Genomic and proteomic analysis of the myeloid differentiation program

Zheng, Liduan; Wang, Le; Yamaga, Shigeru; Bonds, Wesley; Beazer-Barclay, Yasmin; Kluger, Yuval; Gerstein, Mark; Newburger, Peter E.; Berliner, Nancy; Weissman, Sherman M.

doi:10.1182/blood.v98.3.513

Cited by 91 publications

(75 citation statements)

References 33 publications

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“…Increasing genome sequence information for different organisms, development of powerful robots for arraying, and the availability of widely accessible "user-friendly" tools for systematical handling of the genomic analysis output have all accelerated the use of microarrays in basic and clinical research (62). The discrepancies observed between gene expression and protein abundance suggest that posttranslational modalities may be at least as important as changes in mRNA levels in determining the cellular protein composition and provide a cautionary note for efforts to interpret cell composition and function in relation to mRNA levels only (63). Still however, transcriptional analysis can be highly efficient in providing initial novel scientific leads and ideas that subsequently need to be reevaluated and established at the protein and functional levels.…”

Section: Discussionmentioning

confidence: 99%

Novel Insights on Human NK Cells’ Immunological Modalities Revealed by Gene Expression Profiling

Hanna¹,

Bechtel

Zhai

et al. 2004

The Journal of Immunology

143

147

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As part of the innate immune system, human NK cells play a critical role early in the systemic host defense against pathogens and tumor cells. Recent studies suggest a more complex view of NK cell behavior, as different functions and tissue localizing capabilities seem to be preferentially assigned to distinct subpopulations of NK cells, CD56dimCD16+ or CD56brightCD16−. In this study, we used oligonucleotide microarrays to compare the expression profile of ∼20,000 genes in three NK cell subpopulations: peripheral blood-derived CD56dimCD16+, CD56brightCD16−, and in vitro-activated CD16+ NK cells. The differential expression of selected genes was verified by flow cytometry and functional assays. When comparing CD56dimCD16+ and CD56brightCD16− subsets, a new heterogeneous molecular basis for the functional and developmental differences between these two subsets was revealed. Furthermore, systematic analysis of transcriptional changes in activated CD16+ NK cells provided us with a better understanding of NK function in inflamed tissues. We highlight a number of genes that were overexpressed upon activation (e.g., OX40 ligand, CD86, Tim3, galectins, etc.), that enable these cells to directly cross-talk with other innate and adaptive immune effectors. The overexpressed genes assign novel intriguing immunomodulatory functions to activated NK cells, in addition to their potent cytotoxic abilities.

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Section: Discussionmentioning

confidence: 99%

Novel Insights on Human NK Cells’ Immunological Modalities Revealed by Gene Expression Profiling

Hanna¹,

Bechtel

Zhai

et al. 2004

The Journal of Immunology

143

147

View full text Add to dashboard Cite

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“…In eukaryotic systems, mRNA transcript levels often do not correspond with protein quantities (Lian et al 2001;Griffin et al 2002;Cox et al 2005;Kislinger et al 2006;Wilhelm et al 2006;Schmidt et al 2007;Fu et al 2009). For example, in human medulloblastoma cells, there is a relatively poor correlation between steady-state protein and mRNA levels (R = 0.29) (Vogel et al 2010).…”

Section: Discussionmentioning

confidence: 99%

“…In eukaryotic systems, there is a poor correlation between steady-state mRNA and protein levels (Lian et al 2001;Griffin et al 2002;Cox et al 2005;Kislinger et al 2006;Wilhelm et al 2006;Schmidt et al 2007;Fu et al 2009). Although some of this discrepancy can be attributed to mRNA stability and the efficiency of translation initiation, the contribution of alternative splicing (AS) to this problem is largely ignored.…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Frac-seq reveals isoform-specific recruitment to polyribosomes

et al. 2013

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Pre-mRNA splicing is required for the accurate expression of virtually all human protein coding genes. However, splicing also plays important roles in coordinating subsequent steps of pre-mRNA processing such as polyadenylation and mRNA export. Here, we test the hypothesis that nuclear pre-mRNA processing influences the polyribosome association of alternative mRNA isoforms. By comparing isoform ratios in cytoplasmic and polyribosomal extracts, we determined that the alternative products of ∼30% (597/1954) of mRNA processing events are differentially partitioned between these subcellular fractions. Many of the events exhibiting isoform-specific polyribosome association are highly conserved across mammalian genomes, underscoring their possible biological importance. We find that differences in polyribosome association may be explained, at least in part by the observation that alternative splicing alters the cis-regulatory landscape of mRNAs isoforms. For example, inclusion or exclusion of upstream open reading frames (uORFs) in the 5′UTR as well as Alu-elements and microRNA target sites in the 3′UTR have a strong influence on polyribosome association of alternative mRNA isoforms. Taken together, our data demonstrate for the first time the potential link between alternative splicing and translational control of the resultant mRNA isoforms.

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“…The liquid flowing in BHDs may play important roles in tumor growth as it contains hyaluronic acid, adrenalin, noradrenalin, albumin, and microcells (or sanals). In addition, a pro teomic analysis of tissues and liquid from BHDs on rabbit intestinal surfaces [22] composition similar to that usually associated with stem cells [23,24], cancer cells [25], and differentiated myeloid cells [26]. These cells, with vigorous proliferative abilities, show a similar abundance of carbohydrate-or energy-related processes [23−26].…”

Section: Discussionmentioning

confidence: 99%

Bonghan Ducts as Possible Pathways for Cancer Metastasis

Yoo

Kim

Ogay

et al. 2009

Journal of Acupuncture and Meridian Studies

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Objective: The present study has been designed to find a possible new route for the metastasis of cancer cells on the fascia surrounding tumor tissue using a novel technique of trypan blue staining. Materials and Methods: Tumor tissues were grown in the skin of nude mice after subcutaneous inoculation with human lung cancer cells. Trypan blue was recently identified as a dye with specificity for Bonghan ducts (BHDs) and not other tissues, such as blood or lymph vessels or nerves. Results: We demonstrate that the trypan blue staining technique allows the first visualization of BHDs which are connected to tumor tissues. Conclusion: Since BHDs are known to make up a circulatory system corresponding to acu puncture meridians or collaterals, we propose that, in addition to the currently known blood or lymph vessels, BHDs on tumor tissue fascia may be a novel pathway for metastasis.

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Genomic and proteomic analysis of the myeloid differentiation program

Cited by 91 publications

References 33 publications

Novel Insights on Human NK Cells’ Immunological Modalities Revealed by Gene Expression Profiling

Novel Insights on Human NK Cells’ Immunological Modalities Revealed by Gene Expression Profiling

Frac-seq reveals isoform-specific recruitment to polyribosomes

Bonghan Ducts as Possible Pathways for Cancer Metastasis

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