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Minarikova, Petra, Lucie Benesova, Tereza Halkova, et al. "Prognostic Importance of Cell Cycle Regulators Cyclin D1 (CCND1) and Cyclin-Dependent Kinase Inhibitor 1B (CDKN1B/p27) in Sporadic Gastric Cancers." Gastroenterology Research and Practice 2016 (2016): 1–8. http://dx.doi.org/10.1155/2016/9408190.
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Background. Gastric cancer is known for a notable variety in the course of the disease. Clinical factors, such as tumor stage, grade, and localization, are key in patient survival. It is expected that molecular factors such as somatic mutations and gene amplifications are also underlying tumor biological behavior and may serve as factors for prognosis estimation.Aim. The purpose of this study was to examine gene amplifications from a panel of genes to uncover potential prognostic marker candidates.Methods. A panel of gene amplifications including 71 genes was tested by multiplex ligation-dependent probe amplification (MLPA) technique in 76 gastric cancer samples from a Caucasian population. The correlation of gene amplification status with patient survival was determined by the Kaplan-Meier method.Results. The amplification of two cell cycle regulators,CCND1andCDKN1B, was identified to have a negative prognostic role. The medial survival of patients with gastric cancer displaying amplification compared to patients without amplification was 192 versus 725 days forCCND1(P=0.0012) and 165 versus 611 days forCDKN1B(P=0.0098).Conclusion. Gene amplifications ofCCND1andCDKN1Bare potential candidates to serve as prognostic markers for the stratification of patients based on the estimate of survival in the management of gastric cancer patients.
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Dorsey, M., C. Peterson, K. Bray, and C. E. Paquin. "Spontaneous amplification of the ADH4 gene in Saccharomyces cerevisiae." Genetics 132, no. 4 (1992): 943–50. http://dx.doi.org/10.1093/genetics/132.4.943.
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Abstract Five spontaneous amplifications of the ADH4 gene were identified among 1,894 antimycin A-resistant mutants isolated from a diploid strain after growth at 15 degrees. Four of these amplifications are approximately 40-kb linear extrachromosomal palindromes carrying telomere homologous sequences at each end similar to a previously isolated amplification. ADH4 is located at the extreme left end of chromosome VII, and the extrachromosomal fragments appear to be the fusion of two copies of the end of this chromosome. The fifth amplification is a chromosomal amplification carrying an extra copy of ADH4 on both homologs of chromosome VII. These results suggest that the ADH system can be used to study amplification in Saccharomyces cerevisiae.
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Brochet, Mathieu, Elisabeth Couvé, Mohamed Zouine, Claire Poyart, and Philippe Glaser. "A Naturally Occurring Gene Amplification Leading to Sulfonamide and Trimethoprim Resistance in Streptococcus agalactiae." Journal of Bacteriology 190, no. 2 (2007): 672–80. http://dx.doi.org/10.1128/jb.01357-07.
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ABSTRACT Gene amplifications have been detected as a transitory phenomenon in bacterial cultures. They are predicted to contribute to rapid adaptation by simultaneously increasing the expression of genes clustered on the chromosome. However, genome amplifications have rarely been described in natural isolates. Through DNA array analysis, we have identified two Streptococcus agalactiae strains carrying tandem genome amplifications: a fourfold amplification of 13.5 kb and a duplication of 92 kb. Both amplifications were located close to the terminus of replication and originated independently from any long repeated sequence. They probably arose in the human host and showed different stabilities, the 13.5-kb amplification being lost at a frequency of 0.003 per generation and the 92-kb tandem duplication at a frequency of 0.035 per generation. The 13.5-kb tandem amplification carried the five genes required for dihydrofolate biosynthesis and led to both trimethoprim (TMP) and sulfonamide (SU) resistance. Resistance to SU probably resulted from the increased synthesis of dihydropteroate synthase, the target of this antibiotic, whereas the amplification of the whole pathway was responsible for TMP resistance. This revealed a new mechanism of resistance to TMP involving an increased dihydrofolate biosynthesis. This is, to our knowledge, the first reported case of naturally occurring antibiotic resistance resulting from genome amplification in bacteria. The low stability of DNA segment amplifications suggests that their role in antibiotic resistance might have been underestimated.
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Haferlach, Claudia, Vera Grossmann, Melanie Zenger, et al. "Gene Amplifications Are Rare Events in AML and MDS and Are Associated with Complex Karyotype, TP53 Deletions and Very Poor Survival." Blood 118, no. 21 (2011): 2524. http://dx.doi.org/10.1182/blood.v118.21.2524.2524.
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Abstract Abstract 2524 Background: Gene amplifications are usually defined as the presence of more than 6 copies of a gene per cell. These supernumerary copies are located either extrachromosomally in double minutes (small acentric chromosome structures) or intrachromosomally in homogeneously staining regions. Such gene amplifications are rare but recurrent phenomenons in AML and MDS. So far, only small case studies have been reported. Aims: 1) to determine the frequency of gene amplifications in a large AML and MDS cohort, 2) to characterize the amplified regions and accompanying abnormalities, 3) to analyze the impact of specific amplifications on outcome. Patients and Methods: Out of 4,248 AML and 3,689 MDS studied by chromosome banding analysis (CBA) we identified 105 AML patients (2.5%) with gene amplifications (80/3,478 (2.3%) de novo AML, 7/478 (1.5%) s-AML, 18/292 (6.2%) t-AML) and 46 (1.2%) MDS. All cases with gene amplification were studied by 24-color FISH in addition to CBA in order to characterize the amplified regions and the accompanying abnormalities in detail. Further, interphase (IP)-FISH was performed with probes for TP73, HOXD cluster, EVI1, CMYC, JAK2, NUP214, MLL, ZNF4, GLTSCR1, ERG, RUNX1, BCR and CLRF, if 24-color FISH suggested amplification of these genes. In a subcohort of 12 patients genomic arrays (Human CGH Whole-Genome Array, NimbleGen, Madison, WI; Genome-Wide Human SNP Array 6.0, Affymetrix, Santa Clara, CA) were performed to characterize the amplified region in more detail. Results: In 28/151 pts (18.5%) the amplification was located in double minutes and in the remaining 123 cases intrachromosomally (81.5%). The following regions were found to be amplified: 1p (n=1, containing TP73), 2q (n=1, containing HOXD cluster), 3q (n=1, containing EVI1), 7p (n=1), 8q (n=29, containing CMYC in 28/29 pts), 9p (n=2, containing JAK2), 9q (n=1, containing NUP214), 11q (n=81, containing MLL in 80/81 cases), 13q (n=2), chromosome 19 (n=10, containing ZNF4 in 5 cases and GLTSCR1 in 2 cases), 21q (n=19, containing ERG in 16 and RUNX1 in 6 cases), 22q (n=2, containing BCR) and Xp (n=1, containing CLRF). In median, 8 accompanying chromosomal aberrations per cases were observed (range 0–21). 124/151 (82.1%) cases had a complex aberrant karyotype, defined as 4 or more abnormalities. However, in 2 cases the double minutes were the sole abnormalities. Gene amplifications were not observed in patients with disease defining aberration like t(8;21), inv(16), t(15;17) or those carrying NPM1 or CEPBA mutations (mutation status available in 89 and 37 patients, respectively). However, 2 cases with t(6;11)(q27;q23)/MLL-AF6 harbored an amplification of CMYC. In 88 cases the copy number status of TP53 was determined by IP-FISH. A TP53 deletion was detected in 49 (55.7%) pts. Interestingly, 14/16 (87.5%) cases with double minutes compared to 35/72 (48.6%) patients with intrachromosomal gene amplifications showed a TP53 deletion (p=0.004). Only 3 chromosomal regions were amplified in double minutes: 8q24/CMYC (n=14), 11q23/MLL (n=12) and 13q (n=2). In 6 cases with 8q amplification, 2 cases with 11q amplification and 4 cases with 21q amplification genomic arrays were performed. While the amplified region was quite homogeneous in cases with 8q amplification and contained in all cases the CMYC gene, amplified regions on 11q and 21q were heterogeneous and amplified regions were interspersed with regions of deletions. Interestingly, MLL and CBL were amplified in all analyzed cases with 11q23 amplification. In all analyzed cases with 21q22 amplification ERG was located within the amplified region while RUNX1 was amplified in 3/4 cases and deleted in the remaining case. In AML, overall survival was short in cases with gene amplification (median OS 11.3 months) and was particularly short in cases accompanied by complex karyotype (6.3 mo vs 18.6 mo in cases with non-complex karyotype, p=0.049). Conclusions: 1) MLL is the most frequently amplified gene in AML and MDS. 2) Gene amplifications occur predominantly in complex aberrant karyotypes. 3) Prognosis is poor in this subset of cases, and even more dismal if these amplifications are accompanied by complex karyotype. 4) The association of gene amplifications, complex karyotypes and TP53 deletions suggests that the unfavorable prognosis is due to chromosome instability facilitating the occurrence of additional genetic aberrations triggering resistance to chemotherapy. Disclosures: Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Grossmann:MLL Munich Leukemia Laboratory: Employment. Zenger:MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.
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Tang, Yidan, Baiyang Lu, Zhentong Zhu, and Bingling Li. "Establishment of a universal and rational gene detection strategy through three-way junction-based remote transduction." Chemical Science 9, no. 3 (2018): 760–69. http://dx.doi.org/10.1039/c7sc03190d.
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Matsui, Atsuka, Tatsuya Ihara, Hiraku Suda, Hirofumi Mikami, and Kentaro Semba. "Gene amplification: mechanisms and involvement in cancer." BioMolecular Concepts 4, no. 6 (2013): 567–82. http://dx.doi.org/10.1515/bmc-2013-0026.
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AbstractGene amplification was recognized as a physiological process during the development of Drosophila melanogaster. Intriguingly, mammalian cells use this mechanism to overexpress particular genes for survival under stress, such as during exposure to cytotoxic drugs. One well-known example is the amplification of the dihydrofolate reductase gene observed in methotrexate-resistant cells. Four models have been proposed for the generation of amplifications: extrareplication and recombination, the breakage-fusion-bridge cycle, double rolling-circle replication, and replication fork stalling and template switching. Gene amplification is a typical genetic alteration in cancer, and historically many oncogenes have been identified in the amplified regions. In this regard, novel cancer-associated genes may remain to be identified in the amplified regions. Recent comprehensive approaches have further revealed that co-amplified genes also contribute to tumorigenesis in concert with known oncogenes in the same amplicons. Considering that cancer develops through the alteration of multiple genes, gene amplification is an effective acceleration machinery to promote tumorigenesis. Identification of cancer-associated genes could provide novel and effective therapeutic targets.
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Vleugel, Marije M., Reinhard Bos, Horst Buerger та ін. "No Amplifications of Hypoxia-Inducible Factor-1α Gene in Invasive Breast Cancer: A Tissue Microarray Study". Analytical Cellular Pathology 26, № 5-6 (2004): 347–51. http://dx.doi.org/10.1155/2004/532413.
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Objective: Hypoxia Inducible Factor‐1 (HIF‐1) is an important transcription factor that stimulates tumour growth and metastases via several pathways, including angiogenesis and altered metabolism. Activation of HIF‐1 depends on the levels of its α‐subunit, which increase during hypoxia. Recent studies showed that the HIF‐1α gene was amplified in prostate cancer, leading to overexpression of HIF‐1α at normoxia. The aim of this study was to evaluate the presence of HIF‐1α gene amplifications in invasive breast cancer as an explanation for HIF‐1α protein overexpression. Methods: Protein and gene expression of HIF‐1α were analyzed on a tissue microarray of 94 breast cancers by immunohistochemistry and fluorescent in situ hybridization (FISH), respectively. Results: Overexpression of HIF‐1α protein was found in 58/94 (62%) of patients. No amplifications of the HIF‐1α gene were detected. Conclusion: Increased protein levels of HIF‐1α are not associated with amplification of the HIF‐1α gene in human breast cancer. Therefore, other mechanisms than gene amplification must be responsible for HIF‐α overexpression at normoxia.
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Saito, I., R. Groves, E. Giulotto, M. Rolfe, and G. R. Stark. "Evolution and stability of chromosomal DNA coamplified with the CAD gene." Molecular and Cellular Biology 9, no. 6 (1989): 2445–52. http://dx.doi.org/10.1128/mcb.9.6.2445.
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We have compared clones of Syrian hamster cells selected for the first amplification of the CAD gene with clones selected for further amplification. The large domain amplified initially was not reamplified as an intact unit. Instead, subregions were reamplified preferentially, and parts of the initial array were often lost. These events reduced the average amount of coamplified DNA accompanying each copy of the selected gene. The degree of amplification was small in the first step (about three extra copies of CAD per cell), but second-step amplifications to a high copy number (up to 60 extra copies per cell) occurred frequently. After several separate steps of amplification, highly condensed arrays that brought many CAD genes close together were formed. In striking contrast to the stability of these highly amplified arrays, the low-copy chromosomal arrays formed early were quite unstable and were often lost completely within 1 or 2 months of growth without selection. The results suggest that different mechanisms may be involved in the first step of amplification and in the later evolution of an already amplified array.
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Saito, I., R. Groves, E. Giulotto, M. Rolfe, and G. R. Stark. "Evolution and stability of chromosomal DNA coamplified with the CAD gene." Molecular and Cellular Biology 9, no. 6 (1989): 2445–52. http://dx.doi.org/10.1128/mcb.9.6.2445-2452.1989.
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We have compared clones of Syrian hamster cells selected for the first amplification of the CAD gene with clones selected for further amplification. The large domain amplified initially was not reamplified as an intact unit. Instead, subregions were reamplified preferentially, and parts of the initial array were often lost. These events reduced the average amount of coamplified DNA accompanying each copy of the selected gene. The degree of amplification was small in the first step (about three extra copies of CAD per cell), but second-step amplifications to a high copy number (up to 60 extra copies per cell) occurred frequently. After several separate steps of amplification, highly condensed arrays that brought many CAD genes close together were formed. In striking contrast to the stability of these highly amplified arrays, the low-copy chromosomal arrays formed early were quite unstable and were often lost completely within 1 or 2 months of growth without selection. The results suggest that different mechanisms may be involved in the first step of amplification and in the later evolution of an already amplified array.
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Moelans, Cathy B., Hanneke N. Monsuur, Johannes H. de Pinth, Remco D. Radersma, Roel A. de Weger, and Paul J. van Diest. "ESR1 Amplification is Rare in Breast Cancer and is Associated with High Grade and High Proliferation: A Multiplex Ligation-Dependent Probe Amplification Study." Analytical Cellular Pathology 33, no. 1 (2010): 13–18. http://dx.doi.org/10.1155/2010/619180.
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Background: Expression of estrogen receptor alpha (ERα) is predictive for endocrine therapy response and an important prognostic factor in breast cancer. Overexpression of ERα can be caused by estrogen receptor 1 (ESR1) gene amplification and was originally reported to be a frequent event associated with a significantly longer survival for ER-positive women treated with adjuvant tamoxifen monotherapy, which was however questioned by subsequent studies.Methods: This study aimed to reanalyze the frequency of ESR1 amplification by multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridisation (FISH), and to assess clinicopathologic correlations. MLPA was performed in a group of 135 breast cancer patients, and gains/amplifications were subjected to FISH.Results: True ESR1 amplification by MLPA was rare (2%) and only 6% more patients showed a modest gain of ESR1. All MLPA-detected ESR1 amplifications and nearly all ESR1 gains were also FISH amplified and gained, but not all FISH amplifications/gains were MLPA amplified/gained, leading to an overall concordance of only 60% between both techniques. All 3 MLPA and FISH ESR1 amplified cases had high ERα expression, but there was no obvious correlation between ESR1 gain and ER status by IHC. ESR1 gains/amplifications were not associated with HER2 gain/amplification, but seemed to be associated with older age. Surprisingly, ESR1 gain/amplification was not associated with low grade as reported previously, but correlated with high grade and high proliferation. Furthermore, ESR1 gain/amplification by MLPA was not associated with nodal status or tumor size (pT status).Conclusion: ESR1 amplification as detected by MLPA is rare in breast cancer, and seems to be associated with high ERα expression, high age, high grade and high proliferation. This study confirms previous studies that showed differences in the ESR1 amplification frequencies detected by different techniques.
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Fang, Mei-yu, Chun-wei Xu, Wen-xian Wang, et al. "Comparison of the c-MET gene amplification between primary tumor and metastatic lymph nodes in non-small cell lung cancer." Journal of Clinical Oncology 35, no. 15_suppl (2017): e23138-e23138. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.e23138.
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e23138 Background: Activation of c-MET lead to a wide range of biological activities. MET has recently been identified as a novel promising target in NSCLC, some c-MET inhibitors have been developed. The primary aim of this study was to evaluate the c-MET amplification status in advanced NSCLC and compare the consistency of c-MET amplification analyses in metastatic lymph nodes and tumor tissue.Methods: Real-time fluorescent quantitative polymerase chain reaction was used to test the tumor tissues in 368 patients of NSCLCs and 178 paired metastatic lymph nodes samples and compared the amplifications consistency inmetastatic lymph nodesand tissue samples, and analyzed the correlation between c-MET gene amplification and clinical characteristics of patients. Another 5 cases of normal lung tissue were taken as negative control.Results: The c-MET gene amplification rate was 8.97%(33/368) in tumor tissues . Of the178 paired cases, c-MET gene amplification was positive in 7.95%(15/178) cancerous tissuesand18.54%(33/178) in metastatic lymph nodes; Of these patients,13 were positive in the two kinds of samples. 20 cases in the paired group were detected positive c-MET in metastatic lymph nodes but was negative in cancerous tissues; 2 cases in the paired group were detected positive c-MET gene amplification in cancerous tissues but was negative in metastatic lymph nodes,there were statistically significant differences between the two samples (χ2= 45.536, P < 0.001). c-MET gene amplification was detected more in metastatic lymph nodes than the primary cancerous tissue. Consistency was evaluated by consistency test(Kappa = 0.482, P < 0.001).When lymph nodes were used as surrogate samples of primary cancerous tissues, sensitivity was86.67%, the specificity was 87.69%.Conclusions: More c-MET gene amplification positive were detected in metastatic lymph nodes compare with the primary cancerous tissue. c-MET gene amplification detected in lymph node metastases could screen more patients suitable for TKI therapy. Lymph node Metastasis can predict the c-MET gene amplification of primary tumor, and guide the clinical use of gene targeted drugs.
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Suryani, Laksmi Ambarsari, and Efi Sanfitri Harahap. "AMPLIFIKASI GEN 16S-rRNA BAKTERI TERMOFILIK DARI SUMBER AIR PANAS, GUNUNG PANCAR BOGOR." Jurnal Riset Kimia 3, no. 1 (2015): 83. http://dx.doi.org/10.25077/jrk.v3i1.97.
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ABSTRACT Exploration of thermophilic bacteria that produce thermostable enzyme is most useful in application for enzyme base industrial. The aim of of this research is to isolate and amplificate the 16S-rRNA gene from thermophilic bacteria isolate at hotspring, Mount of Pancar, Bogor. The research steps consist of bacteria isolation, chromosomal DNA extraction, and amplification of 16S-rRNA gene. The water sample as source for bacteria was collected from four cauldrons. Temperature and pH for each cauldron are red cauldron 75-80°C, pH 7; black cauldron 55°C, pH 7; white cauldron 57°C, pH 7; and saline cauldron 25°C, pH 6, respectively. The bacteria were cultivated at Luria Bertani (LB) and Thermus media. The chromosomal DNA have been extracted. Gene amplification of 16 S-rRNA have been carried out by using universal primer (Bac F1 and Uni B1). The size of amplicon is ± 1.5kb. Keywords : thermophilic bacteria, chromosomal DNA extraction, amplification of 16S-rRNA gene
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Juarez, Ignacio, Juan Francisco Toro-Fernandez, Christian Vaquero-Yuste, et al. "A Reliable and Standardizable Differential PCR and qPCR Methodology Assesses HER2 Gene Amplification in Gastric Cancer." Biology 10, no. 6 (2021): 516. http://dx.doi.org/10.3390/biology10060516.
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We have applied two PCR techniques, differential PCR (diffPCR) and qPCR for the identification of HER2 gene amplifications in genomic DNA of tumor and distal gastric samples from patients with gastric cancer. The diffPCR technique consists of the simultaneous amplification of the HER2 gene and a housekeeping gene by conventional PCR and the densitometric analysis of the bands obtained. We established a cut-off point based on the mean and standard deviation analyzing the DNA of 30 gastric tissues from patients undergoing non-cancer gastrectomy. diffPCR and qPCR yielded consistent results. HER2-overexpression was detected in 25% of patients and was further confirmed by immunohistochemistry and immunofluorescence. The approaches herein described may serve as complementary and reliable methods to assess HER2 amplification.
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J, Nagalakshmi, Suresh R., S. Archana, and Eswari V. "Study of HER-2 Gene Amplification by Chromogenic in-situ hybridization and HER-2 Protein Amplification by IHC in Breast Cancer using Manual Tissue Microarray Sections." Indian Journal of Pathology: Research and Practice 7, no. 2 (2018): 189–97. http://dx.doi.org/10.21088/ijprp.2278.148x.7218.10.
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Restrepo, Carlos M., Alejandro Llanes, Eymi M. Cedeño, et al. "Environmental Conditions May Shape the Patterns of Genomic Variations in Leishmania panamensis." Genes 10, no. 11 (2019): 838. http://dx.doi.org/10.3390/genes10110838.
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Due to the absence of transcriptional regulation of gene expression in Leishmania parasites, it is now well accepted that several forms of genomic variations modulate the levels of critical proteins through changes in gene dosage. We previously observed many of these variations in our reference laboratory strain of L. panamensis (PSC-1 strain), including chromosomes with an increased somy and the presence of a putative linear minichromosome derived from chromosome 34. Here, we compared the previously described genomic variations with those occurring after exposure of this strain to increasing concentrations of trivalent antimony (SbIII), as well as those present in two geographically unrelated clinical isolates of L. panamensis. We observed changes in the somy of several chromosomes, amplifications of several chromosomal regions, and copy number variations in gene arrays after exposure to SbIII. Occurrence of amplifications potentially beneficial for the Sb-resistant phenotype appears to be associated with the loss of other forms of amplification, such as the linear minichromosome. In contrast, we found no evidence of changes in somy or amplification of relatively large chromosomal regions in the clinical isolates. In these isolates, the predominant amplifications appear to be those that generate genes arrays; however, in many cases, the amplified arrays have a notably higher number of copies than those from the untreated and Sb-treated laboratory samples.
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Steinwald, Peter, Elisa Ledet, Bryce Raymon Christensen, et al. "Cell-free DNA (cfDNA) analysis and evaluation of BRAF amplifications and mutations in metastatic castration-resistant prostate cancer." Journal of Clinical Oncology 36, no. 6_suppl (2018): 255. http://dx.doi.org/10.1200/jco.2018.36.6_suppl.255.
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255 Background: Cell-free DNA (cfDNA) is an accessible method for characterizing tumoral alterations. We report cfDNA screenings of prostate cancer pts positive for BRAF amplifications/mutations in pts with metastatic CRPC. Methods: Guardant360 testing (Guardant Health, Inc.) assesses cell-free DNA analysis using sequencing to identify genomic alterations in 73 cancer-related genes in circulation. A total of 133 metastatic castrate resistant prostate cancer (mCRPC) pts in various stages of therapy had Guardant cfDNA analyses. Treatment histories prior to testing and concurrent cfDNA alterations were analyzed. Results: BRAF amplifications were detected in 32 (24%) mCRPC pts; 5 pts had concurrent BRAF mutations. Of the mutations detected, only one (K601E, n = 2) was a known activating mutation while all others were variants of unknown significance (VUS). One K601E mutation pt had no other cfDNA alterations. Additionally, 4 pts without BRAF amplification had VUS BRAF mutations. BRAF amplification pts had ≥ 2 concurrent gene amplifications/alterations with the median being 8. The most common recurrent amplifications/alterations were AR (75%), p53 (59%), CDK6 (53%), MET (50%), and MYC (50%). Abiraterone (Abi) and/or Enzalutamide (Enza) resistance was associated with BRAF amplification (p = 0.0042). Non-Abi/Enza resistance pts were less likely to have BRAF amplification. The 2 pts with BRAF K601E mutation were treated with targeted protocol therapy without success however one K601E pts was subsequently treated with cabazitaxel+carboplatin which produced a positive clinical response and a 99.79% reduction in PSA. Conclusions: Pts resistant to Abi/Enza have an increased risk of developing BRAF amplifications. BRAF amplifications arise in the context of multiple additional detectable cfDNA alterations. Identification of actionable mutations, such as BRAF K601E, illustrates the potential for cfDNA testing to direct pt treatment. As cfDNA profiling continues to expand, the ability translate alterations into clinically actionable strategies is critical.
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Patterson, Thomas E., Elizabeth B. Albrecht, Paul Nurse, Shelley Sazer, and George R. Stark. "Effects of Genome Position and the DNA Damage Checkpoint on the Structure and Frequency of sod2 Gene Amplification in Fission Yeast." Molecular Biology of the Cell 10, no. 7 (1999): 2199–208. http://dx.doi.org/10.1091/mbc.10.7.2199.
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The Schizosaccharomyces pombe sod2 gene, located near the telomere on the long arm of chromosome I, encodes a Na+ (or Li+)/H+ antiporter. Amplification of sod2 has previously been shown to confer resistance to LiCl. We analyzed 20 independent LiCl-resistant strains and found that the only observed mechanism of resistance is amplification of sod2. The amplicons are linear, extrachromosomal elements either 225 or 180 kb long, containing bothsod2 and telomere sequences. To determine whether proximity to a telomere is necessary for sod2amplification, a strain was constructed in which the gene was moved to the middle of the same chromosomal arm. Selection of LiCl-resistant strains in this genetic background also yielded amplifications ofsod2, but in this case the amplified DNA was exclusively chromosomal. Thus, proximity to a telomere is not a prerequisite for gene amplification in S. pombe but does affect the mechanism. Relative to wild-type cells, mutants with defects in the DNA damage aspect of the rad checkpoint control pathway had an increased frequency of sod2 amplification, whereas mutants defective in the S-phase completion checkpoint did not. Two models for generating the amplified DNA are presented.
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Gallardo, Teresa D., Robert E. Hammer, and Daniel J. Garry. "RNA amplification and transcriptional profiling for analysis of stem cell populations." genesis 37, no. 2 (2003): 57–63. http://dx.doi.org/10.1002/gene.10223.
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Green, M. R., E. Camilleri, M. K. Gandhi, J. Peake, and L. R. Griffiths. "A novel immunodeficiency disorder characterized by genetic amplification of interleukin 25." Genes & Immunity 12, no. 8 (2011): 663–66. http://dx.doi.org/10.1038/gene.2011.50.
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Yoshimoto, Maisa, Silvia Regina Caminada de Toledo, Eliana Maria Monteiro Caran, et al. "MYCN Gene Amplification." American Journal of Pathology 155, no. 5 (1999): 1439–43. http://dx.doi.org/10.1016/s0002-9440(10)65457-0.
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Kelly, B. T., and A. D. Griffiths. "Selective gene amplification." Protein Engineering Design and Selection 20, no. 12 (2007): 577–81. http://dx.doi.org/10.1093/protein/gzm060.
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Difilippantonio, Michael J., Simone Petersen, Hua Tang Chen, et al. "Evidence for Replicative Repair of DNA Double-Strand Breaks Leading to Oncogenic Translocation and Gene Amplification." Journal of Experimental Medicine 196, no. 4 (2002): 469–80. http://dx.doi.org/10.1084/jem.20020851.
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Nonreciprocal translocations and gene amplifications are commonly found in human tumors. Although little is known about the mechanisms leading to such aberrations, tissue culture models predict that they can arise from DNA breakage, followed by cycles of chromatid fusion, asymmetric mitotic breakage, and replication. Mice deficient in both a nonhomologous end joining (NHEJ) DNA repair protein and the p53 tumor suppressor develop lymphomas at an early age harboring amplification of an IgH/c-myc fusion. Here we report that these chromosomal rearrangements are initiated by a recombination activating gene (RAG)-induced DNA cleavage. Subsequent DNA repair events juxtaposing IgH and c-myc are mediated by a break-induced replication pathway. Cycles of breakage-fusion-bridge result in amplification of IgH/c-myc while chromosome stabilization occurs through telomere capture. Thus, mice deficient in NHEJ provide excellent models to study the etiology of unbalanced translocations and amplification events during tumorigenesis.
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Huang, Ta-Chen, Wei-Wu Chen, Ta-Wen Hsu, et al. "Prevalence of gene amplifications of SOX-2, c-MET, and FGFR1 in Asian patients with esophageal squamous cell carcinoma." Journal of Clinical Oncology 31, no. 15_suppl (2013): e15127-e15127. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e15127.
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e15127 Background: Amplifications of SOX-2, c-MET, and FGFR1 have recently been recognized as important molecular derangements with therapeutic implication in squamous cell carcinoma of lung. We investigated the significance of these molecular derangements in esophageal squamous cell carcinoma (ESCC). Methods: Locally advanced ESCC patients who had received curative- intent loco-regional therapy and had available pre-treatment endoscopic biopsy tissues at National Taiwan University Hospital, Taipei, Taiwan, were enrolled. DNA was extracted from formalin-fixed paraffin-embedded tissues. Amplifications of SOX-2, c-MET, and FGFR1 were evaluated by quantitative PCR (TaqMan Copy Number Assay, Applied Biosystems, CA, USA), using TERT as a reference gene. Amplification of specific gene was defined as a copy number more than 4. Results: Forty locally advanced ESCC patients, M: F= 39: 1 with a median age of 56 years (range: 37 to 80), were included. The primary tumors located at cervical, upper thoracic, middle thoracic, and lower thoracic esophagus in 2, 9, 23, and 6 patients, respectively; the tumor staging according to AJCC 2002 version was T3N0, AnyTN1, and M1a in 1, 37, and 2 patients, respectively. Amplifications of SOX-2 and c-MET were identified in 14 (35%) and 7 (17.5%) patients, respectively. No FGFR1 amplification was detected. The amplifications of SOX-2 and c-MET were not associated with any known clinical features of the patients, including gender, age (<60 vs ≧60), primary tumor location, clinical stage, and performance status (ECOG 0, 1). Conclusions: Amplifications of SOX-2 and c-MET, existing in significant portions of Asian patients with ESCC, are worthy of exploration as therapeutic targets of ESCC.
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Martinelli, Erika, Teresa Troiani, Vincenzo Sforza, et al. "Sequential HER2 blockade as effective therapy in chemorefractory, HER2 gene-amplified, RAS wild-type, metastatic colorectal cancer: learning from a clinical case." ESMO Open 3, no. 1 (2018): e000299. http://dx.doi.org/10.1136/esmoopen-2017-000299.
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BackgroundConstitutive activation of HER2-dependent intracellular signalling by HER2 gene amplification or by HER2 mutations has been demonstrated as a mechanism of primary and secondary cancer resistance to cetuximab or panitumumab in preclinical and clinical models of metastatic colorectal cancer (mCRC). Both HER2 Amplification for Colorectal Cancer Enhanced Stratification (HERACLES) cohort A and My Pathway clinical trials provided clinical evidence that anti-HER2 therapies could be active in these patients.Patient and methodsHER2 gene amplification and HER2 protein overexpression analysis were performed in tumour tissue by fluorescence in situ hybridisation and immunohistochemistry. HER2 positivity was defined according to HERACLES CRC-specific HER2 scoring criteria. DNA analysis for multiple assessment of gene mutations or amplifications was carried out with the next-generation sequencing (NGS) Ion AmpliSeq Colon and Lung Cancer Panel and by using a more extensive targeted high-multiplex PCR-based NGS panel (OncoMine Comprehensive Assay).ResultsWe report the clinical case of a patient with HER2 gene amplified and RAS/BRAF wild-type mCRC who experienced a long lasting and relevant clinical efficacy from sequential anti-HER2 therapies (trastuzumab plus lapatinib, pertuzumab plus trastuzumab, trastuzumab emtansine, trastuzumab plus capecitabine) achieving a cumulative clinical benefit of 29 months, after failure of the first three lines of standard treatments, which included all the potentially active drugs in mCRC, and which accounted for only 14 months of disease control. HER gene amplification was confirmed by NGS on two different metastatic lesions during the evolution of the disease.ConclusionThe clinical case highlights the role of HER2 gene amplification as a key genetic driver of cancer development and progression in mCRC and suggests that sequential HER2 blockade could be a potential therapeutic strategy.
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Berg, C., A. Hedrum, A. Holmberg, F. Pontén, M. Uhlén, and J. Lundeberg. "Direct solid-phase sequence analysis of the human p53 gene by use of multiplex polymerase chain reaction and alpha-thiotriphosphate nucleotides." Clinical Chemistry 41, no. 10 (1995): 1461–66. http://dx.doi.org/10.1093/clinchem/41.10.1461.
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Abstract Among the candidate cancer-prognostic genes is the p53 tumor suppressor gene, which, when mutated, plays an important role in the development of many types of cancers. To facilitate robust large-scale DNA analysis of microdissected tumor biopsies, we describe a multiplex/nested PCR approach for a simultaneous outer amplification of exons 4-9 of the human p53 gene with parallel amplification of the HLA-DQB1 locus, involving a total of 14 primers. This approach reduces the required number of cells for analysis and avoids any variation in the amplifications of the individual p53 exons during the common outer amplification step. The HLA sequencing allows sample identification because the DQB1 locus is highly polymorphic and is thereby patient-specific. The p53 and HLA amplicons are analyzed by solid-phase sequencing in a semiautomated format. To improve the DNA sequence quality, we used 2'-deoxyribonucleoside 5'-O-1-thiotriphosphates in the sequencing reactions.
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Wełnicka-Jaskiewicz, M., A. żaczek, K. P. Bielawski, et al. "Gene copy numbers of HER family in breast cancer." Journal of Clinical Oncology 25, no. 18_suppl (2007): 10544. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.10544.
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10544 Background: Most clinicopathological analyses of HER alterations in breast cancer were limited to single HER family members. Since the activation of certain HER receptors is possible only as a result of their dimerization, determining the alterations of all four HER genes may be more relevant. The aim of the study was to estimate the frequency of disorders in all four HER genes, and to determine their correlation with the clinical and histological features in breast cancer patients. Methods: Gene copy number (GCN) of ERBB oncogenes was analyzed with double differential PCR (ddPCR) in a consecutive series of 225 breast cancer patients. Statistical analysis was performed with a set of nonparametric tests. Results: Amplifications of HER1, HER2, HER3 and HER4 were detected in 15%, 26%, 10% and 15% of cases respectively, and deletions in 31%, 2%, 2% and 7% cases respectively. Abnormal GCN of at least one, and at least two oncogenes was found in 65% and 31% of the tumors, respectively. Average GCNs of all HER oncogenes significantly correlated with each other. These correlations were particularly high for HER2/HER3, HER2/HER4 and HER3/HER4 (all p<10-8), and were much stronger in N(+) compared to N(-) tumors. HER1 deletions were associated with the lack of progesterone receptor (p=0.03), whereas HER3 and HER4 amplifications were more common in well differentiated tumors (p=0.03 and 0.047 respectively). At univariate analysis disease-free survival (DFS) and overall survival (OS) were related with T and N stage, and HER1 amplification. The multivariate analysis showed that DFS was influenced by T, N and HER1 amplification, whereas OS by T, N and tumor grade. Conclusions: Our results indicate a key role of HER heterodimers in tumor progression and confirm that HER2 is the preferred partner for other HER oncogenes in this process. Deletions of HER1 were associated with unfavourable characteristics, whereas HER3 and HER4 amplifications may be linked with less aggressive phenotypes. No significant financial relationships to disclose.
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Wei, Zhigang, Jie Wang, Hua Bai, et al. "FGFR1 amplification and EGFR mutation in Chinese squamous cell lung cancer." Journal of Clinical Oncology 30, no. 15_suppl (2012): 7545. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.7545.
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7545 Background: Squamous cell lung cancer (SCC) lacks for effective targeted therapies. FGFR1 amplification has emerged as a potential biomarker. This study aimed to explore clinicopathologic characteristics of FGFR1 amplification in Chinese SCC patients and further explore the correlation between FGFR1 amplification and EGFR mutations. Methods: One hundred seventy-seven SCC patients were included in this retrospective study. Gene copy number of FGFR1 and EGFR mutations were detected by fluorescence in situ hybridization (FISH) and denaturing high-performance liquid chromatography (DHPLC), respectively. Results: FGFR1 amplifications were detected in 24.9% (44/177) Chinese SCC patients. FGFR1 amplification in SCC was more common in male (28.0%, 40/143) and smokers (28.7%, 39/136) than female (11.8%, 4/34, p=0.049) and nonsmokers (12.2%, 5/41, p=0.032). FGFR1 amplification and EGFR mutations were mutually exclusive (p=0.006), fourty-one of 139(29.4%) patients with wild-type EGFR had FGFR1 amplification, while 3 of 38 (7.9%) patients with EGFR mutation had FGFR1 amplification. Conclusions: FGFR1 amplification was common in Chinese squamous cell lung cancer, and mutually exclusive with EGFR mutations.
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Voutsadakis, Ioannis A. "3q26 Amplifications in Cervical Squamous Carcinomas." Current Oncology 28, no. 4 (2021): 2868–80. http://dx.doi.org/10.3390/curroncol28040251.
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Background: Squamous carcinomas of the uterine cervix often carry mutations of the gene encoding for the catalytic sub-unit of kinase PI3K, PIK3CA. The locus of this gene at chromosome 3q26 and neighboring loci are also commonly amplified. The landscape of 3q26-amplified cases have not been previously characterized in detail in cervical cancer. Methods: Published genomic data and associated clinical data from TCGA cervical cancer cohort were analyzed at cBioportal for amplifications in genes at 3q26. The clinical and molecular characteristics of the group of patients with 3q26 amplifications was compared with the group without 3q26 amplifications. Comparative prevalence of amplification and expression of genes at 3q26 in amplified squamous cervical cancer cases were surveyed as well as 3q26 amplifications in cervical cancer cell line databases. Results: Amplification of 3q26 locus is a prevalent molecular lesion in cervical squamous cell carcinomas encountered in about 15% of cases in TCGA cohort of 247 patients. Cancer-related genes commonly amplified from 3q26 include PIK3CA, TBL1XR1, DCUN1D1, SOX2, MECOM, PRKCI, and TERC. Amplified cases do not completely overlap with PIK3CA mutant cases. Differences exist between 3q26-amplified and non-amplified carcinomas in the frequency of mutations and frequency of other amplifications. Most commonly over-expressed genes in 3q26 amplified cases include PIK3CA, TBL1XR1, DCUN1D1, and less commonly SOX2 and PRKCI. Conclusion: The subset of squamous cervical carcinomas with 3q26 amplifications is not overlapping with cancers carrying PIK3CA mutations and contains, besides PIK3CA, other cancer-associated genes that are over-expressed at the mRNA level, including TBL1XR1 and DCUN1D1. DCUN1D1, a regulator of SCF ubiquitin ligase activity, may be a relevant pathogenic player given the importance of ubiquitination and the proteasome in the disease. These observations could form the basis for therapeutic exploitation in this subset of squamous cervical carcinomas.
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Verma, Ajoy Kumar. "Amplification of Hsp 65 Gene and Usage of Restriction Endonuclease for Identification of Non tuberculous Rapid Grower Mycobacterium." Journal of Medical Science And clinical Research 05, no. 04 (2017): 20545–51. http://dx.doi.org/10.18535/jmscr/v5i4.133.
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Litviakov, N. V., M. K. Ibragimova, M. M. Tsyganov, et al. "ASSOCIATION OF THE COMBINATION OF STEMNESS GENE AMPLIFICATIONS AND COPY NUMBER ABERRATIONS OF WNT-SIGNALING GENES IN BREAST TUMORS WITH METASTASIS." Siberian journal of oncology 19, no. 3 (2020): 78–88. http://dx.doi.org/10.21294/1814-4861-2020-19-3-78-88.
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We studied the association between the presence of 2 or more stemness gene amplifications as well as copy number aberrations (CNAs) of WNT signaling genes in residual breast tumor and metastasis. WNT pathway genes associated with metastasis were identified.Material and Methods. The study included 30 patients with breast cancer, who had 2 or more stemness gene amplifications in the residual tumor after neoadjuvant chemotherapy. Fifteen of the thirty patients developed hematogenous metastases; they constituted a group with metastases, the remaining 15 patients entered the second group without metastases. The tumor DNA was examined using a CytoScanHD Array microarray (Affymetrix, USA).Results. By subtracting amplification and deletion frequencies in 852 cytobands between groups with metastases and without metastases, 21 cytobands were identified with the largest difference in deletion and amplification frequencies. They contain 19/150 of WNT genes (12 activators: SKP1, WNT8A, MAPK9, CCND3, FZD9, WNT8B, CCND1, PLCB2, PRKCB, FZD2, WNT3, WNT9B and 7 negative regulators: GSK3B, APC, CSNK2B, SFRP5, BTRC, TCF7L2, CSNK2A2). A point system was developed: when amplifying WNT-signaling activators or deletion of negative regulators, one point was added to the total score, and vice versa when deleting WNT-signaling activators or amplification of negative regulators, one point was taken from the total amount. It was shown that 93% (14/15) of patients with metastases had a total score higher than 0, while 93% (14/15) of patients without metastases had a total score of zero or less than zero. The differences between the groups were statistically significant according to the two-sided Fisher test with a high level of confidence probability (p=0.000003) and the log-rank test (p=0.00004) when assessing non-metastatic survival by the Kaplan-Mayer method.Conclusion. Nineteen WNT signaling genes were identified. Copy number aberrations of these genes in combination with stemness gene amplifications in residual tumors were associated with metastasis. A new highly effective prognostic factor for breast cancer was identified.
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Willis, Scooter, Victor Manuel Villalobos, Brandon Michael Young, Branimir I. Sikic, and Brian Leyland-Jones. "Frequently deleted genes in ovarian cancer as indicators of platinum response." Journal of Clinical Oncology 31, no. 15_suppl (2013): 5583. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.5583.
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5583 Background: Integrating chromosomal deletions/amplifications with sequencing alterations is increasingly important in the determination of key drivers of outcome in cancer (Leary 2008, Curtis 2012). We introduce a novel computational approach, Gene Set Outcome Analysis, to determine gene signatures constrained to regions with frequent deletion or amplification events in ovarian cancer identified by TCGA. Differential expressions of mRNA from these genes are used as a proxy for loss of function from deletions or amplifications. Methods: Gene signatures from each region were evaluated using log-rank test comparing high and low gene expression groups split by cohort mean. In total, 30,119,708 signatures constrained to 47 deleted and 36 amplified regions were tested for PFS for first line platinum treatment in a random 2/3 split of TCGA ovarian cohort (n=262) resulting in 26,271 gene signatures with p < .001. The remaining 1/3 cohort (n=135) and full cohort (n=397) were used as a replication study where 111 signatures have a p < .01 located in 2 deletion and 1 amplification region. The signature with the lowest p-value from each region that validated in the replication study, were evaluated in GSE9891 (n=179) (Tothill 2008) for PFS when treated with platinum and taxol resulting in gene signatures from 2 deletion regions with p<.05. Results: Greater than mean expression in this gene signature [OXTR, SATB1, WNT7A, SH3BP5, CRBN, ATG7, CRELD1, TMEM43] located at 3p23-p26.2 predicts poor response to platinum chemotherapy in TCGA full ovarian cohort (17.9 vs 14 months p = 1.4E-7) and validates in GSE9891 (19.6 vs 13.3 months p = .014). Using a separate, compact gene signature [CAAP1, LRRC19, IFNA8] located at 9p21.2, samples with lower than mean expression demonstrate increased platinum sensitivity in TCGA full ovarian cohort (12.2 vs 18.2 months p = 1.0E-6) and in GSE9891 (15.5 vs 18.6 p = .055). Conclusions: Response to platinum therapy is an important predictor of survival in high-risk ovarian cancer patients. These signatures arising from common deletion and amplification events in ovarian cancer can anticipate platinum sensitivity and merits further study for use in choosing optimal therapies studying platinum resistance mechanisms.
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Takeda, Maiko, Takahiko Kasai, Kinta Hatakeyama, et al. "Association Between Clinicopathological Factors and Genomic Abnormalities Detected by FISH Analysis in Epithelioid Diffuse Malignant Pleural Mesothelioma." International Journal of Surgical Pathology 25, no. 8 (2017): 668–73. http://dx.doi.org/10.1177/1066896917716773.
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Background. Abnormality of genes including 9p21 is known in malignant mesothelioma and we have examined the frequency of gene deletion and amplification using the fluorescence in situ hybridization (FISH) method. We formerly reported that abnormality of the genes was more common in the sarcomatoid type than epithelioid type. In this study, we compared the clinicopathological factors including nuclear grade (NG) and genomic abnormality in epithelioid malignant pleural mesothelioma (MPM). Methods. Using paraffin-embedded tissues of 31 epithelioid MPMs, we investigated the presence of gene abnormalities in the genes 9p21, 1p36, 14q32, 22q12, 5p15, 6p, 8q24, and 7p12 by the FISH method, and compared the results with NG, clinical stage, and prognosis. Results. In the higher NG group of epithelioid MPM, more gene amplifications [in particular 5p15 and 8q24(MYC)] were observed, and clinical stage was more advanced. Cases with the amplification of 7p12(EGFR) tended to exhibit a worse prognosis. The significant correlation between histological differentiation and clinical features such as prognosis was not confirmed. Conclusions. NG status in epithelioid MPM may be related to gene alteration and clinical features.
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Roller, Andreas, Simone Weber, Alexander Kohlmann, et al. "Gene Amplifications In 84 Patients With Acute Myeloid Leukemia and 31 Patients With Myelodysplastic Syndrome Investigated By Array CGH." Blood 122, no. 21 (2013): 3724. http://dx.doi.org/10.1182/blood.v122.21.3724.3724.
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Abstract Background Gains and losses of chromosomal material are frequent in AML and MDS and usually lead to loss or gain of a single copy of a whole chromosome, a chromosome arm or small stretches of the chromosome that may be microscopically invisible. More rarely, amplifications of chromosomal regions (defined as the presence of more than 6 copies of a region per cell) are observed. These supernumerary copies are located either extrachromosomally as small acentric chromosomal structures - so called double-minutes (dmin) - or intrachromosomally as large contiguous stretches of amplified DNA, so called homogeneously staining regions (HSR). Aims Characterize AML and MDS cases with gene amplifications with respect to size, affected genes and accompanying chromosomal abnormalities as well as TP53 status. Patients and Methods 84 AML and 31 MDS cases with cytogenetically visible amplifications were selected for this study. All cases were analyzed by array CGH, chromosome banding analysis, sequencing for TP53 mutations as well as FISH for TP53 deletions. Results The cohort comprised 55 (47.8%) males and 60 (52.2%) females with a median age of 72.0 years (range 38.0 - 90.3 years). A complex karyotype (≥4 aberrations) was present in 92/115 (80.0%) cases (AML=65/84 (77.4%); MDS=27/31 (87.1%)). In total, 385 amplified regions were identified by array CGH. In more detail: 3q26 (AML: n=6; MDS: n=3), 8q24 (AML: n=15; MDS: n=1), 11q21-25 (AML: n=42; MDS: n=13), 13q12 (AML: n=3; MDS: n=1), 13q31 (AML: n=3; MDS: n=2), 19p13 (AML: n=2; MDS: n=4), and 21q21-q22 (AML: n=24; MDS: n=5). The median number of amplified regions was 3 (range 1-18). In 14/115 (12.2%) cases, the amplification was located in dmins (AML: n=11; MDS: n=3) and in 101/115 (87.8%) patients in HSR (AML: n=73; MDS: n=28). In 40 of the latter 101 cases (39.6%) (AML: n=24; MDS: n=16) the amplification was located on a ring chromosome (rc). In patients with complex karyotypes we detected a significantly higher number of amplified regions as compared to non-complex karyotypes (3.5 vs. 2.8; p=0.015). No association between the complexity of the karyotype and the structural type of the amplification (dmin vs rc) was observed. Cases with non-complex karyotypes frequently harbored a 5q deletion (6/23; 26.1%) or chromosome 8 abnormalities (3/23; 13.0%). Within the subgroup of non-complex karyotypes del(5q) cases showed a tendency to a higher number of amplified regions (3.6 vs. 1.9; p=0.140). Further, amplifications of 11q genes were more frequent in complex karyotypes (54.4% vs. 21.7%; p=0.005), whereas 8q amplifications were more frequent in non-complex karyotypes (43.5% vs. 4.4%; p<0.001). We detected a large region on band 11q24, which was amplified in 41/53 (77.4%) cases. This commonly amplified region contains 1,575 genes including the MLL gene. Cases harboring dmins had shorter amplified regions compared to cases with rc (4,428,112.5 bp vs. 18,265,496.9 bp; p=0.028). Moreover, we detected a positive correlation of patients having a rc and gene amplification on chromosome 11q23-25 (p<0.05). On chromosome 3q, 8/9 (88.9%) cases shared a minimal amplified region covering the EVI1 gene. In comparison to samples obtained from healthy donors (n=47), the EVI1 expression was significantly higher in cases with EVI1 amplification (87.4 vs. 0.5; p=0.048). On chromosome 21q the regions of amplifications were heterogeneous. However, we detected a minimal region containing 11 genes including ERG which was amplified in 26/29 (89.7%) patients. ERG expression data was available in 8 cases and was significantly higher compared to a control cohort of AML with normal karyotype (n=331) (729.2 vs. 229.0; p=0.05). On chromosome 8 an amplified region was identified in 15/16 cases. In 14 of these cases (87.5%) the region included MYC. TP53mut were present in 93/115 (80.9%) patients, accompanied by a TP53del in 28/93 (30.1%) cases. Interestingly, cases harboring a TP53mut had more amplified regions compared to TP53wt (3.4 vs. 1.7; p<0.001). Conclusions 1. MLL is the most frequently amplified gene in AML and MDS. 2. Patients with complex karyotypes or TP53mut harbored more amplified regions compared to patients with non-complex karyotypes and TP53wt. 3. Amplifications on 11q were more frequent in complex karyotype whereas gene amplifications on 8q were predominantly observed in non-complex karyotypes. 4. EVI1 and ERG gene amplifications lead to a higher expression of the respective genes. Disclosures: Roller: MLL Munich Leukemia Laboratory: Employment. Weber:MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Zenger:MLL Munich Leukemia Laboratory: Employment. Staller:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.
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Kilgour, Elaine, Xinying Su, Ping Zhan, et al. "Prevalence and prognostic significance of FGF receptor 2 (FGFR2) gene amplification in Caucasian and Korean gastric cancer cohorts." Journal of Clinical Oncology 30, no. 15_suppl (2012): 4124. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.4124.
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4124 Background: Gastric adenocarcinoma is the 4th most common cancer, and many patients present with metastatic or recurrent disease. The prognosis for these patients is poor, with median survival times of 11–12 months. Hence there is a need for identification of potential new drug targets. We have determined the prevalence of FGFR2 gene amplification (FGFR2amp) and its relationship to clinicopathological parameters and survival in Caucasian (n=408) and Korean (n=356) gastric cancers (GC) and determined the overlap with HER2 or cMET gene amplification. Methods: FGFR2, HER2 and cMET gene amplification was assessed by fluorescence in situ hybridisation in GC tissue microarrays from Caucasian and Korean surgically resected gastric carcinomas. Gene amplification was defined as a gene/centromeric probe ratio of ≥2.0 after measuring at least 50 tumour cells. Results: 7% (30/408) of Caucasian and 4% (15/356) of Korean GC showed FGFR2amp, and the incidence was not significantly different between these cohorts (p=0.092). FGFR2amp was significantly associated with lymph node status in both cohorts (p<0.0007, multivariate analysis), and in the Korean cohort with diffuse-type histology, but not with depth of tumour invasion, age or gender. Patients with FGFR2amp showed significantly shorter overall survival in both the Caucasian (HR 2.37, 95% CI 1.6–3.5; p=0.0001) and Korean (HR 2.33, 95% CI 1.28–4.25; p=0.0129) cohorts, by multivariate analysis. There was no overlap between FGFR2amp and HER2 or cMET amplification in the Korean cohort, but two of twenty-six FGFR2amp Caucasian gastric tumours also showed HER2 amplification. Conclusions: This is the first study to demonstrate FGFR2amp, at a prevalence of 4% and 7%, in two large GC cohorts of Asian and Caucasian origin and that FGFR2amp is prognostic and significantly associated with lymph node metastasis. Furthermore, FGFR2amp is generally mutually exclusive with HER2 and cMET amplifications. Based on these observations, FGFR2 inhibitors warrant further investigation in the treatment of FGFR2 amplified GCs.
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Abdalla, D. M., M. A. Hamza, A. E. Kandil, L. K. Younes, and A. F. Sorrour. "MYCN gene amplification and DNA ploidy in peripheral neuroblastic tumors." Journal of Clinical Oncology 27, no. 15_suppl (2009): e22123-e22123. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.e22123.
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e22123 Background: Neuroblastoma is a neuroblastic tumor of the primordial crest cells which are precursors of the sympathetic nervous system and is the most common extracranial solid tumor of childhood comprising between 8 and 10% of all childhood cancers. Neuroblastoma is characterized by a diverse clinical and biological behavior The spectrum of clinical behavior suggests that genetic, biological and morphological features may be useful markers to stratify children with this disease for the most appropriate management Fluorescence in situ hybridization (FISH) is considered the best approach for detection of MYCN amplification because it can detect small copy number gains and copy number heterogeneity among tumor cells. Also, it can determine the source of amplified MYCN signal, whether extrachromosomal double minutes, expanded intrachromosomal region or chromosome 2 aneuploidy. Methods: 30 cases of peripheral neuroblastic tumors were analysed for MYCN oncogene copy number and DNA ploidy using FISH. The 30 cases were divided into: 25 cases of neuroblastoma, 2 cases of ganglioneuroblastoma intermixed, and 3 cases of ganglioneuroma. Results: MYCN oncogene was amplified in 8 out of 30 cases (27.5%). 3 cases showed double minutes, 3 cases showed homogenously staining regions and 2 cases showed both forms of amplification. As regard DNA ploidy, 18 cases were diploid and 12 cases were hyperdiploid. MYCN oncogene amplification was significantly correlated with unfavorable histology, advanced tumor stage increased recurrence and poor survival. Also ploidy was associated with increased recurrence and reduced survival. And so, MYCN oncogene amplification and DNA ploidy were poor prognostic markers and it is recommended that assessment of these factors should be routine in the management of any case of neuroblastoma. Conclusions: 1) MYCN gene amplificahion and DNA plidy are poor prognostic markers 2) They should be measured in every case of peripheral neuroblastic tumors. 3) FISH should be used in the detechion of MYCN oncogene amplification and DNA ploidy No significant financial relationships to disclose.
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Albertson, Donna G. "Gene amplification in cancer." Trends in Genetics 22, no. 8 (2006): 447–55. http://dx.doi.org/10.1016/j.tig.2006.06.007.
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Manguso, Nicholas, Armando E. Giuliano, and Hisashi Tanaka. "circRNA meets gene amplification." Non-coding RNA Investigation 2 (2018): 38. http://dx.doi.org/10.21037/ncri.2018.06.04.
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Beverley, S. M. "Gene Amplification in Leishmania." Annual Review of Microbiology 45, no. 1 (1991): 417–44. http://dx.doi.org/10.1146/annurev.mi.45.100191.002221.
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Bizari, Lucimari, Ana Elizabete Silva, and Eloiza H. Tajara. "Gene amplification in carcinogenesis." Genetics and Molecular Biology 29, no. 1 (2006): 1–7. http://dx.doi.org/10.1590/s1415-47572006000100001.
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DeWitt, Natalie. "Gene amplification for plants." Nature Biotechnology 18, no. 12 (2000): 1233. http://dx.doi.org/10.1038/82312.
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Kafatos, Fotis C., William Orr, and Christos Delidakis. "Developmetally regulated gene amplification." Trends in Genetics 1 (January 1985): 301–6. http://dx.doi.org/10.1016/0168-9525(85)90119-2.
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Kadota, Mitsutaka, Misako Sato, Beverly Duncan, et al. "Identification of Novel Gene Amplifications in Breast Cancer and Coexistence of Gene Amplification with an Activating Mutation of PIK3CA." Cancer Research 69, no. 18 (2009): 7357–65. http://dx.doi.org/10.1158/0008-5472.can-09-0064.
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Paugh, Barbara S., Alberto Broniscer, Chunxu Qu, et al. "Genome-Wide Analyses Identify Recurrent Amplifications of Receptor Tyrosine Kinases and Cell-Cycle Regulatory Genes in Diffuse Intrinsic Pontine Glioma." Journal of Clinical Oncology 29, no. 30 (2011): 3999–4006. http://dx.doi.org/10.1200/jco.2011.35.5677.
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Purpose Long-term survival for children with diffuse intrinsic pontine glioma (DIPG) is less than 10%, and new therapeutic targets are urgently required. We evaluated a large cohort of DIPGs to identify recurrent genomic abnormalities and gene expression signatures underlying DIPG. Patients and Methods Single-nucleotide polymorphism arrays were used to compare the frequencies of genomic copy number abnormalities in 43 DIPGs and eight low-grade brainstem gliomas with data from adult and pediatric (non-DIPG) glioblastomas, and expression profiles were evaluated using gene expression arrays for 27 DIPGs, six low-grade brainstem gliomas, and 66 nonbrainstem low-grade gliomas. Results Frequencies of specific large-scale and focal imbalances varied significantly between DIPGs and nonbrainstem pediatric glioblastomas. Focal amplifications of genes within the receptor tyrosine kinase–Ras–phosphoinositide 3-kinase signaling pathway were found in 47% of DIPGs, the most common of which involved PDGFRA and MET. Thirty percent of DIPGs contained focal amplifications of cell-cycle regulatory genes controlling retinoblastoma protein (RB) phosphorylation, and 21% had concurrent amplification of genes from both pathways. Some tumors showed heterogeneity in amplification patterns. DIPGs showed distinct gene expression signatures related to developmental processes compared with nonbrainstem pediatric high-grade gliomas, whereas expression signatures of low-grade brainstem and nonbrainstem gliomas were similar. Conclusion DIPGs comprise a molecularly related but distinct subgroup of pediatric gliomas. Genomic studies suggest that targeted inhibition of receptor tyrosine kinases and RB regulatory proteins may be useful therapies for DIPG.
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Santos, Luiz Henrique Tolentino, Cibelle Santos Dias, Lucas Amorim Silveira, Messulan Rodrigues Meira, Elisa Susilene Lisboa dos Santos, and Carlos Bernard Moreno Cerqueira-Silva. "Characterization and selection of markers associated with resistance analogous genes as input for genetic analysis of Prosopis juliflora (Sw.) DC." Acta Scientiarum. Technology 43 (June 14, 2021): e51983. http://dx.doi.org/10.4025/actascitechnol.v43i1.51983.
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The characterization and selection of molecular markers are important for genetic pre-breeding programs since they make it possible to choose the most appropriate markers to be used in future research. Therefore, enabling the generation of subsidies for genetic-molecular studies in algabora (Prosopis juliflora (Sw.) DC). The amplification profile was characterized. It was generated from 17 pairs of RGA primers (Resistance Gene Analogs) in 20 samples of genomic DNA of P. juliflora extracted from specimens collected in the city of Itapetinga, Bahia. The amplifications were performed according to previously published laboratory routines and the amplification profiles analyzed from the photodocumentation of the electrophoresis results in 2% agarose gels. Based on the amplification profiles the primer pairs were classified as: Suitable: amplifications in the whole samples and with easy visualization; Reasonable: amplification in parts of the samples and/or difficult to visualize or Inadequate: absence of visible amplification products. Descriptive analyzes associated with the number of generated markers, percentage of polymorphism, expected heterozygosity (He) and the content of polymorphic information (PIC) were also performed. In a nutshell, 12 out of the 17 pairs of RGA primers generated amplification products with easy visualization and only two of these 12 pairs of primers were monomorphic. The percentage of polymorphism varied from 60% to 100%, He and PIC presented an average of 0.21 (ranging from 0 to 0.38) and 0.17 (ranging from 0 to 0.29), respectively. The results confirm that the RGA primers present adequate characteristics for genetic studies in P. juliflora, making it possible to prioritize 12 pairs of primers, which are subject to genetic improvement studies.
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Yun, Tian, Sunan Wang, Bo Jiang, et al. "Significance of Detection of the HER2 Gene and PD-1/PD-L1 in Gastric Cancer." Journal of Oncology 2020 (October 13, 2020): 1–7. http://dx.doi.org/10.1155/2020/8678945.
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Objective. To explore the relationship between the HER2 gene and PD-1/PD-L1 in gastric cancer and its significance. Methods. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) were used to detect HER2 protein expression, HER2 gene amplification, and PD-1/PD-L1 expression in 78 cases of gastric cancer. Results. The expression rate of HER2 protein was 43.6% (34/78), of which 19.4% (14/78) were HER2 3+, 14.1% (11/78) were HER2 2+, and 11.5% (9/78) were HER2 1+. The results showed that 19.2% (15/78) of samples had HER2 gene amplification, 3.8% (3/78) of samples had a HER2/CEP17 ratio <2.0, and 19.2% (15/78) of samples had HER2 gene amplificationf and HER2 copy/cell ≥6.0, as detected by FISH. The positive rate of PD-L1 was 38.5% (30/78) in gastric cancer cells and 50.0% (39/78) in interstitial lymphocytes. The expression of the HER2 gene, PD-L1, and PD-1 in gastric cancer was correlated with the stage and lymph node metastasis of gastric cancer ( P < 0.05 ). Conclusions. The combined detection of the HER2 gene and PD-1/PD-L1 in gastric cancer provides an important reference index for the prognosis of gastric cancer and the benefit of targeted antitumor drugs.
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Smith, David Hersi, Maria Unni Rømer, Niels Frank Jensen, et al. "An explorative analysis of TOP1 copy number alterations in a chemonaive stage III CRC patient cohort." Journal of Clinical Oncology 30, no. 30_suppl (2012): 66. http://dx.doi.org/10.1200/jco.2012.30.30_suppl.66.
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66 Background: Topoisomerase I (TOP1) is the target of TOP1 inhibitor chemotherapy. The TOP1 gene, located at 20q12, is frequently gained in colorectal cancer (CRC). The present study explores the mechanism, frequency and prognostic impact of TOP1 gene alterations in advanced CRC. Methods: Nine CRC cell line metaphase spreads were analyzed with a TOP1 probe in combination with a reference probe covering either the centromeric region of chromosome 20 (CEN20) or chromosome 2 (CEN2). Tissue sections from 154 stage III CRC patients, previously studied with TOP1/CEN20, were analyzed with TOP1/CEN2. Relationships between biomarker status and overall survival (OS), time to recurrence (TTR) in CRC and to local recurrence (LR; rectal cancer only) were analyzed using multivariate statistics. Results: TOP1 alterations were observed in 4 cell line metaphases. In 3 cases, TOP1 gain involved CEN20, indicating either gain of chromosome 20 or 20q. In all cell lines CEN2 was found to reflect chromosomal ploidy levels and therefore the TOP1/CEN2 probe combination was selected to identify TOP1 gene gains (TOP1/CEN2 ratio ≥ 1.5). A total of 151 patient tumor sections were analyzed with TOP1/CEN2. Among these, 99 patients (65.6%) had TOP1 gain of which 15 patients (10 %) harbored TOP1 amplification (TOP1/CEN20 ratio ≥ 2.0). For OS, TOP1 amplification showed a trend towards longer OS and TTR (HR: 0.59; 95% CI: 0.31-1.14; p = 0.11; HR: 0.50; 95% CI: 0.23-1.09; p = 0.08; respectively), whereas TOP1 gain did not. For LR in rectal cancer patients (n=70), TOP1 gains were significantly associated with shorter time to LR (HR: 1.98, 95% CI: 1.02-3.84; p = 0.04), whereas TOP1 amplifications showed a trend towards longer time to LR (HR: 0.40; 95% CI: 0.14-1.11; p = 0.08). Conclusions: TOP1 gene gain occurs frequently in stage III CRC in a mechanism that often includes CEN20. Using CEN2 as a measurement for tumor ploidy levels, we were able to discriminate between gains and amplifications. TOP1 amplifications showed a trend towards longer OS, TTR and time to LR, whereas TOP1 gains were associated with shorter time to LR. Future studies will investigate the difference between TOP1 gains and amplifications in a larger TOP1 inhibitor treated patient population.
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Berezovsky, Artem, Indrani Datta, Ruicong She, Laura Hasselbach, Laila Poisson, and Ana C. deCarvalho. "OTEH-12. Assessing Adaptive Responses to Loss of Extrachromosomal DNA Amplification." Neuro-Oncology Advances 3, Supplement_2 (2021): ii13. http://dx.doi.org/10.1093/noajnl/vdab070.051.
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Abstract Background Oncogene activation through somatic gene amplification happens frequently in GBM, with over 70% of these tumors presenting amplification of at least one putative driver gene, oftentimes in small extrachromosomal circular DNA segments composed of chromatin (ecDNA). A molecularly diverse and representative panel of GBM patient-derived cancer stem-like cells (CSC) and orthotopic mouse xenografts (PDX), which retain the original genomic abnormalities and ecDNA amplifications, was employed to assess adaptive response to the absence of ecDNA amplification. Methods We have isolated ecDNA negative cell populations from two patient-derived models. HF3035 harbors a MET amplification and HF3253 harbors a PDGFRA constitutively active genomic rearrangement and extrachromosomal amplification. We conducted paired, whole RNA-sequencing on 20 HF3253 populations (ecDNA+/-: 6 clones from 3 biological replicate PDXs and 4 clones from 4 in vitro technical replicates) and 12 HF3035 population (ecDNA+/-: 6 clones from 3 biological replicate PDXs). Results Nonparametric differentially expressed gene (DEG) analysis using NOISeqBio (R/Bioconductor), identified 564 differentially expressed genes (482 upregulated in ecDNA(-)) employing a stringent false discovery rate of 0.05. Genes significantly associated with PDGF stimulation, central carbon metabolism, and H3K27me3 were downregulated in ecDNA(-), while genes significantly associated with astrocytic processes, neuronal differentiation, and EGFR signaling were upregulated in ecDNA(-) (EnrichR). We employed an additive linear model with PDX serving as a blocking factor to compare ecDNA+ and ecDNA- populations in both models (R/edgeR). 2071 genes were upregulated in ecDNA+ PDX specimens and 2365 genes were downregulated. Specifically, E2F targets were highly enriched in ecDNA+ populations, in addition to mRNA pre-processing. ecDNA loss primarily targeted glycogen metabolism, NTRK signaling, and inositol phosphate catabolism. Conclusions We have identified PDX-specific and non-specific features to an adaptive response to the loss of ecDNA amplification. Notably, a signature adaptation is an upregulation of seemingly redundant receptor tyrosine kinases.
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Garcia, N., W. Zhang, Y. Wu, and J. Messing. "Evolution of Gene Expression after Gene Amplification." Genome Biology and Evolution 7, no. 5 (2015): 1303–12. http://dx.doi.org/10.1093/gbe/evv075.
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Wahl, G. M., S. Carroll, P. Gaudray, J. Ruiz, and D. von Hoff. "7 Gene transfer models of gene amplification." Cancer Genetics and Cytogenetics 28, no. 1 (1987): 29. http://dx.doi.org/10.1016/0165-4608(87)90286-x.
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Onishchuk, Olga P., Nikolay I. Vorobyov, Nikolay A. Provorov, and Boris V. Simarov. "Symbiotic activity of the alfalfa rhizobia (Sinorhizobium meliloti) strains with the genetically modified transport of dicarboxylic acids." Ecological genetics 7, no. 2 (2009): 3–10. http://dx.doi.org/10.17816/ecogen723-10.
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Inactivation of genes involved in the dicarbyxylic acid transport in alfalfa rhizobia, Sinorhizobium meliloti (structural gene of succinate permease dctA and its transcriptional regulators dctBD, nifA, ntrA) resulted in the full or partial loss of N<sub>2</sub>-fixing activity while amplifications of these genes - in its improvement. It lead to the marked increases of N and C accumulation in alfalfa while its shoot mass was increased by a much lesser degree due to the incomplete N translocation from the roots. Factorial analysis suggested that dctABD amplification was important for improving the symbiotic efficiency in all trials while the effects of dctA, nifA and ntrA amplifications depend on the plant genotypes and growth conditions.