The Experts below are selected from a list of 309 Experts worldwide ranked by ideXlab platform

Hisashi Tanaka - One of the best experts on this subject based on the ideXlab platform.

  • Replication fork integrity and intra-S phase checkpoint suppress Gene Amplification
    Nucleic acids research, 2015
    Co-Authors: Anna A. Kondratova, Takaaki Watanabe, Michael Marotta, Matthew V. Cannon, Anca M. Segall, David Serre, Hisashi Tanaka
    Abstract:

    Gene Amplification is a phenotype-causing form of chromosome instability and is initiated by DNA double-strand breaks (DSBs). Cells with mutant p53 lose G1/S checkpoint and are permissive to Gene Amplification. In this study we show that mammalian cells become proficient for spontaneous Gene Amplification when the function of the DSB repair protein complex MRN (Mre11/Rad50/Nbs1) is impaired. Cells with impaired MRN complex experienced severe replication stress and gained substrates for Gene Amplification during replication, as evidenced by the increase of replication-associated single-stranded breaks that were converted to DSBs most likely through replication fork reversal. Impaired MRN complex directly compromised ATM/ATR-mediated checkpoints and allowed cells to progress through cell cycle in the presence of DSBs. Such compromised intra-S phase checkpoints promoted Gene Amplification independently from mutant p53. Finally, cells adapted to endogenous replication stress by globally suppressing Genes for DNA replication and cell cycle progression. Our results indicate that the MRN complex suppresses Gene Amplification by stabilizing replication forks and by securing DNA damage response to replication-associated DSBs.

  • Abstract #1310: An underlying mechanism of palindromic Gene Amplification in cancer
    Cancer Research, 2009
    Co-Authors: Hisashi Tanaka, Stephen J. Tapscott, Meng-chao Yao
    Abstract:

    The clinical importance of Gene Amplification in cancer has been well recognized, as it is often evident in patients with an unfavorable prognosis and resistance to therapy. Thus, delineating the molecular mechanisms at the beginning of Gene Amplification is necessary in order to achieve early detection and prevention of Gene Amplification. Gene Amplification occurs as a result of structural aberrations of genomic regions. A DNA double strand break (DSB) is a dangerous lesion that leads to structural aberrations. However, how a DSB is processed to a structural aberration that establishes an amplified genomic region is still largely unknown. Using an induced chromosomal DSB in mammalian cell systems, we identified that a prevalent DNA rearrangement at the beginning of Gene Amplification is an inverted duplication (the formation of a large DNA palindrome) that increases the copy number from one to two. Importantly, the formation of palindrome is greatly facilitated by the presence of a short DNA inverted repeat next to the site of DSB. These data indicate that a beginning step of Gene Amplification is a DNA rearrangement between the repeated sequences near a DSB. In order to determine whether the formation of DNA palindromes is associated with Gene Amplification in cancer cells, we have developed a microarray-based approach Genome-wide Analysis of Palindrome Formation (GAPF). GAPF determines the location of DNA palindromes in the genome by hybridizing snap-back DNA, a pool of DNA that is enriched in DNA derived from palindromes on a microarray. Palindromic DNA can form double-stranded DNA by intra-strand annealing after de-naturation and quick re-naturation (snap-back), whereas non-palindromic DNA remains single-stranded after snap-back. Subsequent digestion of single-stranded DNA by nuclease S1 achieves the enrichment of palindromes. Based on the genome-wide locations of DNA palindromes and copy-number gain/loss in colon cancer cells, we show (1) that the location of DNA palindromes are more likely to be amplified, and (2) that DNA palindromes determine the boundaries of a highly amplified region. Consistent with our finding in cell culture model, a pre-existing 29 kb DNA inverted repeat is located at the boundary, strongly suggesting the DNA rearrangement between the repeated sequences as the underlying mechanism of palindrome formation. Therefore, we propose three important components for the underlying mechanism of Gene Amplification in cancer: DNA inverted repeats pre-existing in the genome, DNA palindromes at the beginning of Gene Amplification and highly amplified genomic regions. Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 1310.

  • Palindromic Gene Amplification — an evolutionarily conserved role for DNA inverted repeats in the genome
    Nature Reviews Cancer, 2009
    Co-Authors: Hisashi Tanaka, Meng-chao Yao
    Abstract:

    Gene Amplification is an essential process in several organisms including the ciliate Tetrahymena thermophila . What can Amplification in this model system teach us about mechanisms of Amplification in cancer cells? The clinical importance of Gene Amplification in the diagnosis and treatment of cancer has been widely recognized, as it is often evident in advanced stages of diseases. However, our knowledge of the underlying mechanisms is still limited. Gene Amplification is an essential process in several organisms including the ciliate Tetrahymena thermophila , in which the initiating mechanism has been well characterized. Lessons from such simple eukaryotes may provide useful information regarding how Gene Amplification occurs in tumour cells.

Elena Giulotto - One of the best experts on this subject based on the ideXlab platform.

  • Gene Amplification in human cells knocked down for RAD54
    Genome integrity, 2011
    Co-Authors: Aurora Ruiz-herrera, Alexandra Smirnova, Lela Khouriauli, Solomon G. Nergadze, Chiara Mondello, Elena Giulotto
    Abstract:

    Background In mammalian cells Gene Amplification is a common manifestation of genome instability promoted by DNA double-strand breaks (DSBs). The repair of DSBs mainly occurs through two mechanisms: non-homologous end-joining (NHEJ) and homologous recombination (HR). We previously showed that defects in the repair of DSBs via NHEJ could increase the frequency of Gene Amplification. In this paper we explored whether a single or a combined defect in DSBs repair pathways can affect Gene Amplification.

  • Gene Amplification in human cells knocked down for RAD54
    Genome Integrity, 2011
    Co-Authors: Aurora Ruiz-herrera, Alexandra Smirnova, Lela Khouriauli, Solomon G. Nergadze, Chiara Mondello, Elena Giulotto
    Abstract:

    Background In mammalian cells Gene Amplification is a common manifestation of genome instability promoted by DNA double-strand breaks (DSBs). The repair of DSBs mainly occurs through two mechanisms: non-homologous end-joining (NHEJ) and homologous recombination (HR). We previously showed that defects in the repair of DSBs via NHEJ could increase the frequency of Gene Amplification. In this paper we explored whether a single or a combined defect in DSBs repair pathways can affect Gene Amplification. Results We constructed human cell lines in which the expression of RAD54 and/or DNA-PKcs was constitutively knocked-down by RNA interference. We analyzed their radiosensitivity and their capacity to Generate amplified DNA. Our results showed that both RAD54 and DNA-PKcs deficient cells are hypersensitive to γ-irradiation and Generate methotrexate resistant colonies at a higher frequency compared to the proficient cell lines. In addition, the analysis of the cytoGenetic organization of the amplicons revealed that isochromosome formation is a prevalent mechanism responsible for copy number increase in RAD54 defective cells. Conclusions Defects in the DSBs repair mechanisms can influence the organization of amplified DNA. The high frequency of isochromosome formation in cells deficient for RAD54 suggests that homologous recombination proteins might play a role in preventing rearrangements at the centromeres.

  • Gene Amplification, radiation sensitivity and DNA double-strand breaks.
    Mutation research, 2010
    Co-Authors: Chiara Mondello, Alexandra Smirnova, Elena Giulotto
    Abstract:

    DNA double-strand breaks (DSBs) are one of the main types of damage induced by ionizing radiations. Free DNA ends that are not correctly repaired can be engaged in pathways triggering Gene Amplification. Following Gene Amplification the copy number of a portion of the genome is increased, leading to an enhanced expression of the Genes located in the amplified region. Gene Amplification plays an important role in cancer, being one of the mechanisms of oncoGene activation; in addition, it can confer resistance to chemotherapeutic agents, through the increase in the copy number of Genes coding for drug targets. The presence of Gene Amplification can have a prognostic and a diagnostic value and can help in orienting therapy in specific tumour types. The amplified DNA is primarily produced through recombination-based pathways and can be located either within chromosomes or on extra-chromosomal acentric elements. Studies on the organization of the amplified DNA in tumour cells and in cultured drug resistant cells have suggested that a single DSB can trigger a cascade of events leading to a large number of copies of a region of the genome. In addition, it has been shown that amplified DNA is unstable, further increasing the long-term effect of the initial event. Gene Amplification is a peculiar feature of transformed cells and the ability to amplify is strongly influenced by the cellular Genetic background. Genes involved in DNA damage response and in DNA damage repair can play a role in controlling the Amplification process, in particular, it has been shown that defects in DSB repair functions can increase the frequency of Gene Amplification. In this review, we will discuss the biological significance of Gene Amplification, together with the role of DNA DSBs and DSB repair Genes in the Generation of amplified DNA.

  • Inhibition of Gene Amplification in telomerase deficient immortalized mouse embryonic fibroblasts.
    Carcinogenesis, 2006
    Co-Authors: Paola Rebuzzini, Elena Giulotto, Paola Martinelli, Maria A. Blasco, Chiara Mondello
    Abstract:

    Mutations in Genes important for the preservation of genome stability can increase the frequency of Gene Amplification, a process relevant to tumor development. To investigate whether telomerase, the enzyme deputed to telomere maintenance, also plays a role in Gene Amplification, we studied the Amplification of the carbamyl-P-synthetase, aspartate transcarbamilase, dihydro-orotase (CAD) Gene in immortalized embryonic fibroblasts derived from telomerase knockout mice (mTERC −/− ) of the first and of the sixth Generation. As expected, in 9 out of 10 N-(phosphonacetyl)-l-aspartate (PALA) resistant clones derived from wild-type cells, CAD was amplified; in contrast, in none of the 30 PALA resistant clones isolated from the three mTERC −/− cell lines we could detect CAD Amplification, indicating that, in the absence of telomerase activity, Gene Amplification is inhibited. The causal relationship between mTERC deficiency and lack of Gene Amplification was demonstrated by the restoration of CAD Gene Amplification in two of the three deficient cell lines transfected with mTERC. The lack of Amplification in mTERC deficient cells could be related to a defect in the stabilization of the ends of the amplified chromosomes in the absence of telomerase, to a more General effect of telomerase in the regulation of Gene expression, including Genes involved in Amplification, or to a possible interaction of the telomerase RNA with proteins involved in Gene Amplification.

Chiara Mondello - One of the best experts on this subject based on the ideXlab platform.

  • Gene Amplification in human cells knocked down for RAD54
    Genome integrity, 2011
    Co-Authors: Aurora Ruiz-herrera, Alexandra Smirnova, Lela Khouriauli, Solomon G. Nergadze, Chiara Mondello, Elena Giulotto
    Abstract:

    Background In mammalian cells Gene Amplification is a common manifestation of genome instability promoted by DNA double-strand breaks (DSBs). The repair of DSBs mainly occurs through two mechanisms: non-homologous end-joining (NHEJ) and homologous recombination (HR). We previously showed that defects in the repair of DSBs via NHEJ could increase the frequency of Gene Amplification. In this paper we explored whether a single or a combined defect in DSBs repair pathways can affect Gene Amplification.

  • Gene Amplification in human cells knocked down for RAD54
    Genome Integrity, 2011
    Co-Authors: Aurora Ruiz-herrera, Alexandra Smirnova, Lela Khouriauli, Solomon G. Nergadze, Chiara Mondello, Elena Giulotto
    Abstract:

    Background In mammalian cells Gene Amplification is a common manifestation of genome instability promoted by DNA double-strand breaks (DSBs). The repair of DSBs mainly occurs through two mechanisms: non-homologous end-joining (NHEJ) and homologous recombination (HR). We previously showed that defects in the repair of DSBs via NHEJ could increase the frequency of Gene Amplification. In this paper we explored whether a single or a combined defect in DSBs repair pathways can affect Gene Amplification. Results We constructed human cell lines in which the expression of RAD54 and/or DNA-PKcs was constitutively knocked-down by RNA interference. We analyzed their radiosensitivity and their capacity to Generate amplified DNA. Our results showed that both RAD54 and DNA-PKcs deficient cells are hypersensitive to γ-irradiation and Generate methotrexate resistant colonies at a higher frequency compared to the proficient cell lines. In addition, the analysis of the cytoGenetic organization of the amplicons revealed that isochromosome formation is a prevalent mechanism responsible for copy number increase in RAD54 defective cells. Conclusions Defects in the DSBs repair mechanisms can influence the organization of amplified DNA. The high frequency of isochromosome formation in cells deficient for RAD54 suggests that homologous recombination proteins might play a role in preventing rearrangements at the centromeres.

  • Gene Amplification, radiation sensitivity and DNA double-strand breaks.
    Mutation research, 2010
    Co-Authors: Chiara Mondello, Alexandra Smirnova, Elena Giulotto
    Abstract:

    DNA double-strand breaks (DSBs) are one of the main types of damage induced by ionizing radiations. Free DNA ends that are not correctly repaired can be engaged in pathways triggering Gene Amplification. Following Gene Amplification the copy number of a portion of the genome is increased, leading to an enhanced expression of the Genes located in the amplified region. Gene Amplification plays an important role in cancer, being one of the mechanisms of oncoGene activation; in addition, it can confer resistance to chemotherapeutic agents, through the increase in the copy number of Genes coding for drug targets. The presence of Gene Amplification can have a prognostic and a diagnostic value and can help in orienting therapy in specific tumour types. The amplified DNA is primarily produced through recombination-based pathways and can be located either within chromosomes or on extra-chromosomal acentric elements. Studies on the organization of the amplified DNA in tumour cells and in cultured drug resistant cells have suggested that a single DSB can trigger a cascade of events leading to a large number of copies of a region of the genome. In addition, it has been shown that amplified DNA is unstable, further increasing the long-term effect of the initial event. Gene Amplification is a peculiar feature of transformed cells and the ability to amplify is strongly influenced by the cellular Genetic background. Genes involved in DNA damage response and in DNA damage repair can play a role in controlling the Amplification process, in particular, it has been shown that defects in DSB repair functions can increase the frequency of Gene Amplification. In this review, we will discuss the biological significance of Gene Amplification, together with the role of DNA DSBs and DSB repair Genes in the Generation of amplified DNA.

  • Inhibition of Gene Amplification in telomerase deficient immortalized mouse embryonic fibroblasts.
    Carcinogenesis, 2006
    Co-Authors: Paola Rebuzzini, Elena Giulotto, Paola Martinelli, Maria A. Blasco, Chiara Mondello
    Abstract:

    Mutations in Genes important for the preservation of genome stability can increase the frequency of Gene Amplification, a process relevant to tumor development. To investigate whether telomerase, the enzyme deputed to telomere maintenance, also plays a role in Gene Amplification, we studied the Amplification of the carbamyl-P-synthetase, aspartate transcarbamilase, dihydro-orotase (CAD) Gene in immortalized embryonic fibroblasts derived from telomerase knockout mice (mTERC −/− ) of the first and of the sixth Generation. As expected, in 9 out of 10 N-(phosphonacetyl)-l-aspartate (PALA) resistant clones derived from wild-type cells, CAD was amplified; in contrast, in none of the 30 PALA resistant clones isolated from the three mTERC −/− cell lines we could detect CAD Amplification, indicating that, in the absence of telomerase activity, Gene Amplification is inhibited. The causal relationship between mTERC deficiency and lack of Gene Amplification was demonstrated by the restoration of CAD Gene Amplification in two of the three deficient cell lines transfected with mTERC. The lack of Amplification in mTERC deficient cells could be related to a defect in the stabilization of the ends of the amplified chromosomes in the absence of telomerase, to a more General effect of telomerase in the regulation of Gene expression, including Genes involved in Amplification, or to a possible interaction of the telomerase RNA with proteins involved in Gene Amplification.

Meng-chao Yao - One of the best experts on this subject based on the ideXlab platform.

  • Abstract #1310: An underlying mechanism of palindromic Gene Amplification in cancer
    Cancer Research, 2009
    Co-Authors: Hisashi Tanaka, Stephen J. Tapscott, Meng-chao Yao
    Abstract:

    The clinical importance of Gene Amplification in cancer has been well recognized, as it is often evident in patients with an unfavorable prognosis and resistance to therapy. Thus, delineating the molecular mechanisms at the beginning of Gene Amplification is necessary in order to achieve early detection and prevention of Gene Amplification. Gene Amplification occurs as a result of structural aberrations of genomic regions. A DNA double strand break (DSB) is a dangerous lesion that leads to structural aberrations. However, how a DSB is processed to a structural aberration that establishes an amplified genomic region is still largely unknown. Using an induced chromosomal DSB in mammalian cell systems, we identified that a prevalent DNA rearrangement at the beginning of Gene Amplification is an inverted duplication (the formation of a large DNA palindrome) that increases the copy number from one to two. Importantly, the formation of palindrome is greatly facilitated by the presence of a short DNA inverted repeat next to the site of DSB. These data indicate that a beginning step of Gene Amplification is a DNA rearrangement between the repeated sequences near a DSB. In order to determine whether the formation of DNA palindromes is associated with Gene Amplification in cancer cells, we have developed a microarray-based approach Genome-wide Analysis of Palindrome Formation (GAPF). GAPF determines the location of DNA palindromes in the genome by hybridizing snap-back DNA, a pool of DNA that is enriched in DNA derived from palindromes on a microarray. Palindromic DNA can form double-stranded DNA by intra-strand annealing after de-naturation and quick re-naturation (snap-back), whereas non-palindromic DNA remains single-stranded after snap-back. Subsequent digestion of single-stranded DNA by nuclease S1 achieves the enrichment of palindromes. Based on the genome-wide locations of DNA palindromes and copy-number gain/loss in colon cancer cells, we show (1) that the location of DNA palindromes are more likely to be amplified, and (2) that DNA palindromes determine the boundaries of a highly amplified region. Consistent with our finding in cell culture model, a pre-existing 29 kb DNA inverted repeat is located at the boundary, strongly suggesting the DNA rearrangement between the repeated sequences as the underlying mechanism of palindrome formation. Therefore, we propose three important components for the underlying mechanism of Gene Amplification in cancer: DNA inverted repeats pre-existing in the genome, DNA palindromes at the beginning of Gene Amplification and highly amplified genomic regions. Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 1310.

  • Palindromic Gene Amplification — an evolutionarily conserved role for DNA inverted repeats in the genome
    Nature Reviews Cancer, 2009
    Co-Authors: Hisashi Tanaka, Meng-chao Yao
    Abstract:

    Gene Amplification is an essential process in several organisms including the ciliate Tetrahymena thermophila . What can Amplification in this model system teach us about mechanisms of Amplification in cancer cells? The clinical importance of Gene Amplification in the diagnosis and treatment of cancer has been widely recognized, as it is often evident in advanced stages of diseases. However, our knowledge of the underlying mechanisms is still limited. Gene Amplification is an essential process in several organisms including the ciliate Tetrahymena thermophila , in which the initiating mechanism has been well characterized. Lessons from such simple eukaryotes may provide useful information regarding how Gene Amplification occurs in tumour cells.

Ronald Simon - One of the best experts on this subject based on the ideXlab platform.

  • Estrogen receptor Gene Amplification occurs rarely in ovarian cancer
    Modern Pathology, 2009
    Co-Authors: Rana M Issa, Tobias Grob, Frederik Holst, Matthias Choschzick, Guido Sauter, Annette Lebeau, Luigi Terracciano, Holger Moch, Ronald Simon
    Abstract:

    Amplification of the Gene encoding estrogen receptor- α occurs in about 20% of breast cancers and is an important mechanism for estrogen receptor overexpression in this tumor type. In ovarian cancer, overexpression of estrogen receptor protein has been described in more than two thirds of cases. To study a potential role of estrogen receptor- α Gene Amplification for estrogen receptor overexpression in ovarian cancer, a tumor tissue microarray containing 428 ovarian cancers was analyzed by fluorescence in situ hybridization for estrogen receptor- α Gene Amplification and immunohistochemistry for estrogen receptor expression. The estrogen receptor- α Gene status was successfully determined in 243 of 428 arrayed cancers. Estrogen receptor Gene Amplification was found in 5 of 243 (2%) of tumors. Amplification levels were usually low, with 4–8 estrogen receptor- α Gene copies. However, one case had a high-level Amplification, with more than 30 estrogen receptor- α Gene copies. All five amplified tumors were estrogen receptor positive, with 3 of 5 tumors showing highest (Allred score, 7–8) estrogen receptor levels. The data demonstrate that estrogen receptor- α Amplification occurs only rarely in ovarian cancer.