Biomedical subjects

Aixiang Jiang

Publications and source records attributed to Aixiang Jiang.

4 recordsLinked to original sources

PubMed2006

Semi-supervised learning via penalized mixture model with application to microarray sample classification.

MOTIVATION: It is biologically interesting to address whether human blood outgrowth endothelial cells (BOECs) belong to or are closer to large vessel endothelial cells (LVECs) or microvascular endothelial cells (MVECs) based on global expression profiling. An earlier analysis using a hierarchical clustering and a small set of genes suggested that BOECs seemed to be closer to MVECs. By taking advantage of the two known classes, LVEC and MVEC, while allowing BOEC samples to belong to either of the two classes or to form their own new class, we take a semi-supervised learning approach; for high-dimensional data as encountered here, we propose a penalized mixture model with a weighted L1 penalty to realize automatic feature selection while fitting the model. RESULTS: We applied our penalized mixture model to a combined dataset containing 27 BOEC, 28 LVEC and 25 MVEC samples. Analysis results indicated that the BOEC samples appeared to form their own new class. A simulation study confirmed that, compared with the standard mixture model with or without initial variable selection, the penalized mixture model performed much better in identifying relevant genes and forming corresponding clusters. The penalized mixture model seems to be promising for high-dimensional data with the capability of novel class discovery and automatic feature selection.

Algorithms↗

PubMed2006

A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies.

BACKGROUND: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The "rules" governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. METHODS AND FINDINGS: In an effort to identify new cancer-specific methylation markers, we employed a high-throughput global expression profiling approach in lung cancer cells. We identified 132 genes that have 5' CpG islands, are induced from undetectable levels by 5-aza-2'-deoxycytidine in multiple non-small cell lung cancer cell lines, and are expressed in immortalized human bronchial epithelial cells. As expected, these genes were also expressed in normal lung, but often not in companion primary lung cancers. Methylation analysis of a subset (45/132) of these promoter regions in primary lung cancer (n = 20) and adjacent nonmalignant tissue (n = 20) showed that 31 genes had acquired methylation in the tumors, but did not show methylation in normal lung or peripheral blood cells. We studied the eight most frequently and specifically methylated genes from our lung cancer dataset in breast cancer (n = 37), colon cancer (n = 24), and prostate cancer (n = 24) along with counterpart nonmalignant tissues. We found that seven loci were frequently methylated in both breast and lung cancers, with four showing extensive methylation in all four epithelial tumors. CONCLUSIONS: By using a systematic biological screen we identified multiple genes that are methylated with high penetrance in primary lung, breast, colon, and prostate cancers. The cross-tumor methylation pattern we observed for these novel markers suggests that we have identified a partial promoter hypermethylation signature for these common malignancies. These data suggest that while tumors in different tissues vary substantially with respect to gene expression, there may be commonalities in their promoter methylation profiles that represent targets for early detection screening or therapeutic intervention.

Adenocarcinoma↗

PubMed2003

Distinct roles of catalytic and pexin-like domains in membrane-type matrix metalloproteinase (MMP)-mediated pro-MMP-2 activation and collagenolysis.

Members of the membrane-type matrix metalloproteinase (MT-MMPs) family are dual regulators of extracellular matrix remodeling through direct degradation of extracellular matrix components and activation of other latent MMPs. However, the structural basis of this functional diversity remains poorly understood. In an attempt to dissect the structural determinants for MT-MMP function, we performed domain exchange experiments between MT1-MMP and its close relative MT3-MMP and analyzed the exchange chimeras for pro-MMP-2 activation and collagen degradation at the cellular level. Our results indicate that catalytic domains determine the pattern of pro-MMP-2 activation, whereas pexin-like domains modulate the level of activation. On the other hand, both the catalytic and pexin-like domains of MT1-MMP are required for strong collagenolysis because exchanging either domain with that of MT3-MMP yielded significantly lower activity, and the introduction of the MT1-MMP catalytic or pexin-like domain into MT3-MMP failed to generate any significant enhancement of collagenolytic activity compared with wild-type MT3-MMP. Interestingly, the cytoplasmic domain of MT1-MMP behaves as a negative regulator not only for MT1-MMP itself, but also for MT3-MMP in both pro-MMP-2 activation and collagenolysis, consistent with and extending our recent findings (Jiang, A., Lehti, K., Wang, X., Weiss, S. J., Keski-Oja, J., and Pei, D. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 13693-13698). Taken together, these results demonstrate that domains in MT-MMPs function differently toward a given substrate and thus should be targeted differentially for future therapeutic development.

Animals↗

PubMedDate not supplied

Limited processing of pro-matrix metalloprotease-2 (gelatinase A) overexpressed by transfection in PC-3 human prostate tumor cells: association with restricted cell surface localization of membrane-type matrix metalloproteinase-1.

The expression and activation of matrix metalloproteinases (MMPs) by tumor cells is correlated with progression to invasive and metastatic status. The purpose of this study was to examine the role of increased MMP-2 (gelatinase A) expression in prostate cancer progression utilizing human prostate PC-3 cancer cells that overexpress MMP-2 using gene transfection. PC-3 cells were transfected with pCR-3 vector only and pCR-3 MMP-2 plasmids employing the LipofectAMINE method, and stable transfectants were selected with G418. The expression of MMP-2, tissue inhibitor of metalloproteinase-2 (TIMP-2), and membrane-type MMP 1 (MT1-MMP) in PC-3 parental and transfected cells under serum-free conditions was determined by zymography, immunoblotting, immunofluorescent microscopy, Northern blotting, and/or reverse transcriptase-polymerase chain reaction (RT-PCR). MMP-2 transfected cells produced primarily the proenzyme form of MMP-2; the parental and vector control transfected PC-3 cells did not express any MMP-2 that was detectable by the methods we employed. Treatment of PC-3 MMP-2 transfected cells with Concanavalin A (Con A), in contrast to HT-1080 cells, processed only a small amount of the secreted 72-kd proenzyme to a 62-kd intermediate and a cell-associated 59-kd active form. The low level of secreted pro-MMP-2 processing induced by Con A was inhibited by serine protease inhibitors and was unaffected by cyclic adenosine monophosphate (cAMP). Immunoblotting showed that these cells produced abundant TIMP-2 and lower amounts of MT1-MMP in comparison with Con A-responding HT-1080 cells. HT-1080 cells respond to Con A by translocating MT1-MMP from intracellular localization sites to the plasma membrane, an effect not observed in PC-3 cells. The molecular basis for the low level of processing of pro-MMP-2 by PC-3 cells may be due to an overabundance of TIMP-2 and/or a low level of cell surface active MT1-MMP.

Blotting, Northern↗