Dissecting the transcriptional program of phosphomannomutase 2-deficient cells: Lymphoblastoide B cell lines as a valuable model for congenital disorders of glycosylation studies.

Congenital disorders of glycosylation (CDG) include 150 genetically and clinically heterogeneous diseases, showing significant glycoprotein hypoglycosylation that leads to pathological consequences in multiple organs and systems whose underlying mechanisms are not yet understood. A few cellular and animal models have been used to study specific CDG characteristics, although they have given limited information due to the few CDG mutations tested and the still missing comprehensive molecular and cellular basic research. Here, we provide specific gene expression profiles, based on ribonucleic acid (RNA) microarray analysis, together with some biochemical and cellular characteristics of a total of nine control Epstein-Barr virus-transformed lymphoblastoid B cell lines (B-LCL) and 13 CDG B-LCL from patients carrying severe mutations in the phosphomannomutase 2 (PMM2) gene, strong serum protein hypoglycosylation and neurological symptoms. Significantly dysregulated genes in PMM2-CDG cells included those regulating stress responses, transcription factors, glycosylation, motility, cell junction and, importantly, those related to development and neuronal differentiation and synapse, such as carbonic anhydrase 2 (CA2) and ADAM23. PMM2-CDG-associated biological consequences involved the unfolded protein response, RNA metabolism and the endoplasmic reticulum, Golgi apparatus and mitochondria components. Changes in the transcriptional and CA2 protein levels are consistent with the CDG physiopathology. These results demonstrate the global transcriptional impact in phosphomannomutase 2-deficient cells, reveal CA2 as a potential cellular biomarker and confirm B-LCL as an advantageous model for CDG studies.

Variable Distribution of DOCK-D Proteins between Cytosol and Nucleoplasm in Cell Lines, Effect of Interleukin-4 on DOCK10 in B-Cell Lymphoid Neoplasms, and Validation of a New DOCK10 Antiserum for Immunofluorescence Studies.

Dedicator-of-cytokinesis (DOCK), a family of guanine-nucleotide exchange factors (GEFs), comprises four subfamilies, named from A to D. DOCK-D comprises DOCK9, DOCK10, and DOCK11. The GEF activity involves translocation from the cytoplasm to the plasma membrane (PM), as assessed by the transfection of tagged proteins. However, the cellular localization of endogenous DOCK proteins is poorly understood. In this paper, to gain a better understanding of the role of the DOCK-D proteins, we studied their distribution between cytosol and nucleoplasm in 11 cell lines. DOCK-D proteins were distributed with variable cytosolic or nuclear predominance, although the latter was common for DOCK9 and DOCK11. These results suggest that the DOCK-D proteins may perform new nuclear functions, which remain to be discovered. Furthermore, we found that DOCK10 levels are increased by interleukin-4 (IL-4) in B-cell lymphoid neoplasms other than chronic lymphocytic leukemia (CLL) such as mantle cell lymphoma and diffuse large B-cell lymphoma. We also found evidence for an induction of the cytosolic levels of DOCK10 by IL-4 in CLL. Finally, we obtained a valid DOCK10 antiserum for immunofluorescence (IF) microscopy that, as an antibody against the hemagglutinin (HA) tag, marked PM ruffles and filopodia in HeLa cells with inducible expression of HA-DOCK10.

The roles of Cdc42 and Rac1 in the formation of plasma membrane protrusions in cancer epithelial HeLa cells.

The inducible model of clones generated from the cervical cancer epithelial HeLa cell line has shown the role of DOCK10 as a guanine-nucleotide exchange factor for Rho GTPases Cdc42 and Rac1 and as an inducer of filopodia and plasma membrane (PM) ruffles. In this model, constitutively active (CA) mutants of Cdc42 and Rac1 promote filopodia and ruffles, respectively, as in other models. DOCK9 also induces filopodia and ruffles, although ruffling activity is less prominent. By exploiting this model further, the aim of this work is to provide a more complete understanding of the role of Cdc42 and Rac1, and their interactions with DOCK10 and DOCK9, in regulation of PM protrusions. New clones have been generated from HeLa, including single clones expressing one form of wild-type (WT) or dominant negative (DN) Cdc42 or Rac1, and double clones co-expressing one of them together with either DOCK10 or DOCK9. Expression of WT- and DN-Cdc42 induced filopodia. WT-Cdc42 and, especially, DN-Cdc42 also gave rise to veil protrusions, which were neutralized by DOCK10. Moreover, DN-Cdc42 stimulated the emergence of ruffles, further increased by DOCK10, and WT-Cdc42 also augmented ruffles in presence of DOCK9 and DOCK10. WT-Rac1 greatly increased PM blebbing, as did DN-Rac1 more moderately. In both cases, blebs were enhanced by DOCK10. DN-Rac1 and CA-Rac1 moderately raised filopodia, and DOCK10 and DOCK9 had opposed effects on filopodia (up and down, respectively) in presence of WT-Rac1. As conclusions, we highlight that Cdc42 promotes filopodia regardless of its conformational state, and Rac1 induces blebs in conformations other than CA, especially WT-Rac1, in the inducible HeLa clones. The model could be useful to learn more about the mechanisms underlying PM protrusions.

The role of DOCK10 in the regulation of the transcriptome and aging.

DOCK10, a guanine-nucleotide exchange factor (GEF) for Rac1 and Cdc42 Rho GTPases whose expression is induced by interleukin-4 (IL-4) in B cells, is involved in B cell development and function according to recent studies performed in Dock10-knockout (KO) mice. To investigate whether DOCK10 is involved in regulation of the transcriptome, changes in the gene expression profiles (GEPs) were studied by microarray in three cellular models: DOCK10 expression induced by doxycycline (dox) withdrawal in a stable inducible HeLa clone, DOCK10 expression induced by transient transfection of 293T cells, and wild type (WT) versus KO mouse spleen B cells (SBC). In all three systems, DOCK10 expression determined moderate differences in the GEPs, which were functionally interpreted by gene set enrichment analysis (GSEA). Common signatures significantly associated to expression of DOCK10 were found in all three systems, including the upregulated targets of HOXA5 and the SWI/SNF complex, and EGF signaling. In SBC, Dock10 expression was associated to enrichment of gene sets of Cmyb, integrin, IL-4, Wnt, Rac1, and Cdc42 pathways, and of cellular components such as the immunological synapse and the cell leading edge. Transcription of genes involved in these pathways likely acts as a feedforward mechanism downstream of activation of Rac1 and Cdc42 mediated by DOCK10. Interestingly, a senescence gene set was found significantly associated to WT SBC. To test whether DOCK10 is related to aging, we set out to analyse the survival of the mouse colony, which led to the finding that Dock10-KO mice lived longer than WT mice. Moreover, Dock10-KO mice showed slower loss of their coat during aging. These results indicate a role for Dock10 in senescence. These novel roles of DOCK10 in the regulation of the transcriptome and aging deserve further exploration.

The transcriptional response of mouse spleen B cells to IL-4: Comparison to the response of human peripheral blood B cells.

The Th2 cytokine IL-4 triggers a signaling cascade which activates transcription by STAT6. The goals of the present study are to define the transcriptomic response of mouse spleen B cells (mSBC) to IL-4 used as single stimulus, its specificity compared to human peripheral blood B cells (hPBBC) and to mouse spleen T cells (mSTC), and the pathways affected. Oligonucleotide-based microarrays were performed using two references, the untreated sample and the cells cultured without IL-4, an experimental design which reduces the potential confounding effect of cellular stress during culture. Specificity was addressed by comparing the response of mSBC and our previously published study on hPBBC, of similar design, and a study by other authors on mSTC. We detected an mSBC-specific response (including novel genes, e.g., Sertad4, Lifr, Pmepa1, Epcam, Tbxas1; and common genes, e.g., Usp2, Cst7, Grtp1, and Casp6), an hPBBC-specific response (e.g., CCL17, MTCL1, GCSAM, HOMER2, IL2RA), and a common mSBC/hPBBC response (e.g., CISH, NFIL3, SOCS1, VDR, CDH1). In contrast, the mSBC and mSTC responses were largely divergent. Gene set enrichment analysis (GSEA) was applied for the first time to identify the pathways affected. Both in mSBC and hPBBC, IL-4 activated Myc, the transcriptional machinery itself, cell cycle, mitochondria and respiratory chain, ribosome, proteasome and antigen presentation, and Wnt signaling, and inhibited GPCR signaling. However, significant differences were found in histone demethylation, Nod signaling, and Rho signaling, which were downregulated in mSBC, and in chromatin condensation, which was downregulated in hPBBC. These findings may have therapeutic implications for the treatment of allergic diseases and parasitic infections.

DOCK9 induces membrane ruffles and Rac1 activity in cancer HeLa epithelial cells.

Dedicator-of-cytokinesis (DOCK) proteins are a family of guanine-nucleotide exchange factors (GEF) for Rho GTPases. The DOCK-D homology subfamily comprises DOCK9, DOCK10, and DOCK11. DOCK9 and DOCK11 are GEFs for Cdc42 and induce filopodia, while DOCK10 is a dual GEF for Cdc42 and Rac1 and induces filopodia and ruffles. We provide data showing that DOCK9, the only one of the DOCK-D members that is not considered hematopoietic, is nevertheless expressed at high levels in T lymphocytes, as do DOCK10 and DOCK11, although unlike these, it is not expressed in B lymphocytes. To investigate DOCK9 function, we have created a stable HeLa clone with inducible expression of HA-DOCK9. Induction of expression of HA-DOCK9 produced loss of elongation and polygonal shape of HeLa cells. Regarding membrane protrusions, HA-DOCK9 prominently induced filopodia, but also an increase of membrane ruffles. The latter was consistent with an increase in the levels of activation of Rac1, suggesting that DOCK9 carries a secondary ability to induce ruffles through activation of Rac1.

Dock10 regulates CD23 expression and sustains B-cell lymphopoiesis in secondary lymphoid tissue.

Dock10, a guanine nucleotide exchange factor for the Rho GTPases Rac1 and Cdc42, affects cell morphology, membrane protrusive activity, and cell movement. Dock10 is prominently expressed in lymphoid tissue and upregulated by IL-4 in B cells. To investigate the physiological role of Dock10, WT mice and Dock10 KO mice were used. KO mice showed decreased numbers of B cells in spleen, both follicular B cells and marginal zone B cells, and in peripheral blood, but not in bone marrow. The antiapoptotic effect of IL-4 in vitro, the migratory response to CXCL13 or CCL21 in vitro, and the whole genome expression profile were intact in spleen B cells from KO mice. CD23, the low-affinity receptor for immunoglobulin E, was overexpressed on follicular B cells from KO mice, suggesting that Dock10 negatively regulates membrane CD23 expression. Negative regulation of CD23 expression by Dock10 could play a role in B cell maturation and function.

IL-4 Up-Regulates MiR-21 and the MiRNAs Hosted in the CLCN5 Gene in Chronic Lymphocytic Leukemia.

Interleukin 4 (IL-4) induces B-cell differentiation and survival of chronic lymphocytic leukemia (CLL) cells. MicroRNAs (miRNAs) regulate mRNA and protein expression, and several miRNAs, deregulated in CLL, might play roles as oncogenes or tumor suppressors. We have studied the miRNA profile of CLL, and its response to IL-4, by oligonucleotide microarrays, resulting in the detection of a set of 129 mature miRNAs consistently expressed in CLL, which included 41 differentially expressed compared to normal B cells (NBC), and 6 significantly underexpressed in ZAP-70 positive patients. IL-4 stimulation brought about up-regulation of the 5p and 3p mature variants of the miR-21 gene, which maps immediately downstream to the VMP1 gene, and of the mature forms generated from the miR-362 (3p and 5p), miR-500a (3p), miR-502 (3p), and miR-532 (3p and 5p) genes, which map within the third intron of the CLCN5 gene. Both genes are in turn regulated by IL-4, suggesting that these miRNAs were regulated by IL-4 as passengers from their carrier genes. Their levels of up-regulation by IL-4 significantly correlated with cytoprotection. MiR-21 has been reported to be leukemogenic, associated to bad prognosis in CLL, and the miRNA more frequently overexpressed in human cancer. Up-regulation by IL-4 of miR-21 and the miRNAs hosted in the CLCN5 locus may contribute to evasion of apoptosis of CLL cells. These findings indicate that the IL-4 pathway and the miRNAs induced by IL-4 are promising targets for the development of novel therapies in CLL.

Dock10, a Cdc42 and Rac1 GEF, induces loss of elongation, filopodia, and ruffles in cervical cancer epithelial HeLa cells.

Dock10 is one of the three members of the Dock-D family of Dock proteins, a class of guanine nucleotide exchange factors (GEFs) for Rho GTPases. Its homologs Dock9 and Dock11 are Cdc42 GEFs. Dock10 is required for maintenance of rounded morphology and amoeboid-type movement. Full-length isoforms of Dock10 have been recently cloned. Here, we address GTPase specificity and GEF activity of Dock10. In order of decreasing intensity, Dock10 interacted with nucleotide-free Rac1, Cdc42, and Rac3, and more weakly with Rac2, RhoF, and RhoG. Inducible expression of Dock10 in HeLa epithelial cells promoted GEF activity on Cdc42 and Rac1, and a morphologic change in two-dimensional culture consisting in loss of cell elongation, increase of filopodia, and ruffles. Area in contact with the substrate of cells that spread with non-elongated morphology was larger in cells expressing Dock10. Inducible expression of constitutively active mutants of Cdc42 and Rac1 in HeLa cells also induced loss of elongation. However, Cdc42 induced filopodia and contraction, and Rac1 induced membrane ruffles and flattening. When co-expressed with Dock10, Cdc42 potentiated filopodia, and Rac1 potentiated ruffles. These results suggest that Dock10 functions as a dual GEF for Cdc42 and Rac1, affecting cell morphology, spreading and actin cytoskeleton protrusions of adherent HeLa cells.

The gene expression response of chronic lymphocytic leukemia cells to IL-4 is specific, depends on ZAP-70 status and is differentially affected by an NFκB inhibitor.

Interleukin 4 (IL-4), an essential mediator of B cell development, plays a role in survival of chronic lymphocytic leukemia (CLL) cells. To obtain new insights into the function of the IL-4 pathway in CLL, we analyzed the gene expression response to IL-4 in CLL and in normal B cells (NBC) by oligonucleotide microarrays, resulting in the identification of 232 non-redundant entities in CLL and 146 in NBC (95 common, 283 altogether), of which 189 were well-defined genes in CLL and 123 in NBC (83 common, 229 altogether) (p<0.05, 2-fold cut-off). To the best of our knowledge, most of them were novel IL-4 targets for CLL (98%), B cells of any source (83%), or any cell type (70%). Responses were significantly higher for 54 and 11 genes in CLL and NBC compared to each other, respectively. In CLL, ZAP-70 status had an impact on IL-4 response, since different sets of IL-4 targets correlated positively or negatively with baseline expression of ZAP-70. In addition, the NFκB inhibitor 6-Amino-4-(4-phenoxyphenethylamino)quinazoline, which reversed the anti-apoptotic effect of IL-4, preferentially blocked the response of genes positively correlated with ZAP-70 (e.g. CCR2, SUSD2), but enhanced the response of genes negatively correlated with ZAP-70 (e.g. AUH, BCL6, LY75, NFIL3). Dissection of the gene expression response to IL-4 in CLL and NBC contributes to the understanding of the anti-apoptotic response. Initial evidence of a connection between ZAP-70 and NFκB supports further exploration of targeting NFκB in the context of the assessment of inhibition of the IL-4 pathway as a therapeutic strategy in CLL, especially in patients expressing bad prognostic markers.

Human and mouse DOCK10 splicing isoforms with alternative first coding exon usage are differentially expressed in T and B lymphocytes.

DOCK10 is a member of the dedicator of cytokinesis (DOCK) family of Rho GTPase activators preferentially expressed in lymphocytes. In this paper, we analyzed DOCK10 mRNA diversity produced because of alternative splicing. Alternative first coding exon usage led to 2 main protein-coding transcripts, DOCK10.1 and DOCK10.2. Full-length cDNA clones of both isoforms were obtained from both normal human peripheral blood mononuclear cells and mouse spleen for the first time for human DOCK10.1, mouse DOCK10.1, and mouse DOCK10.2. Human and mouse DOCK10.1 clones corresponded to the protein coding assemblies provided by the National Center for Biotechnology Information as Reference Sequences for DOCK10. Our analysis especially focused on human cDNA clones, of which 63% were alternatively spliced forms involving diverse exons and introns. DOCK10.1 expression was enriched in normal T cells, and DOCK10.2 expression was enriched in normal B cells and chronic lymphocytic leukemia (CLL) B cells. Both isoforms were upregulated in response to interleukin-4 in B cells, both normal and CLL, but not in T cells. Our data suggest that cell-specific mechanisms regulate expression of the alternative first exon variants of DOCK10 in vertebrates.