Tumor and Microenvironment

: 2018  |  Volume : 1  |  Issue : 2  |  Page : 45--54

Commonly expressed genes among cancer stem cells induced from hiPSCs and Obtained from cancer tissues or cell lines

Akimasa Seno1, Masaharu Seno2,  
1 Laboratory of Nano-Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan; Okayama University Research Laboratory for Stem Cell Engineering in Detroit, Integrative Biosciences Center, Wayne State University, Detroit, MI, USA
2 Laboratory of Nano-Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan; Okayama University Research Laboratory for Stem Cell Engineering in Detroit, Integrative Biosciences Center, Wayne State University, Detroit, MI, USA, Japan

Correspondence Address:
Dr. Masaharu Seno
Room 460, Bldg Eng-6, Tsushima-Naka 3-1-1, Kita-Ku, Okayama 700-8530


Introduction: Cancer is one of the serious health problems in worldwide. For the development of radical cancer treatment, cancer stem cells (CSCs) are getting an issue of focus. CSCs are thought to be resistant to chemotherapy and cause metastasis. Although it is very important to understand their characters in detail, the knowledge so far is not sufficient due to their low ratio in tumor tissues. Subjects and Methods: We have induced CSCs from induced pluripotent stem cells (iPSCs) culturing in the conditioned media from cancer-derived cells without introducing genes or mutations. These induced CSCs actually have CSCs-like properties of self-renewal, differentiation potential, and tumorigenicity. In this study, their gene expression data are compared with more than 1000 sets of data from normal stem cells, our CSCs, CSCs obtained from cancer tissues or cell lines and cancer cells, which obtained from Gene Expression Omnibus. Results: Although there were no known cancer stem cell markers which can distinguish CSCs from other cell types, clustering with spherical self-organizing map revealed the expression of NTNG1, ABLIM2, DNM3, EDN1, XLOC_001990, and ISY1-RAB43 are significantly high in CSCs. Conclusion: Their expression should help to find CSCs as the markers in the future. Simultaneously, the function of these genes should become important to be clarified.

How to cite this article:
Seno A, Seno M. Commonly expressed genes among cancer stem cells induced from hiPSCs and Obtained from cancer tissues or cell lines.Tumor Microenviron 2018;1:45-54

How to cite this URL:
Seno A, Seno M. Commonly expressed genes among cancer stem cells induced from hiPSCs and Obtained from cancer tissues or cell lines. Tumor Microenviron [serial online] 2018 [cited 2023 Mar 27 ];1:45-54
Available from: http://www.TMEResearch.org/text.asp?2018/1/2/45/251573

Full Text


Although cancer stem cells (CSCs) and their importance are reported in many papers,[1],[2],[3],[4],[5],[6],[7],[8] their analysis is not sufficiently advanced because of their very small population in cancer tissues and difference depending on patients. During the decade, induced pluripotent stem cells (iPSCs) have been made[9],[10],[11],[12],[13],[14] and CSCs could be induced from them without gene manipulation.[15],[16],[17] In this report, induced CSCs and CSCs found in cancer cell tissues or cancer cell lines were compared with their origins to figure out their differences and similarities using a clustering procedure of spherical self-organizing map (sSOM).[18],[19],[20],[21],[22] This would provide a novel method to understand the relationships of CSCs from different origin.

 Subjects and Methods

Acquisition of data

All data were obtained from Gene Expression Omnibus () in April 2017. Agilent microarray data (Platform GPL16699 or GPL17077) analyzed for human iPSCs or cancer was chosen because the same platform was used for OCC-CSCs (GSE83880). A total of 1170 gene expression data sets, in each of which consisted from 50,170 probes, were obtained from different cells. To eliminate the data sets which are not related to stem cells or cancer and to make comparison clearer, 1036 data sets from the cells were reassigned into four groups: stem cell, OCC-CSC, CSC, and cancer [Table 1]. With all data sets from the four groups, digitalized intensity data were normalized with Bioconductor[23],[24] package agilp (ver. 3.6.0, https://bioconductor.org/packages/release/bioc/html/agilp.html)[25] as directed by maintainer's manual. Briefly, the raw intensity data were mapped to the same ID with IDswop. Mapped data were trimmed with equalizer to include only the set of probes that are common to all data. Then, a baseline file was generated by Baseline, and a set of probe expression data files were normalized by AALoess. Through these procedures, 50,032 probes for 40,105 genes were assessed for the experiments. Expressions of housekeeping genes (ACTB, ATP5F1, GAPDH, GAPDHS, GUSB, HPRT1, PGK1, PPIA, PPIAL4A, RPLP0, PRLP1, RPLP2, RPS18, TBP, TBPL1, TBPL2, TFRC, and YWHAZ) were tested and confirmed expressed equally among all groups [Supplementary Figure 1 [SUPPORTING:1]].{Table 1}

Analyses by sphere self-organizing map

To find genes exhibiting significant expression among each group, averages of normalized expression value from each probe were compared. If it is maximum or minimum among the four groups and the difference from other groups is more than 1, the corresponding gene was nominated as a candidate marker gene of the group. The probes found following this rule were used to map the nodes depicted by the sSOM software “Blossom” (SOM Japan; https://bioconductor.org/packages/release/bioc/html/agilp.html). A virtual probe corresponding to an ideal marker gene has been set maximum or minimum value as normalized expression value in one representative group and set the opposite values in the rest of the groups. Nonsignificant distance (NSD) was calculated between each node on the sphere drawn by sSOM under the default parameters.

Statistical analysis

The significance of gene expression of four groups was tested by one-way ANOVA and Tukey-Kramer method. The critical range (qα, α = 0.05) of four groups consisted with 1,036 samples is 3.64. qs values are shown in figures when it is >qα.


Expressions of known cancer stem cell markers are not always useful to specify cancer stem cells

To evaluate the expression of known CSC marker genes among our OCC-CSCs or other CSCs, their expression levels were analyzed first. A total of 77 probes corresponding to known CSC marker genes were included in the normalized data [Supplementary Figure 2[SUPPORTING:2]] and the representative data are shown in [Figure 1]. Since the CSCs analyzed by Agilent microarray were limited to those derived from ovarian cancer tissue or cell line, we had to compare our OCC-CSCs with the CSCs. In spite of limited origin, the CSCs did not highly express ovarian CSC markers (CD44, CD117, ALDH, CD133, or CD24) or ovarian cancer markers (CA-125, beta-hCG, AFP, CEA, or SCC). Some CSC marker genes such as CDKN2A, ICAM1, and ITGB3 were found highly expressed in this CSC group. This implies these cells were sharing CSC properties and they could be considered as representatives of common CSCs. On the other hand, the gene expression of CD24, KIT, NANOG, POU5F1, and SOX2 was higher in OCC-CSC group than that in the other CSC group and was almost equivalent to that of stem cell group. KIT, KLF4, NCAM1, and some other genes were similarly expressed in OCC-CSC and CSC groups; however, there was no significant difference between the groups of stem cells and OCC-CSC or of CSC and cancer. CD44 and KLF4 are similarly expressed in all groups other than stem cell group. Although some combinations of the gene expression could evoke malignancy of cancer cells, no known “CSC marker” gene commonly appeared expressed in OCC-CSCs and other CSCs. Therefore, evaluation of the gene expression to find which gene is truly expressed as CSC marker gene, which should commonly be expressed in OCC-CSC and CSC in the level higher or lower than in the other cell groups.{Figure 1}

Spherical self-organizing map revealed marker genes for each group

Normalized average expression values from the probes in each group were compared. When it is higher or lower than that of other groups and the difference is more than 1, it was chosen as a candidate probe for a marker representing the group. After this process, they were analyzed by sSOM with a virtually defined ideal probe (IP), which was set with the highest or the lowest expression value in one of the groups. Each IP is shown as a red dot at the center of each sphere [Figure 2]a. Expression similarity between probes is shown as a NSD in [Supplementary Table 1[SUPPORTING:3]] and expressions of five probes which were assigned at the shortest NSD from the IP were shown in [Figure 2]b and [Figure 2]c [summarized in [Table 2]]. Compared with the expression of the genes, they should be marker genes for each group although no known CSC marker gene was listed in OCC-CSC or CSC group.{Figure 2}{Table 2}

Distinguishable cancer stem cell marker genes nominated with spherical self-organizing map

Although the expression of known CSC marker genes does not always distinguish CSCs from cancer cells or stem cells, OCC-CSCs and CSCs focused in this study have been characterized as CSCs.[16],[17],[26],[27] Then, a simple question comes up, “Are there any genes commonly expressed among these CSCs?” To identify genes commonly expressed, their gene expression profiles were reevaluated with modified conditions. Namely, OCC-CSC or CSC group had the genes with the first or the second highest/lowest expression value and as searched for marker genes, there was a difference more than one between the averages of the second and the third groups, when the normalized expression values were compared. As the result, 49 positively expressed genes and 17 negatively expressed genes were nominated in all CSCs [Supplementary Table 2[SUPPORTING:4]]. Especially, eight genes were assigned at a NSD shorter than two, while all other genes were assigned farther apart at more than 2.4. Among the genes, significance is assessed with Tukey-Kramer method. As the result, the expression of six genes for NTNG1, ABLIM2, DNM3, EDN1, XLOC_001990, and ISY1-RAB43 was significant in OCC-CSC and CSC when compared with other two groups [Table 3] and [Figure 3].{Table 3}{Figure 3}


The expression of 40,105 genes in total in 1036 data sets from different cells was compared in this study and six genes, NTNG1, ABLIM2, DNM3, EDN1, XLOC_001990, and ISY1-RAB43 were successfully nominated as the candidates of CSC markers. Among these six genes, little is known about the characteristic expression of the four genes, NTNG1, ABLIM2, DNM3, and EDN1, in cancer or stem cells while the information of XLOC_001990 and ISY1-RAB43 is still obscure.

NTNG1 encodes netrin-G1. This protein was found in P21 mouse cerebellum and thought to be involved in nervous system development.[28] The mutated gene was found in the patient of Rett syndrome.[29] Regarding its relationship with cancer, although it could be a prognostic gene,[30],[31] nothing was revealed yet. ABLIM2, actin-binding LIM protein 2, is only known to bind to F-actin and enhance serum response factor activation.[32] This gene might be involved in metastasis of some cancer cells. Dynamin 3, encoded in DNM3, is a member of guanosine triphosphate-binding protein. When methylation and expression of DNM3 in hepatocellular carcinoma (HCC) cells from 48 patients were compared, the decreased expression of DNM3 was found to correlate with the poor prognosis of the disease.[33] Overexpression of DNM3 was reported to inhibit cell cycle and induce cellular apoptosis in HCC.[34] In breast cancer lines, shRNA of DNM3 inhibited cell motility was inhibited.[35] These reports may imply the function of this gene should depend on the type of cancer. In this paper, the expression of DNM3 was commonly found in all CSCs. OCC-CSCs were induced from human iPSCs in the presence of the conditioned medium of cancer cells derived from various cancer cell lines including both HCC and breast cancer-derived cells.[18] The CSCs were obtained from ovarian cancer cell line or tissue.[26],[36] The function of DNM3 in CSC may not depend on the tissue types of cancer although the function is not clear, and further study is needed.

EDN1 is well-studied gene both in cancer and stem cells among the four genes. This gene codes endothelin-1 (ET-1), which is generally produced by vascular endothelial cells and is considered to be related with the cause of hypertension.[37] The transgenic mice carrying hepatitis B virus antigen are reported to develop HCC with upregulation of EDN1,[38] and, overexpression of EDN1 causes HCC in zebrafish.[39] Moreover, hence, the blockade of ET-1 receptor is reported effective on chemotherapy-resistant ovarian cancer, melanoma, and myeloma.[40],[41],[42] Not only cancer cells ET-1 but also has various effects on mesenchymal stem cells. Pourjafar et al. showed ET-1 effect on survival, angiogenesis, and migration of those cells in vitro,[43] of which properties are also important in CSCs. Taking our results with these reports into consideration, ET-1 should exert a strong effect on CSCs derived not only from iPSCs but also from cancer tissues. The effect of ET-1 on CSCs should be further studied in vitro in the near future.


The authors would like to thank Dr. Heizo Tokutaka for developing sSOM software. The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (GSE113533).[44]

Financial support and sponsorship

This study was financially supported by the followings:

JSPS Grant-in-Aid for Scientific Research (A) No. 25242045 (MS)JSPS Grant-in-Aid for Challenging Exploratory Research No. 26640079 (MS)Long-Range-Research-Initiative from Japan Chemical Industry Association.

Conflicts of interest

There are no conflicts of interest.


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