Correction: Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes

gb-2007-8-1-401 GBJ Correction Correction: Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes De Preter Katleen Vandesompele Jo Heimann Pierre Yigit Nurten Beckman Siv Schramm Alexander Eggert Angelika Stallings L Raymond Benoit Yves Renard Marleen De Paepe Anne Laureys Geneviève Påhlman Sven Speleman Frank franki.speleman@ugent.be

Center for Medical Genetics, Ghent University Hospital, De Pintelaan, B-9000 Ghent, Belgium

Department of Medical Genetics, University Hospital Erasme, Lenniksebaan, B-1070 Brussels, Belgium

Division of Molecular Medicine, Department of Laboratory Medicine, Lund University, University Hospital MAS, SE-20502 Malmö, Sweden

Department of Pediatric Oncology and Hematology, University Hospital of Essen, Hufelandstr., Essen 45122, Germany

Children's Cancer Research Institute, University of Texas Health Science Center, Floyd Curl Drive, Mail Code 7784, San Antonio, Texas 78229-3900, USA

Department of Pediatrics, Ghent University Hospital, De Pintelaan, B-9000 Ghent, Belgium

Department of Pediatrics, UZ Gasthuisberg, Herestraat, B-3000 Leuven, Belgium

Genome Biology 1465-6906 2007 8 1 401 http://genomebiology.com/2007/8/1/401 10.1186/gb-2007-8-1-401 31 1 2007 2007 BioMed Central Ltd

Correction: Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes

Cancer Genome studies

We wish to report some corrections to our study 1, none of which alters the interpretation of the data or the conclusions drawn. After publication, we noticed that one of the micro-array hybridizations (on sample NB11) was performed on the same patient's material as another hybridization (sample NB4; see Table 1; a corrected version of Table 5 1). As this error leads to an incorrect subclassification of the patients into the 'favourable' and 'unfavourable' neuroblastoma subgroups, we would like to exclude this data point from the differential expression analysis of favorable versus unfavorable neuroblastoma given under the heading 'Differential expression analysis of favorable and unfavorable neuroblastoma' in the Results section of 1. Careful reanalysis after exclusion of NB11 did not lead to important changes in the generated gene lists and conclusions; the changes are given in the corrected paragraph and Table 2 (a corrected version of Table 4 1), and the Additional data files 1 and 2 (corrected versions of Additional data files 2 and 3 1) available online with this article.

Table 1

Clinical and genetic data of carefully selected neuroblastoma samples that were included in this study

Sample number

Lab number

% Tumor cells

Stage

MYCN amp

Ploidy

Adrenal localization

Age

Dead/alive

Overall survival (months)

Type

NB1

98T33

Tri

Yes

< 1 year

Alive

76.9

Favorable

NB2

99T84

Tri

< 1 year

Alive

71.8

Favorable

NB3

96T82

Tri

Yes

< 1 year

Alive

115.5

Favorable

NB4

99T129

Tri

Yes

< 1 year

Alive

71.7

Favorable

NB5

01T28

Yes

> 1 year

Dead

5.6

Unfavorable

NB6

03T304

100

Abdominal

> 1 year

Alive

12.0

Unfavorable

NB7

03T236

Yes

> 5 year

Dead

19.4

Unfavorable

NB8

00T54

Tri

Yes

< 1 year

Alive

62.6

Favorable

NB9

00T35

>95

Yes

< 1 year

Dead

13.7

Unfavorable

NB10

99T125

Yes

> 5 year

Alive

79.3

Unfavorable

NB11 = NB4

99T129

Tri

Yes

< 1 year

Alive

71.7

Favorable

NB12

02T192

100

Yes

Abdominal

> 5 year

Dead

16.2

Unfavorable

NB13

D031

>95

Abdominal

> 1 year

Dead

64.8

Unfavorable

NB14

E002

>80

Abdominal

> 1 year

Alive

65.7

Unfavorable

NB15

E037

>80

Abdominal

> 1 year

Alive

45.3

Unfavorable

NB16

E044

>80

Yes

< 1 year

Alive

37.0

Unfavorable

NB17

E121

>80

Yes

Abdominal

> 1 year

Dead

78.4

Unfavorable

NB18

04T121

Yes

> 1 year

Dead

Unfavorable

Samples were subdivided into favorable or unfavorable type based on MYCN amplification, ploidy and age at diagnosis. *Neuroblastoma or nodular gan-glioneuroblastoma. ND, not determined or unknown.

Table 2

Genes that are differentially expressed in favorable vs unfavorable neuroblastoma

Favorable NB > unfavorable NB

NBGS

Favorable NB < unfavorable NB

NBGS

neuroblast < favorable NB

neuroblast < favorable NB, neuroblast < unfavorable NB

AKAP7

FABP6

ARL4C

IGLJ3

22q

ASPN

NEFL

BCL2

18q

NPY

CALB1

neuroblast < unfavorable NB

CAMK2B

22q

ALK

CD24

ASCL1

12q

CDC42

BCL11A

DDAH1

BIRC5

17q

DNAPTP6

19p

EPB41L3

18p

CALCB

11p

FAM70A

CCL18

17q

KIFAP3

CCL21

OPHN1

CCNB1

PPAN

19p

CD74

PRKCB1

16p

CRH

REEP1

CSPG3

19p

RGS7

CXCR4

RNF11

DYNC1I1

SCD5

F12

SERINC1

GFRA2

ST6GALNAC5

IGHA1

14q

SV2C

IGHG3

14q

neuroblast > favorable NB, neuroblast > unfavorable NB

IGHM

14q

CACNA2D3

IGKC

DLK1

14q

IGLC1

22q

HBG1

11p

IGLC2

22q

HBG2

11p

LMO3

12p

neuroblast > unfavorable NB

MMP9

20q

ALDH3A2

17p

MYCN

DBH

NEFH

22q

DLC1

ODC1

EYA1

OGDHL

10q

GCH1

14q

P2RX5

17p

HBA1

16p

PRAME

22q

HBA2

16p

RPS4Y1

NTRK1

SERPINF1

17p

PTPRD

SIX3

PTPRK

SST

SFRP1

TNFRSF10B

SLC18A1

TWIST1

TFAP2B

XAGE1

TLN2

15q

neuroblast > favorable NB

RNU2

17q

neuroblast > favorable NB, neuroblast > unfavorable NB

C11orf43

11p

Genes that are differentially expressed compared with neuroblasts among the differentially expressed genes in favorable neuroblastoma (NB) vs unfavorable NB, with an indication of the number of neuroblastoma microarray studies in which these genes were found through NBGS analysis. NBGS, Neuroblastoma Gene Server.

We also noticed that sample NB1 is stage 1 instead of stage 4S and that sample NB2 was not localized to the adrenals (see Table 1).

Results

Differential expression analysis of favorable and unfavorable neuroblastoma

So far, most published microarray studies on neuroblastomas mainly compared favorable with unfavorable neuroblastomas in order to identify prognostic markers or pathways that are involved in these clearly different neuroblastoma tumor types. In order to add value to such an analysis, we contrasted similar differentially expressed gene lists with the normal neuroblast expression profile (Additional data file 1). In a first step, we compared the differentially expressed genes between these two tumor types with published prognostic gene lists. We found that 23 of the 193 genes on our list were previously reported, including the well established markers MYCN, NTRK1, and CD44 (see NBGS analysis in Additional data file 2). This overlap demonstrates the validity of the selected neuroblastoma panel and their expression profile. Subsequently, we looked for the corresponding gene expression levels of the differentially expressed genes in the normal counterpart cells, aiming to select neuroblastoma candidate genes. Of the 100 genes that are more highly expressed in favorable tumors (compared to unfavorable) 41 also have a significant differential expression (either higher or lower) compared to neuroblasts, whereas 43 of the 93 genes that are more highly expressed in unfavorable tumors exhibit differential expression compared to the neuroblasts (Table 2).

From this analysis, a few putative positional tumor suppressor candidates emerge: CDC42 on 1p36, CACNA2D3 on 3p21 and DLK1 on 14q. The latter two genes are of particular interest because they are highly expressed in neuroblasts and favorable neuroblastomas and their expression is significantly lower in unfavorable neuroblastomas. Among the genes that are more highly expressed in unfavorable neurob-lastomas than in favorable ones and neuroblasts, the proven oncogenic transcription factor MYCN emerges (and putative downstream genes KIFAP3, OPHN1, RGS7, ASCL1, ODC1, TWIST1 and TYMS, according to NBGS), as well as several other genes that have been identified or studied in the context of neuroblastoma such as ALK and PRAME, and positional candidates on 17q including BIRC5 and RNU2.

Additional data files

Additional data files 1 and 2 containing the corrected data available online with this article.

Additional data file 1

Corrected version of Additional data file 2

Corrected version of Additional data file 2 [1].

Click here for file

Additional data file 2

Corrected version of Additional data file 3

Corrected version of Additional data file 3 [1].

Click here for file

Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes. De Preter K Vandesompele J Heimann P Yigit N Beckman S Schramm A Eggert A Stallings RL Benoit Y Renard M Genome Biol 2006 7 R84 10.1186/gb-2006-7-9-r84 16989664 1794547