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Yin Cheng, Jun Wang,
Jiaofang Shao,
Qiyun Chen,
Fan Mo,
Liang Ma,
Xu Han,
Jing Zhang,
Chen Chen,
Cixiong Zhang,
Shuyong Lin,
Jiekai Yu,
Shu Zheng,
Sheng-Cai Lin,
Biaoyang Lin
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ABSTRACT: We described an approach of identifying single nucleotide polymorphisms (SNPs) in complete genomic regions of key genes including promoters, exons, introns, and downstream sequences by combining long-range polymerase chain reaction (PCR) or NimbleGen sequence capture with next-generation sequencing. Using the adenomatous polyposis coli (APC) gene as an example, we identified 210 highly reliable SNPs by next-generation sequencing analysis program MAQ and Samtools, of which 69 were novel ones, in the 123-kb APC genomic region in 27 pair of colorectal cancers and normal adjacent tissues. We confirmed all of the eight randomly selected high-quality SNPs by allele-specific PCR, suggesting that our false discovery rate is negligible. We identified 11 SNPs in the exonic region, including one novel SNP that was not previously reported. Although 10 of them are synonymous, they were predicted to affect splicing by creating or removing exonic splicing enhancers or exonic splicing silencers. We also identified seven SNPs in the upstream region of the APC gene, three of which were only identified in the cancer tissues. Six of these upstream SNPs were predicted to affect transcription factor binding. We also observed that long-range PCR was better in capturing GC-rich regions than the NimbleGen sequence capture technique.
Omics: a journal of integrative biology 06/2010; 14(3):315-25. · 2.29 Impact Factor
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ABSTRACT: Osteonecrosis of the femoral head (ONFH) is a devastating disease that can result in a femoral head collapse. By proteomics analysis, we identified 1,967 proteins with two or more unique peptides from ONFH and from control bones with a false discovery rate of 4.8%. Using spectral counting, we identified 141 overexpressed and 56 underexpressed proteins comparing ONFH bones to the controls. GSEA (gene set enrichment analysis) revealed that proteins overexpressed in ONFH are enriched for gene sets related to multiple myeloma and adult T-cell lymphoma (ATL), and to JAK2-dependent genes. We confirmed the underexpression of CHST2 (isoform 1 of carbohydrate sulfotransferase 2), a key protein involved in biosynthesis of chondroitin sulfate proteoglycans, and the underexpression of GPCR26 (G-protein coupled receptor 26), a protein that mediates intracellular calcium mobilization, in ONFH bones compared to controls. Taken together, our data suggest that biosynthesis of chondroitin sulfate proteoglycans and cation transport and mobilization may be a key process involved in the pathogenesis of ONFH. Our analysis sheds new light on the understanding of the pathogenesis of ONFH.
Omics: a journal of integrative biology 12/2009; 13(6):453-66. · 2.29 Impact Factor
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ABSTRACT: Personalized medicine heralds the future of medicine. The 2009 Westlake International Conference on Personalized Medicine held from May 29-31, 2009, in Hangzhou, China (www.westlakeconference.org) brought together approximately 200 participants and over 40 presenters from a dozen countries. The conference was discussed in detail, with focus on the following major areas of personalized medicine: preventative and predictive medicine, cancer systems biology and therapy, physiology and artificial liver systems, nanotechnology and informatics, proteomics and systems pathology, genomics and pharmacogenomics, and epigenetics and new techniques. During the conference, the Asian Association of Systems Biology and Medicine (AASBM) was officially formed, and the ad hoc steering members for each of the major Asian countries were appointed to recruit key players from each country. The IBC (Interdisciplinary Bio Central) journal was suggested as the official journal for the AASBM, as it is a truly open journal (www.ibc7.org). The Web site for AASBM will be aasbm.org.
Omics: a journal of integrative biology 09/2009; 13(4):285-9. · 2.29 Impact Factor
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ABSTRACT: Asthenozoospermia (AS) is a common cause of human male infertility. In one study, more than 80% of the samples from infertile men had reduced sperm motility. Seminal plasma is a mixture of secretions from the testis, epididymis and several male accessory glands, including the prostate, seminal vesicles and Cowper's gland. Studies have shown that seminal plasma contains proteins that are important for sperm motility. To further explore the pathophysiological character of AS, we separated the seminal plasma proteins from AS patients and healthy donors using sodium dodecyl sulfate polyacrylamide gel electrophoresis and in-gel digestion, and then subjected the proteins to liquid chromatography-mass spectrometry (LC-MS/MS) analysis. A total of 741 proteins were identified in the seminal plasma, with a false discovery rate of 3.3%. Using spectral counting, we found that 45 proteins were threefold upregulated and 56 proteins were threefold downregulated in the AS group when compared with the control. Most of these proteins originated from the epididymis and prostate. This study identified a rich source of biomarker candidates for male infertility and indicates that functional abnormalities of the epididymis and prostate can contribute to AS. We identified DJ-1-a protein that has been shown elsewhere to be involved in the control of oxidative stress (OS)-as a downregulated protein in AS seminal plasma. The levels of DJ-1 in AS seminal plasma were about half of those in the control samples. In addition, the levels of reactive oxygen species were 3.3-fold higher in the AS samples than in the controls. Taken together, these data suggest that downregulation of DJ-1 is involved in OS in semen, and therefore affects the quality of the semen.
Asian Journal of Andrology 06/2009; 11(4):484-91. · 1.52 Impact Factor
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ABSTRACT: Hepatocellular carcinoma (HCC) is the fifth most frequent neoplasm with more than 500 000 new cases diagnosed yearly. Novel liver cancer biomarkers are needed. By tandem mass spectrometry, we analyzed the secretomes of 12 individual paired samples of liver cancer and adjacent normal tissues and identified 1528 proteins with >2 unique peptide hits. The false discovery rate was 3.4%. Using spectral counting, we found 87 proteins in the HCC group and 86 proteins in the normal group that showed fivefold overexpression. These proteins provided a rich source of biomarker candidates. We presented a novel paradigm in combining biomarkers that include an up-regulated cancer biomarker and a down-regulated organ-enriched marker, and identified chitinase-3-like protein 1(CHI3L1) and mannan-binding lectin serine peptidase 2 (MASP2) as the top biomarker pair for HCC diagnosis using integrative transcriptomics and proteomics analysis. Using ELISA assays, we further evaluated this biomarker pair in a separate cohort of 25 serum samples of liver cancer patients and 15 age-matched normal controls. The combined marker pair (YKL40/MASP2 ratio) performed better than either marker alone with an AUC of 0.97 for liver cancer diagnosis. Further validation of the biomarker pair in HCC patients versus disease controls and independent cohorts is warranted.
PROTEOMICS - CLINICAL APPLICATIONS 04/2009; 3(5):541 - 551. · 1.81 Impact Factor
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Biaoyang Lin, Jun Wang,
Xu Hong,
Xiaowei Yan,
Daehee Hwang,
Ji-Hoon Cho,
Danielle Yi,
Angelita G Utleg,
Xuefeng Fang,
Dustin E Schones,
Keji Zhao,
Gilbert S Omenn,
Leroy Hood
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ABSTRACT: The androgen receptor (AR) plays important roles in the development of male phenotype and in different human diseases including prostate cancers. The AR can act either as a promoter or a tumor suppressor depending on cell types. The AR proliferative response program has been well studied, but its prohibitive response program has not yet been thoroughly studied.
Previous studies found that PC3 cells expressing the wild-type AR inhibit growth and suppress invasion. We applied expression profiling to identify the response program of PC3 cells expressing the AR (PC3-AR) under different growth conditions (i.e. with or without androgens and at different concentration of androgens) and then applied the newly developed ChIP-seq technology to identify the AR binding regions in the PC3 cancer genome. A surprising finding was that the comparison of MOCK-transfected PC3 cells with AR-transfected cells identified 3,452 differentially expressed genes (two fold cutoff) even without the addition of androgens (i.e. in ethanol control), suggesting that a ligand independent activation or extremely low-level androgen activation of the AR. ChIP-Seq analysis revealed 6,629 AR binding regions in the cancer genome of PC3 cells with an FDR (false discovery rate) cut off of 0.05. About 22.4% (638 of 2,849) can be mapped to within 2 kb of the transcription start site (TSS). Three novel AR binding motifs were identified in the AR binding regions of PC3-AR cells, and two of them share a core consensus sequence CGAGCTCTTC, which together mapped to 27.3% of AR binding regions (1,808/6,629). In contrast, only about 2.9% (190/6,629) of AR binding sites contains the canonical AR matrix M00481, M00447 and M00962 (from the Transfac database), which is derived mostly from AR proliferative responsive genes in androgen dependent cells. In addition, we identified four top ranking co-occupancy transcription factors in the AR binding regions, which include TEF1 (Transcriptional enhancer factor), GATA (GATA transcription factors), OCT (octamer transcription factors) and PU1 (PU.1 transcription factor).
Our data provide a valuable data set in understanding the molecular basis for growth inhibition response program of the AR in prostate cancer cells, which can be exploited for developing novel prostate cancer therapeutic strategies.
PLoS ONE 02/2009; 4(8):e6589. · 4.09 Impact Factor
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ABSTRACT: Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched.
We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events.
Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data.
BMC Bioinformatics 01/2009; 9:537. · 2.75 Impact Factor
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ABSTRACT: We are now witnessing a new genomic revolution due to the arrival and continued advancements in the next-generation high-throughput sequencing technologies, which encompass sequencing by synthesis including fluorescent in situ sequencing (FISSEQ) and pyrosequencing, sequencing by ligation including using polony amplification and supported oligonucleotide detection (SOLiD), sequencing by hybridization in combination with sequencing-by-ligation and nanopore technology, nanopore sequencing and other novel sequencing technologies using nano-transistor array, scanning tunneling microscopy and nanowire molecule sensors etc. We review here major technologies and recent patents for achieving high-throughput, ultra-fast, extremely cheap, and highly accurate sequencing. We will see enormous impacts of these next-generation sequencing methods for solving complex biological problems and for ushering in the practice of personalized medicine.
Recent Patents on Biomedical Engineering 01/2008; 2008(1):60-67.
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ABSTRACT: The recent high-resolution neutron and synchrotron diffraction measurements by Fauth et al. [Phys. Rev. B 65, 060401(R) (2002)] demonstrated the existence of an intermediate spin state in half-doped La1/2Ba1/2CoO3 which is accompanied by a long-range tetragonal Jahn-Teller distortion. In this paper we find that the charge uniform ferromagnetic intermediate spin state strongly couples to the Jahn-Teller effect and is stable only at moderate distortion of 1%. While the calculated magnetic moment of this state is in agreement with the experimentally measured one, the corresponding orbital ordering is the nearest-neighboring alternating d3x2-r2/d3y2-r2, instead of the observed uniform d3z2-r2 orbital ordering. A calculation is carried out using the self-consistent unrestricted Hartree-Fock approximation on a realistic multiband d-p Hubbard Hamiltonian and a generalized Jahn-Teller coupling model, in which all possible spin-, charge-, and orbital-ordered states are considered.
Phys. Rev. B. 08/2002; 66(6).
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ABSTRACT: Based on a self-consistent mean-field approach, we study electronic structures of two types of doped manganites, Pr0.55(Ca0.75Sr0.25)0.45MnO3 (PCSMO) and Pr0.7Ca0.3MnO3, by considering both the double-exchange mechanism and Jahn-Teller effect. It is found that for PCSMO either ferromagnetically metallic state or charge-ordered insulator state is stable in a reasonable parameter range, while for Pr0.7Ca0.3MnO3 the metallic phase cannot be a stable state. These results are consistent with experimental observations that a persistent laser-induced insulator-metal transition could occur in PCSMO, whereas no stable metallic state was detected in Pr0.7Ca0.3MnO3.
Phys. Rev. B. 74(1).
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ABSTRACT: We have investigated theoretically the hydrostatic pressure effect on the electronic and magnetic properties of the doped bilayer manganites La2−2xSr1+2xMn2O7 (0.30⩽x⩽0.48). The key observation is the anisotropic variations of lattice parameters of the separate bilayers under the hydrostatic pressure, which in turn leads to the different changes between the intra- and interlayer hopping amplitudes of electrons and an additional energy level splitting of the two eg orbits x2−y2 and 3z2−r2 of Mn ions. It was found that these two factors from pressure have opposite effects on the orbital occupation properties of the system and the competition between them can cause very different behaviors depending on the doping concentrations. Our results of magnetic and orbital order variations at different doping levels are consistent with recent experiments.
Phys. Rev. B. 76(13).
