High WBP5 expression correlates with elevation of HOX genes levels and is associated with inferior survival in patients with acute myeloid leukaemia

Preliminary study on molecular mechanism of COVID-19 intervention by Polygonum cuspidatum through computer bioinformatics

To explore the mechanism of action of Polygonum cuspidatum in intervening in coronavirus disease 2019 using a network pharmacology approach and to preliminarily elucidate its mechanism. The active ingredients and action targets of P cuspidatum were classified and summarized using computer virtual technology and molecular informatics methods. The active ingredients and relevant target information of P cuspidatum were identified using the TCM Systematic Pharmacology Database and Analysis Platform, the TCM Integrated Pharmacology Research Platform v2.0, and the SwissTarget database. The GENECARDS database was used to search for COVID-19 targets. The STRING database was analyzed and combined with Cytoscape 3.7.1 software to construct a protein interaction network map to screen the core targets. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was then performed. The core compound, polydatin, was selected and the core targets were analyzed by computer virtual docking using software such as discovery studio autodock tool. In vitro cell models were constructed to experimentally validate the activity of the core compound, polydatin. By computer screening, we identified 9 active ingredients and their corresponding 286 targets from P cuspidatum. A search of the GENECARDS database for COVID-19 yielded 303 core targets. By mapping the active ingredient targets to the disease targets, 27 overlapping targets could be extracted as potential targets for the treatment of COVID-19 with P cuspidatum. In addition, the enrichment analysis of Kyoto Encyclopedia of Genes and Genomes pathway on core targets showed that the coronavirus disease, MAPK signaling pathway, NF kappa B signaling pathway, and other signaling pathways were highly enriched. Combined with the degree-high target analysis in the protein interaction network, it was found to be mainly concentrated in the NF-kappaB (NF-κB) signaling pathway, indicating that the NF-κB signaling pathway may be an important pathway for P cuspidatum intervention. In vitro assays showed no effect of 0.1 to 10 μM polydatin on cell viability, but an inhibitory effect on the transcriptional activity of NF-κB-RE. Molecular docking showed stable covalent bonding of polydatin molecules with Il-1β protein at residue leu-26, TNF protein ser-60, residue gly-121, and residue ile-258 of ICAM-1 protein, indicating a stable docking result. The treatment of COVID-19 with P cuspidatum is characterized by multi-component, multi-target, and multi-pathway, which can exert a complex network of regulatory effects through the interaction between different targets, providing a new idea and basis for further exploration of the mechanism of action of P cuspidatum in the treatment of COVID-19.

Reversal of MYB-dependent suppression of MAFB expression overrides leukaemia phenotype in MLL-rearranged AML

The transcription factor MYB plays a pivotal role in haematopoietic homoeostasis and its aberrant expression is involved in the genesis and maintenance of acute myeloid leukaemia (AML). We have previously demonstrated that not all AML subtypes display the same dependency on MYB expression and that such variability is dictated by the nature of the driver mutation. However, whether this difference in MYB dependency is a general trend in AML remains to be further elucidated. Here, we investigate the role of MYB in human leukaemia by performing siRNA-mediated knock-down in cell line models of AML with different driver lesions. We show that the characteristic reduction in proliferation and the concomitant induction of myeloid differentiation that is observed in MLL-rearranged and t(8;21) leukaemias upon MYB suppression is not seen in AML cells with a complex karyotype. Transcriptome analyses revealed that MYB ablation produces consensual increase of MAFB expression in MYB-dependent cells and, interestingly, the ectopic expression of MAFB could phenocopy the effect of MYB suppression. Accordingly, in silico stratification analyses of molecular data from AML patients revealed a reciprocal relationship between MYB and MAFB expression, highlighting a novel biological interconnection between these two factors in AML and supporting new rationales of MAFB targeting in MLL-rearranged leukaemias.

Differential expression of mRNA 3'-end isoforms in cervical and ovarian cancers

Early diagnosis and therapeutic targeting are continuing challenges for gynecological cancers. Here, we focus on cancer transcriptomes and describe the differential expression of 3'UTR isoforms in patients using an algorithm to detect differential poly(A) site usage. We find primarily 3'UTR shortening cases in cervical cancers compared with the normal cervix. We show differential expression of alternate 3'-end isoforms of FOXP1, VPS4B, and OGT in HPV16-positive patients who develop high-grade cervical lesions compared with the infected but non-progressing group. In contrast, in ovarian cancers, 3'UTR lengthening is more evident compared with normal ovary tissue. Nevertheless, highly malignant ovarian tumors have unique 3'UTR shortening events (e.g., CHRAC1, SLC16A1, and TOP2A), some of which correlate with upregulated protein levels in tumors. Overall, our study shows isoform level deregulation in gynecological cancers and highlights the complexity of the transcriptome. This transcript diversity could help identify novel cancer genes and provide new possibilities for diagnosis and therapy.

Evaluation of the HOXA9 and MEIS1 genes as a potential biomarker in adult acute myeloid leukemia

Background

Acute myeloid leukemia (AML) is a heterogeneous disorder encompassing a set of hematopoietic tumors that develop when the myeloid precursor cells undergo disproportionate clonal proliferation. Homeobox A 9 (HOXA9) is a pioneer transcription factor in AML pathogenesis along with its cofactor myeloid ecotropic integration site 1 (MEIS1). Our work aimed to evaluate the different expression levels of HOXA9 and MEIS1 genes and their diagnostic and prognostic significance in adult Egyptian patients with de novo AML. The study was carried out on 91 de novo AML Egyptian patients and 41 healthy individuals. Bone marrow samples were obtained from both patients and controls and then tested by reverse transcription-quantitative polymerase chain reaction to assess the mRNA expression in the studied genes.

Results

HOXA9 and MEIS1 gene expression levels were significantly elevated in AML patients compared to controls (p < 0.001). There was a statistically significant positive correlation between HOXA9 and MEIS1 gene expression in AML patients. However, there was no association between HOXA9 and MEIS1 gene expression levels and disease-free survival (DFS) and overall survival (OS) (p = 0.264 and 0.351, respectively).

Conclusion

HOXA9 and MEIS1 genes are highly expressed in Egyptian AML patients, suggesting their interesting pathogenic role in AML. They could be used as markers for the diagnosis of AML, but not for the disease prognosis.

Somatic FOXC1 insertion mutation remodels the immune microenvironment and promotes the progression of childhood acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is the most common malignant hematological diseases in children. An immunosuppressive microenvironment, particularly regulatory T cell (Treg) infiltration, has been documented to be highly associated with childhood ALL. This present study, based on genetic factors, was aimed at investigating the mutations potentially involved in the immunosuppressive microenvironment in childhood ALL. After whole-exome sequencing was used on DNA extracted from the T cells of ALL bone marrow samples, we found the FOXC1 H446HG induced a increased Treg while decreased cytotoxic T lymphocyte (CTL) in bone marrow. The mutation of FOXC1 in T cell promoted the proliferation of leukemia cells in vitro and in vivo. CpG islands formed by insertion mutation led to an abnormal increase in exon methylation and were associated with the suppression of FOXC1. Decreased FOXC1 attenuated the transcription of HDAC1, thus resulting in the activation of KLF10 through increasing H3K27 acetylation in the promoter region. In conclusion, the de novo insertion mutation in FOXC1 induced suppression of FOXC1, thereby promoting a Treg/CTL shift in the ALL immune microenvironment. The FOXC1 H446HG mutation might be a potential therapeutic target for ALL in the future.

Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions

BACKGROUND

One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes at the core of key macroevolutionary changes, their origin and organismal function are generally poorly understood.

RESULTS

Here, we identify several previously unreported transposable element domestication events in the human and mouse genomes. Among them, we find a remarkable molecular domestication that gave rise to a multigenic family in placental mammals, the Bex/Tceal gene cluster. These genes, which act as hub proteins within diverse signaling pathways, have been associated with neurological features of human patients carrying genomic microdeletions in chromosome X. The Bex/Tceal genes display neural-enriched patterns and are differentially expressed in human neurological disorders, such as autism and schizophrenia. Two different murine alleles of the cluster member Bex3 display morphological and physiopathological brain modifications, such as reduced interneuron number and hippocampal electrophysiological imbalance, alterations that translate into distinct behavioral phenotypes.

CONCLUSIONS

We provide an in-depth understanding of the emergence of a gene cluster that originated by transposon domestication and gene duplication at the origin of placental mammals, an evolutionary process that transformed a non-functional transposon sequence into novel components of the eutherian genome. These genes were integrated into existing signaling pathways involved in the development, maintenance, and function of the CNS in eutherians. At least one of its members, Bex3, is relevant for higher brain functions in placental mammals and may be involved in human neurological disorders.

Molecular update on biology of Wilms Tumor 1 gene and its applications in acute myeloid leukemia

Wilms tumor gene 1 (WT1) is an important gene which is involved in growth and development of many organs. It is identified as a tumor suppressor gene in nephroblastoma. However, its role as a tumor oncogene has been highlighted by many studies in haematological as well as non haematological malignant neoplasm. The expression of WT1 on leukemic blast cells sensitised us to explore its impact on neoplastic phenomenon. WT1 is has been found both mutated as well as over expressed in different subsets of acute myeloid leukemia (AML). WT1 is a gene has been used as a biomarker for diagnosis, monitoring of minimal residual disease (MRD) and detection of relapse for molecular remission in AML. It also has potential of being a predictive molecular predictive biomarker for the treatment of leukemic cases after allogeneic transplantation. The WT1 specific expression on blast cells and its interaction with cytotoxic T cell has also been explored for its potential usage WT1 based immunotherapy. Here, we are reviewing molecular updates of WT1 gene and discuss its potential clinical applications as a predictive molecular biomarker for diagnosis, as MRD detection and as immunotherapy in AML.