Genomic Alterations, Gene Expression Profiles and Functional Enrichment of Normal-Karyotype Acute Myeloid Leukaemia Based on Targeted Next-Generation Sequencing
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Patient Samples and Ethics Statement
2.2. Targeted DNA Sequencing Using Archer Dx
2.3. Sanger Sequencing
2.4. RNA Sequencing
2.5. Functional and Pathway Enrichment Analysis of Genes with Somatic Variants Using WEB-Based Gene Set Analysis Toolkit (WebGestalt) for Overrepresentation Analysis (ORA)
2.6. Statistical Analysis
3. Results
3.1. Demographic and Clinical Summary of Patients in This Study
3.2. Variants Discovered in This Study
3.3. Size of FLT3 Internal Tandem Duplication (ITD)
3.4. Evaluation of Somatic Variants Detected at Presentation and CR1/CR2
3.5. CEBPA Mutation and Gene Expression Profile
3.6. Functional and Pathway Enrichment Analysis of 26 Genes with Somatic Variants Using WebGestalt ORA Analysis
4. Discussion
Significance of the Study
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Patient Details | ||||||||
---|---|---|---|---|---|---|---|---|
DX1 | DX2 | DX3 | DX4 | DX5 | DX6 | DX7 | DX8 | |
Demographic data | ||||||||
Age | 31 | 29 | 54 | 55 | 36 | 49 | 45 | 21 |
Ethnicity | Malay | Malay | Indian | Malay | Chinese | Malay | Indian | Malay |
Gender | Female | Female | Female | Female | Female | Female | Male | Male |
No. of mutations | 3 | 3 | 1 | 1 | 1 | 3 | 1 | 5 |
Karyotype | ||||||||
G-banding | 46 (X,X) [19] | 46 (X,X) [19] | 46 (X,X) [19] | 46 (X,X) [19] | 46 (X,X) [19] | 46 (X,X) [19] | 46 (X,Y) [19] | 46 (X,Y) [19] |
Cell counts | ||||||||
White blood cell count (109/L) | 26.9 | 57.7 | 31.1 | 170 | 19.5 | 45.8 | 39.5 | 152.8 |
Haemoglobin (g/dL) | 7.3 | 8.1 | 8.1 | 8.4 | 11.3 | 7.9 | 9.9 | 6.1 |
Platelet (109/L) | 32 | 76 | 83 | 70 | 68 | 21 | 22 | 27 |
% Blast (PB) | 20% | 55% | 89% | 90% | 40% | 90% | 95% | 94% |
% Blast (BMA) | 90% | 80% | 90% | 92% | 90% | 96% | 90% | 95% |
Flow cytometry immunophenotyping | ||||||||
Aberrant antigen expression | CD2+ | CD2+ | - | CD56+ | CD2+ | - | - | - |
Gene mutations | ||||||||
Leukaemia Q-Fusion (30 fusion genes) | Negative | Negative | Negative | Negative | Negative | Negative | Negative | Negative |
FLT3-ITD | Detected | wt | wt | Detected | wt | Detected | Detected | wt |
NPM1 mutation | Detected | Detected | Detected | Detected | wt | Detected | Detected | wt |
Archer HGC VariantPlex Myeloid Panel | ||||||||
Genes with pathogenic/likely pathogenic somatic variants/ITD | CBL | CBL | IDH2 | TET2 | CEBPA | FLT3 | IDH1 | CEBPA |
DNMT3A | IDH1 | NPM1 | NPM1 | IDH2 | NPM1 | CUX1 | ||
RUNX1 | LUC7L2 | FLT3-ITD | U2AF2 | FLT3-ITD | GATA2 | |||
STAG2 | NPM1 | NPM1 | IDH1 | |||||
NPM1 | FLT3-ITD | LUC7L2 | ||||||
FLT3-ITD | WT1 | |||||||
FLT3-ITD insertion length (Archer HGC) | 42 | - | - | 45 | - | 54 | 144 | - |
Number of mutations per patients | 4 | 3 | 1 | 1 | 1 | 3 | 1 | 5 |
DEG | ||||||||
Upregulated genes | EZH2 | EZH2 | CUX1 | CUX1 | EZH2 | ANKRD26 | CUX1 | EZH2 |
FLT3 | FLT3 | FLT3 | ETV6 | CEBPA | CUX1 | FLT3 | CEBPA | |
HRAS | HRAS | GATA2 | FLT3 | CUX1 | FLT3 | GATA2 | CUX1 | |
IDH1 | LUC7L2 | LUC7L2 | GATA2 | DNMT3A | GATA2 | NPM1 | DNMT3A | |
NPM1 | NPM1 | NPM1 | LUC7L2 | FLT3 | LUC7L2 | RUNX1 | ETV6 | |
RUNX1 | SMC1A | RUNX1 | NPM1 | GATA2 | NPM1 | WT1 | FLT3 | |
U2AF2 | WT1 | RUNX1 | IDH1 | RUNX1 | GATA2 | |||
WT1 | NPM1 | SMC1A | IDH1 | |||||
WT1 | LUC7L2 | |||||||
NPM1 | ||||||||
Downregulated genes | ATRX | ATRX | CBL | CBL | CBL | CBL | CBL | TET2 |
CBL | CBL | NOTCH1 | NOTCH1 | NOTCH1 | NOTCH1 | KDM6A | STAG2 | |
KDM6A | KDM6A | PPM1D | PPM1D | PPM1D | PPM1D | NOTCH1 | RAD21 | |
NOTCH1 | NOTCH1 | RAD21 | RAD21 | RAD21 | RAD21 | PPM1D | PPM1D | |
PPM1D | PPM1D | STAG2 | STAG2 | STAG2 | STAG2 | RAD21 | NOTCH1 | |
RAD21 | RAD21 | TET2 | TET2 | TET2 | TET2 | STAG2 | KDM6A | |
STAG2 | STAG2 | TET2 | CBL | |||||
TET2 | TET2 | |||||||
ELN 2017 Classification | ||||||||
Prognosis | Intermediate | Good | Good | Intermediate | Good | Intermediate | Intermediate | Good |
Treatment Protocol | ||||||||
Induction | DA 3+7 | DA 3+7 | DA 3+7 | DA 3+7 | DA 3+7 | DA 3+7 | DA 3+7 | DA 3+7 |
Consolidation | MIDAC/HIDAC | HIDAC/HIDAC/HIDAC | MIDAC/HIDAC/FLAG | MIDAC/FLAG/HIDAC | MIDAC/HIDAC/ARAC | MIDAC/FLAG/FLAG | MIDAC/HIDAC/ARAC | FLAG-IDA/HIDAC/ARAC |
SCT | Nil | Nil | Nil | Allo-SCT after CR1 | Nil | Auto-SCT after CR1 | Allo-SCT after CR1 | Allo-SCT after CR2 |
Response to treatment | ||||||||
Remission status | CR1 | CR1 | CR1 | CR1 | CR1 | CR1 | CR1 | CR2 |
OS | >5 | >5 | >5 | >5 | >5 | >5 | >5 | >5 |
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Share and Cite
Ambayya, A.; Razali, R.; Sulong, S.; Zulkefli, E.S.; Yap, Y.Y.; Sathar, J.; Hassan, R. Genomic Alterations, Gene Expression Profiles and Functional Enrichment of Normal-Karyotype Acute Myeloid Leukaemia Based on Targeted Next-Generation Sequencing. Cancers 2023, 15, 1386. https://doi.org/10.3390/cancers15051386
Ambayya A, Razali R, Sulong S, Zulkefli ES, Yap YY, Sathar J, Hassan R. Genomic Alterations, Gene Expression Profiles and Functional Enrichment of Normal-Karyotype Acute Myeloid Leukaemia Based on Targeted Next-Generation Sequencing. Cancers. 2023; 15(5):1386. https://doi.org/10.3390/cancers15051386
Chicago/Turabian StyleAmbayya, Angeli, Rozaimi Razali, Sarina Sulong, Ezzanie Suffya Zulkefli, Yee Yee Yap, Jameela Sathar, and Rosline Hassan. 2023. "Genomic Alterations, Gene Expression Profiles and Functional Enrichment of Normal-Karyotype Acute Myeloid Leukaemia Based on Targeted Next-Generation Sequencing" Cancers 15, no. 5: 1386. https://doi.org/10.3390/cancers15051386