Prognostic stratification improvement by integrating ID1/ID3/IGJ gene expression signature and immunophenotypic profile in adult patients with B-ALL

Transcriptomic analysis of mRNAs in human whole blood identified age-specific changes in healthy individuals

Older age is one of the most important shared risk factors for multiple chronic diseases, increasing the medical burden to contemporary societies. Current research focuses on identifying aging biomarkers to predict aging trajectories and developing interventions aimed at preventing and delaying the progression of multimorbidity with aging. Here, a transcriptomic changes analysis of whole blood genes with age was conducted. The age-related whole blood gene-expression profiling datasets were downloaded from the Gene Expression Omnibus (GEO) database. We screened the differentially expressed genes (DEGs) between healthy young and old individuals and performed functional enrichment analysis. Cytoscape with Cytohubba and MCODE was used to perform an interaction network of DEGs and identify hub genes. In addition, ROC curves and correlation analysis were used to evaluate the accuracy of hub genes. In total, we identified 29 DEGs between young and old samples that were enriched mainly in immunoglobulin binding and complex, humoral immune response, and immune response-activating signaling pathways. In combination with the PPI network and topological analysis, 4 hub genes (IGLL5, Jchain, POU2AF1, and Bach2) were identified. Pearson analysis showed that the expression changes of these hub genes were highly correlated with age. Among them, 3 hub genes (IGLL5, POU2AF1, and Bach2) were identified with good accuracy (AUC score > 0.7), indicating that these genes were the best indicators of age. Together, our results provided potential biomarkers IGLL5, POU2AF1, and Bach2 to identify individuals at high early risk of age-related disease to be targeted for early interventions and contribute to understanding the molecular mechanisms in the progression of aging.

Multi-Organ Nutrigenomic Effects of Dietary Grapes in a Mouse Model

As a whole food, the potential health benefits of table grapes have been widely studied. Some individual constituents have garnered great attention, particularly resveratrol, but normal quantities in the diet are meniscal. On the other hand, the grape contains hundreds of compounds, many of which have antioxidant potential. Nonetheless, the achievement of serum or tissue concentrations of grape antioxidants sufficient to mediate a direct quenching effect is not likely, which supports the idea of biological responses being mediated by an indirect catalytic-type response. We demonstrate herein with Hsd:ICR (CD-1® Outbred, 18-24 g, 3-4 weeks old, female) mice that supplementation of a semi-synthetic diet with a grape surrogate, equivalent to the human consumption of 2.5 servings per day for 12 months, modulates gene expression in the liver, kidney, colon, and ovary. As might be expected when sampling changes in a pool of over 35,000 genes, there are numerous functional implications. Analysis of some specific differentially expressed genes suggests the potential of grape consumption to bolster metabolic detoxification and regulation of reactive oxygen species in the liver, cellular metabolism, and anti-inflammatory activity in the ovary and kidney. In the colon, the data suggest anti-inflammatory activity, suppression of mitochondrial dysfunction, and maintaining homeostasis. Pathway analysis reveals a combination of up- and down-regulation in the target tissues, primarily up-regulated in the kidney and down-regulated in the ovary. More broadly, based on these data, it seems logical to conclude that grape consumption leads to modulation of gene expression throughout the body, the consequence of which may help to explain the broad array of activities demonstrated in diverse tissues such as the brain, heart, eye, bladder, and colon. In addition, this work further supports the profound impact of nutrigenomics on mammalian phenotypic expression.

Novel gene signature reveals prognostic model in acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is a type of hematological malignancy and has a poor prognosis. In our study, we aimed to construct a prognostic model of ALL by identifying important genes closely related to ALL prognosis. We obtained transcriptome data (RNA-seq) of ALL samples from the GDC TARGET database and identified differentially expressed genes (DEGs) using the “DESeq” package of R software. We used univariate and multivariate cox regression analyses to screen out the prognostic genes of ALL. In our results, the risk score can be used as an independent prognostic factor to predict the prognosis of ALL patients [hazard ratio (HR) = 2.782, 95% CI = 1.903–4.068, p < 0.001]. Risk score in clinical parameters has high diagnostic sensitivity and specificity for predicting overall survival of ALL patients, and the area under curve (AUC) is 0.864 in the receiver operating characteristic (ROC) analysis results. Our study evaluated a potential prognostic signature with six genes and constructed a risk model significantly related to the prognosis of ALL patients. The results of this study can help clinicians to adjust the treatment plan and distinguish patients with good and poor prognosis for targeted treatment.

Genetic Profiling in Children With Acute Lymphoblastic Leukemia Referred for Allogeneic Hematopoietic Stem Cell Transplantation

Introduction

Hematopoietic stem cell transplantation (HSCT) is the essential and often the only curative therapeutic option in high risk and relapsed pediatric acute lymphoblastic leukemia (ALL).

Methods

The objective of the study was to investigate whole-genome expression in children with high risk or relapsed ALL referred for HSCT. Gene expression was assessed in 18 children with ALL referred for HSCT (10 high risk, 8 relapsed; median age of 9.4 years) and in a control group of 38 obese children (median age of 14.1 years). Whole-genome expression was assessed in leukocytes using GeneChip® HumanGene 1.0 ST microarray.

Results

The analysis of genomic profiles revealed a significantly lower expression of 21 genes with a defined function, involved in immunoglobulin production, lymphocyte function, or regulation of DNA processing in ALL patients referred for HSCT compared with the control group.

Conclusion

Genome expression of patients with ALL in remission referred to HSCT revealed deep immunosuppression of both B-cell and T-cell lineages, which may increase the probability of donor cell engraftment.

Combination of the PI3K inhibitor Idelalisib with the conventional cytostatics cytarabine and dexamethasone leads to changes in pathway activation that induce anti-proliferative effects in B lymphoblastic leukaemia cell lines

BACKGROUND

The introduction of combined conventional cytostatics and pathway-specific inhibitors has opened new treatment options for several cancer types including hematologic neoplasia such as leukaemias. As the detailed understanding of the combination-induced molecular effects is often lacking, the identification of combination-induced molecular mechanisms bears significant value for the further development of interventional approaches.

METHODS

Combined application of conventional cytostatic agents (cytarabine and dexamethasone) with the PI3K-inhibitor Idelalisib was analysed on cell-biologic parameters in two acute pro-B lymphoblastic leukaemia (B-ALL) cell lines. In particular, for comparative characterisation of the molecular signatures induced by the combined and mono application, whole transcriptome sequencing was performed. Emphasis was placed on pathways and genes exclusively regulated by drug combinations.

RESULTS

Idelalisib + cytostatics combinations changed pathway activation for, e.g., "Retinoblastoma in cancer", "TGF-b signalling", "Cell cycle" and "DNA-damage response" to a greater extent than the two cytostatics alone. Analyses of the top-20 regulated genes revealed that both combinations induce characteristic gene expression changes.

CONCLUSION

A specific set of genes was exclusively deregulated by the drug combinations, matching the combination-specific anti-proliferative cell-biologic effects. The addition of Idelalisib suggests minor synergistic effects which are rather to be classified as additive.

Paradoxical role of Id proteins in regulating tumorigenic potential of lymphoid cells

A family of transcription factors known as Id proteins, or inhibitor of DNA binding and differentiation, is capable of regulating cell proliferation, survival and differentiation, and is often upregulated in multiple types of tumors. Due to their ability to promote self-renewal, Id proteins have been considered as oncogenes, and potential therapeutic targets in cancer models. On the contrary, certain Id proteins are reported to act as tumor suppressors in the development of Burkitt's lymphoma in humans, and hepatosplenic and innate-like T cell lymphomas in mice. The contexts and mechanisms by which Id proteins can serve in such contradictory roles to determine tumor outcomes are still not well understood. In this review, we explore the roles of Id proteins in lymphocyte development and tumorigenesis, particularly with respect to inhibition of their canonical DNA binding partners known as E proteins. Transcriptional regulation by E proteins, and their antagonism by Id proteins, act as gatekeepers to ensure appropriate lymphocyte development at key checkpoints. We re-examine the derailment of these regulatory mechanisms in lymphocytes that facilitate tumor development. These mechanistic insights can allow better appreciation of the context-dependent roles of Id proteins in cancers and improve considerations for therapy.

Epigenetics in Hematological Malignancies

Acute leukemias are hematologic malignancies with aggressive behavior especially in adult population. With the introduction of new gene expression and sequencing technologies there have been advances in the knowledge of the genetic landscape of acute leukemias. A more detailed analysis allows for the identification of additional alterations in epigenetic regulators that have a profound impact in cellular biology without changes in DNA sequence. These epigenetic alterations disturb the physiological balance between gene activation and gene repression and contribute to aberrant gene expression, contributing significantly to the leukemic pathogenesis and maintenance. We review epigenetic changes in acute leukemia in relation to what is known about their mechanism of action, their prognostic role and their potential use as therapeutic targets, with important implications for precision medicine.