Wafa Amer - Academia.edu (original) (raw)

Papers by Wafa Amer

Research paper thumbnail of THU-453-Dissecting the landscape of (epi-)genetic alterations during sequential evolution of liver cancer

Journal of Hepatology, 2019

Research paper thumbnail of Tumor tracking and evolution analysis of hepatocellular carcinoma progression by ultra-deep sequencing of the entire mitochondrial genome

Journal of Liver, May 20, 2016

Research paper thumbnail of Communication and System Relevance in Liver Damage and Regeneration January 21 – 22 , 2016

Poster Abstracts Falk Foundation Dr. Falk Pharma Workshop Communication and System Relevance in L... more Poster Abstracts Falk Foundation Dr. Falk Pharma Workshop Communication and System Relevance in Liver Damage

Research paper thumbnail of Comprehensive Analysis of Disease Related Nuclear and Mitochondrial Genes in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the third most lethal cancer due to late detection, high recurr... more Hepatocellular carcinoma (HCC) is the third most lethal cancer due to late detection, high recurrence and limited therapeutics. Although genetic alterations have been recently studied by whole genome or whole exome next generation sequencing, a comprehensive analysis of HCC relevant genes on lesions with low and high grade of dedifferentiation is missing. Herein, I aimed to study the nuclear and mitochondrial genomic alterations in order to characterize HCC development and clonality. First, for target enrichment of HCC relevant genes and mt-genome, gene loci of relevance had to be selected and primer sets designed. Subsequent ultra-deep sequencing revealed that in accordance with previous studies, the β-catenin gene (CTNNB1) was shown to be the most frequently mutated oncogene, whereas the TP53 and AXIN1 genes were the most frequently mutated tumour suppressor genes. Interestingly, CTNNB1 mutations were detected in lesions with early as well as advanced HCC stage, confirming its rol...

Research paper thumbnail of Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis

Research paper thumbnail of Evolution analysis of heterogeneous non-small cell lung carcinoma by ultra-deep sequencing of the mitochondrial genome

Scientific Reports, 2017

Accurate assessment of tumour heterogeneity is an important issue that influences prognosis and t... more Accurate assessment of tumour heterogeneity is an important issue that influences prognosis and therapeutic decision in molecular pathology. Due to the shortage of protective histones and a limited DNA repair capacity, the mitochondrial (mt)-genome undergoes high variability during tumour development. Therefore, screening of mt-genome represents a useful molecular tool for assessing precise cell lineages and tracking tumour history. Here, we describe a highly specific and robust multiplex PCR-based ultra-deep sequencing technology for analysis of the whole mt-genome (wmt-seq) on low quality-DNA from formalin-fixed paraffin-embedded tissues. As a proof of concept, we applied the wmt-seq technology to characterize the clonal relationship of non-small cell lung cancer (NSCLC) specimens with multiple lesions (N = 43) that show either different histological subtypes (group I) or pulmonary adenosquamous carcinoma as striking examples of a mixed-histology tumour (group II). The application...

Research paper thumbnail of P0318 : Ultra-deep sequencing of multiplex-PCR enriched hotspot and disease-related targets in hepatocellular carcinoma

Journal of Hepatology, 2015

Research paper thumbnail of Promoter regulation of the miR-29a/b1 gene by transforming growth factor-β in hepatic stellate cells and in hepatoma cells

Zeitschrift für Gastroenterologie, 2015

Research paper thumbnail of Comprehensive analysis of informative target disease relevant nuclear genes and the whole mitochondrial genome in hepatocellular carcinoma by Multiplex PCR and Ultra-Deep Sequencing

Zeitschrift für Gastroenterologie, 2015

ABSTRACT Hepatocellular carcinoma (HCC) are highly malignant tumors triggered by a wide variety o... more ABSTRACT Hepatocellular carcinoma (HCC) are highly malignant tumors triggered by a wide variety of genetic alterations. Importantly, they show multicentric occurrence characterized by a nodule-in-nodule pattern. In the present study, we investigate the occurrence of disease related nuclear mutations and whole mitochondrial genomic variants by a comprehensive ultra-deep sequencing approach as a novel tool for hepatocellular cancer follow-up and prognosis. Macrodissected 48 HCC nodules, representing different tumor grades, and adjacent non-cancerous tissues from HCC patients were studied. Hot spot mutation screening of nuclear DNA (nDNA) was performed using a multiplex PCR approach covering 40 disease relevant gene regions by a total of 394 amplicons. The mitochondrial (mt) genome is highly susceptible to DNA alterations due to the lack of protective histones and a limited repair system. Therefore, we were using mt-variations as a way of focal cancer barcoding and tracking. Thus, 108 primer sets spanning the whole mtDNA were designed and automatic single PCR set-up was established using the Biomek robotic system. Target enriched libraries of mtDNA and nDNA were sequenced by means of the MiSeq platform and data analysis was performed by the CLC Cancer Research Workbench. Whole mt-genome analysis revealed high frequency of variants in the D-Loop region and the MT-CYB gene. In particular, in HCC nodules of non-cirrhotic origin a wide spectrum of mt-variants with high frequency were identified. However, highly frequent mt-variants occur not only in HCC nodules but also in peri-tumorous parenchymal foci raising the possibility that mtDNA mutations might precede nuclear alterations and play a role in the pre-tumor machinery. Furthermore, the occurrence of identical mt-variants in different nodules of one liver sample indicates the monoclonal HCC origin. Most notably, the increasing numbers of mt-variants as well as the increasing frequency of a particular mt-hot-spot mutation refer to the progression of the HCC dedifferentiation. This accumulation of mt-hot-spot variants in highly dedifferentiated nodules was associated with an enrichment of nuclear mutations as shown in the RPS6KA3, TP53, ARID2, ARID1A or the ATM gene. In conclusion, screening of mitochondrial genome by ultra-deep sequencing is a reliable and useful molecular tool to identify pre-tumorous nodules with high transformation potential and to illustrate tumor clonality and history. Early appearance and high frequency of mt-hot spot mutations associated with HCC development and nuclear genomic alterations provide novel insights in cancer diagnostics and therapeutic approaches.

Research paper thumbnail of TGF-beta mediates transcriptional repression of miR–29 a/b1 during liver fibrosis

Zeitschrift für Gastroenterologie, 2012

Research paper thumbnail of Transcriptional promoter regulation of the miR-29a/b1 gene in hepatoma cells

Zeitschrift für Gastroenterologie, 2013

Research paper thumbnail of miR-125b regulates the Lin-28/IGF-II axis during hepatocellular carcinogenesis

Zeitschrift für Gastroenterologie, 2013

Research paper thumbnail of Analysis of microsatellite instability by microfluidic-based electrophoresis

Methods in molecular biology (Clifton, N.J.), 2013

Microsatellites are short repetitive sequences of two, three, or four bases, prone to base mispai... more Microsatellites are short repetitive sequences of two, three, or four bases, prone to base mispairing. Microsatellite instability (MSI) occurs frequently in various types of cancer due to a defective DNA mismatch repair system. Therefore, MSI analysis is an important tool in clinical research and molecular diagnostics. Mostly, polyacrylamide gel electrophoresis or capillary electrophoresis of labeled microsatellite sequences is used for the detection of MSI. Here we present a microfluidic-based electrophoresis technology for MSI analyses. Defined loci of microsatellites were PCR amplified and amplicons were analyzed by microfluidic-based electrophoresis. The electropherogram profiles of tumor and non-tumor derived DNA clearly revealed an individual pattern identifying differences in tumor-associated microsatellites. Detection of MSI by microfluidics turned out to be a simple and efficient procedure but less laborious than conventional approaches. Thus, the chip-based microfluidic el...

Research paper thumbnail of P0289 : Evolution analysis by deep sequencing revealed high impact of the mitochondrial genome in hepatocellular carcinoma initiation and progression

Journal of Hepatology, 2015

Research paper thumbnail of THU-453-Dissecting the landscape of (epi-)genetic alterations during sequential evolution of liver cancer

Journal of Hepatology, 2019

Research paper thumbnail of Tumor tracking and evolution analysis of hepatocellular carcinoma progression by ultra-deep sequencing of the entire mitochondrial genome

Journal of Liver, May 20, 2016

Research paper thumbnail of Communication and System Relevance in Liver Damage and Regeneration January 21 – 22 , 2016

Poster Abstracts Falk Foundation Dr. Falk Pharma Workshop Communication and System Relevance in L... more Poster Abstracts Falk Foundation Dr. Falk Pharma Workshop Communication and System Relevance in Liver Damage

Research paper thumbnail of Comprehensive Analysis of Disease Related Nuclear and Mitochondrial Genes in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the third most lethal cancer due to late detection, high recurr... more Hepatocellular carcinoma (HCC) is the third most lethal cancer due to late detection, high recurrence and limited therapeutics. Although genetic alterations have been recently studied by whole genome or whole exome next generation sequencing, a comprehensive analysis of HCC relevant genes on lesions with low and high grade of dedifferentiation is missing. Herein, I aimed to study the nuclear and mitochondrial genomic alterations in order to characterize HCC development and clonality. First, for target enrichment of HCC relevant genes and mt-genome, gene loci of relevance had to be selected and primer sets designed. Subsequent ultra-deep sequencing revealed that in accordance with previous studies, the β-catenin gene (CTNNB1) was shown to be the most frequently mutated oncogene, whereas the TP53 and AXIN1 genes were the most frequently mutated tumour suppressor genes. Interestingly, CTNNB1 mutations were detected in lesions with early as well as advanced HCC stage, confirming its rol...

Research paper thumbnail of Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis

Research paper thumbnail of Evolution analysis of heterogeneous non-small cell lung carcinoma by ultra-deep sequencing of the mitochondrial genome

Scientific Reports, 2017

Accurate assessment of tumour heterogeneity is an important issue that influences prognosis and t... more Accurate assessment of tumour heterogeneity is an important issue that influences prognosis and therapeutic decision in molecular pathology. Due to the shortage of protective histones and a limited DNA repair capacity, the mitochondrial (mt)-genome undergoes high variability during tumour development. Therefore, screening of mt-genome represents a useful molecular tool for assessing precise cell lineages and tracking tumour history. Here, we describe a highly specific and robust multiplex PCR-based ultra-deep sequencing technology for analysis of the whole mt-genome (wmt-seq) on low quality-DNA from formalin-fixed paraffin-embedded tissues. As a proof of concept, we applied the wmt-seq technology to characterize the clonal relationship of non-small cell lung cancer (NSCLC) specimens with multiple lesions (N = 43) that show either different histological subtypes (group I) or pulmonary adenosquamous carcinoma as striking examples of a mixed-histology tumour (group II). The application...

Research paper thumbnail of P0318 : Ultra-deep sequencing of multiplex-PCR enriched hotspot and disease-related targets in hepatocellular carcinoma

Journal of Hepatology, 2015

Research paper thumbnail of Promoter regulation of the miR-29a/b1 gene by transforming growth factor-β in hepatic stellate cells and in hepatoma cells

Zeitschrift für Gastroenterologie, 2015

Research paper thumbnail of Comprehensive analysis of informative target disease relevant nuclear genes and the whole mitochondrial genome in hepatocellular carcinoma by Multiplex PCR and Ultra-Deep Sequencing

Zeitschrift für Gastroenterologie, 2015

ABSTRACT Hepatocellular carcinoma (HCC) are highly malignant tumors triggered by a wide variety o... more ABSTRACT Hepatocellular carcinoma (HCC) are highly malignant tumors triggered by a wide variety of genetic alterations. Importantly, they show multicentric occurrence characterized by a nodule-in-nodule pattern. In the present study, we investigate the occurrence of disease related nuclear mutations and whole mitochondrial genomic variants by a comprehensive ultra-deep sequencing approach as a novel tool for hepatocellular cancer follow-up and prognosis. Macrodissected 48 HCC nodules, representing different tumor grades, and adjacent non-cancerous tissues from HCC patients were studied. Hot spot mutation screening of nuclear DNA (nDNA) was performed using a multiplex PCR approach covering 40 disease relevant gene regions by a total of 394 amplicons. The mitochondrial (mt) genome is highly susceptible to DNA alterations due to the lack of protective histones and a limited repair system. Therefore, we were using mt-variations as a way of focal cancer barcoding and tracking. Thus, 108 primer sets spanning the whole mtDNA were designed and automatic single PCR set-up was established using the Biomek robotic system. Target enriched libraries of mtDNA and nDNA were sequenced by means of the MiSeq platform and data analysis was performed by the CLC Cancer Research Workbench. Whole mt-genome analysis revealed high frequency of variants in the D-Loop region and the MT-CYB gene. In particular, in HCC nodules of non-cirrhotic origin a wide spectrum of mt-variants with high frequency were identified. However, highly frequent mt-variants occur not only in HCC nodules but also in peri-tumorous parenchymal foci raising the possibility that mtDNA mutations might precede nuclear alterations and play a role in the pre-tumor machinery. Furthermore, the occurrence of identical mt-variants in different nodules of one liver sample indicates the monoclonal HCC origin. Most notably, the increasing numbers of mt-variants as well as the increasing frequency of a particular mt-hot-spot mutation refer to the progression of the HCC dedifferentiation. This accumulation of mt-hot-spot variants in highly dedifferentiated nodules was associated with an enrichment of nuclear mutations as shown in the RPS6KA3, TP53, ARID2, ARID1A or the ATM gene. In conclusion, screening of mitochondrial genome by ultra-deep sequencing is a reliable and useful molecular tool to identify pre-tumorous nodules with high transformation potential and to illustrate tumor clonality and history. Early appearance and high frequency of mt-hot spot mutations associated with HCC development and nuclear genomic alterations provide novel insights in cancer diagnostics and therapeutic approaches.

Research paper thumbnail of TGF-beta mediates transcriptional repression of miR–29 a/b1 during liver fibrosis

Zeitschrift für Gastroenterologie, 2012

Research paper thumbnail of Transcriptional promoter regulation of the miR-29a/b1 gene in hepatoma cells

Zeitschrift für Gastroenterologie, 2013

Research paper thumbnail of miR-125b regulates the Lin-28/IGF-II axis during hepatocellular carcinogenesis

Zeitschrift für Gastroenterologie, 2013

Research paper thumbnail of Analysis of microsatellite instability by microfluidic-based electrophoresis

Methods in molecular biology (Clifton, N.J.), 2013

Microsatellites are short repetitive sequences of two, three, or four bases, prone to base mispai... more Microsatellites are short repetitive sequences of two, three, or four bases, prone to base mispairing. Microsatellite instability (MSI) occurs frequently in various types of cancer due to a defective DNA mismatch repair system. Therefore, MSI analysis is an important tool in clinical research and molecular diagnostics. Mostly, polyacrylamide gel electrophoresis or capillary electrophoresis of labeled microsatellite sequences is used for the detection of MSI. Here we present a microfluidic-based electrophoresis technology for MSI analyses. Defined loci of microsatellites were PCR amplified and amplicons were analyzed by microfluidic-based electrophoresis. The electropherogram profiles of tumor and non-tumor derived DNA clearly revealed an individual pattern identifying differences in tumor-associated microsatellites. Detection of MSI by microfluidics turned out to be a simple and efficient procedure but less laborious than conventional approaches. Thus, the chip-based microfluidic el...

Research paper thumbnail of P0289 : Evolution analysis by deep sequencing revealed high impact of the mitochondrial genome in hepatocellular carcinoma initiation and progression

Journal of Hepatology, 2015