ETV6-RUNX1 interacts with a region in SPIB intron 1 to regulate gene expression in pre-B-cell acute lymphoblastic leukemia

Genetic Profiling of Acute and Chronic Leukemia via Next-Generation Sequencing: Current Insights and Future Perspectives

Leukemia is a heterogeneous group of hematologic malignancies characterized by distinct genetic and molecular abnormalities. Advancements in genomic technologies have significantly transformed the diagnosis, prognosis, and treatment strategies for leukemia. Among these, next-generation sequencing (NGS) has emerged as a powerful tool, enabling high-resolution genomic profiling that surpasses conventional diagnostic approaches. By providing comprehensive insights into genetic mutations, clonal evolution, and resistance mechanisms, NGS has revolutionized precision medicine in leukemia management. Despite its transformative potential, the clinical integration of NGS presents challenges, including data interpretation complexities, standardization issues, and cost considerations. However, continuous advancements in sequencing platforms and bioinformatics pipelines are enhancing the reliability and accessibility of NGS in routine clinical practice. The expanding role of NGS in leukemia is paving the way for improved risk stratification, targeted therapies, and real-time disease monitoring, ultimately leading to better patient outcomes. This review highlights the impact of NGS on leukemia research and clinical applications, discussing its advantages over traditional diagnostic techniques, key sequencing approaches, and emerging challenges. As precision oncology continues to evolve, NGS is expected to play an increasingly central role in the diagnosis and management of leukemia, driving innovations in personalized medicine and therapeutic interventions.

An insight into the concept of neuroinflammation and neurodegeneration in Alzheimer's disease: targeting molecular approach Nrf2, NF-κB, and CREB

Alzheimer's disease (AD) is a most prevalent neurologic disorder characterized by cognitive dysfunction, amyloid-β (Aβ) protein accumulation, and excessive neuroinflammation. It affects various life tasks and reduces thinking, memory, capability, reasoning and orientation ability, decision, and language. The major parts responsible for these abnormalities are the cerebral cortex, amygdala, and hippocampus. Excessive inflammatory markers release, and microglial activation affect post-synaptic neurotransmission. Various mechanisms of AD pathogenesis have been explored, but still, there is a need to debate the role of NF-κB, Nrf2, inflammatory markers, CREB signaling, etc. In this review, we have briefly discussed the signaling mechanisms and function of the NF-ĸB signaling pathway, inflammatory mediators, microglia activation, and alteration of autophagy. NF-κB inhibition is a current strategy to counter neuroinflammation and neurodegeneration in the brain of individuals with AD. In clinical trials, numbers of NF-κB modulators are being examined. Recent reports revealed that molecular and cellular pathways initiate complex pathological competencies that cause AD. Moreover, this review will provide extensive knowledge of the cAMP response element binding protein (CREB) and how these nuclear proteins affect neuronal plasticity.

The Landscape of Secondary Genetic Rearrangements in Pediatric Patients with B-Cell Acute Lymphoblastic Leukemia with t(12;21)

The most frequent chromosomal rearrangement in childhood B-cell acute lymphoblastic leukemia (B-ALL) is translocation t(12;21)(p13;q22). It results in the fusion of the ETV6::RUNX1 gene, which is active in the regulation of multiple crucial cellular pathways. Recent studies hypothesize that many translocations are influenced by RAG-initiated deletions, as well as defects in the RAS and NRAS pathways. According to a "two-hit" model for the molecular pathogenesis of pediatric ETV6::RUNX1-positive B-ALL, the t(12;21) translocation requires leukemia-causing secondary mutations. Patients with ETV6::RUNX1 express up to 60 different aberrations, which highlights the heterogeneity of this B-ALL subtype and is reflected in differences in patient response to treatment and chances of relapse. Most studies of secondary genetic changes have concentrated on deletions of the normal, non-rearranged ETV6 allele. Other predominant structural changes included deletions of chromosomes 6q and 9p, loss of entire chromosomes X, 8, and 13, duplications of chromosome 4q, or trisomy of chromosomes 21 and 16, but the impact of these changes on overall survival remains unclarified. An equally genetically diverse group is the recently identified new B-ALL subtype ETV6::RUNX1-like ALL. In our review, we provide a comprehensive description of recurrent secondary mutations in pediatric B-ALL with t(12;21) to emphasize the value of investigating detailed molecular mechanisms in ETV6::RUNX1-positive B-ALL, both for our understanding of the etiology of the disease and for future clinical advances in patient treatment and management.

Establishment and validation of an aging-related risk signature associated with prognosis and tumor immune microenvironment in breast cancer

BACKGROUND

Breast cancer (BC) is a highly malignant and heterogeneous tumor which is currently the cancer with the highest incidence and seriously endangers the survival and prognosis of patients. Aging, as a research hotspot in recent years, is widely considered to be involved in the occurrence and development of a variety of tumors. However, the relationship between aging-related genes (ARGs) and BC has not yet been fully elucidated.

MATERIALS AND METHODS

The expression profiles and clinicopathological data were acquired in the Cancer Genome Atlas (TCGA) and the gene expression omnibus (GEO) database. Firstly, the differentially expressed ARGs in BC and normal breast tissues were investigated. Based on these differential genes, a risk model was constructed composed of 11 ARGs via univariate and multivariate Cox analysis. Subsequently, survival analysis, independent prognostic analysis, time-dependent receiver operating characteristic (ROC) analysis and nomogram were performed to assess its ability to sensitively and specifically predict the survival and prognosis of patients, which was also verified in the validation set. In addition, functional enrichment analysis and immune infiltration analysis were applied to reveal the relationship between the risk scores and tumor immune microenvironment, immune status and immunotherapy. Finally, multiple datasets and real-time polymerase chain reaction (RT-PCR) were utilized to verify the expression level of the key genes.

RESULTS

An 11-gene signature (including FABP7, IGHD, SPIB, CTSW, IGKC, SEZ6, S100B, CXCL1, IGLV6-57, CPLX2 and CCL19) was established to predict the survival of BC patients, which was validated by the GEO cohort. Based on the risk model, the BC patients were divided into high- and low-risk groups, and the high-risk patients showed worse survival. Stepwise ROC analysis and Cox analyses demonstrated the good performance and independence of the model. Moreover, a nomogram combined with the risk score and clinical parameters was built for prognostic prediction. Functional enrichment analysis revealed the robust relationship between the risk model with immune-related functions and pathways. Subsequent immune microenvironment analysis, immunotherapy, etc., indicated that the immune status of patients in the high-risk group decreased, and the anti-tumor immune function was impaired, which was significantly different with those in the low-risk group. Eventually, the expression level of FABP7, IGHD, SPIB, CTSW, IGKC, SEZ6, S100B, CXCL1, IGLV6-57 and CCL19 was identified as down-regulated in tumor cell line, while CPLX2 up-regulated, which was mostly similar with the results in TCGA and Human Protein Atlas (HPA) via RT-PCR.

CONCLUSIONS

In summary, our study constructed a risk model composed of ARGs, which could be used as a solid model for predicting the survival and prognosis of BC patients. Moreover, this model also played an important role in tumor immunity, providing a new direction for patient immune status assessment and immunotherapy selection.

Development of dynamical network biomarkers for regulation in Epstein-Barr virus positive peripheral T cell lymphoma unspecified type

Background: This study was performed to identify key regulatory network biomarkers including transcription factors (TFs), miRNAs and lncRNAs that may affect the oncogenesis of EBV positive PTCL-U. Methods: GSE34143 dataset was downloaded and analyzed to identify differentially expressed genes (DEGs) between EBV positive PTCL-U and normal samples. Gene ontology and pathway enrichment analyses were performed to illustrate the potential function of the DEGs. Then, key regulators including TFs, miRNAs and lncRNAs involved in EBV positive PTCL-U were identified by constructing TF-mRNA, lncRNA-miRNA-mRNA, and EBV encoded miRNA-mRNA regulatory networks. Results: A total of 96 DEGs were identified between EBV positive PTCL-U and normal tissues, which were related to immune responses, B cell receptor signaling pathway, chemokine activity. Pathway analysis indicated that the DEGs were mainly enriched in cytokine-cytokine receptor interaction and chemokine signaling pathway. Based on the TF network, hub TFs were identified regulate the target DEGs. Afterwards, a ceRNA network was constructed, in which miR-181(a/b/c/d) and lncRNA LINC01744 were found. According to the EBV-related miRNA regulatory network, CXCL10 and CXCL11 were found to be regulated by EBV-miR-BART1-3p and EBV-miR-BHRF1-3, respectively. By integrating the three networks, some key regulators were found and may serve as potential network biomarkers in the regulation of EBV positive PTCL-U. Conclusion: The network-based approach of the present study identified potential biomarkers including transcription factors, miRNAs, lncRNAs and EBV-related miRNAs involved in EBV positive PTCL-U, assisting us in understanding the molecular mechanisms that underlie the carcinogenesis and progression of EBV positive PTCL-U.

Expression and Clinical Significance of Spi-B in B-cell Acute Lymphoblastic Leukemia

Spi-B, a member of the E26 transformation-specific (ETS) family of transcription factors, plays an important role in B cell differentiation. Spi-B also functions in development of diffuse large B-cell lymphoma; thus, we hypothesized that it may participate in leukemogenesis of B-cell acute lymphoblastic leukemia (B-ALL). To test this hypothesis, we first generated an anti-Spi-B monoclonal antibody that recognized Spi-B on formalin-fixed, paraffin-embedded tissue sections. This antibody, designated S28-5, selectively stained B cell nuclei at the pre-plasma cell stage (including centrocytes and centroblasts in germinal centers) and nuclei of plasmacytoid dendritic cells, but not fully differentiated plasma cells, T cells, macrophages, or follicular dendritic cells. Employing S28-5, we then performed immunohistochemical staining of bone marrow aspiration biopsy specimens obtained from B-ALL patients (n=62). Cases that showed stronger nuclear S28-5 signals than T-cell ALL were scored positive. In 26 (42%) of 62 specimens, leukemic cells showed nuclear Spi-B expression, and positivity was associated with patient age at diagnosis, and serum uric acid and creatinine levels. Moreover, Spi-B-positive patients demonstrated significantly shorter overall survival than did Spi-B-negative patients. These results suggest that Spi-B expression may serve as a prognostic indicator of B-ALL.

Inference of age-associated transcription factor regulatory activity changes in single cells

Transcription factors (TFs) control cell identity and function. How their activity is altered during healthy aging is critical for an improved understanding of aging and disease risk, yet relatively little is known about such changes at cell-type resolution. Here we present and validate a TF activity estimation method for single cells from the hematopoietic system that is based on TF regulons, and apply it to a mouse single-cell RNA-sequencing atlas, to infer age-associated differentiation activity changes in the immune cells of different organs. This revealed an age-associated signature of macrophage dedifferentiation, which is shared across tissue types, and aggravated in tumor-associated macrophages. By extending the analysis to all major cell types, we reveal cell-type and tissue-type-independent age-associated alterations to regulatory factors controlling antigen processing, inflammation, collagen processing and circadian rhythm, that are implicated in age-related diseases. Finally, our study highlights the limitations of using TF expression to infer age-associated changes, underscoring the need to use regulatory activity inference methods.

SPIB acts as a tumor suppressor by activating the NFkB and JNK signaling pathways through MAP4K1 in colorectal cancer cells

Spi-B transcription factor (SPIB) is a member of the E-twenty-six (ETS) transcription factor family. Previous studies have shown that the expression of SPIB is downregulated in human colorectal cancer tissues. The purpose of our study was to explore the biological function and related mechanism of SPIB in colorectal cancer cells. Our study found that SPIB could inhibit the proliferation, migration and invasion of CRC cells; inhibit angiogenesis; and induce CRC cells cycle arrest in G2/M phase and promote the apoptosis of CRC cells. We also found that compared with the control group, the 50% inhibitory concentration (IC50) values of oxaliplatin and 5-FU in the SPIB overexpression group were significantly reduced. Western blot results showed that the overexpression of SPIB upregulated cleaved-PARP(c-PARP), nuclear factor kB p65 (NFkB p65), phospho-NFkB p65 (p-NFkB P65), JNK1, and C-Jun protein expression levels compared with the control group. The silence of SPIB downregulated c-PARP, NFκB p65, p-NFκB p65, JNK1, and C-Jun protein expression levels. A dual-luciferase reporter assay showed that SPIB could activate the promoter of MAP4K1 and enhance the expression of MAP4K1. After silencing MAP4K1, the protein expression levels of c-PARP, NFkB P65, p-NFkB P65, JNK1, and C-Jun were downregulated. In summary, we found that SPIB is a tumor suppressor in colorectal cancer cells and that SPIB sensitizes colorectal cancer cells to oxaliplatin and 5-FU, SPIB exerts its anti-colorectal cancer effect by activating the NFkB and JNK signaling pathways through MAP4K1. The above findings may provide a reference for new molecular markers and therapeutic targets for CRC.