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Global comparison of chromosome X genes of pulmonary telocytes with mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells, and lymphocytes.

Zhu Y, Zheng M, Song D, Ye L, Wang X - J Transl Med (2015)

Bottom Line: We compared gene expression profiles in chromosome X of pulmonary TCs with mesenchymal stem cells (MSC), fibroblasts (Fb), alveolar type II cells (ATII), airway basal cells (ABC), proximal airway cells (PAC), CD8(+) T cells come from bronchial lymph nodes (T-BL), or CD8(+) T cells from lungs (T-L) by global analyses, and selected the genes which were consistently up or down regulated (>1 fold) in TCs compared to other cells as TC-specific genes.The functional and characteristic networks were identified and compared by bioinformatics tools.According to the selected TC-specific genes, we infer that pulmonary TCs function as modulators which may enhance cellular growth and migration, resist senescence, protect cells from external stress, regulate immune responses, participate in tissue remodeling and repair, regulate neural function, and promote vessel formation.

View Article: PubMed Central - PubMed

Affiliation: Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Bioinformatics, Fudan University, Shanghai, China. zhu.yichun@zs-hospital.com.

ABSTRACT

Background: Telocytes (TCs) are suggested as a new type of interstitial cells with specific telopodes. Our previous study evidenced that TCs differed from fibroblasts and stem cells at the aspect of gene expression profiles. The present study aims to search the characters and patterns of chromosome X genes of TC-specific or TC-dominated gene profiles and fingerprints, investigate the network of principle genes, and explore potential functional association.

Methods: We compared gene expression profiles in chromosome X of pulmonary TCs with mesenchymal stem cells (MSC), fibroblasts (Fb), alveolar type II cells (ATII), airway basal cells (ABC), proximal airway cells (PAC), CD8(+) T cells come from bronchial lymph nodes (T-BL), or CD8(+) T cells from lungs (T-L) by global analyses, and selected the genes which were consistently up or down regulated (>1 fold) in TCs compared to other cells as TC-specific genes. The functional and characteristic networks were identified and compared by bioinformatics tools.

Results: We selected 31 chromosome X genes as the TC-specific or dominated genes, among which 8 up-regulated (Flna, Msn, Cfp, Col4a5, Mum1l1, Rnf128, Syn1, and Srpx2) and 23 down-regulated (Abcb7, Atf1, Ddx26b, Drp2, Fam122b, Gyk, Irak1, Lamp2, Mecp2, Ndufb11, Ogt, Pdha1, Pola1, Rab9, Rbmx2, Rhox9, Thoc2, Vbp1, Dkc1, Nkrf, Piga, Tmlhe and Tsr2), as compared with other cells.

Conclusions: Our data suggested that gene expressions of chromosome X in TCs are different with those in other cells in the lung tissue. According to the selected TC-specific genes, we infer that pulmonary TCs function as modulators which may enhance cellular growth and migration, resist senescence, protect cells from external stress, regulate immune responses, participate in tissue remodeling and repair, regulate neural function, and promote vessel formation.

No MeSH data available.


Related in: MedlinePlus

Hierarchical cluster analysis. Hierarchical cluster analysis of the differentially expressed genes on chromosomes X among telocytes (TCs), mesenchymal stem cells (MSCs), fibroblasts (Fbs), lymphocytes from lungs (T-LL) and from bronchial lymph nodes (T-BL), alveolar type II cells (ATII), proximal airway cells (PAC) and airway basal cells (ABC)
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Fig1: Hierarchical cluster analysis. Hierarchical cluster analysis of the differentially expressed genes on chromosomes X among telocytes (TCs), mesenchymal stem cells (MSCs), fibroblasts (Fbs), lymphocytes from lungs (T-LL) and from bronchial lymph nodes (T-BL), alveolar type II cells (ATII), proximal airway cells (PAC) and airway basal cells (ABC)

Mentions: Hierarchical clustering of genes in chromosomes X was performed by TIGR Multi-experiment Viewer (MeV v4.9) (Fig. 1). Gene expression data were normalized and imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Up- or down-regulated folds of TCs genes were calculated by comparing with other cells, after the averages of gene expression in cells were obtained from the raw data of multi-databases. The up-regulated folds were defined as the normalized gene expression values of TC5 or TC10 divide those of other cells, while the down-regulated folds were defined as the expression values of other cells devide those of TC5 or TC10. We selected the genes which were consistently up or down regulated (>1 fold) in both TC5 and TC10 as compared to other cells as TC-specific genes (Additional file 1: Table S1).Fig. 1


Global comparison of chromosome X genes of pulmonary telocytes with mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells, and lymphocytes.

Zhu Y, Zheng M, Song D, Ye L, Wang X - J Transl Med (2015)

Hierarchical cluster analysis. Hierarchical cluster analysis of the differentially expressed genes on chromosomes X among telocytes (TCs), mesenchymal stem cells (MSCs), fibroblasts (Fbs), lymphocytes from lungs (T-LL) and from bronchial lymph nodes (T-BL), alveolar type II cells (ATII), proximal airway cells (PAC) and airway basal cells (ABC)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4587873&req=5

Fig1: Hierarchical cluster analysis. Hierarchical cluster analysis of the differentially expressed genes on chromosomes X among telocytes (TCs), mesenchymal stem cells (MSCs), fibroblasts (Fbs), lymphocytes from lungs (T-LL) and from bronchial lymph nodes (T-BL), alveolar type II cells (ATII), proximal airway cells (PAC) and airway basal cells (ABC)
Mentions: Hierarchical clustering of genes in chromosomes X was performed by TIGR Multi-experiment Viewer (MeV v4.9) (Fig. 1). Gene expression data were normalized and imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Up- or down-regulated folds of TCs genes were calculated by comparing with other cells, after the averages of gene expression in cells were obtained from the raw data of multi-databases. The up-regulated folds were defined as the normalized gene expression values of TC5 or TC10 divide those of other cells, while the down-regulated folds were defined as the expression values of other cells devide those of TC5 or TC10. We selected the genes which were consistently up or down regulated (>1 fold) in both TC5 and TC10 as compared to other cells as TC-specific genes (Additional file 1: Table S1).Fig. 1

Bottom Line: We compared gene expression profiles in chromosome X of pulmonary TCs with mesenchymal stem cells (MSC), fibroblasts (Fb), alveolar type II cells (ATII), airway basal cells (ABC), proximal airway cells (PAC), CD8(+) T cells come from bronchial lymph nodes (T-BL), or CD8(+) T cells from lungs (T-L) by global analyses, and selected the genes which were consistently up or down regulated (>1 fold) in TCs compared to other cells as TC-specific genes.The functional and characteristic networks were identified and compared by bioinformatics tools.According to the selected TC-specific genes, we infer that pulmonary TCs function as modulators which may enhance cellular growth and migration, resist senescence, protect cells from external stress, regulate immune responses, participate in tissue remodeling and repair, regulate neural function, and promote vessel formation.

View Article: PubMed Central - PubMed

Affiliation: Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Bioinformatics, Fudan University, Shanghai, China. zhu.yichun@zs-hospital.com.

ABSTRACT

Background: Telocytes (TCs) are suggested as a new type of interstitial cells with specific telopodes. Our previous study evidenced that TCs differed from fibroblasts and stem cells at the aspect of gene expression profiles. The present study aims to search the characters and patterns of chromosome X genes of TC-specific or TC-dominated gene profiles and fingerprints, investigate the network of principle genes, and explore potential functional association.

Methods: We compared gene expression profiles in chromosome X of pulmonary TCs with mesenchymal stem cells (MSC), fibroblasts (Fb), alveolar type II cells (ATII), airway basal cells (ABC), proximal airway cells (PAC), CD8(+) T cells come from bronchial lymph nodes (T-BL), or CD8(+) T cells from lungs (T-L) by global analyses, and selected the genes which were consistently up or down regulated (>1 fold) in TCs compared to other cells as TC-specific genes. The functional and characteristic networks were identified and compared by bioinformatics tools.

Results: We selected 31 chromosome X genes as the TC-specific or dominated genes, among which 8 up-regulated (Flna, Msn, Cfp, Col4a5, Mum1l1, Rnf128, Syn1, and Srpx2) and 23 down-regulated (Abcb7, Atf1, Ddx26b, Drp2, Fam122b, Gyk, Irak1, Lamp2, Mecp2, Ndufb11, Ogt, Pdha1, Pola1, Rab9, Rbmx2, Rhox9, Thoc2, Vbp1, Dkc1, Nkrf, Piga, Tmlhe and Tsr2), as compared with other cells.

Conclusions: Our data suggested that gene expressions of chromosome X in TCs are different with those in other cells in the lung tissue. According to the selected TC-specific genes, we infer that pulmonary TCs function as modulators which may enhance cellular growth and migration, resist senescence, protect cells from external stress, regulate immune responses, participate in tissue remodeling and repair, regulate neural function, and promote vessel formation.

No MeSH data available.


Related in: MedlinePlus