Prognostic significance of NT5E/CD73 in neuroblastoma and its function in CSC stemness maintenance

Combined single-cell RNA sequencing and mendelian randomization to identify biomarkers associated with necrotic apoptosis in intervertebral disc degeneration

BACKGROUND

Intervertebral disc degeneration (IDD) is associated with back pain; back pain is a world-wide contributor to poor quality of life, while necroptosis has the characteristics of necroptosis and apoptosis, however, its role in IDD is still unclear. Therefore, the aim of this study was to identify biomarkers associated with necroptosis in IDD.

PURPOSE

To explore biomarkers associated with necroptosis in IDD, reveal the pathogenesis of IDD, as well as provide new directions for the diagnosis and treatment of this disease.

STUDY DESIGN/SETTINGS

Retrospective cohort study. Our study employs scRNA-seq coupled with MR analysis to investigate the causal relationship between necroptosis and IDD, laying a foundational groundwork for unveiling the intricate pathogenic mechanisms of this condition.

METHODS

Data quality control and normalisation was executed in single-cell dataset, GSE205535. Then, different cell types were obtained by cell annotation through marker genes. Subsequently, chi-square test was employed to assess the distribution difference of different cell types between IDD and control to screen key cells. AUCell was applied to calculate necroptosis-related genes (NRGs) scores of all cell types, further key cells were divided into high and low NRGs groups according to the median AUC scores of different cell types. Afterwards, the differentially expressed genes (DEGs) within the 2 score groups were screened. Then, the genes that had causal relationship with IDD were selected as biomarkers by univariate and multivariate Mendelian randomization (MR) analysis. Finally, the expression of biomarkers in different cell types and pseudo-time analysis was analyzed separately.

RESULTS

In GSE205535, 16 different cell populations identified by UMAP cluster analysis were further annotated to 8 cell types using maker genes. Afterwards, 53 DEGs were screened between the high and low NRGs groups. In addition, 9 genes with causal relationship with IDD were obtained by univariate MR analysis, further multivariate MR analysis proved that NT5E and TMEM158 had a direct causal relationship with IDD, which were used as biomarkers in this study. This study not only found that the expression levels of NT5E and TMEM158 were higher in IDD group, but also found that fibrochondrocytes and inflammatory chondrocytes were the key cells of NT5E and TMEM158, respectively. In the end, the biomarkers had the same expression trend in the quasi-time series, and both of them from high to low and then increased.

CONCLUSION

NT5E and TMEM158, as biomarkers of necroptotic apoptotic IDD, were causally associated with IDD.

CLINICAL SIGNIFICANCE

The understanding of chondrocytes as key cells provides new perspectives for deeper elucidation of the pathogenesis of IDD, improved diagnostic methods, and the development of more effective treatments. These findings are expected to provide a more accurate and personalised approach to clinical diagnosis and treatment, thereby improving the prognosis and quality of life of patients with IDD.

Proteasome Inhibition Reprograms Chromatin Landscape in Breast Cancer

The 26S proteasome is the major protein degradation machinery in cells. Cancer cells use the proteasome to modulate gene expression networks that promote tumor growth. Proteasome inhibitors have emerged as effective cancer therapeutics, but how they work mechanistically remains unclear. Here, using integrative genomic analysis, we discovered unexpected reprogramming of the chromatin landscape and RNA polymerase II (RNAPII) transcription initiation in breast cancer cells treated with the proteasome inhibitor MG132. The cells acquired dynamic changes in chromatin accessibility at specific genomic loci termed differentially open chromatin regions (DOCR). DOCRs with decreased accessibility were promoter proximal and exhibited unique chromatin architecture associated with divergent RNAPII transcription. Conversely, DOCRs with increased accessibility were primarily distal to transcription start sites and enriched in oncogenic superenhancers predominantly accessible in non-basal breast tumor subtypes. These findings describe the mechanisms by which the proteasome modulates the expression of gene networks intrinsic to breast cancer biology.

SIGNIFICANCE

Our study provides a strong basis for understanding the mechanisms by which proteasome inhibitors exert anticancer effects. We find open chromatin regions that change during proteasome inhibition, are typically accessible in non-basal breast cancers.

Purinergic system in cancer stem cells

Accumulating evidence supports the idea that cancer stem cells (CSCs) are those with the capacity to initiate tumors, generate phenotypical diversity, sustain growth, confer drug resistance, and orchestrate the spread of tumor cells. It is still controversial whether CSCs originate from normal stem cells residing in the tissue or cancer cells from the tumor bulk that have dedifferentiated to acquire stem-like characteristics. Although CSCs have been pointed out as key drivers in cancer, knowledge regarding their physiology is still blurry; thus, research focusing on CSCs is essential to designing novel and more effective therapeutics. The purinergic system has emerged as an important autocrine-paracrine messenger system with a prominent role at multiple levels of the tumor microenvironment, where it regulates cellular aspects of the tumors themselves and the stromal and immune systems. Recent findings have shown that purinergic signaling also participates in regulating the CSC phenotype. Here, we discuss updated information regarding CSCs in the purinergic system and present evidence supporting the idea that elements of the purinergic system expressed by this subpopulation of the tumor represent attractive pharmacological targets for proposing innovative anti-cancer therapies.

Proteasome inhibition reprograms chromatin landscape in breast cancer

The 26S proteasome is the major protein degradation machinery in cells. Cancer cells use the proteasome to modulate gene expression networks that promote tumor growth. Proteasome inhibitors have emerged as effective cancer therapeutics, but how they work mechanistically remains unclear. Here, using integrative genomic analysis, we discovered unexpected reprogramming of the chromatin landscape and RNAPII transcription initiation in breast cancer cells treated with the proteasome inhibitor MG132. The cells acquired dynamic changes in chromatin accessibility at specific genomic loci termed Differentially Open Chromatin Regions (DOCRs). DOCRs with decreased accessibility were promoter proximal and exhibited unique chromatin architecture associated with divergent RNAPII transcription. Conversely, DOCRs with increased accessibility were primarily distal to transcription start sites and enriched in oncogenic super enhancers predominantly accessible in non-basal breast tumor subtypes. These findings describe the mechanisms by which the proteasome modulates the expression of gene networks intrinsic to breast cancer biology.

Highlights

Proteasome inhibition uncovers de novo Differential Open Chromatin Regions (DOCRs) in breast cancer cells. Proteasome inhibitor sensitive promoters exhibit a distinctive chromatin architecture with discrete transcription initiation patterns.Proteasome inhibition reprograms accessibility of super enhancers.Proteasome inhibitor sensitive super enhancers distinguish basal from non-basal breast cancer subtypes.

ATP and Adenosine Metabolism in Cancer: Exploitation for Therapeutic Gain

Adenosine is an evolutionary ancient metabolic regulator linking energy state to physiologic processes, including immunomodulation and cell proliferation. Tumors create an adenosine-rich immunosuppressive microenvironment through the increased release of ATP from dying and stressed cells and its ectoenzymatic conversion into adenosine. Therefore, the adenosine pathway becomes an important therapeutic target to improve the effectiveness of immune therapies. Prior research has focused largely on the two major ectonucleotidases, ectonucleoside triphosphate diphosphohydrolase 1/cluster of differentiation (CD)39 and ecto-5'-nucleotidase/CD73, which catalyze the breakdown of extracellular ATP into adenosine, and on the subsequent activation of different subtypes of adenosine receptors with mixed findings of antitumor and protumor effects. New findings, needed for more effective therapeutic approaches, require consideration of redundant pathways controlling intratumoral adenosine levels, including the alternative NAD-inactivating pathway through the CD38-ectonucleotide pyrophosphatase phosphodiesterase (ENPP)1-CD73 axis, the counteracting ATP-regenerating ectoenzymatic pathway, and cellular adenosine uptake and its phosphorylation by adenosine kinase. This review provides a holistic view of extracellular and intracellular adenosine metabolism as an integrated complex network and summarizes recent data on the underlying mechanisms through which adenosine and its precursors ATP and ADP control cancer immunosurveillance, tumor angiogenesis, lymphangiogenesis, cancer-associated thrombosis, blood flow, and tumor perfusion. Special attention is given to differences and commonalities in the purinome of different cancers, heterogeneity of the tumor microenvironment, subcellular compartmentalization of the adenosine system, and novel roles of purine-converting enzymes as targets for cancer therapy. SIGNIFICANCE STATEMENT: The discovery of the role of adenosine as immune checkpoint regulator in cancer has led to the development of novel therapeutic strategies targeting extracellular adenosine metabolism and signaling in multiple clinical trials and preclinical models. Here we identify major gaps in knowledge that need to be filled to improve the therapeutic gain from agents targeting key components of the adenosine metabolic network and, on this basis, provide a holistic view of the cancer purinome as a complex and integrated network.