impaired differentiation are central to the development of c... more Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation respectively in pooled CRISPR screening formats. We then constructed a dual reporter system that simultaneously monitors aberrant stem cell-like and differentiation activity in the same CRC cell line, improving our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the SWI/SNF BAF complex as a negative regulator of differenti...
International Journal of Molecular Sciences, 2022
We developed a human melanoma model using the HT168-M1 cell line to induce IFN-α2 resistance in v... more We developed a human melanoma model using the HT168-M1 cell line to induce IFN-α2 resistance in vitro (HT168-M1res), which was proven to be maintained in vivo in SCID mice. Comparing the mRNA profile of in vitro cultured HT168-M1res cells to its sensitive counterpart, we found 79 differentially expressed genes (DEGs). We found that only a 13-gene core of the DEGs was stable in vitro and only a 4-gene core was stable in vivo. Using an in silico cohort of IFN-treated melanoma tissues, we validated a differentially expressed 9-gene core of the DEGs. Furthermore, using an in silico cohort of immune checkpoint inhibitor (ICI)-treated melanoma tissues, we tested the predictive power of the DEGs for the response rate. Analysis of the top four upregulated and top four downregulated genes of the DEGs identified WFDC1, EFNA3, DDX10, and PTBP1 as predictive genes, and analysis of the “stable” genes of DEGs for predictive potential of ICI response revealed another 13 genes, out of which CDCA4, ...
Magyar onkologia, 2021
Negative predictive markers of the anti-EGFR antibody therapies are RAS or BRAF mutations, while ... more Negative predictive markers of the anti-EGFR antibody therapies are RAS or BRAF mutations, while left sidedness can be considered as a positive predictor. Here we analyzed 97 wild type RAS metastatic colorectal cancers looking for the prognostic and predictive roles of EGFR protein expression. We found that right-sided colorectal cancers are characterized by significantly higher EGFR protein expression as compared to left-sided ones, irrespective of the primary or metastatic tissue analysis. Furthermore, tumors with multiple organ involvement are characterized by significantly higher EGFR protein expression as compared to single organ ones. In the homogenous cetuximab treated cohort (n=90) we have found that lower than the applied EGFR protein expression cut-off was associated with favorable survival. In the multivariate analysis only sidedness proved to be a strong independent predictor, however sidedness is an EGFR-dependent predictor of anti-EGFR therapy.
Experimental Dermatology, 2019
Tumor cell invasion is one of the key processes during cancer progression, leading to life‐threat... more Tumor cell invasion is one of the key processes during cancer progression, leading to life‐threatening metastatic lesions in melanoma. As methylation of cancer‐related genes plays a fundamental role during tumorigenesis and may lead to cellular plasticity which promotes invasion, our aim was to identify novel epigenetic markers on selected invasive melanoma cells. Using Illumina BeadChip assays and Affymetrix Human Gene 1.0 microarrays, we explored the DNA methylation landscape of selected invasive melanoma cells and examined the impact of DNA methylation on gene expression patterns. Our data revealed predominantly hypermethylated genes in the invasive cells affecting the neural crest differentiation pathway and regulation of the actin cytoskeleton. Integrative analysis of the methylation and gene expression profiles resulted in a cohort of hypermethylated genes (IL12RB2, LYPD6B, CHL1, SLC9A3, BAALC, FAM213A, SORCS1, GPR158, FBN1 and ADORA2B) with decreased expression. On the other ...
Pathology & Oncology Research, 2019
Right-and left-sided colorectal cancers (RSCRC and LSCRC, respectively) are different development... more Right-and left-sided colorectal cancers (RSCRC and LSCRC, respectively) are different developmentally, genetically and prognostically. Clinical data also indicate that they respond differently to anti-EGFR therapies. The role of EGFR protein expression in KRAS wild type colorectal cancer is also controversial. Here we have used a cohort of anti-EGFR antibody treated KRAS-wild type colorectal cancer patients (n = 97) to analyse the prognostic role of EGFR protein expression in relation to sidedness. In our cohort EGFR copy number, determined by FISH, was not associated with the level of EGFR protein, assessed by immunohistochemistry and measured by H-scoring. There was a significantly higher EGFR H-score detected in RSCRC as compared to LSCRC in primary tumors (p = 0.04). Furthermore, in a proportion of cases (n = 31) metastatic tissues were also available and their analysis also found a significantly higher EGFR H-score in metastases of RSCRC compared to LSCRC (p = 0.018). Kaplan Meyer survival analysis demonstrated that anti-EGFR antibody therapies were more effective in case of LSCRC compared to RSCRC. Although in case of progression-free survival data just indicated a trend (p = 0.065), in case of overall survival the difference was significant favouring LSCRC (p = 0.047). These data demonstrated for the first time that the EGFR protein expression is significantly higher in KRAS wild type RSLCL as compared to LSCRC. Meanwhile it is somewhat unexpected that the lower EGFR protein expression was found to be associated with better efficacy of anti-EGFR antibody therapies of colorectal cancer, the finding of which must be further validated.
Acta Oncologica, 2019
Background: Chemotherapeutic agents are often mutagenic. Induction of mutation associated neo-epi... more Background: Chemotherapeutic agents are often mutagenic. Induction of mutation associated neo-epitopes is one of the mechanisms by which chemotherapy is thought to increase the number of tumor-infiltrating lymphocytes, but the clinical relevance of this triggered immune response is not known. We decided to investigate, whether treatment with various chemotherapeutic agents with significantly different mutagenic capacity induce a significantly different number of stromal tumor-infiltrating lymphocytes (StrTIL) in the clinical setting. Methods: 112 breast carcinoma cases treated with pre-operative chemotherapy were selected for the study. According to chemotherapy regimen 28/112 patients received platinum-based, 42/112 cyclophosphamide-based and 42/112 anthracycline-based chemotherapy. The percentage of stromal tumor-infiltrating lymphocytes (StrTIL) was evaluated on hematoxylineosin stained slides of pre-treatment core biopsy (pre-StrTIL) and post-treatment surgical tumor samples (post-StrTIL), according to the most recent recommendation of International TILs Working Group. In survival analyses, TIL changes (∆StrTIL) were calculated from the difference between post-StrTIL and pre-StrTIL. Results: Of the 112 cases, 58.0% (n=65) were hormone receptor (HR) positive and 42.0% (n=47) were HR negative. There was a trend of higher post-StrTIL compared to pre-StrTIL (median 6.25% vs. 3.00%; p<0.001). When analyzing the pre-StrTIL and post-StrTIL among the three treatment groups, we experienced significant StrTIL increase independently of the treatment applied. Based on the results of survival analyses both post-StrTIL and ∆StrTIL was found to be independent prognostic factor in HR negative cases. Each 1% increase in post-StrTIL reduced the hazard of distant metastases development by 2.6% (hazard ratio: 0.974; this material for any purpose without crediting the original authors.
Cancers, 2021
Malignant melanoma is one of the most aggressive skin cancers with high potential of visceral dis... more Malignant melanoma is one of the most aggressive skin cancers with high potential of visceral dissemination. Since the information about melanoma genomics is mainly based on primary tumors and lymphatic or skin metastases, an autopsy-based visceral metastasis biobank was established. We used copy number variation arrays (N = 38 samples) to reveal organ specific alterations. Results were partly completed by proteomic analysis. A significant increase of high-copy number gains was found in an organ-specific manner, whereas copy number losses were predominant in brain metastases, including the loss of numerous DNA damage response genes. Amplification of many immune genes was also observed, several of them are novel in melanoma, suggesting that their ectopic expression is possibly underestimated. This “immunogenic mimicry” was exclusive for lung metastasis. We also provided evidence for the possible autocrine activation of c-MET, especially in brain and lung metastases. Furthermore, freq...
Cancers, Mar 10, 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
bioRxiv (Cold Spring Harbor Laboratory), Feb 3, 2023
Despite advancements in early cancer detection and prevention methods, colorectal cancer (CRC) re... more Despite advancements in early cancer detection and prevention methods, colorectal cancer (CRC) remains a significant global health problem. It is the third most common cancer and the second leading cause of cancer-related deaths worldwide. Additionally, there has been a marked increase of incidence in young adults, and the reasons for this tendency are not fully understood. Therefore, the need for more effective diagnostic methods of assessing disease risk at early stage is crucial.
PurposeDue to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (cc... more PurposeDue to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (ccRCC) has not benefitted from targeted synthetic lethality-based therapies. We investigated whether nucleotide excision repair (NER) deficiency is present in an identifiable subset of ccRCC cases that would render those tumors sensitive to therapy targeting this specific DNA repair pathway aberration.Experimental DesignWe used functional assays that detect UV-induced 6-4 pyrimidine-pyrimidone photoproducts to quantify NER deficiency in ccRCC cell lines. We also measured sensitivity to irofulven, an experimental cancer therapeutic agent that specifically targets cells with inactivated transcription-coupled nucleotide excision repair (TC-NER). In order to detect NER deficiency in clinical biopsies, we assessed whole exome sequencing data for the presence of an NER deficiency associated mutational signature previously identified in ERCC2 mutant bladder cancer.ResultsFunctional assays showed ...