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

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

10.1101/2021.10.02.21264452 ◽

2021 ◽

Author(s):

Takanori Hasegawa ◽

Masanori Kakuta ◽

Rui Yamaguchi ◽

Noriaki Sato ◽

Tatsuya Mikami ◽

...

Keyword(s):

Gut Microbiome ◽

Copy Number ◽

Japanese Population ◽

Metabolic Response ◽

Positive Association ◽

Gene Copy ◽

P Value ◽

Copy Numbers ◽

Obesity And Diabetes ◽

Amylase Genes

Amylase genes reside in a structurally complex locus, and their copy numbers vary greatly, especially among agricultural races. Amylase genes seem to shape the metabolic response to dietary starch, and several studies have reported their association with obesity. Besides, the effect of amylase copy numbers seems to depend on lifestyle, and 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 in a northern Japanese population. 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), which can partly explain the mechanism underlying obesity and diabetes in populations with high amylase copy numbers.

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

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.e18029 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. e18029-e18029

Author(s):

Natalya N. Timoshkina ◽

Natalia A. Petrusenko ◽

Vera P. Nikitina ◽

Diana A. Spiridonova ◽

Ekaterina V. Verenikina ◽

...

Keyword(s):

Cervical Cancer ◽

Copy Number ◽

Gene Dosage ◽

Total Sample ◽

Gene Copy ◽

Relative Copy Number ◽

Genomic Changes ◽

Copy Numbers ◽

Cyp1a1 Gene ◽

Gene Copy Numbers

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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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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Relationship between amount of esterase and gene copy number in insecticide-resistant Myzus persicae (Sulzer)

Biochemical Journal ◽

10.1042/bj3390737 ◽

1999 ◽

Vol 339 (3) ◽

pp. 737-742 ◽

Cited By ~ 55

Author(s):

Linda M. FIELD ◽

Roger L. BLACKMAN ◽

Chris TYLER-SMITH ◽

Alan L. DEVONSHIRE

Keyword(s):

Gene Amplification ◽

Myzus Persicae ◽

Copy Number ◽

Transcriptional Control ◽

Gene Copy Number ◽

Gene Copy ◽

Copy Numbers ◽

And Function ◽

Gene Copy Numbers

Overproduction of the insecticide-degrading esterases, E4 and FE4, in peach-potato aphids, Myzus persicae (Sulzer), depends on both gene amplification and transcriptional control, the latter being associated with changes in DNA methylation. The structure and function of the aphid esterase genes have been studied but the determination of their copy number has proved difficult, a common problem with gene amplification. We have now used a combination of pulsed-field gel electrophoresis and quantitative competitive PCR to determine relative esterase gene copy numbers in aphid clones with different levels of insecticide resistance (R1, R2 and R3). There are approx. 4-fold increases between susceptible, R1, R2 and R3 aphids, reaching a maximum of approx. 80 times more genes in R3; this gives proportionate increases in esterase protein relative to susceptible aphids. Thus there is no overexpression of the amplified genes, in contrast with what was thought previously. For E4 genes, the loss of 5-methylcytosine is correlated with a loss of expression, greatly decreasing the amount of enzyme relative to the copy number.

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Quantitation of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes

10.1101/2021.08.05.455335 ◽

2021 ◽

Author(s):

Audrey Garcia ◽

Tri Le ◽

Paul Jankowski ◽

Kadir Yanac ◽

Qiuyan Yuan ◽

...

Keyword(s):

Wastewater Treatment ◽

Treatment Plant ◽

Enteric Viruses ◽

Gene Copy ◽

P Value ◽

E Coli ◽

Copy Numbers ◽

Gene Copies ◽

Average Gene ◽

Gene Copy Numbers

We investigated the potential use and quantitation of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA and RNA enteric viruses, as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantitated in the extracted samples via quantitative PCR using TaqMan assays. The average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.0547 and 0.7986) than the average gene copies assessed in the effluents for Adenovirus and crAssphage (DNA viruses), Pepper Mild Mottle Virus (RNA virus), and uidA in terms of both volume and biomass. A significant reduction of these enteric viruses was observed consistently in activated sludge samples compared with those for raw sewage. Corresponding reductions in gene copies per volume and gene copies per biomass were also seen for uidA but were not statistically significant (p-value = 0.8769 and p-value = 0.6353, respectively). The higher gene copy numbers of enteric viruses and E. coli observed in the effluents may be associated with the 12-hour hydraulic retention time in the facility. Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA. This indicate that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used as complementary viral indicators of human fecal pollution.

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

10.21203/rs.3.rs-39782/v2 ◽

2020 ◽

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 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, and the relationship between KIAA0101 protein expression and other clinicopathological parameters was 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), and 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 be detectable in matched-non-cancerous tissues. Significant correlations between the expression of KIAA0101 protein and p53 tumor suppressor protein (p=0.002), and Ki-67 proliferation marker protein (p=0.017) were found. However, KIAA0101 protein levels were not correlated with patient age, tumor size, or the expression of AFP and HBsAg.Conclusions: KIAA0101/PCLAF mRNA and protein overexpressionis 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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