Data on affected cancer-related genes in pediatric t(12;21)-positive acute lymphoblastic leukemia patients harboring unbalanced der(6)t(X;6) translocations.

The t(12;21)(p13;q22), leading to ETV6/RUNX1 fusion, is of importance for leukemogenesis in acute lymphoblastic leukemia but is not sufficient for the leukemic transformation. Acquired secondary chromosomal aberrations are necessary for overt leukemia but their complete nature and genes involved are still elusive. In our recent publication, "Oligo-based aCGH analysis reveals cryptic unbalanced der(6)t(X;6) in pediatric t(12;21)-positive acute lymphoblastic leukemia", we identified acquired common concurrent regions with 6q deletion and Xq duplication E. Kjeldsen (2016) [1]. The present article provides data on genes that are associated with hematological malignancy and other cancers located in these common regions of chromosomal aberrations.

Specifications Table

Value of the data

Non-random concurrent Xq duplication and 6q deletion in pediatric t(12;21)-positive ALLs may point to important secondary aberrations for leukemogenesis.

16 out of 59 cancer-related genes located in the aberrant genomic regions were associated with hematological malignancy.

The findings add to the spectrum of acquired secondary aberrations in t(12;21)-positive ALLs.

Data

A search at the repository Network of Cancer Genes (NCG5.0) [2] revealed 27 cancer-related genes in the common region of duplication Xq25-qter (genomic pos. 121,657,255-155,232,907) of which seven genes are described to be associated with hematological malignancy, including STAG2, SMARCA1, PHF6, MAGEC3, PASD1, DUSP9, and RPL10 (Table 1). A search for cancer-related genes in the common region of deletion on 6q16.1-qter (genomic pos. 95,958,513–171,025,515) revealed 32 genes of which nine genes are associated with hematological malignancy, including PRDM1, FYN, ROS1, EYA4, SGK1, TNFAIP3, CCDC28A, ECT2L, and ESR1 (Table 2). The tables also summarize current knowledge of the function(s) of the proteins encoded by the involved genes.

Table 1

Twenty-seven cancer related genes located in the common region of amplification in Xq25-qter, pos. 121,657,255–155,232,907.

Genes	CytoBand	Cancer Type or sitea	Protein function	Ref.
GRIA3	Xq25	Pancreas	Cellular processesSignal transduction	[3]
STAG2	Xq25	MultipleBladderLeukemiaEwing sarcomaGlioblastoma	Cell cycle	[4][5][6][7][8][9], [10]
DCAF12L2	Xq25	Glioblastoma	No functional information	[11]
SMARCA1	Xq25	Lymphoma	Cell cycleCellular metabolismDNA/RNA metabolism and transcriptionDevelopmentRegulation of intracellular processes and metabolismRegulation of transcription	[12]
XPNPEP2	Xq26.1	Lung	Cellular metabolism	[13]
BCORL1	Xq26.1	GliomaIntracranial	Cellular metabolismDNA/RNA metabolism and transcriptionRegulation of intracellular processes and metabolismRegulation of transcription	[14], [15]
ELF4	Xq26.1	Multiple	Cellular metabolismDNA/RNA metabolism and transcriptionImmune system responseRegulation of intracellular processes and metabolismRegulation of transcription	[4]
FRMD7	Xq26.2	Glioblastoma	No functional information	[11]
GPC3	Xq26.2	Multiple	No functional information	[4]
PHF6	Xq26.2	MultipleLeukemia	Cellular metabolismDNA/RNA metabolism and transcriptionRegulation of intracellular processes and metabolismRegulation of transcription	[4][7][16]
SAGE1	Xq26.3	Pancreas	No functional information	[17]
GPR112	Xq26.3	Cholangio-carcinoma	Signal transduction	[18]
RBMX	Xq26.3	Endometrial	DNA/RNA metabolism and transcriptionRegulation of transcription	[19]
ZIC3	Xq26.3	Liver	Cellular metabolismDNA/RNA metabolism and transcriptionDevelopmentRegulation of intracellular processes and metabolismRegulation of transcription	[20]
MAGEC3	Xq27.2	LeukemiaLymphoma	No functional information	[16][12]
MAGEC1	Xq27.1	MelanomaHead and neck	No functional information	[21][22]
MAGEC2	Xq27.2	Head and neck	No functional information	[22]
SPANXN2	Xq27.3	Gastric	No functional information	[23]
AFF2	Xq28	Breast	Development	[19]
PASD1	Xq28	Lymphoma	Signal transduction	[24]
MAGEA6	Xq28	Pancreas	No functional information	[25]
ATP2B3	Xq28	Multiple	Cellular processes	[4]
DUSP9	Xq28	Lymphoma	Cellular metabolismCellular processesRegulation of intracellular processes and metabolismSignal transduction	[12]
RPL10	Xq28	MultipleLeukemia	Cellular metabolismRegulation of transcription	[4][16]
PLXNA3	Xq28	Neuroblastoma	Cell cycleCell motility and interactionsDevelopmentRegulation of intracellular processes and metabolismSignal transduction	[26]
F8	Xq28	Pancreas	Cell response to stimuliImmune system responseMulticellular activities	[3]
MTCP1	Xq28	Multiple	No functional information	[4]

Hematological malignancies are in bold.

Table 2

Thirty-two cancer related genes located in the common region of deletion on 6q16.1-qter, pos. 95,958,513–171,025,515.

Genes	CytoBand	Cancer type or Sitea	Protein function	Ref.
MCHR2	6q16.2	Lung	Signal transduction	[27]
PRDM1	6q21	Lymphoma	Cellular metabolismDNA/RNA metabolism and transcriptionRegulation of intracellular processes and metabolismRegulation of transcription	[12]
FOXO3	6q21	Multiple	Cell CycleCellular metabolismDNA/RNA metabolism and transcriptionDevelopmentMulticellular activitiesRegulation of intracellular processes and metabolismRegulation of transcription	[4]
FYN	6q21	Lymphoma	Cell response to stimuliCellular metabolismCellular processesImmune system responseMulticellular activitiesSignal transduction	[28]
LAMA4	6q21	BladderIntracranial	Cell motility and interactionsDevelopment	[5][14]
DSE	6q22.1	Liver	Cellular metabolism	[29]
RFX6	6q22.1	Glioblastoma	Cellular metabolismDNA/RNA metabolism and transcriptionRegulation of intracellular processes and metabolismRegulation of transcription	[11]
ROS1	6q22.1	MultipleLungLeukemia	Cellular metabolismCellular processesSignal transduction	[4], [27], [30]
GOPC	6q22.1	MultipleLung	Cellular metabolismCellular processesRegulation of intracellular processes and metabolism	[4][31]
TBC1D32	6q22.31	Glioblastoma	Regulation of intracellular processes and metabolismSignal transduction	[32]
PTPRK	6q22.33	Melanoma	Cellular metabolismCellular processes	[21]
LAMA2	6q22.33	Cholangio-carcinoma	Cell motilityDevelopment	[33]
EYA4	6q23.2	ColorectalLungLeukemia	Cell response to stimuliCellular metabolismRegulation of intracellular processes and metabolismRegulation of transcription	[34][35][36]
SGK1	6q23.2	LymphomaEndometrial	Cell cycleCellular metabolismCellular processes	[24][37][38]
MYB	6q23.3	MultipleGlioma	Cellular metabolismDNA/RNA metabolism and transcriptionRegulation of intracellular processes and metabolismRegulation of transcription	[4][39]
BCLAF1	6q23.3	Lung	Cell cycleCellular metabolismDNA/RNA metabolism and transcriptionDevelopmentRegulation of intracellular processes and metabolismRegulation of transcription	[40]
MAP7	6q23.3	Colorectal	Cellular processesDevelopment	[41]
MAP3K5	6q23.3	Melanoma	Cell cycleCellular metabolismCellular processesDevelopmentRegulation of intracellular processes and metabolismSignal tranduction	[42]
TNFAIP3	6q23.3	Lymphoma	Cell cycleDevelopmentRegulation of intracellular processes and metabolismSignal tranduction	[12][43]
CCDC28A	6q24.1	Leukemia	No functional information	[44]
ECT2L	6q24.1	MultipleLeukemia	Signal transdcution	[4][45]
GRM1	6q24.3	LungChondronmyxoid fibroma	Multicellular activitiesSignal transduction	[27][46]
ESR1	6q25.1	BreastEndometrialLeukemia	Cell cycleCellular metabolismDNA/RNA metabolism and transcriptionDevelopmentRegulation of intracellular processes and metabolismRegulation of transcriptionSignal transduction	[47][48]
SYNE1	6q25.1-q25.2	BladderEsophagealNasopharyngealHead and neck	Cellular processesDevelopment	[5][49][50][22]
ARID1B	6q25.3	NeuroblastomaBreastLungLiver	Cellular metabolismDNA/RNA metabolism and transcriptionRegulation of intracellular processes and metabolismRegulation of transcription	[51][52][53][54][20]
EZR	6q25.3	Multiple	Cell motility and interactionsCellular processesDevelopmentRegulation of intracellular processes and metabolism	[4]
IGF2R	6q25.3	PancreasGlioma	Cellular processesSignal transduction	[55][56]
MAP3K4	6q26	Endometrial	Cellular metabolismCellular processesRegulation of intracellular processes and metabolismSignal transduction	[57]
QKI	6q26	Glioma	Cellular metabolismCellular processesDNA/RNA metabolism and transcriptionRegulation of intracellular processes and metabolismRegulation of transcription	[39]
C6orf118	6q27	Esophageal	No functional information	[49]
FGFR1OP	6q27	Multiple	Cell cycleRegulation of intracellular processes and metabolism	[4]
MLLT4	6q27	Multiple	Signal transduction	[4]

Hematological malignancies are in bold.

Experimental design, materials and methods

By oligobased aCGH analysis of three pediatric t(12;21)-positive ALLs we recently identified a common region of duplication on Xq (genomic pos. 121,657,255–155,232,907) and a common region of deletion on 6q (genomic pos. 95,958,513–171,025,515) [1]. This genomic information was used to search the web-based Network of Cancer Genes (NCG5.0) [2]. The resulting information of genes located in these common regions of aberrations were listed in the tables without filtering.

Subject area	Biology
More specific subject area	Cancer genomics
Type of data	Tables
How data was acquired	Search was performed in the repository Network of Cancer Genes
Data format	Analyzed
Experimental factors	Bone marrow samples of t(12;21)-positive ALLs were analyzed by oligo-based array-comparative genomic hybridization, which identified a group of patients with der(6)t(X;6).
Experimental features	A common region of duplication on Xq and a common region of deletion on 6q were determined in our recent publication and used for the repository search.
Data source location	Aarhus, Denmark
Data accessibility	Data is with this article