Gene networks in basal cell carcinoma of the eyelid, analyzed using gene expression profiling

Abstract

Basal cell carcinoma (BCC) is the most frequent malignant tumor of the eyelid; it progresses slowly and rarely metastasizes. However, BCC of the eyelid is partially invasive and can extend to the surrounding ocular adnexa even if appropriate treatment is performed. To understand the molecular mechanism underlying its pathogenesis, global gene expression analysis of surgical tissue samples of BCC of the eyelid (n=2) and normal human epidermal keratinocytes was performed using a GeneChip ® system. The histopathological examination of surgically removed eyelid tissues showed the tumor nest composed with small basaloid. In the samples from patients 1 and 2, 687 and 713 genes were identified, respectively, demonstrating ≥5.0-fold higher expression than that noted in normal human epidermal keratinocytes. For the 640 genes with upregulated expression in both patient samples, Ingenuity ® pathway analysis showed that the gene network in BCC of the eyelid included many BCC-associated genes, such as the following: BCL2 apoptosis regulator; Patched-1; and SRY-box 9. In addition, unique gene networks related to cancer cell growth, tumorigenesis, and cell survival were identified. These results of integrating microarray analyses provide further insights into the molecular mechanisms involved in BCC of the eyelid and may provide a therapeutic approach for this disease.

Pathological mutations reveal the key role of the cytosolic iRhom2 N-terminus for phosphorylation-independent 14-3-3 interaction and ADAM17 binding, stability, and activity

“…List of used experiment IDs for indicated tissue and primary cells: a) murine heart: MM-00170 [ 73 ], MM-00253 [ 22 ], MM-00257 [ 124 ], MM-00262 [ 3 ], MM-00300 [ 85 ], MM-00322, [ 107 ], MM-00330 [ 57 ], MM-00368 [ 9 ], MM-00384 [ 118 ], MM-00476 [ 1 ], MM-00485 [ 78 ], MM-00492 [ 115 ], MM-00497 [ 97 ], MM-00507 [ 97 ], MM-00561 [ 86 ], MM-00834 [ 108 ], MM-00841 [ 68 ], MM-01538 [ 31 ], MM-01642 [ 62 ], MM-01875 [ 62 ]; b) murine primary fibroblast (dermis): MM-00159 (Vallender et al 2006), MM-00180 (Vallender et al 2006), MM-00627 [ 32 ], MM-00724 [ 32 ]; c) murine primary keratinocytes: MM-01215 [ 4 ]; d) healthy human epidermis tissue (biopsy): HS-02924 [ 30 ]; e) human primary keratinocytes (untreated): HS-02625 [ 121 ], HS-02787 [ 15 ], HS-02490 [ 105 ], HS-00220 [ 90 ]; f) human primary keratinocytes (treated with TNFα, IFNα, IFNγ or IL4; 24 h): HS-02490 [ 105 ]; g) human primary keratinocytes (treated with 10 ng/ml I IFNγ; 96 h): HS-02625 [ 121 ]; h) human primary fibroblasts (untreated): HS-00393, HS-00481 [ 18 ], HS-00805 [ 112 ], HS-00928 [ 117 ], HS-00963, HS-00989 [ 104 ], HS-01109 [ 113 ], HS-01279 [ 64 ], HS-01311 [ 36 ], HS-01326 [ 114 ], HS-02421 [ 102 ],i) primary artery smooth muscle cells (heart): HS-00478 [ 96 ]; j) primary bronchial smooth muscle cells: HS-00039 [ 13 ]; k) healthy oesophagus squamous tissue (biopsy): HS-01298 [ 116 ], HS-00217, HS-00017 [ 88 ], HS-01525 [ 93 ]; squamous cell carcinoma (grade G1): HS-01298 [ 116 ]; oesophagus adenocarcinoma: HS-00002; HS-01298 [ 116 ]; Barrett´s oesophagus (pre-malignant): HS-01298 [ 116 ]; primary macrophages: HS-01265; primary...…”

Pathological mutations reveal the key role of the cytosolic iRhom2 N-terminus for phosphorylation-independent 14-3-3 interaction and ADAM17 binding, stability, and activity

“…List of used experiment IDs for indicated tissue and primary cells: a) murine heart: MM-00170 (Muchir et al, 2007), MM-00253 (Dufour et al, 2007), MM-00257 (Zhao et al, 2007), MM-00262 (Alcendor et al, 2007), MM-00300 (Ramchandran et al, 2006), MM-00322, (Thorrez et al, 2008), MM-00330 (Lattin et al, 2008), MM-00368 (Barger et al, 2008), MM-00384 (Wong et al, 2010), MM-00476 (Abd Alla et al, 2016), MM-00485 (Oka et al, 2011), MM-00492 (Wang et al, 2016), MM-00497 (Shuai et al, 2011), MM-00507 (Shuai et al, 2011), MM-00561 (Ricard et al, 2010), MM-00834 (Traister et al, 2013), MM-00841 (Mercader et al, 2012), MM-01538 (Gambino et al, 2013), MM-01642 (Lucas et al, 2014), MM-01875 (Lucas et al, 2014); b) murine primary fibroblast (dermis): MM-00159 (Vallender and Lahn, 2006), MM-00180 (Vallender and Lahn, 2006), MM-00627 (Garinis et al, 2009), MM-00724 (Garinis et al, 2009); c) murine primary keratinocytes: MM-01215 (Allende et al, 2013); d) healthy human epidermis tissue (biopsy): HS-02924 (Esaki et al, 2015); e) human primary keratinocytes (untreated): HS-02625 (Yunoki et al, 2018), HS-02787 (Busch et al, 2008), HS-02490 (Swindell et al, 2012), HS-00220 (Sa et al, 2007); f) human primary keratinocytes (treated with TNFα, IFNα, IFNγ or IL4; 24 h): HS-02490 (Swindell et al, 2012); g) human primary keratinocytes (treated with 10 ng/ml I IFNγ; 96 h): HS-02625 (Yunoki et al, 2018); h) human primary fibroblasts (untreated): HS-00393, HS-00481 (Chen et al, 2008), HS-00805 (Verkerk et al, 2009), HS-00928 (Wang et al, 2012), HS-00963, HS-00989 (Strunnikova et al, 2009), HS-01109 (Visser et al, 2012), HS-01279 (Marchina et al, 2014), HS-01311 (Henrichsen et al, 2011), HS-01326 (Voets et al, 2012), HS-02421 (Smith et al, 2008); i) primary artery smooth muscle cells (heart): HS-00478 (Shalhoub et al, 2010); j) primary bronchial smooth muscle cells: HS-00039 (Bosse et al, 2007); k) healthy oesophagus squamous tissue (biopsy): HS-01298 (Wang et al, 2013), HS-00217, HS-00017 (Roth et al, 2006), HS-01525 (Sato et al, 2013); squamous cell carcinoma (grade G1): HS-01298 (Wang et al, 2013); oesophagus adenocarcinoma: HS-00002; HS-01298 (Wang et al, 2013); Barrett’s oesophagus (pre-malignant): HS-01298 (Wang et al, 2013); primary macrophages: HS-0...…”

Prediction of Diagnostic Gene Biomarkers Associated with Immune Infiltration for Basal Cell Carcinoma

“…The GEO query package 18 in R software was used to extract the BCC expression datasets, GSE103439, 19 GSE7553, 20 and GSE42109, 21 from the GEO database and corresponding sequencing data from our research group ( https://www.ncbi.nlm.nih.gov/geo/ ) (version 3.6.5, http://r-project.org/ ). The samples in the dataset were all Homo sapiens .…”