31 research outputs found
Abundance-Ratio-Based Semiquantitative Analysis of Site-Specific N‑Linked Glycopeptides Present in the Plasma of Hepatocellular Carcinoma Patients
Aberrant structures
of site-specific N-linked glycans are closely
associated with the tumorigenesis of hepatocellular carcinoma (HCC),
one of the most common fatal cancers worldwide. Vitronectin (VTN)
is considered a candidate glycobiomarker of HCC. In this study, we
describe a reliable and simple quantification strategy based on abundance
ratios of site-specific N-linked glycopeptides of VTN to screen for
potential biomarkers. A total of 14 unique N-linked glycans corresponding
to 27 unique N-linked glycopeptides were characterized at three N-linked
sites (Asn-86, -169, and -242) present in VTN. These glycans could
be good candidate markers for HCC. Among these glycans, the abundance
ratio of two representative glycoforms (fucosyl vs non-fucosyl) was
significantly increased in HCC plasma relative to normal plasma. This
strategy was also successfully applied to another potential HCC biomarker,
haptoglobin. Furthermore, we demonstrate that our approach employing
tandem mass tag (TMT) and target N-linked glycopeptides of VTN is
a useful tool for quantifying specific glycans in HCC plasma relative
to normal plasma. Our strategy represents a simple and potentially
useful screening platform for the discovery of cancer-specific glycobiomarkers
Proteogenomic Analysis of Human Chromosome 9‑Encoded Genes from Human Samples and Lung Cancer Tissues
The Chromosome-centric Human Proteome
Project (C-HPP) was recently
initiated as an international collaborative effort. Our team adopted
chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic
analysis to catalog Chr 9-encoded proteins from normal tissues, lung
cancer cell lines, and lung cancer tissues. Approximately 74.7% of
the Chr 9 genes of the human genome were identified, which included
approximately 28% of missing proteins (46 of 162) on Chr 9 compared
with the list of missing proteins from the neXtProt Master Table (2013-09).
In addition, we performed a comparative proteomics analysis between
normal lung and lung cancer tissues. On the basis of the data analysis,
15 proteins from Chr 9 were detected only in lung cancer tissues.
Finally, we conducted a proteogenomic analysis to discover Chr 9-residing
single nucleotide polymorphisms (SNP) and mutations described in the
COSMIC cancer mutation database. We identified 21 SNPs and four mutations
containing peptides on Chr 9 from normal human cells/tissues and lung
cancer cell lines, respectively. In summary, this study provides valuable
information of the human proteome for the scientific community as
part of C-HPP. The mass spectrometry proteomics data have been deposited
to the ProteomeXchange Consortium with the data set identifier PXD000603
Proteogenomic Analysis of Human Chromosome 9‑Encoded Genes from Human Samples and Lung Cancer Tissues
The Chromosome-centric Human Proteome
Project (C-HPP) was recently
initiated as an international collaborative effort. Our team adopted
chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic
analysis to catalog Chr 9-encoded proteins from normal tissues, lung
cancer cell lines, and lung cancer tissues. Approximately 74.7% of
the Chr 9 genes of the human genome were identified, which included
approximately 28% of missing proteins (46 of 162) on Chr 9 compared
with the list of missing proteins from the neXtProt Master Table (2013-09).
In addition, we performed a comparative proteomics analysis between
normal lung and lung cancer tissues. On the basis of the data analysis,
15 proteins from Chr 9 were detected only in lung cancer tissues.
Finally, we conducted a proteogenomic analysis to discover Chr 9-residing
single nucleotide polymorphisms (SNP) and mutations described in the
COSMIC cancer mutation database. We identified 21 SNPs and four mutations
containing peptides on Chr 9 from normal human cells/tissues and lung
cancer cell lines, respectively. In summary, this study provides valuable
information of the human proteome for the scientific community as
part of C-HPP. The mass spectrometry proteomics data have been deposited
to the ProteomeXchange Consortium with the data set identifier PXD000603
Proteogenomic Analysis of Human Chromosome 9‑Encoded Genes from Human Samples and Lung Cancer Tissues
The Chromosome-centric Human Proteome
Project (C-HPP) was recently
initiated as an international collaborative effort. Our team adopted
chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic
analysis to catalog Chr 9-encoded proteins from normal tissues, lung
cancer cell lines, and lung cancer tissues. Approximately 74.7% of
the Chr 9 genes of the human genome were identified, which included
approximately 28% of missing proteins (46 of 162) on Chr 9 compared
with the list of missing proteins from the neXtProt Master Table (2013-09).
In addition, we performed a comparative proteomics analysis between
normal lung and lung cancer tissues. On the basis of the data analysis,
15 proteins from Chr 9 were detected only in lung cancer tissues.
Finally, we conducted a proteogenomic analysis to discover Chr 9-residing
single nucleotide polymorphisms (SNP) and mutations described in the
COSMIC cancer mutation database. We identified 21 SNPs and four mutations
containing peptides on Chr 9 from normal human cells/tissues and lung
cancer cell lines, respectively. In summary, this study provides valuable
information of the human proteome for the scientific community as
part of C-HPP. The mass spectrometry proteomics data have been deposited
to the ProteomeXchange Consortium with the data set identifier PXD000603
Proteogenomic Analysis of Human Chromosome 9‑Encoded Genes from Human Samples and Lung Cancer Tissues
The Chromosome-centric Human Proteome
Project (C-HPP) was recently
initiated as an international collaborative effort. Our team adopted
chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic
analysis to catalog Chr 9-encoded proteins from normal tissues, lung
cancer cell lines, and lung cancer tissues. Approximately 74.7% of
the Chr 9 genes of the human genome were identified, which included
approximately 28% of missing proteins (46 of 162) on Chr 9 compared
with the list of missing proteins from the neXtProt Master Table (2013-09).
In addition, we performed a comparative proteomics analysis between
normal lung and lung cancer tissues. On the basis of the data analysis,
15 proteins from Chr 9 were detected only in lung cancer tissues.
Finally, we conducted a proteogenomic analysis to discover Chr 9-residing
single nucleotide polymorphisms (SNP) and mutations described in the
COSMIC cancer mutation database. We identified 21 SNPs and four mutations
containing peptides on Chr 9 from normal human cells/tissues and lung
cancer cell lines, respectively. In summary, this study provides valuable
information of the human proteome for the scientific community as
part of C-HPP. The mass spectrometry proteomics data have been deposited
to the ProteomeXchange Consortium with the data set identifier PXD000603
Anal Human Papillomavirus Infection among HIV-Infected Men in Korea
<div><p>Background</p><p>Little is known about the epidemiology on human papillomavirus (HPV) infection among HIV-infected men in Korea. The objective of this study was to determine the prevalence, genotype distribution and risk factors associated with anal HPV infection among HIV-infected men in Korea.</p><p>Methods</p><p>A single-center cross-sectional study was conducted with HIV-infected men in Korea. Participants completed a detailed sexual behavior risk factor questionnaire. Anal samples were collected for cytology and HPV genotyping. Factors associated with anal HPV infection were assessed using multivariable logistic regression, stratifying by sexual behaviour.</p><p>Results</p><p>A total of 201 HIV-infected men were included in the study: 133 were from men who have sex with men (MSM) and 68 from men who have sex with women (MSW). Any anal HPV infection was detected in 82.7% of HIV-infected MSM and in 51.5% of HIV- infected MSW (<i>P</i> < 0.001). High-risk HPV (HR-HPV) prevalence was higher among MSM (47.4%) than MSW (25.0%; <i>P</i> = 0.002). The HR-HPV types identified most frequently were HPV 16 (11%), HPV 18 (9.9%), and HPV 58 (5%) in MSM, and HPV 58(11%) and HPV 16 (8.9%) in MSW. Prevalence of any HPV types in 9-valent vaccine types was higher among MSM than MSW (47.4% vs 22.1%. <i>P</i> = 0.001). Abnormal anal cytology was more commonly detected in MSM than MSW (42.9% vs.19.1%, <i>P</i> < 0.001). In HIV-infected MSM, higher number of lifetime male sex partners was significantly associated with any anal HPV infection, but age was a significant risk factor associated with anal HR-HPV infection.</p><p>Conclusion</p><p>Anal HPV infection was highly prevalent in HIV-infected MSM in Korea, and also commonly found in HIV-infected MSW. In HIV-infected MSM, the significant risk factor for being infected with any HPV infection was lifetime number of male sexual partners, and with anal oncogenic HPV infection was age.</p></div
Prevalence of Human papillomavirus (HPV) infection and abnormal anal cytology.
<p>Prevalence of Human papillomavirus (HPV) infection and abnormal anal cytology.</p
Univariable and multivariable analyses of determinants of anal human papillomavirus infection in HIV-infected Men who have sex with men.
<p>Univariable and multivariable analyses of determinants of anal human papillomavirus infection in HIV-infected Men who have sex with men.</p
Human papillomavirus (HPV) genotypic distribution among HIV-infected Men who have sex with men and among HIV-infected men who have sex with women.
<p>(MSM, men who have sex with men; MSW, men who have sex with women; U, untypeable)</p