Relative gene copy numbers in various patterns of cervical cancer growth.

e18029 Background: Numerous studies on cervical cancer confirm an important role of specific genomic changes in the onset and development of cervical intraepithelial neoplasia and their effect on the progression of cervical cancer. Solid tumors are characterized by genomic changes leading to a change in the DNA sequence copy number. The purpose of the study was to reveal changes in the relative copy number of the ESR1, ESR2, GPER1, STS, SULT1A1, SULT1E1, CYP1A1, CYP1A2 genes responsible for the reception and metabolism of estrogens in cervical tissues in endophytic and exophytic patterns of tumor growth in order to find predictive markers of malignancy. Methods: The study included 40 patients aged 28-65 years with cervical cancer of endophytic (n = 20) and exophytic (n = 20) growth patterns. Eligibility criteria included a morphologically confirmed cervical squamous cell cancer T1b-2aN0M0, stage I-II. The Thermo Scientific GeneJET FFPE DNA Purification Kit was used for the DNA extraction from FFPE blocks of tumor and healthy tissues. DNA concentrations were measured on the Qubit 2.0 fluorimeter (Invitrogen, USA) using the Quant-iT dsDNA High-Sensitivity (HS) Assay Kit (Invitrogen, USA). Results: The relative copy number of the GPER1, SULT1A1, CYP1A1 genes in tumor samples increased (p < 0.05) compared with normal tissues in the total sample of patients diagnosed with cervical cancer. In contrast to the total sample, an increase in the SULT1A1 gene dosage did not reach a statistically significant level in any group (p = 0.242 and p = 0.157); the copy number of the GPER1 locus significantly increased only in the group with the endophytic growth pattern (p = 0.040), as well as the CYP1A2 gene dosage (p = 0.025). Patients of 36-55 years with endophytic tumors showed a statistically significant (p < 0.05) increase in the GPER1 and CYP1A1 gene copy numbers with the rates of 41.7% and 66.7%, respectively, as well as an increased amplification of the CYP1A2 gene in 41.67% of patients. In women of 56-75 years with endophytic tumors, an increase in the copy numbers of the ESR2, GPER1, SULT1A1 genes was observed with a frequency of 50%, 100% and 75%, respectively. Patients aged 20-35 and 36-55 years with exophytic tumors showed a statistically significant (p < 0.05) increase in the CYP1A1 gene copy numbers in 33.33% and 45.45%, respectively. Conclusions: The results suggest the use of the GPER1, SULT1A1 and CYP1A1 gene copy numbers as biomarkers of cervical tumors.

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Photo-Induced Electron Transfer Real-Time PCR for Detection ofPlasmodium falciparum plasmepsin 2Gene Copy Number

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00317-18 ◽

2018 ◽

Vol 62 (8) ◽

Cited By ~ 1

Author(s):

Samaly Santos Souza ◽

Mariangela L'Episcopia ◽

Carlo Severini ◽

Venkatachalam Udhayakumar ◽

Naomi W. Lucchi

Keyword(s):

Electron Transfer ◽

Real Time ◽

Real Time Pcr ◽

Copy Number ◽

Gene Copy ◽

Content Type ◽

Copy Numbers ◽

Ofplasmodium Falciparum ◽

Photo Induced Electron Transfer ◽

Gene Copy Numbers

ABSTRACTPiperaquine is an important partner drug used in artemisinin-based combination therapies (ACTs). An increase in theplasmepsin 2and3gene copy numbers has been associated with decreased susceptibility ofPlasmodium falciparumto piperaquine in Cambodia. Here, we developed a photo-induced electron transfer real-time PCR (PET-PCR) assay to quantify the copy number of theP. falciparumplasmepsin 2gene (PfPM2) that can be used in countries whereP. falciparumis endemic to enhance molecular surveillance.

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Plasmodium copy number variation scan: gene copy numbers evaluation in haploid genomes

Malaria Journal ◽

10.1186/s12936-016-1258-x ◽

2016 ◽

Vol 15 (1) ◽

Cited By ~ 10

Author(s):

Johann Beghain ◽

Anne-Claire Langlois ◽

Eric Legrand ◽

Laura Grange ◽

Nimol Khim ◽

...

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Gene Copy ◽

Copy Numbers ◽

Number Variation ◽

Gene Copy Numbers

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High levels of copy number variation of ampliconic genes across major human Y haplogroups

10.1101/230342 ◽

2017 ◽

Author(s):

Danling Ye ◽

Arslan Zaidi ◽

Marta Tomaszkiewicz ◽

Corey Liebowitz ◽

Michael DeGiorgio ◽

...

Keyword(s):

Copy Number Variation ◽

Y Chromosome ◽

Copy Number ◽

Gene Copy Number ◽

Gene Families ◽

Digital Pcr ◽

Gene Copy ◽

Copy Numbers ◽

Number Variation ◽

Gene Copy Numbers

AbstractDue to its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups. Overall, only three gene families (DATZ, RBMY, TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of an individual could not be predicted based on his ampliconic gene copy numbers. Finally, we found a significant correlation between copy number variation and individual’s height (for three gene families), but not between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.

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Epidermal Growth Factor Receptor Copy Number Alterations Correlate With Poor Clinical Outcome in Patients With Head and Neck Squamous Cancer

Journal of Clinical Oncology ◽

10.1200/jco.2006.06.6605 ◽

2007 ◽

Vol 25 (16) ◽

pp. 2164-2170 ◽

Cited By ~ 262

Author(s):

Stephane Temam ◽

Hidetoshi Kawaguchi ◽

Adel K. El-Naggar ◽

Jaroslav Jelinek ◽

Hongli Tang ◽

...

Keyword(s):

Clinical Outcome ◽

Copy Number ◽

Growth Factor Receptor ◽

Gene Copy ◽

Copy Number Alterations ◽

Egfr Gene ◽

Copy Numbers ◽

Epidermal Growth ◽

Gene Copy Numbers

Purpose Overexpression of epidermal growth factor receptor (EGFR) is common in head and neck squamous cell carcinoma (HNSCC). Recent studies showed that EGFR inhibitors are effective for patients with HNSCC. This study analyzed the genetic nature of EGFR gene in HNSCC and its clinical correlations. Patients and Methods The EGFR gene copy numbers in 134 HNSCC tumors were determined using quantitative real-time polymerase chain reaction. The status of EGFR gene copy numbers was analyzed with clinical parameters including clinical outcome. Mutation status of EGFR exons 18, 19, and 21 was determined in the HNSCC tumors. Results Aberrant EGFR copy numbers were found in 32 (24%) of 134 tumors, including 22 (17%) with increased copy number and 10 (7%) with decreased copy number. Patients whose tumors had EGFR copy number alterations (particularly patients with increased copy numbers) had significantly poorer overall, cancer-specific, and disease-free survivals compared with patients with normal copy numbers (P < .0001). At 5 years after initial diagnosis, 20 (91%) of the 22 patients with increased copy numbers died of disease compared with 30 (29%) of the 102 patients with normal copy number. No mutations on EGFR exons 18, 19, and 21 were detected in any of the tumors. Conclusion A subset of HNSCC manifests EGFR copy number alterations, and this is associated with a poor clinical outcome, suggesting a biologic role of the alterations. The rare mutation or small deletion at EGFR exons 18 to 21 indicates a minimal role of these events in HNSCC.

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Impact of Salivary and Pancreatic Amylase Gene Copy Numbers on Diabetes, Obesity, and Functional Profiles of Microbiome in Northern Japanese Population

10.21203/rs.3.rs-1033850/v1 ◽

2021 ◽

Author(s):

Takanori Hasegawa ◽

Masanori Kakuta ◽

Rui Yamaguchi ◽

Noriaki Sato ◽

Tatsuya Mikami ◽

...

Keyword(s):

Gut Microbiome ◽

Copy Number ◽

Positive Association ◽

Gene Copy ◽

P Value ◽

Copy Numbers ◽

Obesity And Diabetes ◽

Complex Locus ◽

Gene Copy Numbers ◽

Functional Profiles

Abstract Amylase genes reside in a structurally complex locus, and their copy numbers vary greatly, and several studies have reported their association with obesity. The mechanism of this effect was partially explained by changes in the oral and gut microbiome compositions; however, a detailed mechanism has been unclarified. In this study, we showed their association with diabetes in addition to obesity, and further discovered a plausible mechanism of this association based on the function of commensal bacterial. First, we confirmed that the amylase copy number in the population tends to be larger than that reported in other studies and that there is a positive association between obesity and diabetes (p=1.95E-2 and 3.28E-2). Second, we identified that relative abundance of some genus level microbiome, Capnocytophaga, Dialister, and previously reported bacteria, were significantly associated with amylase copy numbers. Finally, through functional gene-set analysis using shotgun sequencing, we observed that the abundance of genes in the Acarbose pathway in the gut microbiome was significantly decreased with an increase in the amylase copy number (p-value = 5.80E-4). Our findings can partly explain the mechanism underlying obesity and diabetes in populations with high amylase copy numbers.

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Analysis of gene copy number in esophageal patient-derived tumor xenografts.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.e13648 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. e13648-e13648

Author(s):

Ekaterina A. Lukbanova ◽

Natalya N. Timoshkina ◽

Evgeniy N. Kolesnikov ◽

Mikhail A Kozhushko ◽

Sergei Kit ◽

...

Keyword(s):

Esophageal Cancer ◽

Copy Number ◽

Cancer Biology ◽

Clonal Selection ◽

Gene Copy ◽

Normal Donor ◽

Relative Copy Number ◽

Copy Numbers ◽

Tumor Tissues ◽

Pdx Models

e13648 Background: Patient-derived tumor xenograft (PDX) models are a valuable resource for studying cancer biology and antitumor drug evaluation. The suitability of tumor models in vivo depends on how accurately they mimic a human disease and reproduce the histotype and molecular genetic features of a human tumor. The purpose of the study was to create a PDX model of human cancer and analyze its characteristics. Methods: PDX models of esophageal cancer were obtained by transplanting a tumor fragment from a patient with esophageal squamous cell carcinoma to the BALB/c Nude athymic mice (n = 10 for one PDX generation). Preservation of the tumor histotype was confirmed histologically (hematoxylin and eosin staining). 5 PDX were generated. An analysis of the relative copy number of the YAP1 and KDM6A genes (Real-Time qPCR) in xenograft and donor tumor tissues was performed in each generation. Results: A decrease in the copy numbers of the YAP1 and KDM6A genes by 3.8 and 2.2 times, respectively, was observed in PDX tumor samples (F3 generation) compared to normal donor tissues (p < 0.05). This trend maintained in F4 and F5 generation PDX samples. No changes in the copy numbers of the YAP1 and KDM6A genes were detected in PDX tumor samples in F1 and F2 generations. A cluster analysis (Hierarchical Clustering, Euclidean distance) demonstrated that samples of the first and second generations of esophageal cancer PDX models were closest to the patient tumor tissues in gene copy numbers. Conclusions: Later generations of esophageal cancer PDX models are characterized by changes in the genes copy numbers due to changes in the tumor and clonal selection. Early PDX generations better reproduce genetic, molecular and morphological features of tumors.

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The ribosomal RNA gene cluster in aneuploid chickens: evidence for increased gene dosage and regulation of gene expression.

The Journal of Cell Biology ◽

10.1083/jcb.101.5.1749 ◽

1985 ◽

Vol 101 (5) ◽

pp. 1749-1756 ◽

Cited By ~ 28

Author(s):

D E Muscarella ◽

V M Vogt ◽

S E Bloom

Keyword(s):

Ribosomal Rna ◽

Gene Dosage ◽

Regulation Of Gene Expression ◽

Nucleolar Organizer ◽

Nucleolus Organizer ◽

Rrna Genes ◽

Gene Copy ◽

Multiple Generations ◽

Copy Numbers ◽

Gene Copy Numbers

In the chicken, the nucleolus organizer regions, or sites of the genes encoding 18S, 5.8S, and 28S ribosomal RNA (rRNA), map to one pair of microchromosomes that can be identified by silver nitrate cytochemistry. This nucleolar organizer chromosome also contains the major histocompatibility complex. Chickens aneuploid for this chromosome have been identified and reproduced for over seven generations. Crossing two trisomic parents results in the production of viable disomic, trisomic, and tetrasomic progeny, showing two, three, and four nucleoli and nucleolar organizers per cell, respectively. A molecular analysis of rRNA genes was undertaken to establish the gene copy numbers in the aneuploid genotypes, and to determine if elevated numbers of rRNA genes are stably maintained and inherited over multiple generations. Gene copy numbers were determined using hybridization analysis of erythrocyte DNA obtained from individuals comprising a family which segregated disomic, trisomic, and tetrasomic genotypes. The values obtained were 290, 420, and 570 rDNA repeats per cell for disomic, trisomic, and tetrasomic animals, respectively. These results provide molecular confirmation of the two aneuploid states and show that elevated gene copy numbers have been maintained over multiple generations. Fibroblasts derived from disomic and tetrasomic embryos were found to grow at similar rates in culture, and mature rRNA levels in chicken embryo fibroblasts from disomic, trisomic and tetrasomic embryos were also found to have similar levels of mature rRNA. Therefore, despite the increase in rDNA content, the level of rRNA is regulated to diploid amounts in aneuploid fibroblasts.

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Measuring the buffering capacity of gene silencing in Saccharomyces cerevisiae

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2111841118 ◽

2021 ◽

Vol 118 (49) ◽

pp. e2111841118

Author(s):

Kenneth Wu ◽

Namrita Dhillon ◽

Kelvin Du ◽

Rohinton T. Kamakaka

Keyword(s):

Gene Silencing ◽

Gene Dosage ◽

Gene Copy ◽

Promoter Strength ◽

Protein Levels ◽

Copy Numbers ◽

Upstream Activating Sequence ◽

Functional Consequences ◽

Gene Copy Numbers ◽

Silent State

Gene silencing in budding yeast is mediated by Sir protein binding to unacetylated nucleosomes to form a chromatin structure that inhibits transcription. Transcriptional silencing is characterized by the high-fidelity transmission of the silent state. Despite its relative stability, the constituent parts of the silent state are in constant flux, giving rise to a model that silent loci can tolerate such fluctuations without functional consequences. However, the level of tolerance is unknown, and we developed methods to measure the threshold of histone acetylation that causes the silent chromatin state to switch to the active state as well as to measure the levels of the enzymes and structural proteins necessary for silencing. We show that loss of silencing required 50 to 75% acetyl-mimic histones, though the precise levels were influenced by silencer strength and upstream activating sequence (UAS) enhancer/promoter strength. Measurements of repressor protein levels necessary for silencing showed that reducing SIR4 gene dosage two- to threefold significantly weakened silencing, though reducing the gene copy numbers for Sir2 or Sir3 to the same extent did not significantly affect silencing suggesting that Sir4 was a limiting component in gene silencing. Calculations suggest that a mere twofold reduction in the ability of acetyltransferases to acetylate nucleosomes across a large array of nucleosomes may be sufficient to generate a transcriptionally silent domain.

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PCNA-associated factor (KIAA0101/PCLAF) overexpression and gene copy number alterations in hepatocellular carcinoma tissues

BMC Cancer ◽

10.1186/s12885-021-07994-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Anchalee Tantiwetrueangdet ◽

Ravat Panvichian ◽

Pattana Sornmayura ◽

Surasak Leelaudomlipi ◽

Jill A. Macoska

Keyword(s):

Hepatocellular Carcinoma ◽

Protein Expression ◽

Gene Amplification ◽

Copy Number ◽

Gene Copy Number ◽

Gene Copy ◽

Mrna Levels ◽

Ki 67 ◽

Copy Numbers ◽

Gene Copy Numbers

Abstract Background PCNA-associated factor, the protein encoded by the KIAA0101/PCLAF gene, is a cell-cycle regulated oncoprotein that regulates DNA synthesis, maintenance of DNA methylation, and DNA-damage bypass, through the interaction with the human sliding clamp PCNA. KIAA0101/PCLAF is overexpressed in various cancers, including hepatocellular carcinoma (HCC). However, it remains unknown whether KIAA0101/PCLAF overexpression is coupled to gene amplification in HCC. Methods KIAA0101/PCLAF mRNA expression levels were assessed by quantitative real-time PCR (qRT-PCR) in 40 pairs of snap-frozen HCC and matched-non-cancerous tissues. KIAA0101/PCLAF gene copy numbers were evaluated by droplet digital PCR (ddPCR) in 36 pairs of the tissues, and protein expression was detected by immunohistochemistry (IHC) in 81 pairs of formalin-fixed paraffin-embedded (FFPE) tissues. The KIAA0101/PCLAF gene copy number alteration and RNA expression was compared by Spearman correlation. The relationships between KIAA0101 protein expression and other clinicopathological parameters, including Ki-67, p53, and HBsAg protein expression in HCC tissues, were evaluated using Chi-square test. Results Our results demonstrated that KIAA0101/PCLAF mRNA levels were significantly higher in HCC than in the matched-non-cancerous tissues (p < 0.0001). The high KIAA0101/PCLAF mRNA levels in HCC were associated with poor patient survival. The KIAA0101/PCLAF gene was not amplified in HCC, and KIAA0101/PCLAF gene copy numbers were not associated with KIAA0101/PCLAF transcript levels. KIAA0101 protein was overexpressed in the majority of HCC tissues (77.8%) but was not detectable in matched-non-cancerous tissues. Significant correlations between the expression of KIAA0101 protein in HCC tissues and p53 tumor suppressor protein (p = 0.002) and Ki-67 proliferation marker protein (p = 0.017) were found. However, KIAA0101 protein levels in HCC tissues were not correlated with patient age, tumor size, serum AFP level, or the HBsAg expression. Conclusions KIAA0101/PCLAF mRNA and protein overexpression is frequently observed in HCC but without concurrent KIAA0101/PCLAF gene amplification. Significant correlations between the expression of KIAA0101 protein and p53 and Ki-67 proteins were observed in this study. Thus, detection of KIAA0101/PCLAF mRNA/protein might be used, along with the detection of p53 and Ki-67 proteins, as potential biomarkers to select candidate patients for further studies of novel HCC treatment related to these targets.

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