Genetic abnormalities associated with acute lymphoblastic leukemia

A newly identified gene Ahed plays essential roles in murine haematopoiesis

The development of haematopoiesis involves the coordinated action of numerous genes, some of which are implicated in haematological malignancies. However, the biological function of many genes remains elusive and unknown functional genes are likely to remain to be uncovered. Here, we report a previously uncharacterised gene in haematopoiesis, identified by screening mutant embryonic stem cells. The gene, 'attenuated haematopoietic development (Ahed)', encodes a nuclear protein. Conditional knockout (cKO) of Ahed results in anaemia from embryonic day 14.5 onward, leading to prenatal demise. Transplantation experiments demonstrate the incapacity of Ahed-deficient haematopoietic cells to reconstitute haematopoiesis in vivo. Employing a tamoxifen-inducible cKO model, we further reveal that Ahed deletion impairs the intrinsic capacity of haematopoietic cells in adult mice. Ahed deletion affects various pathways, and published databases present cancer patients with somatic mutations in Ahed. Collectively, our findings underscore the fundamental roles of Ahed in lifelong haematopoiesis, implicating its association with malignancies.

Integrated systems biology analysis of acute lymphoblastic leukemia: unveiling molecular signatures and drug repurposing opportunities

Acute lymphoblastic leukemia (ALL) is a hematological malignancy characterized by aberrant proliferation and accumulation of lymphoid precursor cells within the bone marrow. The tyrosine kinase inhibitor (TKI), imatinib mesylate, has played a significant role in the treatment of Philadelphia chromosome-positive ALL (Ph + ALL). However, the achievement of durable and sustained therapeutic success remains a challenge due to the development of TKI resistance during the clinical course.The primary objective of this investigation is to propose a novel and efficacious treatment approach through drug repositioning, targeting ALL and its Ph + subtype by identifying and addressing differentially expressed genes (DEGs). This study involves a comprehensive analysis of transcriptome datasets pertaining to ALL and Ph + ALL in order to identify DEGs associated with the progression of these diseases to identify possible repurposable drugs that target identified hub proteins.The outcomes of this research have unveiled 698 disease-related DEGs for ALL and 100 for Ph + ALL. Furthermore, a subset of drugs, specifically glipizide for Ph + ALL, and maytansine and isoprenaline for ALL, have been identified as potential candidates for therapeutic intervention. Subsequently, cytotoxicity assessments were performed to confirm the in vitro cytotoxic effects of these selected drugs on both ALL and Ph + ALL cell lines.In conclusion, this study offers a promising avenue for the management of ALL and Ph + ALL through drug repurposed drugs. Further investigations are necessary to elucidate the mechanisms underlying cell death, and clinical trials are recommended to validate the promising results obtained through drug repositioning strategies.

A Bayesian quantile joint modeling of multivariate longitudinal and time-to-event data

Linear mixed models are traditionally used for jointly modeling (multivariate) longitudinal outcomes and event-time(s). However, when the outcomes are non-Gaussian a quantile regression model is more appropriate. In addition, in the presence of some time-varying covariates, it might be of interest to see how the effects of different covariates vary from one quantile level (of outcomes) to the other, and consequently how the event-time changes across different quantiles. For such analyses linear quantile mixed models can be used, and an efficient computational algorithm can be developed. We analyze a dataset from the Acute Lymphocytic Leukemia (ALL) maintenance study conducted by Tata Medical Center, Kolkata. In this study, the patients suffering from ALL were treated with two standard drugs (6MP and MTx) for the first two years, and three biomarkers (e.g. lymphocyte count, neutrophil count and platelet count) were longitudinally measured. After treatment the patients were followed nearly for the next three years, and the relapse-time (if any) for each patient was recorded. For this dataset we develop a Bayesian quantile joint model for the three longitudinal biomarkers and time-to-relapse. We consider an Asymmetric Laplace Distribution (ALD) for each outcome, and exploit the mixture representation of the ALD for developing a Gibbs sampler algorithm to estimate the regression coefficients. Our proposed model allows different quantile levels for different biomarkers, but still simultaneously estimates the regression coefficients corresponding to a particular quantile combination. We infer that a higher lymphocyte count accelerates the chance of a relapse while a higher neutrophil count and a higher platelet count (jointly) reduce it. Also, we infer that across (almost) all quantiles 6MP reduces the lymphocyte count, while MTx increases the neutrophil count. Simulation studies are performed to assess the effectiveness of the proposed approach.

A Bayesian joint model for multivariate longitudinal and time-to-event data with application to ALL maintenance studies

The most common type of cancer diagnosed among children is the Acute Lymphocytic Leukemia (ALL). A study was conducted by Tata Translational Cancer Research Center (TTCRC) Kolkata, in which 236 children (diagnosed as ALL patients) were treated for the first two years (approximately) with two standard drugs (6MP and MTx) and were then followed nearly for the next 3 years. The goal is to identify the longitudinal biomarkers that are associated with time-to-relapse, and also to assess the effectiveness of the drugs. We develop a Bayesian joint model in which a linear mixed model is used to jointly model three biomarkers (i.e. white blood cell count, neutrophil count, and platelet count) and a semi-parametric proportional hazards model is used to model the time-to-relapse. Our proposed joint model can assess the effects of different covariates on the progression of the biomarkers, and the effects of the biomarkers (and the covariates) on time-to-relapse. In addition, the proposed joint model can impute the missing longitudinal biomarkers efficiently. Our analysis shows that the white blood cell (WBC) count is not associated with time-to-relapse, but the neutrophil count and the platelet count are significantly associated with it. We also infer that a lower dose of 6MP and a higher dose of MTx jointly result in a lower relapse probability in the follow-up period. Interestingly, we find that relapse probability is the lowest for the patients classified into the "high-risk" group at presentation. The effectiveness of the proposed joint model is assessed through the extensive simulation studies.

The emerging role of microRNA-22 in the Leukemia: experimental and clinical implications

MicroRNAs (miRNAs) are short noncoding RNAs, approximately 20-24 nucleotides long that negatively regulate gene expression by either inhibiting translation or cleaving complementary mRNA to participate in various biological processes. Accumulating evidence has indicated that miRNAs are widely present in hematological cancers, particularly leukemia, exhibiting either upregulation or downregulation in leukemia patients compared with healthy controls. These miRNAs have a pivotal role in the development, progression and metastasis of leukemia, as well as in the prognosis and/or relapse of patients. miR-22 is one of the abnormally expressed miRNAs in a variety of leukemia diseases, and is considered to be one of the few cancer suppressors. Recent research has demonstrated that miR-22 is involved in the regulation of leukemia cell proliferation, differentiation and apoptosis, and could be a promising biomarker and prognostic indicator for leukemia. Here, we summarize all relevant findings that carry out experimental investigation and clinical analyses, aiming to elucidate the comprehensive implications of miR-22 in various types of leukemia for the development of new therapeutic and prognostic strategies and new drug targets for the treatment of leukemia.

Immuno-Stimulating Activity of 1,25-Dihydroxyvitamin D in Blood Cells from Five Healthy People and in Blasts from Five Patients with Leukemias and Pre-Leukemic States

(1) Hematological malignancies are characterized by an immortalization, uncontrolled proliferation of blood cells and their differentiation block, followed by the loss of function. The primary goal in the treatment of leukemias is the elimination of rapidly proliferating leukemic cells (named blasts). However, chemotherapy, which removes proliferating blasts, also prevents the remaining immune cells from being activated. Acute leukemias affect elderly people, who are often not fit to survive aggressive chemotherapy. Therefore, there is a need of milder treatment, named differentiation therapy, which might simulate the immune system of the patient. 1,25-Dihydroxyvitamin D, or low-calcemic analogs of this compound, were proposed as supporting therapy in acute leukemias. (2) Bone marrow blasts from patients with hematological malignancies, and leukocytes from healthy volunteers were ex vivo exposed to 1,25-dihydroxyvitamin D, and then their genomes and transcriptomes were investigated. (3) Our analysis indicates that 1,25-dihydroxyvitamin D regulates in blood cells predominantly genes involved in immune response, such as CAMP (cathelicidin antimicrobial peptide), CP (ceruloplasmin), CXCL9 (C-X-C motif chemokine ligand 9), CD14 (CD14 molecule) or VMO1 (vitelline membrane outer layer 1 homolog). This concerns blood cells from healthy people, as well as blasts from patients with hematological malignancies. In addition, in one patient, 1,25-dihydroxyvitamin D significantly downregulated transcription of genes responsible for cell division and immortalization. (4) In conclusion, the data presented in this paper suggest that addition of 1,25-dihydroxyvitamin D to the currently available treatments would stimulate immune system, inhibit proliferation and reduce immortal potential of blasts.

A Bayesian joint model for multivariate longitudinal and time-to-event data with application to ALL maintenance studies

The most common type of cancer diagnosed among children is the acute lymphocytic leukemia (ALL). A study was conducted by Tata Translational Cancer Research Center (TTCRC) Kolkata, in which 236 children (diagnosed as ALL patients) were treated for the first two years (approximately) with two standard drugs (6MP and MTx) and were then followed nearly for the next three years. The goal is to identify the longitudinal biomarkers that are associated with time-to-relapse, and also to assess the effectiveness of the drugs. We develop a Bayesian joint model in which a linear mixed model is used to jointly model three biomarkers (i.e. white blood cell count, neutrophil count, and platelet count) and a semi-parametric proportional hazards model is used to model the time-to-relapse. Our proposed joint model can assess the effects of different covariates on the progression of the biomarkers, and the effects of the biomarkers (and the covariates) on time-to-relapse. In addition, the proposed joint model can impute the missing longitudinal biomarkers efficiently. Our analysis shows that the white blood cell (WBC) count is not associated with time-to-relapse, but the neutrophil count and the platelet count are significantly associated with it. We also infer that a lower dose of 6MP and a higher dose of MTx jointly result in a lower relapse probability in the follow-up period. Interestingly, we find that relapse probability is the lowest for the patients classified into the "high-risk" group at presentation. The effectiveness of the proposed joint model is assessed through the extensive simulation studies.

Meta-analysis of the Prognostic Value of microRNA-22 in Leukemia Patients

Objective: The pathogenesis of leukemia is complex and there are no effective diagnostic and prognostic indicators. Previous studies showed that microRNA-22 (miR-22) has altered expression level in multiple leukemia subtypes, which is associated with the survival outcomes of leukemia. Methods: According to the constituted retrieval strategy, eligible studies were included from January 2010 to November 2022 by searching database. The pooled Risk Ratio (RR) and 95% confidence intervals (CI) were used to study the relationship between miR-22 and survival. Stata12.0 was used for meta-analysis. Differential expression analysis was conducted based on expression profile of miRNA. Results: Four English articles were included containing a total of 215 leukemia patients. Data showed that the pooled RR for overall survival (OS) was 1.558 (95% CI: 1.197-2.028, P < .01). Subgroup analysis for OS of acute myeloid leukemia patients and the RFS of plasma cell leukemia patients were statistically significant with different expression levels of miR-22 (RR:1.495, 95%CI:1.141-1.958, P < .01 and RR:1.517, 95%CI:1.114-2.065, P < .01, respectively). Moreover, all data included had no significant heterogeneity and publication bias. Conclusions: miR-22 is associated with the survival outcome of leukemia patients suggesting that miR-22 may be a promising prognostic biomarker for this patient population, and the expression level of miR-22 in ALL patients down-regulated.

Emerging roles of circRNAs in leukemia and the clinical prospects: An update

BACKGROUND

Circular RNAs (circRNAs) are a new category of endogenous non-protein coding RNAs (ncRNAs), and show the characteristics of high conservation, stability, and tissue specificity. Due to rapid advances in next-generation sequencing and transcriptome profiling technologies, circRNAs have been widely discovered in many organisms and participated in the development and progress of a variety of diseases. As a type of molecular sponge, circRNAs mainly absorb micro RNAs competitively and interplay with RNA-binding proteins to modulate the splicing as well as transcription of target genes.

METHODS

This review is based on a literature search using the Medline database. Search terms used were "circular RNAs and leukemia," "circRNAs and leukemia," "circRNAs and acute lymphoblastic leukemia," "circRNAs and chronic lymphoblastic leukemia," "circRNAs and acute myeloid leukemia," "circRNAs and chronic myeloid leukemia," and "circRNAs, biomarker, and hematological system."

RESULTS

CircRNAs have been proven as potential biomarkers and therapeutic targets in a variety of tumors. Recent research has found that circRNAs aberrantly exist in hematological cancers, especially leukemia, and are significantly associated with the incidence, progress, and metastasis of diseases as well as the prognosis of patients.

CONCLUSION

The current work summarizes the latest findings on circRNAs in various types of leukemia, aiming to propose prospective therapies and new drug screening methods for the treatment of leukemia.

KCTD15 deregulation is associated with alterations of the NF-κB signaling in both pathological and physiological model systems

Like other KCTD proteins, KCTD15 is involved in important albeit distinct biological processes as cancer, neural crest formation, and obesity. Here, we characterized the role of KCTD15 in different physiological/pathological states to gain insights into its diversified function(s). The silencing of KCTD15 in MLL-rearranged leukemia models induced attenuation of the NF-κB pathway associated with a downregulation of pIKK-β and pIKB-α. Conversely, the activation of peripheral blood T cells upon PMA/ionomycin stimulation remarkably upregulated KCTD15 and, simultaneously, pIKK-β and pIKB-α. Moreover, a significant upregulation of KCTD15 was also observed in CD34 hematopoietic stem/progenitor cells where the NF-κB pathway is physiologically activated. The association between KCTD15 upregulation and increased NF-κB signaling was confirmed by luciferase assay as well as KCTD15 and IKK-β proximity ligation and immunoprecipitation experiments. The observed upregulation of IKK-β by KCTD15 provides a novel and intriguing interpretative key for understanding the protein function in a wide class of physiological/pathological conditions ranging from neuronal development to cancer and obesity/diabetes.

TYK2 in Cancer Metastases: Genomic and Proteomic Discovery

Simple Summary

Cancer deaths are predominantly due to metastases rather than the primary tumors, and thus there is an urgent need for the discovery of more effective drug therapies for metastatic cancer. Recent genomics, transcriptomics, and proteomics studies have identified tyrosine kinase 2 (TYK2) as an oncogene that is frequently mutated or overexpressed in many types of cancer and metastases. A member of the Janus kinase (JAK) family, TYK2 mediates the signals of numerous cytokines involved in immune and inflammatory signaling. In cancer cells, activation of TYK2 can lead to decreased cell death as well as increased cell growth and invasion. Multiple drugs that specifically block TYK2 or JAKs are currently FDA-approved or in clinical trials. In this review, we provide an overview of the screening, molecular, and animal studies that have characterized the role of TYK2 in cancer and metastases, and the potential of TYK2 inhibitors as effective cancer therapies.

Abstract

Advances in genomic analysis and proteomic tools have rapidly expanded identification of biomarkers and molecular targets important to cancer development and metastasis. On an individual basis, personalized medicine approaches allow better characterization of tumors and patient prognosis, leading to more targeted treatments by detection of specific gene mutations, overexpression, or activity. Genomic and proteomic screens by our lab and others have revealed tyrosine kinase 2 (TYK2) as an oncogene promoting progression and metastases of many types of carcinomas, sarcomas, and hematologic cancers. TYK2 is a Janus kinase (JAK) that acts as an intermediary between cytokine receptors and STAT transcription factors. TYK2 signals to stimulate proliferation and metastasis while inhibiting apoptosis of cancer cells. This review focuses on the growing evidence from genomic and proteomic screens, as well as molecular studies that link TYK2 to cancer prevalence, prognosis, and metastasis. In addition, pharmacological inhibition of TYK2 is currently used clinically for autoimmune diseases, and now provides promising treatment modalities as effective therapeutic agents against multiple types of cancer.

Dual targeting of MTOR as a novel therapeutic approach for high-risk B-cell acute lymphoblastic leukemia

Children of Hispanic/Latino ancestry have increased incidence of high-risk B-cell acute lymphoblastic leukemia (HR B-ALL) with poor prognosis. This leukemia is characterized by a single-copy deletion of the IKZF1 (IKAROS) tumor suppressor and increased activation of the PI3K/AKT/mTOR pathway. This identifies mTOR as an attractive therapeutic target in HR B-ALL. Here, we report that IKAROS represses MTOR transcription and IKAROS' ability to repress MTOR in leukemia is impaired by oncogenic CK2 kinase. Treatment with the CK2 inhibitor, CX-4945, enhances IKAROS activity as a repressor of MTOR, resulting in reduced expression of MTOR in HR B-ALL. Thus, we designed a novel therapeutic approach that implements dual targeting of mTOR: direct inhibition of the mTOR protein (with rapamycin), in combination with IKAROS-mediated transcriptional repression of the MTOR gene (using the CK2 inhibitor, CX-4945). Combination treatment with rapamycin and CX-4945 shows synergistic therapeutic effects in vitro and in patient-derived xenografts from Hispanic/Latino children with HR B-ALL. These data suggest that such therapy has the potential to reduce the health disparity in HR B-ALL among Hispanic/Latino children. The dual targeting of oncogene transcription, combined with inhibition of the corresponding oncoprotein provides a paradigm for a novel precision medicine approach for treating hematological malignancies.

Cancer incidence and survival trends among infants in the United States from 1975 to 2014

BACKGROUND

Cancer among infants (<1 year old) has unique epidemiologic, clinical, and genetic characteristics compared with cancer in older children. Nonetheless, data on secular trends in infant cancer incidence and survival in the United States is sparse.

METHODS

Population-based data from nine areas of the Surveillance Epidemiology and End Results (SEER) were used to estimate the incidence, average annual percentage change (APC) for trends, and survival of malignant neoplasm among infants from 1975 to 2014. Data were stratified by gender, race, registry, and cancer type.

RESULTS

There were 3437 new infant cancer cases with an overall incidence of 23.6/100 000. Neuroblastoma was the most common infant malignancy (6.5/100 000), followed by leukemia (3.8/100 000), and brain and central nervous system tumors (3.3/100 000). The incidence rate increased significantly from 1975 to 2014 (APC 0.68; 95% CI 0.30-1.06; P < .05). Variations in overall incidence rates were uneven across SEER registry geographic areas, with the lowest rates among both males and females in New Mexico. Relative to other racial distribution, infant cancer rates were highest among Whites. The relative survival rates improved over time for all tumors except for renal, sarcomas, and germ cells and were not significantly different by gender or race.

CONCLUSIONS

Cancer incidence among infants increased over time largely driven by leukemia, germ cell, and sarcoma mainly among male infants. The overall survival for infant cancer has improved over the past 40 years, especially since 1990 for hepatic tumors, lymphoma, and leukemia. Further research is needed to explore the potential impacts of genetic, environmental, and perinatal factors for possible explanations for these increased cancer incidence trends.

IKAROS and CK2 regulate expression of BCL-XL and chemosensitivity in high-risk B-cell acute lymphoblastic leukemia

High-risk B-cell acute lymphoblastic leukemia (B-ALL) is an aggressive disease, often characterized by resistance to chemotherapy. A frequent feature of high-risk B-ALL is loss of function of the IKAROS (encoded by the IKZF1 gene) tumor suppressor. Here, we report that IKAROS regulates expression of the BCL2L1 gene (encodes the BCL-XL protein) in human B-ALL. Gain-of-function and loss-of-function experiments demonstrate that IKAROS binds to the BCL2L1 promoter, recruits histone deacetylase HDAC1, and represses BCL2L1 expression via chromatin remodeling. In leukemia, IKAROS' function is impaired by oncogenic casein kinase II (CK2), which is overexpressed in B-ALL. Phosphorylation by CK2 reduces IKAROS binding and recruitment of HDAC1 to the BCL2L1 promoter. This results in a loss of IKAROS-mediated repression of BCL2L1 and increased expression of BCL-XL. Increased expression of BCL-XL and/or CK2, as well as reduced IKAROS expression, are associated with resistance to doxorubicin treatment. Molecular and pharmacological inhibition of CK2 with a specific inhibitor CX-4945, increases binding of IKAROS to the BCL2L1 promoter and enhances IKAROS-mediated repression of BCL2L1 in B-ALL. Treatment with CX-4945 increases sensitivity to doxorubicin in B-ALL, and reverses resistance to doxorubicin in multidrug-resistant B-ALL. Combination treatment with CX-4945 and doxorubicin show synergistic therapeutic effects in vitro and in preclinical models of high-risk B-ALL. Results reveal a novel signaling network that regulates chemoresistance in leukemia. These data lay the groundwork for clinical testing of a rationally designed, targeted therapy that combines the CK2 inhibitor, CX-4945, with doxorubicin for the treatment of hematopoietic malignancies.

High frequency of the risk allele of rs4132601 and rs11978267 from the IKZF1 gene in indigenous Mexican population

Background

IKZF1 is a relevant gene associated with the pathogenesis of acute lymphoblastic leukemia, and the rs4132601 (T>G) and rs11978267 (A>G) polymorphisms have been associated with the development of this disease in several populations. The aim of this study was to determine the allelic and genotypic frequencies of the rs4132601 and rs11978267 polymorphisms in two indigenous Mexican groups (Cora and Huichol) and Mestizo populations from Nayarit, Mexico, and compare them with the frequencies of both polymorphisms in other populations of the world.

Methods

One hundred, 116, and 100 subjects from the Mestizo, Huichol, and Cora populations, respectively, all of them residents of the state of Nayarit, Mexico, were analyzed. The frequencies of rs4132601 and rs11978267 were determined by allelic discrimination using TaqMan assays.

Results

The allelic frequencies of rs4132601 were as follows: Mestizo group T = 0.74, G = 0.26; Cora T = 0.745, G = 0.255; and Huichol T = 0.47, G = 0.53. In the case of the rs11978267 polymorphism, the allelic frequencies were Mestizo A = 0.745, G = 0.255; Cora A = 0.735, G = 0.265; and Huichol A = 0.457, G = 0.543. For each population, both polymorphisms were in Hardy–Weinberg equilibrium.

Conclusion

The Huichol population from Nayarit presented the highest frequencies of the risk allele reported to date in the whole world for both rs4132601 and rs11978267 polymorphisms.

Mutations Encountered in Acute Lymphoblastic Leukemia: A Retrospective Study in a Teaching Hospital in Jeddah, Saudi Arabia

Background

Acute lymphoblastic leukemia (ALL) is an invasive cancer that results from the malignant conversion and rapid replication of white blood cells and hematopoietic stem cells that supply multiple lymphocytes. Harmful gene mutations occur in more than two-thirds of patients with ALL; however, these mutations have not been extensively identified in Saudi Arabia.

Aim

The aim of this study was to identify the types of mutations in patients with ALL at King Abdulaziz University Hospital (KAUH) in Jeddah. In addition, we identified the most common mutations.

Methods

A retrospective study was performed on patients who were diagnosed with ALL from January 2009 to January 2019 at the Department of Hematology at KAUH. Our target population comprised patients diagnosed with ALL, including all age groups and both sexes. Patients were excluded if they had Down syndrome or central nervous system involvement, Li-Fraumeni syndrome, or neurofibromatosis.

Results

Of the 130 patients with ALL, 101 (77.77%) were children. The number of men (n=81) was substantially more than that of women (n=49). The data showed that 13.1% of our patients had mutations, and they occurred more frequently in patients with B-cell lymphoblastic ALL (B-ALL) than in those with T-cell lymphoblastic ALL (T-ALL). Several mutations, including BCR-ABL and ETV6/RUNX1, were more common in B-ALL, whereas the MLL-F0X04mutation was more commonly observed in T-ALL. There was a significant difference between the types of ALL and the genes involved (p=0.039). One female patient had translocation t(X;11)(q26;q23) (MLL-F0X04), which is a rare mutation.

Conclusion

In summary, 13.1% of our study population had mutations. The BCR-ABL fusion gene was the most frequent mutation in patients at KAUH, and it occurred at a higher rate in B-ALL. Moreover, we detected other mutations, such as ETV6/RUNX1 and MLL-F0X04. The gene mutations were significantly different between B-ALL and T-ALL.

Clinical value of RAG1 expression and IKZF1 deletions in Philadelphia negative pediatric B cell precursor acute lymphoblastic leukemia

This study aimed to address the clinical impact of recombination-activating gene (RAG1) expression and tumor suppressor IKZF1 gene deletions in Philadelphia negative B-cell precursor acute lymphoblastic leukemia (B-ALL) patients. Fifty newly diagnosed pediatric Philadelphia negative B-ALL patients were included in this study. Using Bone Marrow samples, RAG1 expression was assessed by real time PCR and IKZF1 deletions were determined by multiplex real-time quantitative PCR. The expression of RAG1 was significantly higher in B-ALL patients as compared to the controls (p < .001). The B-ALL patients with RAG1 high expression (≥median) had lower response to induction of remission, shorter DFS, shorter overall survival, higher blast cells, and white cell counts in the peripheral blood as compared to those with low RAG1 expression levels (p < .01 for all). Likewise, there was significant association between IKZF1 deletion and high RAG1 expression. Based on our findings RAG1 high expression and IKZF1 deletions were associated with adverse prognosis in Philadelphia negative B-ALL. RAG1 could be used as therapeutic target in the treatment of B-ALL.

A Case of Acute Lymphocytic Leukaemia with t(3;13) and Central Nervous System Leukemia after Allogenic Cord Blood Transplantation

Background:

Acute lymphoblastic leukemia (ALL) is a neoplastic cancer characterized by clonal expansion of leukemic cells in lymph organs and bone marrow. Lots of kinds of different chromosomal translocations can be found in those leukemic cells. However, the role of abnormal chromosomes and genes in leukemogenesis is not yet fully understood. Identifying new chromosomal translocations can facilitate a better understanding of pathogenesis of this disease.

Case presentation:

We report a rare case of acute lymphocytic leukaemia with t(3;13)(q29, q21). The patient was diagnosed pre-B-ALL with no abnormal chromosomal or gene fusion and achieved complete remission (CR) after induction chemotherapy; 10 months later, she relapsed in the consolidation, with cytogenetics tests showing 46, XX, t(3;13)(q29, q21). Given no CR after two chemotherapy regimens, the patient received salvage cord blood transplantation. Regular intrathecal methotrexate was applied to prevent central nervous system leukemia. Good graft versus leukemia was induced by daily injection of a low dose of IL-2 2 months post-transplantation. Minimal residual disease negativity was maintained until central nervous system (CNS) leukemia was found 8 months after transplantation. A whole exome sequencing was performed. Nine driver mutation genes and seven tumor genes were found.

Conclusions:

We highly suspect that the relapse in the CNS after transplantation is associated with a rare chromosomal translocation.

Observation of the molecular genetics among children with acute lymphoblastic leukemia: A retrospective study based on the SEER database

Acute lymphoblastic leukemia (ALL) is one of the most common malignancies of the hematologic system in children. Typically, ALL children with various genetic changes show different incidences, development, and prognoses. This study aimed to analyze the incidence of molecular genetic subtype among ALL children based on their clinical information, and to further investigate the relationship of genetic varieties with the prognostic factors.From 2010 to 2016, a total of 888 ALL children with TEL-AML1 fusion gene, hyperdiploidy, hypodiloidy, IL3-IGH rearranged, E2A PBX1 fusion gene, BCR-ABL1 fusion gene, or mixed lineage leukemia (MML) rearranged were selected and analyzed through the Surveillance, Epidemiology, and End Results database.Our results suggested that, ALL children who lived in the Northern Plains were more likely to experience genetic varieties. In addition, the TEL-AML1 fusion gene, hyperdiploidy, and hypodiloidy were more likely to be detected in ALL children aged 1 to 9 years, while MLL rearrangement was probably detected among ALL children aged <1 year. On the other hand, the 5-year overall survival varied depending on different regions (East: 42.21%; Alaska: 0.001%; Northern Plains: 1.8%; Pacific Coast: 16.3%; and Southwest: 8%), races (African American: 44.5%; white: 18.2%; and Other: 16.3%), and genetic features (TEL-AML1: 10.1%; hyperdiploidy: 19.4%; hypodiloidy: 64.7%; IL3-IGH: 0.01%; E2A PBX1: 14.2%; BCR-ABL1: 15.2%; MLL rearranged: 12.3%).In conclusion, our study found that genetic varieties among ALL children were closely related to their prognoses, and the detection rate of genetic molecules was associated with the age, race, and living area of children.

Evidence-based review of genomic aberrations in B-lymphoblastic leukemia/lymphoma: Report from the cancer genomics consortium working group for lymphoblastic leukemia

Clinical management and risk stratification of B-lymphoblastic leukemia/ lymphoma (B-ALL/LBL) depend largely on identification of chromosomal abnormalities obtained using conventional cytogenetics and Fluorescence In Situ Hybridization (FISH) testing. In the last few decades, testing algorithms have been implemented to support an optimal risk-oriented therapy, leading to a large improvement in overall survival. In addition, large scale genomic studies have identified multiple aberrations of prognostic significance that are not routinely tested by existing modalities. However, as chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) technologies are increasingly used in clinical management of hematologic malignancies, these abnormalities may be more readily detected. In this article, we have compiled a comprehensive, evidence-based review of the current B-ALL literature, focusing on known and published subtypes described to date. More specifically, we describe the role of various testing modalities in the diagnosis, prognosis, and therapeutic relevance. In addition, we propose a testing algorithm aimed at assisting laboratories in the most effective detection of the underlying genomic abnormalities.

Identification and Characterization of Novel Fusion Genes with Potential Clinical Applications in Mexican Children with Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia is the most common type of childhood cancer worldwide. Mexico City has one of the highest incidences and mortality rates of this cancer. It has previously been recognized that chromosomal translocations are important in cancer etiology. Specific fusion genes have been considered as important treatment targets in childhood acute lymphoblastic leukemia (ALL). The present research aimed at the identification and characterization of novel fusion genes with potential clinical implications in Mexican children with acute lymphoblastic leukemia. The RNA-sequencing approach was used. Four fusion genes not previously reported were identified: CREBBP-SRGAP2B, DNAH14-IKZF1, ETV6-SNUPN, ETV6-NUFIP1. Although a fusion gene is not sufficient to cause leukemia, it could be involved in the pathogenesis of the disease. Notably, these new translocations were found in genes encoding for hematopoietic transcription factors which are known to play an important role in leukemogenesis and disease prognosis such as IKZF1, CREBBP, and ETV6. In addition, they may have an impact on the prognosis of Mexican pediatric patients with ALL, with the potential to be included in the current risk stratification schemes or used as therapeutic targets.

Recent advances in the biology and treatment of B-cell acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is a hematologic malignancy arising from precursors of the lymphoid lineage. Conventional cytotoxic chemotherapies have resulted in high cure rates of up to 90% in pediatric ALL, but the outcomes for adult patients remain suboptimal with 5-year survival rates of only 30%-40%. Over the last decade, major advances have been made in our understanding and management of ALL. Identification of new prognostic genomic markers and incorporation of minimal residual diseases' assessment into therapeutic protocols have improved risk stratification and treatment strategies. The use of pediatric-inspired regimens for adolescent and young adults, and the advent of tyrosine kinase inhibitors and novel targeted therapies, including monoclonal antibodies and chimeric antigen receptor T cells, have redefined the therapeutic paradigm of ALL, and significantly improved the outcomes. In this article, we will provide an overview of the current knowledge regarding the biology and treatment of ALL, and highlight recent diagnostic and therapeutic advances made in this area over the past 5 years.

OncoKids: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies

The OncoKids panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 ng) and RNA (20 ng) and is compatible with formalin-fixed, paraffin-embedded and frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; and amplification events in 24 genes. The RNA content includes 1421 targeted gene fusions. We describe the validation of this panel by using a large cohort of 192 unique clinical samples that included a wide range of tumor types and alterations. Robust performance was observed for analytical sensitivity, reproducibility, and limit of detection studies. The results from this study support the use of OncoKids for routine clinical testing of a wide variety of pediatric malignancies.

Philadelphia chromosome-like acute lymphoblastic leukemia: A review of the genetic basis, clinical features, and therapeutic options

Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a recently identified high-risk subtype of B-lineage ALL (B-ALL), characterized by a gene expression profile similar to that of Philadelphia-positive (Ph+) ALL, but without the hallmark BCR-ABL1 oncoprotein. Ph-like ALL represents approximately 15% of childhood ALL and its frequency rises with age, peaking among adolescents, and young adults with B-ALL. This subtype is associated with adverse clinical features, persistence of minimal residual disease, and a poor prognosis despite modern chemotherapy regimens. While Ph-like ALL lacks the BCR-ABL1 fusion, it is characterized by a diverse spectrum of kinase fusions and cytokine receptor gene rearrangements that may be similarly amenable to molecularly targeted therapies. While survival rates for childhood ALL have drastically improved with intensive conventional chemotherapy, Ph-like ALL represents a novel paradigm of precision medicine in ALL. This review aims to provide a comprehensive review of the clinical picture and genetic basis of Ph-like ALL and to illustrate how these findings can translate into tailored targeted therapies with the hopes of improving the outcomes of Ph-like ALL patients.

New Challenges in Targeting Signaling Pathways in Acute Lymphoblastic Leukemia by NGS Approaches: An Update

The identification and study of genetic alterations involved in various signaling pathways associated with the pathogenesis of acute lymphoblastic leukemia (ALL) and the application of recent next-generation sequencing (NGS) in the identification of these lesions not only broaden our understanding of the involvement of various genetic alterations in the pathogenesis of the disease but also identify new therapeutic targets for future clinical trials. The present review describes the main deletions, amplifications, sequence mutations, epigenetic lesions, and new structural DNA rearrangements detected by NGS in B-ALL and T-ALL and their clinical importance for therapeutic procedures. We reviewed the molecular basis of pathways including transcriptional regulation, lymphoid differentiation and development, TP53 and the cell cycle, RAS signaling, JAK/STAT, NOTCH, PI3K/AKT/mTOR, Wnt/β-catenin signaling, chromatin structure modifiers, and epigenetic regulators. The implementation of NGS strategies has enabled important mutated genes in each pathway, their associations with the genetic subtypes of ALL, and their outcomes, which will be described further. We also discuss classic and new cryptic DNA rearrangements in ALL identified by mRNA-seq strategies. Novel cooperative abnormalities in ALL could be key prognostic and/or predictive biomarkers for selecting the best frontline treatment and for developing therapies after the first relapse or refractory disease.

Aberrant Wnt Signaling in Leukemia

The Wnt signaling pathway is essential in the development and homeostasis of blood and immune cells, but its exact role is still controversial and is the subject of intense research. The malignant counterpart of normal hematopoietic cells, leukemic (stem) cells, have hijacked the Wnt pathway for their self-renewal and proliferation. Here we review the multiple ways dysregulated Wnt signaling can contribute to leukemogenesis, both cell autonomously as well as by changes in the microenvironment.

Genetic abnormalities associated with acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) occurs with high frequency in childhood and is associated with high mortality in adults. Recent technical advances in next‐generation sequencing have shed light on genetic abnormalities in hematopoietic stem/progenitor cells as the precursor to ALL pathogenesis. Based on these genetic abnormalities, ALL is now being reclassified into newly identified subtypes. Philadelphia chromosome‐like B‐lineage ALL is one of the new high‐risk subtypes characterized by genetic alterations that activate various signaling pathways, including those involving cytokine receptors, tyrosine kinases, and epigenetic modifiers. Philadelphia chromosome‐like ALL is essentially heterogeneous; however, deletion mutations in the IKZF1 gene encoding the transcription factor IKAROS underlie many cases as a key factor inducing aggressive phenotypes and poor treatment responses. Whole‐genome sequencing studies of ALL patients and ethnically matched controls also identified inherited genetic variations in lymphoid neoplasm‐related genes, which are likely to increase ALL susceptibility. These findings are directly relevant to clinical hematology, and further studies on this aspect could contribute to accurate diagnosis, effective monitoring of residual disease, and patient‐oriented therapies.