The clinical relevance of inosine triphosphate pyrophosphohydrolase(Itpa) genotypes in pediatric acute lymphoblastic leukemia

Genomic studies of pediatric acute lymphoblastic leukemia (ALL) have shown remarkable heterogeneity in initial diagnosis, with multiple (sub)clones harboring lesions in relapse-associated genes. However, the clinical relevance of these subclonal alterations remains unclear. We assessed the clinical relevance and prognostic value of subclonal alterations in the relapse-associated genes IKZF1, CREBBP, KRAS, NRAS, PTPN11, TP53, NT5C2, and WHSC1 in 503 ALL cases. Using Molecular Inversion Probe sequencing and breakpoint-spanning PCR we reliably detected alterations below 1% allele frequency. We identified 660 genomic alterations in 285 diagnosis samples of which 495 (75%) were subclonal. RAS pathway mutations were common, particularly in minor subclones, and comparisons between RAS hotspot mutations revealed differences in their capacity to drive clonal expansion in ALL. We did not find an association of subclonal alterations with unfavorable outcome. Particularly for IKZF1, an established prognostic marker in ALL, all clonal but none of the subclonal alterations were preserved at relapse. We conclude that, for the genes tested, there is no basis to consider subclonal alterations detected at diagnosis for risk group stratification of ALL treatment.

Download Full-text

Faculty Opinions recommendation of Epigenetics in pediatric acute lymphoblastic leukemia.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.731120594.793548064 ◽

2018 ◽

Author(s):

Kenneth Ramos

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Lymphoblastic Leukemia ◽

Pediatric Acute Lymphoblastic Leukemia

Download Full-text

Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia

Scientific Reports ◽

10.1038/s41598-021-95109-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shumaila Sayyab ◽

Anders Lundmark ◽

Malin Larsson ◽

Markus Ringnér ◽

Sara Nystedt ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Large Scale ◽

Somatic Mutations ◽

Lymphoblastic Leukemia ◽

Clonal Evolution ◽

Point Mutations ◽

Driver Genes ◽

Protein Coding ◽

Pediatric Acute Lymphoblastic Leukemia ◽

Evolutionary Trajectories

AbstractThe mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.

Download Full-text

Pediatric acute lymphoblastic leukemia complicated by secondary hemophagocytic lymphohistiocytosis

Pediatric Blood & Cancer ◽

10.1002/pbc.22064 ◽

2009 ◽

Vol 53 (3) ◽

pp. 491-492 ◽

Cited By ~ 14

Author(s):

Omer Devecioglu ◽

Sema Anak ◽

Didem Atay ◽

Pinar Aktan ◽

Esra Devecioglu ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Hemophagocytic Lymphohistiocytosis ◽

Lymphoblastic Leukemia ◽

Pediatric Acute Lymphoblastic Leukemia ◽

Secondary Hemophagocytic Lymphohistiocytosis

Download Full-text

Advances in the Diagnosis and Treatment of Pediatric Acute Lymphoblastic Leukemia

Journal of Clinical Medicine ◽

10.3390/jcm10091926 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1926

Author(s):

Hiroto Inaba ◽

Ching-Hon Pui

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Detailed Analysis ◽

Residual Disease ◽

Lymphoblastic Leukemia ◽

Survival Rates ◽

Treatment Strategies ◽

Chemotherapeutic Agents ◽

Response To Treatment ◽

Pediatric Acute Lymphoblastic Leukemia ◽

Therapeutic Implications

The outcomes of pediatric acute lymphoblastic leukemia (ALL) have improved remarkably during the last five decades. Such improvements were made possible by the incorporation of new diagnostic technologies, the effective administration of conventional chemotherapeutic agents, and the provision of better supportive care. With the 5-year survival rates now exceeding 90% in high-income countries, the goal for the next decade is to improve survival further toward 100% and to minimize treatment-related adverse effects. Based on genome-wide analyses, especially RNA-sequencing analyses, ALL can be classified into more than 20 B-lineage subtypes and more than 10 T-lineage subtypes with prognostic and therapeutic implications. Response to treatment is another critical prognostic factor, and detailed analysis of minimal residual disease can detect levels as low as one ALL cell among 1 million total cells. Such detailed analysis can facilitate the rational use of molecular targeted therapy and immunotherapy, which have emerged as new treatment strategies that can replace or reduce the use of conventional chemotherapy.

Download Full-text

Unravelling the Sequential Interplay of Mutational Mechanisms during Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia

Genes ◽

10.3390/genes12020214 ◽

2021 ◽

Vol 12 (2) ◽

pp. 214

Author(s):

Željko Antić ◽

Stefan H. Lelieveld ◽

Cédric G. van der Ham ◽

Edwin Sonneveld ◽

Peter M. Hoogerbrugge ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

De Novo ◽

Lymphoblastic Leukemia ◽

Clonal Evolution ◽

Leukemic Cells ◽

Proliferative Potential ◽

Disease Evolution ◽

Pediatric Acute Lymphoblastic Leukemia ◽

First Relapse ◽

Mutational Processes

Pediatric acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and is characterized by clonal heterogeneity. Genomic mutations can increase proliferative potential of leukemic cells and cause treatment resistance. However, mechanisms driving mutagenesis and clonal diversification in ALL are not fully understood. In this proof of principle study, we performed whole genome sequencing of two cases with multiple relapses in order to investigate whether groups of mutations separated in time show distinct mutational signatures. Based on mutation allele frequencies at diagnosis and subsequent relapses, we clustered mutations into groups and performed cluster-specific mutational profile analysis and de novo signature extraction. In patient 1, who experienced two relapses, the analysis unraveled a continuous interplay of aberrant activation induced cytidine deaminase (AID)/apolipoprotein B editing complex (APOBEC) activity. The associated signatures SBS2 and SBS13 were present already at diagnosis, and although emerging mutations were lost in later relapses, the process remained active throughout disease evolution. Patient 2 had three relapses. We identified episodic mutational processes at diagnosis and first relapse leading to mutations resembling ultraviolet light-driven DNA damage, and thiopurine-associated damage at first relapse. In conclusion, our data shows that investigation of mutational processes in clusters separated in time may aid in understanding the mutational mechanisms and discovery of underlying causes.

Download Full-text