Open Access

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

  • Katleen De Preter1,
  • Jo Vandesompele1,
  • Pierre Heimann2,
  • Nurten Yigit1,
  • Siv Beckman3,
  • Alexander Schramm4,
  • Angelika Eggert4,
  • Raymond L Stallings5,
  • Yves Benoit6,
  • Marleen Renard7,
  • Anne De Paepe1,
  • Geneviève Laureys6,
  • Sven Påhlman3 and
  • Frank Speleman1Email author
Genome Biology20078:401

DOI: 10.1186/gb-2007-8-1-401

Published: 31 January 2007

The Research to this article has been published in Genome Biology 2006 7:R84

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

95

1

No

Tri

Yes

< 1 year

Alive

76.9

Favorable

NB2

99T84

90

1

No

Tri

No

< 1 year

Alive

71.8

Favorable

NB3

96T82

90

1

No

Tri

Yes

< 1 year

Alive

115.5

Favorable

NB4

99T129

90

1

No

Tri

Yes

< 1 year

Alive

71.7

Favorable

NB5

01T28

90

4

Yes

Di

Yes

> 1 year

Dead

5.6

Unfavorable

NB6

03T304

100

3*

No

Di

Abdominal

> 1 year

Alive

12.0

Unfavorable

NB7

03T236

90

4

No

ND

Yes

> 5 year

Dead

19.4

Unfavorable

NB8

00T54

70

1

No

Tri

Yes

< 1 year

Alive

62.6

Favorable

NB9

00T35

>95

4

Yes

Di

Yes

< 1 year

Dead

13.7

Unfavorable

NB10

99T125

80

3

No

Di

Yes

> 5 year

Alive

79.3

Unfavorable

NB11 = NB4

99T129

90

1

No

Tri

Yes

< 1 year

Alive

71.7

Favorable

NB12

02T192

100

4

Yes

Di

Abdominal

> 5 year

Dead

16.2

Unfavorable

NB13

D031

>95

4

No

Di

Abdominal

> 1 year

Dead

64.8

Unfavorable

NB14

E002

>80

4

No

ND

Abdominal

> 1 year

Alive

65.7

Unfavorable

NB15

E037

>80

4

No

ND

Abdominal

> 1 year

Alive

45.3

Unfavorable

NB16

E044

>80

4

No

ND

Yes

< 1 year

Alive

37.0

Unfavorable

NB17

E121

>80

4

Yes

ND

Abdominal

> 1 year

Dead

78.4

Unfavorable

NB18

04T121

60

3

Yes

Di

Yes

> 1 year

Dead

6

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

6q

-

FABP6

5q

-

ARL4C

2q

-

IGLJ3

22q

1

ASPN

9q

-

NEFL

8p

-

BCL2

18q

1

NPY

7p

-

CALB1

8q

-

neuroblast < unfavorable NB

CAMK2B

22q

2

ALK

2p

-

CD24

6q

-

ASCL1

12q

1

CDC42

1p

1

BCL11A

2p

-

DDAH1

1p

-

BIRC5

17q

3

DNAPTP6

2q

-

C3

19p

-

EPB41L3

18p

1

CALCB

11p

-

FAM70A

Xq

-

CCL18

17q

-

KIFAP3

1q

1

CCL21

9p

-

OPHN1

Xq

-

CCNB1

5q

1

PPAN

19p

-

CD74

5q

-

PRKCB1

16p

1

CRH

8q

-

REEP1

2p

-

CSPG3

19p

-

RGS7

1q

2

CXCR4

2q

2

RNF11

1p

-

DYNC1I1

7q

-

SCD5

4q

2

F12

5q

-

SERINC1

6q

1

GFRA2

8p

-

ST6GALNAC5

1p

-

IGHA1

14q

2

SV2C

5q

-

IGHG3

14q

-

neuroblast > favorable NB, neuroblast > unfavorable NB

IGHM

14q

-

CACNA2D3

3p

-

IGKC

2p

1

DLK1

14q

2

IGLC1

22q

-

HBG1

11p

-

IGLC2

22q

-

HBG2

11p

-

LMO3

12p

1

neuroblast > unfavorable NB

MMP9

20q

1

ALDH3A2

17p

1

MYCN

2p

9

DBH

9q

1

NEFH

22q

-

DLC1

8p

-

ODC1

2p

3

EYA1

8q

-

OGDHL

10q

-

GCH1

14q

1

P2RX5

17p

-

HBA1

16p

-

PRAME

22q

1

HBA2

16p

-

RPS4Y1

Yp

1

NTRK1

1q

4

SERPINF1

17p

-

PTPRD

9p

-

SIX3

2p

-

PTPRK

6q

-

SST

3q

1

SFRP1

8p

1

TNFRSF10B

8p

2

SLC18A1

8p

-

TWIST1

7p

1

TFAP2B

6p

-

XAGE1

Xp

-

TLN2

15q

1

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.

Declarations

Authors’ Affiliations

(1)
Center for Medical Genetics, Ghent University Hospital
(2)
Department of Medical Genetics, University Hospital Erasme
(3)
Division of Molecular Medicine, Department of Laboratory Medicine, Lund University, University Hospital MAS
(4)
Department of Pediatric Oncology and Hematology, University Hospital of Essen
(5)
Children's Cancer Research Institute, University of Texas Health Science Center
(6)
Department of Pediatrics, Ghent University Hospital
(7)
Department of Pediatrics, UZ Gasthuisberg

References

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

Copyright

© BioMed Central Ltd 2007

Advertisement