Conjoined Genes as Common Events in Childhood Acute Lymphoblastic Leukemia
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Code | Age | Sex | Phenotype | BM Blasts % | Translocations | DNA Index | Steroid Response | MRD Risk Stratification |
---|---|---|---|---|---|---|---|---|
#8 | 16 | M | BII | 86 | NEG | 1 | PGR | HR |
#11 | 15 | M | BII | 80 | NEG | 1 | PGR | HR |
#12 | 3 | F | BI | 73 | NEG | 1 | PGR | HR |
#13 | 4 | F | BIII | 78 | NEG | 1 | PGR | HR |
#15 | 9 | F | BII | 74 | NEG | 1 | PGR | HR |
#16 | 11 | M | BIII | 90 | NEG | 1 | PGR | HR |
#6 | 1 | M | BII | 94 | NEG | 1 | PGR | SR |
#7 | 5 | M | BII | 70 | NEG | 1 | PGR | SR |
#9 | 15 | M | BII | 94 | NEG | 1 | PGR | SR |
#14 | 8 | M | BII/BIII | 90 | NEG | 1 | PGR | SR |
Conjoined Genes | Gene Orientation * | 5′ Gene | 3′ Gene | 5′ Breakpoint | 3′ Breakpoint | Annotation | Our ALL Cohort (Case ID#) | AML ** | T-ALL (Leucegene) ** | T-ALL (COG) ** | B-ALL** | TCGA Solid Tumors *** |
---|---|---|---|---|---|---|---|---|---|---|---|---|
LRRC61::ZBED6CL | +/+ | LRRC61 | ZBED6CL | 7:150328742 | 7:150330107 | - | 1/10 (#14) | 17/27 | 8/12 | 6/14 | 0/20 | THCA (1/20) |
ZNF250::COMMD5 | +/+ | ZNF250 | COMMD5 | 8:144880365 | 8:144851395 | GenBank | 1/10 (#14) | 15/27 | 9/12 | 4/14 | 4/20 | LGG (1/20), PRAD (1/20) |
RP11-305L7.3::RP11-305L7.1 | +/+ | RP11-305L7.3 | RP11-305L7.1 | 9:91163005 | 9:91106671 | RefSeq | 1/10 (#13) | 10/27 | 8/12 | 3/14 | 1/20 | BLCA (1/20), BRCA (1/20), SKCM (1/20) |
RP11-556E13.1::RP11-346D6.6 | +/+ | RP11-556E13.1 | RP11-346D6.6 | 10:52561006 | 10:52463332 | 1/10 (#11) | 9/27 | 2/12 | 0/14 | 0/20 | LUAD (1/20), SKCM (1/20) | |
OPN4::LDB3 | +/+ | OPN4 | LDB3 | 10:86666848 | 10:86668669 | GenBank, RefSeq | 1/10 (#16) | 0/27 | 0/12 | 0/14 | 2/20 | BRCA (1/20), CESC (1/20), KIRC (6/20), LGG (9/20), SKCM (1/20) |
C14orf37::RP11-999E24.3 | +/+ | C14orf37 | RP11-999E24.3 | 14:58003907 | 14:57994417 | RefSeq | 1/10 (#13) | 2/27 | 0/12 | 0/14 | 0/20 | KIRC (1/20), LGG (1/20) |
RP11-1360M22.11::RP11-810K23.8 | +/+ | RP11-1360M22.11 | RP11-810K23.8 | 15:20012876 | 15:21019524 | - | 1/10 (#13) | 5/27 | 3/12 | 4/14 | 0/20 | KIRC (1/20), LGG (1/20) |
IGF1R::RP11-35O15.2 | +/+ | IGF1R | RP11-35O15.2 | 15:98649675 | 15:98660230 | GenBank | 2/10 (#6,#7) | 8/27 | 3/12 | 0/14 | 3/20 | BRCA (1/20), CESC (2/20), LGG (1/20) |
NHLRC4::PIGQ | +/+ | NHLRC4 | PIGQ | 16:568989 | 16:574066 | Ensembl, UCSC, Vega, ConjoinG, FusionHub | 2/10 (#7,#8) | 12/27 | 7/12 | 6/14 | 10/20 | BRCA (2/20), COAD (2/20), KIRC (1/20) |
MAPK3::GDPD3 | +/+ | MAPK3 | GDPD3 | 16:30114203 | 16:30113437 | - | 1/10 (#11) | 10/27 | 5/12 | 4/14 | 4/20 | BRCA (1/20), LGG (1/20) |
TRAPPC1::KCNAB3 | +/+ | TRAPPC1 | KCNAB3 | 17:7930527 | 17:7927826 | ConjoinG, FusionHub | 1/10 (#11) | 0/27 | 1/12 | 2/14 | 0/20 | CESC (2/20) |
Conjoined Genes | Gene Orientation * | 5′ Gene | 3′ Gene | 5′ Breakpoint | 3′ Breakpoint | Annotation | Our ALL Cohort (Case Id#) | AML ** | T-ALL (Leucegene) ** | T-ALL (COG) ** | B-ALL ** |
---|---|---|---|---|---|---|---|---|---|---|---|
CTB-26E19.1::COL23A1 | +/+ | CTB-26E19.1 | COL23A1 | 5:178442931 | 5:178306919 | - | 1/10 (#11) | 2/27 | 7/12 | 7/14 | 3/20 |
SURF1::MED22 | +/+ | SURF1 | MED22 | 9:133351836 | 9:133345252 | - | 2/10 (#6,#7) | 1/27 | 2/12 | 0/14 | 0/20 |
SURF1::MED22 | +/+ | SURF1 | MED22 | 9:133351836 | 9:133346700 | - | 1/10 (#13) | 6/27 | 4/12 | 0/14 | 1/20 |
CACUL1::RP11-427L15.2 | +/+ | CACUL1 | RP11-427L15.2 | 10:118693702 | 10:118692438 | - | 2/10 (#7,#11) | 3/27 | 1/12 | 0/14 | 1/20 |
TMEM86A::RP11-1081L13.4 | +/+ | TMEM86A | RP11-1081L13.4 | 11:18702116 | 11:18706818 | - | 1/10 (#7) | 1/27 | 1/12 | 1/14 | 0/20 |
RP11-20D14.3::RIMKLB | +/+ | RP11-20D14.3 | RIMKLB | 12:8668831 | 12:8713811 | - | 9/10 (#6,#7,#9,#8,#11,#12,#13,#15,#16) | 17/27 | 1/12 | 1/14 | 16/20 |
RP11-397H6.1::RP11-541G9.1 | +/+ | RP11-397H6.1 | RP11-541G9.1 | 12:97033423 | 12:97185076 | - | 1/10 (#13) | 0/27 | 0/12 | 0/14 | 0/20 |
CCPG1::PIGBOS1 | +/+ | CCPG1 | PIGBOS1 | 15:55355634 | 15:55317867 | - | 2/10 (#6,#13) | 14/27 | 2/12 | 6/14 | 0/20 |
AC019118.3::AC019118.2 | +/+ | AC019118.3 | AC019118.2 | 2:3145547 | 2:2966675 | - | 2/10 (#14,#16) | 0/27 | 1/12 | 0/14 | 4/20 |
RP11-87G24.3::RP11-87G24.6 | +/+ | RP11-87G24.3 | RP11-87G24.6 | 17:76963893 | 17:76957657 | - | 6/10 (#7,#8,#12,#13,#14,#16) | 3/27 | 9/12 | 6/14 | 6/20 |
KLHL22::SCARF2 | +/+ | KLHL22 | SCARF2 | 22:20446443 | 22:20430557 | Ensembl, UCSC, Vega, ConjoinG, FusionHub | 4/10 (#9,#12,#13,#15) | 14/27 | 8/12 | 5/14 | 4/20 |
PPP1R3F::LL0XNC01-7P3.1 | +/+ | PPP1R3F | LL0XNC01-7P3.1 | X:49270873 | X:49273514 | GenBank | 1/10 (#7) | 2/27 | 0/12 | 0/14 | 0/20 |
MYNN::RP11-362K14.7 | +/+ | MYNN | RP11-362K14.7 | 3:169786730 | 3:169793627 | - | 2/10 (#8,#14) | 8/27 | 4/12 | 4/14 | 0/20 |
FAM200B::BST1 | +/+ | FAM200B | BST1 | 4:15687148 | 4:15711807 | RefSeq | 2/10 (#13,#14) | 3/27 | 2/12 | 0/14 | 0/20 |
Fusions | Gene Orientation * | 5′ Gene | 3′ Gene | 5′ Breakpoint | 3′ Breakpoint | Annotation | Our ALL Cohort (Case ID#) | AML ** | T-ALL (Leucegene) ** | T-ALL (COG) ** | B-ALL ** |
---|---|---|---|---|---|---|---|---|---|---|---|
IK::FBXW2 | +/− | IK | FBXW2 | 5:140659164 | 9:120792947 | - | 1/10 (#13) | 0/27 | 0/12 | 0/14 | 0/20 |
ZNF444::HLA-B | +/− | ZNF444 | HLA-B | 19:56160570 | 6:31355372 | - | 1/10 (#9) | 1/27 | 3/12 | 0/14 | 0/20 |
PAX5::POM121C | +/+ | PAX5 | POM121C | 9:36966549 | 7:75441583 | - | 1/10 (#6) | 0/27 | 0/12 | 0/14 | 0/20 |
NFX1::DICER1 | +/− | NFX1 | DICER1 | 9:33290597 | 14:95141748 | - | 1/10 (#9) | 0/27 | 0/12 | 0/14 | 0/20 |
DCAF8::ZNF836 | −/− | DCAF8 | ZNF836 | 1:160220067 | 19:52156511 | - | 1/10 (#14) | 0/27 | 0/12 | 0/14 | 0/20 |
DMD::STAMBPL1 | −/+ | DMD | STAMBPL1 | X:32216916 | 10:88893871 | - | 1/10 (#13) | 0/27 | 0/12 | 0/14 | 0/20 |
SLFNL1::SMPD2 | −/+ | SLFNL1 | SMPD2 | 1:41022123 | 6:109441113 | - | 1/10 (#16) | 0/27 | 0/12 | 0/14 | 0/20 |
RP11-148O21.2::ATG4B | −/+ | RP11-148O21.2 | ATG4B | 8:11558702 | 2:241672559 | - | 1/10 (#7) | 0/27 | 0/12 | 0/14 | 0/20 |
TMEM263::CD47 | +/− | TMEM263 | CD47 | 12:106971137 | 3:108055566 | - | 1/10 (#11) | 0/27 | 0/12 | 0/14 | 0/20 |
INPP5A::SETD7 | +/− | INPP5A | SETD7 | 10:132607956 | 4:139548119 | - | 1/10 (#7) | 0/27 | 0/12 | 0/14 | 0/20 |
ZC3H12D::RP11-445F6.2 | −/+ | ZC3H12D | RP11-445F6.2 | 6:149456666 | 6:139271659 | - | 1/10 (#14) | 0/27 | 0/12 | 0/14 | 0/20 |
NUP214::ABL1 | −/− | NUP214 | ABL1 | 9:131230769 | 9:130854801 | FusionHub, Atlas Genetics Oncology | 1/10 (#16) | 0/27 | 0/12 | 0/14 | 0/20 |
MAML2::FAT3 | −/+ | MAML2 | FAT3 | 11:96091892 | 11:92352096 | - | 1/10 (#15) | 0/27 | 0/12 | 0/14 | 0/20 |
MNT::CLUH | −/− | MNT | CLUH | 17:2400640 | 17:2704564 | - | 2/10 (#9,#11) | 3/27 | 2/12 | 0/14 | 0/20 |
TSKS::ARRDC2 | −/+ | TSKS | ARRDC2 | 19:49746470 | 19:18007338 | - | 1/10 (#11) | 0/27 | 0/12 | 0/14 | 0/20 |
MAEA::CTBP1 | +/− | MAEA | CTBP1 | 4:1289982 | 4:1238337 | FusionHub, Atlas Genetics Oncology | 2/10 (#7,#12) | 9/27 | 3/12 | 6/14 | 2/20 |
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Severgnini, M.; D’Angiò, M.; Bungaro, S.; Cazzaniga, G.; Cifola, I.; Fazio, G. Conjoined Genes as Common Events in Childhood Acute Lymphoblastic Leukemia. Cancers 2022, 14, 3523. https://doi.org/10.3390/cancers14143523
Severgnini M, D’Angiò M, Bungaro S, Cazzaniga G, Cifola I, Fazio G. Conjoined Genes as Common Events in Childhood Acute Lymphoblastic Leukemia. Cancers. 2022; 14(14):3523. https://doi.org/10.3390/cancers14143523
Chicago/Turabian StyleSevergnini, Marco, Mariella D’Angiò, Silvia Bungaro, Giovanni Cazzaniga, Ingrid Cifola, and Grazia Fazio. 2022. "Conjoined Genes as Common Events in Childhood Acute Lymphoblastic Leukemia" Cancers 14, no. 14: 3523. https://doi.org/10.3390/cancers14143523