# Antigenic and Genotypic Similarity between Primary Glioblastomas and Their Derived Neurospheres

Authors: Valentina Caldera; Marta Mellai; Laura Annovazzi; Angela Piazzi; Michele Lanotte; Paola Cassoni; Davide Schiffer
Journal: Journal of Oncology
 (2011)

---

## Abstract

Formation of neurospheres (NS) in cultures of glioblastomas (GBMs), with self-renewal, clonogenic capacities, and tumorigenicity following transplantation into immunodeficient mice, may denounce the existence of brain tumor stem cells (BTSCs) in vivo. In sixteen cell lines from resected primary glioblastomas, NS showed the same genetic alterations as primary tumors and the expression of stemness antigens. Adherent cells (AC), after adding 10% of fetal bovine serum (FBS) to the culture, were genetically different from NS and prevailingly expressed differentiation antigens. NS developed from a highly malignant tumor phenotype with proliferation, circumscribed necrosis, and high vessel density. Beside originating from transformed neural stem cells (NSCs), BTSCs may be contained within or correspond to dedifferentiated cells after mutation accumulation, which reacquire the expression of stemness antigens.


---

## Body

## 1. Introduction

In leukemias, rare tumor cells show extensive proliferative and self-renewal potential and are responsible for maintaining the tumor clone [1]; similar cells were subsequently described in gliomas [2–4]. They were called brain tumor stem cells (BTSCs), believed to be responsible for tumor growth, recurrence and resistance to therapies and, supposedly, to derive from neural stem cells (NSCs) transformation and to be related to restricted unipotent or multipotent progenitors [5–7]. They share with NSCs antigenic properties of stemness, such as Nestin, Musashi-1, CD133, and SOX2 expression [8]; it has been suggested to better identify them on the basis of their functional competence than as cell types [9]. A derivation from dedifferentiated tumor cells that re-acquire stem cell-like properties has also been hypothesized [3, 10, 11].Beside common antigenic properties with NSCs, BTSCs share genetic properties with primary tumor cells. Their existence in tumors is indirectly demonstrated by the generation, from tumor samples put in culture, of neurospheres (NS) and, by adding 10% of fetal bovine serum (FBS), of adherent cells (AC) with different capacities of self-renewal, differentiation, clonogenicity, and tumorigenicity. The demonstration of BTSCs in vitro may be influenced by the methodological procedures employed and may have different expression modalities [12, 13]. For example, using N29 and N32 tumor models, it has been demonstrated that NS formation is not necessary to enrich for tumorigenic cells, due to the fact that AC can display high clonogenicity in vitro, tumorigenicity in vivo, and high expression of CD133 and Nestin [14].Recently, two transcription factors have been proposed as putative markers of stemness: sex determining region of Y chromosome (Sry)-related high mobility group box2 (SOX2) and repressor element-1 silencing transcription/neuron-restrictive silencer factor (REST/NRSF). SOX2 belongs to a family of transcription factors expressed in the central nervous system (CNS) at early stages of development [15] and it is expressed in malignant gliomas at both mRNA and protein level [16]. The second putative marker is REST/NRSF (REST), which represses transcription of several neuronal genes by binding to a DNA regulatory motif known as repressor element 1/neuron-restrictive silencer element (RE1/NRSE) [17]. REST is highly expressed in NSCs and its transcription is blocked as they exit the cell cycle and differentiate [18].There is no possibility to demonstrate the existence of BTSCs in tumors before surgical intervention as to be useful for therapeutic strategies. Specific phenotypes have been shown to be related with the derivation of NS from surgical samples [19, 20], but it has not yet been definitively established whether the phenotypical heterogeneity influences [21] or not [22] the occurrence of BTSCs.In a series of GBMs we wanted to verify from the genetic and antigenic point of view the relationship between NS with AC and the primary tumor phenotype.


## 2. Materials and Methods

### 2.1. Patients

The investigation was carried out on 16 partially resected primary hemispheric GBMs (CV1-20) operated on at the Department of Neuroscience, Neurosurgical Unit, University of Turin. Histological diagnosis of GBM was performed according to WHO guidelines [23]. The mean age of the patients was 62 years (range: 23–76 years). Ten patients were males, and 6 were females.The patient stratification was as follows: out of 16 GBM patients, 10 received postoperative standard radiation therapy (RT) (60 Gy total dose in 27–30 fractions administeredvia a LINAC). Among the 10 irradiated patients, 8 received standard Temozolomide (TMZ) therapy (75 mg/m2/daily for 6 weeks), followed by adjuvant TMZ (200 mg/m2 from day 1 to day 5 every 4 weeks for 6–12 cycles). Two patients received TMZ, but no radiation therapy. Of the remaining patients, 2 did not receive any treatment because of low Karnofsky Performance Status (KPS), and 2 were lost at follow up. All patients are still alive with the exception of 2 patients who died 3 months following surgery.A viable sample from the dissected tumor was divided into three serial slices: one was stored at −80°C for molecular genetics and frozen sections, one was fixed in buffered-formalin and embedded in paraffin (FFPE) and one was washed, minced, and enzymatically dissociated for expansion in culture. A peripheral blood sample was obtained from each patient and was stored at −20°C. All patients provided informed consent allowing for the use of tumor specimens for molecular and cell culture studies. The study was approved by the Ethics Committee of the University Hospital of Turin.


### 2.2. Histology, Immunohistochemistry (IHC), and Immunofluorescence (IF)

Haematoxylin and eosin stain (H&E) was performed on 4μm paraffin sections.IHC was performed on 4μm paraffin sections using a Ventana Full BenchMark automatic immunostainer (Ventana Medical Systems Inc., Tucson, AZ, USA). UltraView Universal DAB Detection Kit was used as detection system. The antibodies used are listed in Table 1. Heat-induced epitope retrieval (HIER) was performed in Tris-EDTA, pH 8 (Ventana Medical Systems). Negative controls were obtained by omitting the primary antibody.Table 1
List of antibodies.
AntibodySourceDilution IHCDilution WBCodeCompanyNestin*,°Mouse1 : 200—MAB5326ChemiconNestin*,°Rabbit1 : 2001 : 1000AB5922ChemiconGFAP°Mouse1 : 200—M0761DakoCytomationGFAP°Rabbit1 : 2001 : 1000Z0334DakoCytomationCD133°Mouse1 : 201 : 250130-090-422Miltenyi BiotecMusashi-1°Rabbit1 : 2001 : 500AB5977ChemiconSOX2*,°Rabbit1 : 50—sc-20088Santa Cruz Biotec.SOX2*,°Mouse1 : 1001 : 250MAB2018R&D SystemsREST*,°Rabbit1 : 150—IHC-00141Bethyl LaboratoriesRESTRabbit—1 : 2500A300-540ABethyl LaboratoriesGalC*,°Mouse1 : 200—MAB342ChemiconβIII-Tubulin*,°Mouse1 : 250—MAB1637ChemiconKi-67/MIB-1*Mouse1 : 100—M7240DakoCytomationMGMTMouse—1 : 400MS-470-P0Lab Vision Corp.α-TubulinRabbit—1 : 5000LF-PA0146LabFrontierCD34MousePre-diluted—790-2927Ventana*HIER required.°tested by IF.Double immunohistochemistry was performed using Nestin, GFAP, and CD34 antibodies with ultraView Universal Alkaline Phosphatase Red Detection Kit as chromogen (Ventana Medical Systems).IF was performed on frozen sections, NS and AC. Goat anti-rabbit FITC-conjugated IgG and rabbit anti-mouse TRITC-conjugated IgG antibodies were used. Cell nuclei were stained with DAPI. The antibodies used are listed in Table1. Observations were made on a Zeiss Axioskop fluorescence microscope (Karl Zeiss, Oberkochen, Germany) equipped with an AxioCam5MR5c and coupled to an Imaging system (AxioVision Release 4.5, Zeiss).


### 2.3. In Vitro Cultures

Tumor tissue was processed as previously described [24]. Culture conditions were the following: for NS, Dulbecco’s modified Eagle’s medium (DMEM)/F-12 with 10 ng/mL bFGF (basic fibroblast growth factor) and 20 ng/mL EGF (epidermal growth factor); for AC, DMEM with 10% fetal bovine serum (FBS). Both cultures were maintained at 5% O2/CO2. GBM reference cell lines were U87-MG and 010627 (Galli R, DIBIT San Raffaele, Milan) for both AC and NS.All cell cultures were periodically checked forMycoplasmacontamination (e-Myco Mycoplasma PCR Detection kit, iNtRON Biotechnology, Korea).For population analyses, cells were plated at 200,000 cells/cm2, and the resulting spheres were collected every 4–6 days. The total number of viable cells was assessed at each passage by Trypan blue (Sigma, St. Louis, MO, USA).Clonogenic assays were performed as previously described [25]. Briefly, NS were dissociated into single cells and plated into a 96-well plate for the subsphere-forming assay by limiting dilution. Single-cell suspensions were diluted and plated at 1-2 cells/well. After plating, cells were monitored, and only wells containing a single cell were considered for the analysis. Wells were scored for sphere formation following one month of culture.Differentiation assays were performed by mitogen withdrawal and the addition of 3% FBS to the culture.


### 2.4. Tumorigenicity

It was tested by transplanting NS and AC from each sample intoNOD SCIDmice (Charles River, Calco, Italy). Two microliters of a 1 × 108 cells/mL suspension were stereotactically injected into the right striatum according to the procedure described in Galli et al. [3]. Mouse brains were treated with FFPE using the same procedures as described for primary tumors. Injections were carried out at the H. S. Raffaele, Milan.


### 2.5. Ethics Statement

All animals were handled in strict accordance with good animal practice as defined by the relevant international (Directive 86/609/EEC and recommendation 2007/526/EC from the European community) and national (Legislative Decree 116/92 and law n. 413/1993) directives and according to protocols approved by the Animal Care and Use Committee of the H. S. Raffaele (IACUC #316).


### 2.6. DNA Extraction

Genomic DNA was extracted from frozen tumor samples according to a standard phenol-chloroform protocol. DNA extraction from cell lines was performed with the QIAmp DNA Mini Kit (Qiagen GmbH, Hamburg, Germany) and from peripheral blood by a salting-out procedure. The genetic analyses described below were carried out on primary tumors, NS and AC.


### 2.7. Loss of Heterozygosity (LOH) Analysis

Allelic imbalances were determined by LOH analyses of microsatellite markers. Highly polymorphic markers were selected based on their heterozygosity and position on the five most frequently deleted chromosomes in gliomas (Table2). Microsatellites were amplified in multiplex reactions by PCR with fluorescently labeled primers (Applied Biosystems). Amplification was performed with a standard touchdown protocol. Following electrophoresis on an ABI 3130 Genetic Analyzer (Applied Biosystems), data were collected by GeneMapper v4.0 software (Applied Biosystems). LOH was determined by measuring the peak height ratio between the two alleles (allelic ratio) in constitutive (N1/N2) and tumor (T1/T2) DNA samples. Allelic imbalance was calculated from the ratio of N1/N2 to T1/T2. Values less than 0.5 and greater than 1.5 were considered evidence of LOH [26].Table 2
Microsatellites markers used for LOH analysis.
RegionSTRLocusRepeatMax. het*PCR primers 5′ to 3 (forward/reverse)1pD1S5081p36.23(AC)n0.812AGCTGGGGAATATATGTNTCATATTGTGGAAGGCCAACTCD1S4961p36.1-p34.3(AC)n0.815TCTCTATGCATCTATGCATCTATCTGCATTTGTCTGGGTTCTTD1S27241p33(AC)n0.821TCAAGTCCCAGGAGGATTCCACTGTGTTATTTAGCAGGATD1S4571p13.3(AC)n0.742GGGGGCAATAACACAAAGGAGCCTGGAGCCAAGAGTGCTA9pD9S1579p22.2(AC)n0.849AGCAAGGCAAGCCACATTTCTGGGGATGCCCAGATAACTATATCD9S1719p21.1(AC)n0.804AGCTAAGTGAACCTCATCTCTGTCTACCCTAGCACTGATGGTATAGTCT10qD10S21210q26.3(AC)n0.74GAAGTAAAGCAAGTTCTATCCACGGAAGTAAAGCAAGTTCTATCCACGD10S19010q26.11(AC)n0.863GTGTTTGGGTCATGGAGATGAGGCAAAGCAGGAGCAD10S56210q25.3(AC)n0.715CCTGGCAGATGGAGGTTTCGGAGTGCTTCCTTAAAATAC17pTP53 Alu17p13.1(AAAAT)n0.594ACTCCAGCCTGGGCAATAAGAGCTACAAAACATCCCCTACCAAACAGCD17S52017p13(AC)n0.854GGAGAAAGTGATACAAGGGATAGTTAGATTAATACCCACC19qD19S41219q13.33(AC)n0.812TGAGCGACAGAATGAGACTACATCTTACTGAATGCTTGCD19S21919q13.32(AC)n0.77GTGAGCCAAGATTGTGCCGACTATTTCTGAGACAGATTCCCASTR: Short Tandem Repeat.*Maximum heterozygosity.


### 2.8. EGFR Amplification Status

As in previous studies, EGFR amplification status (GeneBank sequence NM_005228) was assessed by Fragment Analysis and Capillary Electrophoresis (CE) on an ABI 3130 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). INF-γ was used as reference house-keeping gene. The amplification status of the EGFR gene was determined by measuring the EGFR/INF-γ ratio. A ratio greater than 2.09 was considered evidence of more than two copies of the EGFR gene.


### 2.9. MGMT Promoter Hypermethylation Status

MGMT promoter hypermethylation status (GeneBank sequence NM_002412) was determined by Methylation Specific Polymerase Chain Reaction (MS-PCR) followed by CE as previously reported [27]. Sodium bisulfite modification was performed with the MethylEasy DNA Bisulphite Modification Kit (Human Genetic Signatures Pty Ltd, Macquarie Park, Sydney, Australia) [27]. CpGenome Universal Methylated DNA (Chemicon International Inc., Temecula, CA, USA), and normal lymphocyte DNA samples were used as methylated and unmethylated controls, respectively. Primer sequences for MS-PCR and amplification conditions were previously reported [28]. Following electrophoresis using an ABI 3130 Genetic Analyzer (Applied BioSystems), data were collected by the GeneMapper Software v4.0 for fragment analysis (Applied BioSystems). The peak height ratio between peaks for the methylated and unmethylated allele was determined. Values greater than 0.1 were scored as evidence of the methylated status of the MGMT gene.


### 2.10. TP53, PTEN, EGFR, IDH1, and IDH2 Mutation Analysis

The entire coding region of PTEN (exons 1–9) (GeneBank sequence NM_000314) and TP53 (exons 1–11) (GeneBank sequence NM_000546), the tyrosine kinase domain (TK) (exons 18–24) of EGFR (GeneBank sequence NM_005228), and codons R132 of IDH1 (GeneBank sequence NM_005896) and R172 of IDH2 (GeneBank sequence NM_002168) were investigated for variations by direct sequencing. A minimum of 50 bp of each flanking intronic sequence was also analyzed. All fragments were amplified by PCR using a standard touchdown protocol. Primer sequences and PCR conditions are available on request. Amplicons were analyzed by direct DNA sequencing on an ABI 3130 Genetic Analyzer using the BigDye Terminator version 1.1 Cycle Sequencing Kit. The reported nucleotide and amino acid numbering is relative to the transcription start site (+1) corresponding to the A of the ATG on the corresponding GeneBank reference sequences.To establish if each putative mutation was somatic (i.e., tumor specific) or germ-line, the corresponding patient’s constitutional DNA was also analyzed when available.


### 2.11. Bioinformatic Analysis

In silico predictions of the putative functional effects of missense mutations in genes coding for TP53, PTEN, and EGFR amplification were determined by PMUT (http://mmb.pcb.ub.es/PMut/), PolyPhen (http://genetics.bwh.harvard.edu/pph/), and SNAP (http://cubic.bioc.columbia.edu/services/SNAP/) programs.The effect of the intronic variants on splicing was evaluated by SpliceView (http://bioinfo2.itb.cnr.it/sun/webgene/) and NNSplice (http://biologyhelp.awardspace.com/desc.php?id=147&type=biotech) software programs.


### 2.12. Western Blotting Analysis

Frozen tissue and cultured cells (NS and AC) were homogenized in a lysis buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1% v/v Igepal, 2% sodium dodecyl sulfate (SDS), 0.5% sodium deoxycholate, 10 mM EDTA) supplemented with Protease Inhibitor Cocktail (Sigma), 2 mM sodium orthovanadate, and 10 mM sodium fluoride. Tissues were sonicated with three, 10-s bursts. Whole protein extracts were quantified by BCA Protein Assay Kit (Pierce Biotechnology, Rockford, IL, USA) and equal amounts were resolved in 10% SDS-PAGE gels and transferred onto PVDF membranes (Immobilon-P, Millipore, Bedford, MA). Blots were probed with the antibodies listed in Table1. Membranes were then incubated with the appropriate HRP-conjugated secondary antibodies and proteins were detected by enhanced chemiluminescence (Millipore). An anti-α-Tubulin antibody was used to normalize sample loading and transfer. Band intensity was quantified by densitometry using NIH Image J software (RSB, NIMH, Bethesda, MD, USA).


## 2.1. Patients

The investigation was carried out on 16 partially resected primary hemispheric GBMs (CV1-20) operated on at the Department of Neuroscience, Neurosurgical Unit, University of Turin. Histological diagnosis of GBM was performed according to WHO guidelines [23]. The mean age of the patients was 62 years (range: 23–76 years). Ten patients were males, and 6 were females.The patient stratification was as follows: out of 16 GBM patients, 10 received postoperative standard radiation therapy (RT) (60 Gy total dose in 27–30 fractions administeredvia a LINAC). Among the 10 irradiated patients, 8 received standard Temozolomide (TMZ) therapy (75 mg/m2/daily for 6 weeks), followed by adjuvant TMZ (200 mg/m2 from day 1 to day 5 every 4 weeks for 6–12 cycles). Two patients received TMZ, but no radiation therapy. Of the remaining patients, 2 did not receive any treatment because of low Karnofsky Performance Status (KPS), and 2 were lost at follow up. All patients are still alive with the exception of 2 patients who died 3 months following surgery.A viable sample from the dissected tumor was divided into three serial slices: one was stored at −80°C for molecular genetics and frozen sections, one was fixed in buffered-formalin and embedded in paraffin (FFPE) and one was washed, minced, and enzymatically dissociated for expansion in culture. A peripheral blood sample was obtained from each patient and was stored at −20°C. All patients provided informed consent allowing for the use of tumor specimens for molecular and cell culture studies. The study was approved by the Ethics Committee of the University Hospital of Turin.


## 2.2. Histology, Immunohistochemistry (IHC), and Immunofluorescence (IF)

Haematoxylin and eosin stain (H&E) was performed on 4μm paraffin sections.IHC was performed on 4μm paraffin sections using a Ventana Full BenchMark automatic immunostainer (Ventana Medical Systems Inc., Tucson, AZ, USA). UltraView Universal DAB Detection Kit was used as detection system. The antibodies used are listed in Table 1. Heat-induced epitope retrieval (HIER) was performed in Tris-EDTA, pH 8 (Ventana Medical Systems). Negative controls were obtained by omitting the primary antibody.Table 1
List of antibodies.
AntibodySourceDilution IHCDilution WBCodeCompanyNestin*,°Mouse1 : 200—MAB5326ChemiconNestin*,°Rabbit1 : 2001 : 1000AB5922ChemiconGFAP°Mouse1 : 200—M0761DakoCytomationGFAP°Rabbit1 : 2001 : 1000Z0334DakoCytomationCD133°Mouse1 : 201 : 250130-090-422Miltenyi BiotecMusashi-1°Rabbit1 : 2001 : 500AB5977ChemiconSOX2*,°Rabbit1 : 50—sc-20088Santa Cruz Biotec.SOX2*,°Mouse1 : 1001 : 250MAB2018R&D SystemsREST*,°Rabbit1 : 150—IHC-00141Bethyl LaboratoriesRESTRabbit—1 : 2500A300-540ABethyl LaboratoriesGalC*,°Mouse1 : 200—MAB342ChemiconβIII-Tubulin*,°Mouse1 : 250—MAB1637ChemiconKi-67/MIB-1*Mouse1 : 100—M7240DakoCytomationMGMTMouse—1 : 400MS-470-P0Lab Vision Corp.α-TubulinRabbit—1 : 5000LF-PA0146LabFrontierCD34MousePre-diluted—790-2927Ventana*HIER required.°tested by IF.Double immunohistochemistry was performed using Nestin, GFAP, and CD34 antibodies with ultraView Universal Alkaline Phosphatase Red Detection Kit as chromogen (Ventana Medical Systems).IF was performed on frozen sections, NS and AC. Goat anti-rabbit FITC-conjugated IgG and rabbit anti-mouse TRITC-conjugated IgG antibodies were used. Cell nuclei were stained with DAPI. The antibodies used are listed in Table1. Observations were made on a Zeiss Axioskop fluorescence microscope (Karl Zeiss, Oberkochen, Germany) equipped with an AxioCam5MR5c and coupled to an Imaging system (AxioVision Release 4.5, Zeiss).


## 2.3. In Vitro Cultures

Tumor tissue was processed as previously described [24]. Culture conditions were the following: for NS, Dulbecco’s modified Eagle’s medium (DMEM)/F-12 with 10 ng/mL bFGF (basic fibroblast growth factor) and 20 ng/mL EGF (epidermal growth factor); for AC, DMEM with 10% fetal bovine serum (FBS). Both cultures were maintained at 5% O2/CO2. GBM reference cell lines were U87-MG and 010627 (Galli R, DIBIT San Raffaele, Milan) for both AC and NS.All cell cultures were periodically checked forMycoplasmacontamination (e-Myco Mycoplasma PCR Detection kit, iNtRON Biotechnology, Korea).For population analyses, cells were plated at 200,000 cells/cm2, and the resulting spheres were collected every 4–6 days. The total number of viable cells was assessed at each passage by Trypan blue (Sigma, St. Louis, MO, USA).Clonogenic assays were performed as previously described [25]. Briefly, NS were dissociated into single cells and plated into a 96-well plate for the subsphere-forming assay by limiting dilution. Single-cell suspensions were diluted and plated at 1-2 cells/well. After plating, cells were monitored, and only wells containing a single cell were considered for the analysis. Wells were scored for sphere formation following one month of culture.Differentiation assays were performed by mitogen withdrawal and the addition of 3% FBS to the culture.


## 2.4. Tumorigenicity

It was tested by transplanting NS and AC from each sample intoNOD SCIDmice (Charles River, Calco, Italy). Two microliters of a 1 × 108 cells/mL suspension were stereotactically injected into the right striatum according to the procedure described in Galli et al. [3]. Mouse brains were treated with FFPE using the same procedures as described for primary tumors. Injections were carried out at the H. S. Raffaele, Milan.


## 2.5. Ethics Statement

All animals were handled in strict accordance with good animal practice as defined by the relevant international (Directive 86/609/EEC and recommendation 2007/526/EC from the European community) and national (Legislative Decree 116/92 and law n. 413/1993) directives and according to protocols approved by the Animal Care and Use Committee of the H. S. Raffaele (IACUC #316).


## 2.6. DNA Extraction

Genomic DNA was extracted from frozen tumor samples according to a standard phenol-chloroform protocol. DNA extraction from cell lines was performed with the QIAmp DNA Mini Kit (Qiagen GmbH, Hamburg, Germany) and from peripheral blood by a salting-out procedure. The genetic analyses described below were carried out on primary tumors, NS and AC.


## 2.7. Loss of Heterozygosity (LOH) Analysis

Allelic imbalances were determined by LOH analyses of microsatellite markers. Highly polymorphic markers were selected based on their heterozygosity and position on the five most frequently deleted chromosomes in gliomas (Table2). Microsatellites were amplified in multiplex reactions by PCR with fluorescently labeled primers (Applied Biosystems). Amplification was performed with a standard touchdown protocol. Following electrophoresis on an ABI 3130 Genetic Analyzer (Applied Biosystems), data were collected by GeneMapper v4.0 software (Applied Biosystems). LOH was determined by measuring the peak height ratio between the two alleles (allelic ratio) in constitutive (N1/N2) and tumor (T1/T2) DNA samples. Allelic imbalance was calculated from the ratio of N1/N2 to T1/T2. Values less than 0.5 and greater than 1.5 were considered evidence of LOH [26].Table 2
Microsatellites markers used for LOH analysis.
RegionSTRLocusRepeatMax. het*PCR primers 5′ to 3 (forward/reverse)1pD1S5081p36.23(AC)n0.812AGCTGGGGAATATATGTNTCATATTGTGGAAGGCCAACTCD1S4961p36.1-p34.3(AC)n0.815TCTCTATGCATCTATGCATCTATCTGCATTTGTCTGGGTTCTTD1S27241p33(AC)n0.821TCAAGTCCCAGGAGGATTCCACTGTGTTATTTAGCAGGATD1S4571p13.3(AC)n0.742GGGGGCAATAACACAAAGGAGCCTGGAGCCAAGAGTGCTA9pD9S1579p22.2(AC)n0.849AGCAAGGCAAGCCACATTTCTGGGGATGCCCAGATAACTATATCD9S1719p21.1(AC)n0.804AGCTAAGTGAACCTCATCTCTGTCTACCCTAGCACTGATGGTATAGTCT10qD10S21210q26.3(AC)n0.74GAAGTAAAGCAAGTTCTATCCACGGAAGTAAAGCAAGTTCTATCCACGD10S19010q26.11(AC)n0.863GTGTTTGGGTCATGGAGATGAGGCAAAGCAGGAGCAD10S56210q25.3(AC)n0.715CCTGGCAGATGGAGGTTTCGGAGTGCTTCCTTAAAATAC17pTP53 Alu17p13.1(AAAAT)n0.594ACTCCAGCCTGGGCAATAAGAGCTACAAAACATCCCCTACCAAACAGCD17S52017p13(AC)n0.854GGAGAAAGTGATACAAGGGATAGTTAGATTAATACCCACC19qD19S41219q13.33(AC)n0.812TGAGCGACAGAATGAGACTACATCTTACTGAATGCTTGCD19S21919q13.32(AC)n0.77GTGAGCCAAGATTGTGCCGACTATTTCTGAGACAGATTCCCASTR: Short Tandem Repeat.*Maximum heterozygosity.


## 2.8. EGFR Amplification Status

As in previous studies, EGFR amplification status (GeneBank sequence NM_005228) was assessed by Fragment Analysis and Capillary Electrophoresis (CE) on an ABI 3130 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). INF-γ was used as reference house-keeping gene. The amplification status of the EGFR gene was determined by measuring the EGFR/INF-γ ratio. A ratio greater than 2.09 was considered evidence of more than two copies of the EGFR gene.


## 2.9. MGMT Promoter Hypermethylation Status

MGMT promoter hypermethylation status (GeneBank sequence NM_002412) was determined by Methylation Specific Polymerase Chain Reaction (MS-PCR) followed by CE as previously reported [27]. Sodium bisulfite modification was performed with the MethylEasy DNA Bisulphite Modification Kit (Human Genetic Signatures Pty Ltd, Macquarie Park, Sydney, Australia) [27]. CpGenome Universal Methylated DNA (Chemicon International Inc., Temecula, CA, USA), and normal lymphocyte DNA samples were used as methylated and unmethylated controls, respectively. Primer sequences for MS-PCR and amplification conditions were previously reported [28]. Following electrophoresis using an ABI 3130 Genetic Analyzer (Applied BioSystems), data were collected by the GeneMapper Software v4.0 for fragment analysis (Applied BioSystems). The peak height ratio between peaks for the methylated and unmethylated allele was determined. Values greater than 0.1 were scored as evidence of the methylated status of the MGMT gene.


## 2.10. TP53, PTEN, EGFR, IDH1, and IDH2 Mutation Analysis

The entire coding region of PTEN (exons 1–9) (GeneBank sequence NM_000314) and TP53 (exons 1–11) (GeneBank sequence NM_000546), the tyrosine kinase domain (TK) (exons 18–24) of EGFR (GeneBank sequence NM_005228), and codons R132 of IDH1 (GeneBank sequence NM_005896) and R172 of IDH2 (GeneBank sequence NM_002168) were investigated for variations by direct sequencing. A minimum of 50 bp of each flanking intronic sequence was also analyzed. All fragments were amplified by PCR using a standard touchdown protocol. Primer sequences and PCR conditions are available on request. Amplicons were analyzed by direct DNA sequencing on an ABI 3130 Genetic Analyzer using the BigDye Terminator version 1.1 Cycle Sequencing Kit. The reported nucleotide and amino acid numbering is relative to the transcription start site (+1) corresponding to the A of the ATG on the corresponding GeneBank reference sequences.To establish if each putative mutation was somatic (i.e., tumor specific) or germ-line, the corresponding patient’s constitutional DNA was also analyzed when available.


## 2.11. Bioinformatic Analysis

In silico predictions of the putative functional effects of missense mutations in genes coding for TP53, PTEN, and EGFR amplification were determined by PMUT (http://mmb.pcb.ub.es/PMut/), PolyPhen (http://genetics.bwh.harvard.edu/pph/), and SNAP (http://cubic.bioc.columbia.edu/services/SNAP/) programs.The effect of the intronic variants on splicing was evaluated by SpliceView (http://bioinfo2.itb.cnr.it/sun/webgene/) and NNSplice (http://biologyhelp.awardspace.com/desc.php?id=147&type=biotech) software programs.


## 2.12. Western Blotting Analysis

Frozen tissue and cultured cells (NS and AC) were homogenized in a lysis buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1% v/v Igepal, 2% sodium dodecyl sulfate (SDS), 0.5% sodium deoxycholate, 10 mM EDTA) supplemented with Protease Inhibitor Cocktail (Sigma), 2 mM sodium orthovanadate, and 10 mM sodium fluoride. Tissues were sonicated with three, 10-s bursts. Whole protein extracts were quantified by BCA Protein Assay Kit (Pierce Biotechnology, Rockford, IL, USA) and equal amounts were resolved in 10% SDS-PAGE gels and transferred onto PVDF membranes (Immobilon-P, Millipore, Bedford, MA). Blots were probed with the antibodies listed in Table1. Membranes were then incubated with the appropriate HRP-conjugated secondary antibodies and proteins were detected by enhanced chemiluminescence (Millipore). An anti-α-Tubulin antibody was used to normalize sample loading and transfer. Band intensity was quantified by densitometry using NIH Image J software (RSB, NIMH, Bethesda, MD, USA).


## 3. Results

### 3.1. Histology

Slices from the 16 tumor samples used for histological analyses were serial to those used for cell culture. The following phenotypic features characterized 4 of the 6 samples from which NS generated and 3 of the 9 samples from which AC generated: high cell density, high number of mitoses, a Ki-67/MIB-1 labeling index (LI) between 25% and 30%, circumscribed necroses with pseudo-palisading, high vessel density, and perivascular cuffings of tumor cells (Figure1).Histological and immunohistochemical aspects of phenotypic areas from which NS and AC generated. (a) High cell density, nuclear pleomorphism, scanty cytoplasms, and visible mitoses, H&E. (b) High Ki-67/MIB.1 LI, DAB. (c) The external slope of a circumscribed necrosis, H&E. (d) High vessel density, H&E. (e) Hypercellular perivascular cuffings. GFAP is more positive than Nestin (f), DAB. Scale bar 50μm.
(a)(b)(c)(d)(e)(f)


### 3.2. Immunohistochemistry of Primary Tumors

Nestin was variably expressed in all GBMs, but its distribution did not completely overlap with that of GFAP. As a matter of fact, Nestin expression was higher than GFAP expression, considering both the number of positive cells and the same cells (Figures2(a) and 2(b)). SOX2 and REST, which are diffusely expressed in all GBMs, reached the highest intensity in the areas the phenotype of which has been above described and around vessels (Figures 2(c) and 2(d)).Immunohistochemistry of a parallel section of Figure1. (a) Poor GFAP expression. (b) High Nestin expression. (c) SOX2 is highly expressed in nuclei of the external slope of circumscribed necrosis. (d) REST expression, all DAB. (e) CD133-positive area, frozen section. (f) Musashi-1-positive area. Scale bar 50 μm.
(a)(b)(c)(d)(e)(f)


### 3.3. Immunofluorescence of Primary Tumors (Frozen Sections)

As determined by analysis of frozen sections, CD133 and Musashi-1 were sporadically expressed in areas of variable size or in single cells (Figures2(e) and 2(f)).


### 3.4. In Vitro Culture Assay

NS and AC were observed in cultures from 6 (CV1, CV7, CV10, CV13, CV17, and CV20) and 9 (CV1, CV2, CV3, CV4, CV6, CV8, CV9, CV10, and CV17) of the 16 samples, respectively (37.5% and 56.3%). Cells derived from CV10 primarily grew as AC, occasionally forming cell aggregates attached to the culture plate. When CV10 aggregates were transferred to a low-adherent culture plate with DMEM/F-12 medium and mitogens, they gave rise to NS. In cells derived from CV1, in addition to NS, occasional AC were observed when cultured with DMEM/F-12 and mitogens. Alternatively, cultures derived from CV17 developed both NS and AC in their respective media conditions.NS cultures were verified to contain true BTSCs by assessing their long-term self-renewing ability by population analysis. Cells grown in culture with growth factors proliferated as nonadherent, multicellular spheres (Figure3(a)), whereas cells grown with serum proliferated as an adherent monolayer with an initial heterogeneous morphology which later became homogeneous with resemblance to fibroblasts (Figure 4(a)) and showing astrocytic, oligodendrocytic, or neuronal differentiation (Figures 4(b)–4(d)). Growth rates of NS and AC are illustrated in Figures 5(a) and 5(b). Figure 5(c) shows the different growth rates between NS and AC of the same cell line.Immunofluorescence of NS cultured in serum-free medium. (a) NS. (b) Cytoplasmic expression of CD133. (c) Musashi-1 expression in the cytoplasms. (d) Nestin expression in the cytoplasms. Nuclei are counterstained with DAPI (blue). (e) SOX2 expression in nuclei. (f) REST expression in nuclei. Scale bar 50μm.
(a)(b)(c)(d)(e)(f)Immunofluorescence of AC cultured in serum-containing medium. (a) Monolayer of adherent cells. (b) GFAP expression in the cytoplasms. (c) Cytoplasmic expression of GalC. (d) Cytoplasmic expression ofβ-III Tubulin. Nuclei are counterstained with DAPI (blue). Scale bar 50 μm.
(a)(b)(c)(d)Growth rates of NS and AC. (a) Growth curves of NS cultured in serum-free medium supplemented with mitogens from CV1, CV7, CV10, CV13, CV17, CV20, and reference cell lines U87-MG and 010627. (b) Growth curves of AC cultured in serum containing medium from CV2, CV3, CV4, CV6, CV8, CV9, CV10, CV17 (CV1 is not included), and reference cell lines U87-MG and 010627. (c) Comparison between NS and AC curves.
(a)(b)(c)The subsphere-forming assay performed by limiting dilution demonstrated that the clonogenic efficiency of all NS to form subspheres from individual NS cells was 7–9%.By differentiation assays NS demonstrated their multipotency showing after 7 days from the addition of 3% serum an astrocytic, oligodendrocytic and neuronal differentiation (Figures6(a)–6(c)). Upon intracranial transplantation, NS developed tumors in mice, whereas AC did not developed tumors or showed a reduced tumorigenicity in two cases (data not shown), demonstrating that NS populations included true BTSCs. Details of intracranial transplantations will be discussed in a separate manuscript.Immunofluorescence of differentiation of NS after addition of 3% serum. (a) Cytoplasmic expression ofβIII-Tubulin (red). (b) Cytoplasmic expression of GFAP (green). (c) Cytoplasmic expression of GalC (red). Nuclei are counterstained with DAPI (blue). Scale bar 50 μm.
(a)(b)(c)


### 3.5. Immunofluorescent Analysis of Cell Lines

NS and AC showed different antigenic expression patterns. Nestin was strongly expressed in NS, along with SOX2 and REST, whereas CD133 and Musashi-1 were only sporadically expressed (Figures3(b)–3(f)). GFAP was expressed in cells from only one sample (CV7). AC, in contrast, showed decreased Nestin expression and increased GFAP expression when compared with NS. Both CD133 and Musashi-1 expression was almost completely absent in AC. Nuclear expression of SOX2 and REST was lower in AC when compared to NS.Comparisons of primary tumors, NS and AC are shown in Table3. The expression of antigens indicative of stemness was highest in primary tumors and NS, whereas the expression of antigens indicative of differentiation was highest in AC.Table 3
Primary tumors, NS and AC. Immunohistochemistry and immunofluorescence.
(a)AntibodiesFFPE sectionsCV1CV7CV10CV13CV17CV20GFAP+++++±βIII-Tubulin−−+−−−GalC−−−−−−Nestin+++++++++++CD133−
*−
*±
*±
*±
*+Musashi-1−
*−
*±
*±
*−
*+SOX2++++++++++++REST++++++++++++AntibodiesNSCV1CV7CV10CV13CV17CV20GFAP±+±−−−βIII-Tubulin−++−−±GalC−+±−−±Nestin+++++±CD133+++±−−Musashi-1++±±−−SOX2++++++REST++++++(b)AntibodiesFFPE sectionsCV1CV2CV3CV4CV6CV8CV9CV10CV17GFAP+++++++++++βIII-Tubulin±−+−−−−−−GalC−−−−−−−−−Nestin+++++++++CD133−
*−
*±
*±
*±
*−
*−−−Musashi-1−
*−
*±
*±
*−
*−
*−−−SOX2+++++++++REST+++++++++AntibodiesACCV1CV2CV3CV4CV6CV8CV9CV10CV17GFAP+++++++++βIII-Tubulin+++−±±−−+GalC−++−+±−−+Nestin+++++++++CD133−−+−±−−−+Musashi-1±−+−±±−−+SOX2−−−−+°±+°++°REST−−−++°++°−+°*Tested by IF on primary tumor frozen sections. °Cytoplasmic staining. +Moderate expression intensity.++High expression intensity. ± Barely visible. − Negative.


### 3.6. Molecular Genetics

The derivation of NS and AC from the respective primary tumors was confirmed by genotyping of the 13 microsatellite markers used for LOH analysis.Genetic alterations in primary tumors and in the matched NS or AC are summarized in Table4. Their frequency is consistent with the primary nature of GBMs. No significant differences in the frequency of genetic or epigenetic alterations were observed between primary tumors generating cell lines and those not generating cell lines. In addition, no differences were observed between primary tumors generating NS or AC. LOH on chromosomes 1p, 9p, 10q, 17p, and 19q, EGFR amplification, MGMT promoter hypermethylation as well as PTEN and TP53 mutations was identified with similar frequency in primary tumors and NS, but not in AC. In primary tumors, PTEN mutations were detected in 56.2% of cases, whereas only 31.2% of cases showed TP53 mutations. The TK domain of the gene coding for EGFR was found to be mutated in only one primary tumor (CV6) generating AC. This previously undescribed mutation was a somatic synonymous nucleotide substitution (c.2904C > T, p.F968F). All observed nucleotide sequence variations are reported in Table 5. No point mutations were identified in codons R132 or R172 of IDH1 and IDH2 genes, respectively.Table 4
Frequency of genetic and epigenetic alterations in primary tumors, NS and AC.
Molecular markerPrimary GBM (%)NS (%)AC* (%)LOH 1p, 9p, 10q, 17p, 19q16 (100)6 (100)0 (0)EGFR amplification8 (50)3 (45)0 (0)MGMT hypermethylation9 (50)4 (66.7)0 (0)TP53 mutations5 (31.2)3 (50)0 (0)PTEN mutations9 (56.2)4 (66.7)2 (22.2)EGFR mutations1 (<1)0 (0)0 (0)p.R132 IDH10 (0)0 (0)0 (0)p.R172 IDH20 (0)0 (0)0 (0)*An exception is CV10 in which NS generated from AC. AC showed the same molecular profile of NS.Table 5
Spectrum of the identified sequence variations.
GeneCDS variationAA variationLocationrefSNP IDFunctionNumber of heterozygous patientsTP53IVS3−29C>Aap.?IVS3rs178833231c.215G>Cp.R72PExon 4rs1042522Functional polymorphism6IVS4+5G>Ca,dp.?IVS4de novoSplice variant1c.388C>Adp.L130IExon 5de novoMissense1c.473G>Tb,cp.R158LExon 5Missense1c.527G>Ab,cp.C176YExon 5Missense1c.639A>Gbp.R213RExon 6rs1800372Nonsense2IVS6+31A>Gap.?IVS6rs34949160No splice variant3IVS6+62G>Aap.?IVS6rs1625895No splice variant7IVS6−36G>Cap.?IVS6rs17880604No splice variant1c.713G>Ab,cp.C238YExon 7Missense1IVS7−35A>Ga,dp.?IVS7de novoNo splice variant1c.817C>Tb,cp.R273CExon 8rs1625895Missense2c.832C>Tb,cp.P278SExon 8Missense1PTENc.170_171insTcp.L57fs*5Exon 3Frame-shift and stop codon1IVS3+1G>Ta,cp.?IVS3No splice variantc.328C>Tcp.Q110*Exon 5Stop codon1c.371G>Adp.C124YExon 5de novoMissense1c.388C>Tcp.R130*Exon 5Stop codon1c.395G>Acp.G132DExon 5Missense1c.538T>Cdp.Y180HExon 6de novoMissense1c.541delCdp.L181fs*1Exon 6de novoFrame-shift and stop codon1IVS6+2T>Gap.?IVS6de novoSplice variant1c.754G>Ap.D252NExon 7de novoMissense1IVS8+32T>Gap.?IVS8rs555895No splice variant8c.954_957delTACTcp.L318fs*2Exon 8Frame-shift and stop codon1c.1061C>Td,ep.P354LExon 9Missense1EGFRIVS18+19G>Aap.?IVS18rs173371074IVS18+100C>Tap.?IVS18rs172903362IVS19−60T>Cap.?IVS19rs102414515c.2361A>Gp.Q787QExon 20rs1050171Nonsense11c.2508C>Tp.R836RExon 21rs17290559Nonsense1c.2709C>Tp.T903TExon 23rs1140475Nonsense6c.2904C>Tdp.F968FExon 24de novoNonsense1aThe numbering of intronic variations is relative to the first (+) or the last (−1) nucleotide of the corresponding intron.bPreviously reported as somatic mutation in gliomas or glioma cell lines at the International Agency for Research on Cancer (http://www-p53.iarc.fr/).cPreviously reported in gliomas or glioma cell lines in the Catalogue of Somatic Mutations in Cancer (http://www.sanger.ac.uk/genetics/CGP/cosmic/).dVariations identified de novo in gliomas in the present study.eAlready present in the patient’s constitutive DNA.With respect to LOH analysis, the specific spectrum of LOH present in primary tumors was detected only in NS. LOH of 10q was present in all primary tumors, followed by LOH of 9p in 8 of the 16 cases (50%). LOH of 1p, 17p, and 19q was observed only occasionally. The allelic imbalance was partial in all primary tumors and complete in NS (Figure7). No detectable LOH was identified in AC. In line with these data, MGMT was hypermethylated in 50% of primary tumors and in 63.7% of NS. Remarkably, AC from CV10 showed a molecular profile typical of NS.Figure 7
Genetic analysis for CV17 primary tumor, NS, AC, and brain tumor developed in mouse after transplantation of CV17 NS. LOH on CV17 primary tumor, NS, AC, constitutive DNA, and on brain tumor developed after NS transplantion intoNod Scidmice. Electropherograms show allelic imbalances for the following microsatellite markers: D1S457 (green), D9S171 (red), D10S562 (red), TP53-Alu (green), and D19S412 (blue). For all markers, primary tumor shows a partial allelic imbalance in comparison with the constitutive DNA, which is complete in NS, with the exception of D1S457 and TP53-Alu, and in CV17 mouse brain tumor. Arrows indicate, for each marker, the allelic imbalance in primary tumor, NS and in mouse brain tumor.


### 3.7. Western Blotting Analysis

Western blotting analysis confirmed a higher prevalence of antigens indicative of stemness in primary tumors and NS when compared to AC, in which antigens indicative of differentiation were more highly expressed. MGMT expression was consistent with the MGMT promoter hypermethylation status (Figure8(a)). Densitometric analyses of the antigens studied in NS, AC, and the corresponding primary tumors are reported in Figures 8(b) and 8(c).Western blotting analysis of the different antigens studied in cell lines (NS and AC) and in primary tumors. (a) Stemness antigens and differentiation antigens prevail in NS and AC, respectively. (b) Densitometric quantification of bands in NS and in the corresponding primary tumors. (c) Densitometric quantification of bands in AC and in the corresponding primary tumors.
(a)(b)(c)


## 3.1. Histology

Slices from the 16 tumor samples used for histological analyses were serial to those used for cell culture. The following phenotypic features characterized 4 of the 6 samples from which NS generated and 3 of the 9 samples from which AC generated: high cell density, high number of mitoses, a Ki-67/MIB-1 labeling index (LI) between 25% and 30%, circumscribed necroses with pseudo-palisading, high vessel density, and perivascular cuffings of tumor cells (Figure1).Histological and immunohistochemical aspects of phenotypic areas from which NS and AC generated. (a) High cell density, nuclear pleomorphism, scanty cytoplasms, and visible mitoses, H&E. (b) High Ki-67/MIB.1 LI, DAB. (c) The external slope of a circumscribed necrosis, H&E. (d) High vessel density, H&E. (e) Hypercellular perivascular cuffings. GFAP is more positive than Nestin (f), DAB. Scale bar 50μm.
(a)(b)(c)(d)(e)(f)


## 3.2. Immunohistochemistry of Primary Tumors

Nestin was variably expressed in all GBMs, but its distribution did not completely overlap with that of GFAP. As a matter of fact, Nestin expression was higher than GFAP expression, considering both the number of positive cells and the same cells (Figures2(a) and 2(b)). SOX2 and REST, which are diffusely expressed in all GBMs, reached the highest intensity in the areas the phenotype of which has been above described and around vessels (Figures 2(c) and 2(d)).Immunohistochemistry of a parallel section of Figure1. (a) Poor GFAP expression. (b) High Nestin expression. (c) SOX2 is highly expressed in nuclei of the external slope of circumscribed necrosis. (d) REST expression, all DAB. (e) CD133-positive area, frozen section. (f) Musashi-1-positive area. Scale bar 50 μm.
(a)(b)(c)(d)(e)(f)


## 3.3. Immunofluorescence of Primary Tumors (Frozen Sections)

As determined by analysis of frozen sections, CD133 and Musashi-1 were sporadically expressed in areas of variable size or in single cells (Figures2(e) and 2(f)).


## 3.4. In Vitro Culture Assay

NS and AC were observed in cultures from 6 (CV1, CV7, CV10, CV13, CV17, and CV20) and 9 (CV1, CV2, CV3, CV4, CV6, CV8, CV9, CV10, and CV17) of the 16 samples, respectively (37.5% and 56.3%). Cells derived from CV10 primarily grew as AC, occasionally forming cell aggregates attached to the culture plate. When CV10 aggregates were transferred to a low-adherent culture plate with DMEM/F-12 medium and mitogens, they gave rise to NS. In cells derived from CV1, in addition to NS, occasional AC were observed when cultured with DMEM/F-12 and mitogens. Alternatively, cultures derived from CV17 developed both NS and AC in their respective media conditions.NS cultures were verified to contain true BTSCs by assessing their long-term self-renewing ability by population analysis. Cells grown in culture with growth factors proliferated as nonadherent, multicellular spheres (Figure3(a)), whereas cells grown with serum proliferated as an adherent monolayer with an initial heterogeneous morphology which later became homogeneous with resemblance to fibroblasts (Figure 4(a)) and showing astrocytic, oligodendrocytic, or neuronal differentiation (Figures 4(b)–4(d)). Growth rates of NS and AC are illustrated in Figures 5(a) and 5(b). Figure 5(c) shows the different growth rates between NS and AC of the same cell line.Immunofluorescence of NS cultured in serum-free medium. (a) NS. (b) Cytoplasmic expression of CD133. (c) Musashi-1 expression in the cytoplasms. (d) Nestin expression in the cytoplasms. Nuclei are counterstained with DAPI (blue). (e) SOX2 expression in nuclei. (f) REST expression in nuclei. Scale bar 50μm.
(a)(b)(c)(d)(e)(f)Immunofluorescence of AC cultured in serum-containing medium. (a) Monolayer of adherent cells. (b) GFAP expression in the cytoplasms. (c) Cytoplasmic expression of GalC. (d) Cytoplasmic expression ofβ-III Tubulin. Nuclei are counterstained with DAPI (blue). Scale bar 50 μm.
(a)(b)(c)(d)Growth rates of NS and AC. (a) Growth curves of NS cultured in serum-free medium supplemented with mitogens from CV1, CV7, CV10, CV13, CV17, CV20, and reference cell lines U87-MG and 010627. (b) Growth curves of AC cultured in serum containing medium from CV2, CV3, CV4, CV6, CV8, CV9, CV10, CV17 (CV1 is not included), and reference cell lines U87-MG and 010627. (c) Comparison between NS and AC curves.
(a)(b)(c)The subsphere-forming assay performed by limiting dilution demonstrated that the clonogenic efficiency of all NS to form subspheres from individual NS cells was 7–9%.By differentiation assays NS demonstrated their multipotency showing after 7 days from the addition of 3% serum an astrocytic, oligodendrocytic and neuronal differentiation (Figures6(a)–6(c)). Upon intracranial transplantation, NS developed tumors in mice, whereas AC did not developed tumors or showed a reduced tumorigenicity in two cases (data not shown), demonstrating that NS populations included true BTSCs. Details of intracranial transplantations will be discussed in a separate manuscript.Immunofluorescence of differentiation of NS after addition of 3% serum. (a) Cytoplasmic expression ofβIII-Tubulin (red). (b) Cytoplasmic expression of GFAP (green). (c) Cytoplasmic expression of GalC (red). Nuclei are counterstained with DAPI (blue). Scale bar 50 μm.
(a)(b)(c)


## 3.5. Immunofluorescent Analysis of Cell Lines

NS and AC showed different antigenic expression patterns. Nestin was strongly expressed in NS, along with SOX2 and REST, whereas CD133 and Musashi-1 were only sporadically expressed (Figures3(b)–3(f)). GFAP was expressed in cells from only one sample (CV7). AC, in contrast, showed decreased Nestin expression and increased GFAP expression when compared with NS. Both CD133 and Musashi-1 expression was almost completely absent in AC. Nuclear expression of SOX2 and REST was lower in AC when compared to NS.Comparisons of primary tumors, NS and AC are shown in Table3. The expression of antigens indicative of stemness was highest in primary tumors and NS, whereas the expression of antigens indicative of differentiation was highest in AC.Table 3
Primary tumors, NS and AC. Immunohistochemistry and immunofluorescence.
(a)AntibodiesFFPE sectionsCV1CV7CV10CV13CV17CV20GFAP+++++±βIII-Tubulin−−+−−−GalC−−−−−−Nestin+++++++++++CD133−
*−
*±
*±
*±
*+Musashi-1−
*−
*±
*±
*−
*+SOX2++++++++++++REST++++++++++++AntibodiesNSCV1CV7CV10CV13CV17CV20GFAP±+±−−−βIII-Tubulin−++−−±GalC−+±−−±Nestin+++++±CD133+++±−−Musashi-1++±±−−SOX2++++++REST++++++(b)AntibodiesFFPE sectionsCV1CV2CV3CV4CV6CV8CV9CV10CV17GFAP+++++++++++βIII-Tubulin±−+−−−−−−GalC−−−−−−−−−Nestin+++++++++CD133−
*−
*±
*±
*±
*−
*−−−Musashi-1−
*−
*±
*±
*−
*−
*−−−SOX2+++++++++REST+++++++++AntibodiesACCV1CV2CV3CV4CV6CV8CV9CV10CV17GFAP+++++++++βIII-Tubulin+++−±±−−+GalC−++−+±−−+Nestin+++++++++CD133−−+−±−−−+Musashi-1±−+−±±−−+SOX2−−−−+°±+°++°REST−−−++°++°−+°*Tested by IF on primary tumor frozen sections. °Cytoplasmic staining. +Moderate expression intensity.++High expression intensity. ± Barely visible. − Negative.


## 3.6. Molecular Genetics

The derivation of NS and AC from the respective primary tumors was confirmed by genotyping of the 13 microsatellite markers used for LOH analysis.Genetic alterations in primary tumors and in the matched NS or AC are summarized in Table4. Their frequency is consistent with the primary nature of GBMs. No significant differences in the frequency of genetic or epigenetic alterations were observed between primary tumors generating cell lines and those not generating cell lines. In addition, no differences were observed between primary tumors generating NS or AC. LOH on chromosomes 1p, 9p, 10q, 17p, and 19q, EGFR amplification, MGMT promoter hypermethylation as well as PTEN and TP53 mutations was identified with similar frequency in primary tumors and NS, but not in AC. In primary tumors, PTEN mutations were detected in 56.2% of cases, whereas only 31.2% of cases showed TP53 mutations. The TK domain of the gene coding for EGFR was found to be mutated in only one primary tumor (CV6) generating AC. This previously undescribed mutation was a somatic synonymous nucleotide substitution (c.2904C > T, p.F968F). All observed nucleotide sequence variations are reported in Table 5. No point mutations were identified in codons R132 or R172 of IDH1 and IDH2 genes, respectively.Table 4
Frequency of genetic and epigenetic alterations in primary tumors, NS and AC.
Molecular markerPrimary GBM (%)NS (%)AC* (%)LOH 1p, 9p, 10q, 17p, 19q16 (100)6 (100)0 (0)EGFR amplification8 (50)3 (45)0 (0)MGMT hypermethylation9 (50)4 (66.7)0 (0)TP53 mutations5 (31.2)3 (50)0 (0)PTEN mutations9 (56.2)4 (66.7)2 (22.2)EGFR mutations1 (<1)0 (0)0 (0)p.R132 IDH10 (0)0 (0)0 (0)p.R172 IDH20 (0)0 (0)0 (0)*An exception is CV10 in which NS generated from AC. AC showed the same molecular profile of NS.Table 5
Spectrum of the identified sequence variations.
GeneCDS variationAA variationLocationrefSNP IDFunctionNumber of heterozygous patientsTP53IVS3−29C>Aap.?IVS3rs178833231c.215G>Cp.R72PExon 4rs1042522Functional polymorphism6IVS4+5G>Ca,dp.?IVS4de novoSplice variant1c.388C>Adp.L130IExon 5de novoMissense1c.473G>Tb,cp.R158LExon 5Missense1c.527G>Ab,cp.C176YExon 5Missense1c.639A>Gbp.R213RExon 6rs1800372Nonsense2IVS6+31A>Gap.?IVS6rs34949160No splice variant3IVS6+62G>Aap.?IVS6rs1625895No splice variant7IVS6−36G>Cap.?IVS6rs17880604No splice variant1c.713G>Ab,cp.C238YExon 7Missense1IVS7−35A>Ga,dp.?IVS7de novoNo splice variant1c.817C>Tb,cp.R273CExon 8rs1625895Missense2c.832C>Tb,cp.P278SExon 8Missense1PTENc.170_171insTcp.L57fs*5Exon 3Frame-shift and stop codon1IVS3+1G>Ta,cp.?IVS3No splice variantc.328C>Tcp.Q110*Exon 5Stop codon1c.371G>Adp.C124YExon 5de novoMissense1c.388C>Tcp.R130*Exon 5Stop codon1c.395G>Acp.G132DExon 5Missense1c.538T>Cdp.Y180HExon 6de novoMissense1c.541delCdp.L181fs*1Exon 6de novoFrame-shift and stop codon1IVS6+2T>Gap.?IVS6de novoSplice variant1c.754G>Ap.D252NExon 7de novoMissense1IVS8+32T>Gap.?IVS8rs555895No splice variant8c.954_957delTACTcp.L318fs*2Exon 8Frame-shift and stop codon1c.1061C>Td,ep.P354LExon 9Missense1EGFRIVS18+19G>Aap.?IVS18rs173371074IVS18+100C>Tap.?IVS18rs172903362IVS19−60T>Cap.?IVS19rs102414515c.2361A>Gp.Q787QExon 20rs1050171Nonsense11c.2508C>Tp.R836RExon 21rs17290559Nonsense1c.2709C>Tp.T903TExon 23rs1140475Nonsense6c.2904C>Tdp.F968FExon 24de novoNonsense1aThe numbering of intronic variations is relative to the first (+) or the last (−1) nucleotide of the corresponding intron.bPreviously reported as somatic mutation in gliomas or glioma cell lines at the International Agency for Research on Cancer (http://www-p53.iarc.fr/).cPreviously reported in gliomas or glioma cell lines in the Catalogue of Somatic Mutations in Cancer (http://www.sanger.ac.uk/genetics/CGP/cosmic/).dVariations identified de novo in gliomas in the present study.eAlready present in the patient’s constitutive DNA.With respect to LOH analysis, the specific spectrum of LOH present in primary tumors was detected only in NS. LOH of 10q was present in all primary tumors, followed by LOH of 9p in 8 of the 16 cases (50%). LOH of 1p, 17p, and 19q was observed only occasionally. The allelic imbalance was partial in all primary tumors and complete in NS (Figure7). No detectable LOH was identified in AC. In line with these data, MGMT was hypermethylated in 50% of primary tumors and in 63.7% of NS. Remarkably, AC from CV10 showed a molecular profile typical of NS.Figure 7
Genetic analysis for CV17 primary tumor, NS, AC, and brain tumor developed in mouse after transplantation of CV17 NS. LOH on CV17 primary tumor, NS, AC, constitutive DNA, and on brain tumor developed after NS transplantion intoNod Scidmice. Electropherograms show allelic imbalances for the following microsatellite markers: D1S457 (green), D9S171 (red), D10S562 (red), TP53-Alu (green), and D19S412 (blue). For all markers, primary tumor shows a partial allelic imbalance in comparison with the constitutive DNA, which is complete in NS, with the exception of D1S457 and TP53-Alu, and in CV17 mouse brain tumor. Arrows indicate, for each marker, the allelic imbalance in primary tumor, NS and in mouse brain tumor.


## 3.7. Western Blotting Analysis

Western blotting analysis confirmed a higher prevalence of antigens indicative of stemness in primary tumors and NS when compared to AC, in which antigens indicative of differentiation were more highly expressed. MGMT expression was consistent with the MGMT promoter hypermethylation status (Figure8(a)). Densitometric analyses of the antigens studied in NS, AC, and the corresponding primary tumors are reported in Figures 8(b) and 8(c).Western blotting analysis of the different antigens studied in cell lines (NS and AC) and in primary tumors. (a) Stemness antigens and differentiation antigens prevail in NS and AC, respectively. (b) Densitometric quantification of bands in NS and in the corresponding primary tumors. (c) Densitometric quantification of bands in AC and in the corresponding primary tumors.
(a)(b)(c)


## 4. Discussion

One important question is whether GBMs are heterogeneous with respect to their BTSC content. Basically, it has been demonstrated that different subsets of BTSCs with different proliferative, clonogenic, and tumorigenic properties exist in GBMs [3]. Moreover, chemosensitivity of highly infiltrative GBMs has been demonstrated to be associated with a stem cell-like phenotype, that is, with the expression of Nestin, Vimentin, and Musashi-1 [3, 29]. In a study no difference was found among several samples from the same tumor as for their BTSC content [22], but in another study the existence of at least two types of BTSCs from different regions of the same tumor has been demonstrated; they showed different genetic anomalies and tumorigenic potentials, even though the cells were considered to derive from common ancestors [21]. The demonstration of BTSCs largely depends on the technical procedures, but in most studies only approximately 30% of GBMs generate NS [22]. Selecting differently glioma initiating cells, for example by autofluorescence, these can be found in all glioma types [30].In our GBM series, the development of NS in culture is largely dependent on the occurrence in primary tumors of what is known as the most malignant phenotype of GMB, composed of small hyperchromatic and rapidly dividing cells, with vessel hyperdensity and circumscribed necroses [23]. In the present study, the most important observation is that the frequency of the genetic and epigenetic alterations is very similar between primary tumors and NS, showing a strong genotypic concordance. This is particularly remarkable in the case of LOH profiles, which are present with the same spectrum in both primary tumors and NS, but not in AC. This observation is consistent with previous data [31]. The allelic imbalance was partial in primary tumors and complete in NS. In AC, no detectable genetic or epigenetic alteration similar to that of the corresponding primary tumor was observed, with the exception of occasional PTEN mutations. The MGMT hypermethylation status and the EGFR amplification status showed a similar frequency between primary tumors and NS, but not between primary tumors and AC. The same is true for the mutation spectrum of TP53 and PTEN genes. In 3 of our cases, both NS and AC developed from the same tumor sample indicating that cells with different potential can coexist in the same tumor. Interestingly, in 1 of these 3 cases, AC generating NS showed the same molecular profile as NS.The prevalence of Nestin upon GFAP and the expression of stemness antigens in perivascular cuffings and in areas with vessel hyperdensity of primary tumors is in line with the preference of BTSCs for perivascular niches [32–34]. The latter recapitulate normal NSCs and the vasculature of developing nervous system [35, 36]; on the other hand, BTSCs in gliomas mediate vascular proliferation via VEGF [37, 38].The different behavior of NS and AC may be due to showing the former full stemness properties and appearing the latter as the product of cell differentiation. NS could be transformed NSCs from germinal zones, subventricular zone (SVZ), or subgranular zone (SGZ), or from dedifferentiated elements of the astrocytic lineage [39], whereas AC could represent a differentiating cell type. Intermediated behaviors have been observed in our material, as it has been already shown [20].The generation of NS from a tumor sample mostly when it shows the mentioned phenotype may suggest that BTSCs arise from or are contained in the novel, proliferating and dedifferentiated clones which develop following mutation accumulation or epigenetic events during malignant transformation and substitute the predecessorsvia competitive selection [10]. This hypothesis, previously considered [3, 8, 10, 11], regards dedifferentiated cells as regressed to an embryonic state reacquiring a stem cell-like status. Embryonic regression has been previously invoked, for example, for reactive astrocytes reexpressing Nestin [40, 41].Our observations concern a very important debated question, that is, the cell composition of a starting tumor tissue. It is not clear whether a major role is played by the occurrence of BTSCs in the tissue or by culture conditions. On the other hand, a clear distinction between NS and AC is still debated concerning self-renewal, clonogenicity and tumorigenicity, and intermediate stages between them exist; terms such as semiadherent cells have been coined for them [20]. This is confirmed by the behavior of CV1, CV10, and CV17 of our series.Stemness, therefore, might not be a property of a specific cell type, but a status which encompasses the early steps of the cytogenesis. It is conceivable that in the process of differentiation during cytogenesis there is a point, represented by progenitors, beyond which stemness ceases. In the same way, considering the process of tumor cell dedifferentiation from more differentiated stages, through the development of new clones there should be a point beyond which stemness reappears. From the different stages of differentiation and dedifferentiation, different stemness potentials could be recognized, explaining intermediate properties (Figure9). A similar problem has been presented and exhaustively discussed in relation to leukemias [42].Figure 9
Scheme of a hypothetical distribution of stemness during differentiation and dedifferentiation. Stemness decreases from the stage of neural stem cells toward progenitors and adult cells. Conversely, in tumors it increases to a maximum in the stage of brain tumor stem cells.The high expression of SOX2 and REST in primary tumors and NS is a stemness property. In our samples, SOX2 not only correlated with the malignancy grade, but it was also overexpressed in the GBM phenotype from which NS could be generated and even amplified as in NS [43]. SOX2 is therefore a proliferation and stemness factor. REST has been shown to display tumor-suppressor activity [44] and oncogenic functions in medulloblastoma [45]. REST is overexpressed in NSC and in medulloblastomas [46, 47]. We did not find in our samples even a slight REST amplification [48]; however, it is overexpressed in the primary tumor phenotype generating NS. The most commonly held position is that REST could maintain stem cell status [49].



---

*Source: 314962-2011-08-18.xml*