ALKBH family members as novel biomarkers and prognostic factors in human breast cancer

Spatial and single-cell analyses uncover links between ALKBH1 and tumor-associated macrophages in gastric cancer

BACKGROUND

AlkB homolog 1, histone H2A dioxygenase (ALKBH1), a crucial enzyme involved in RNA demethylation in humans, plays a significant role in various cellular processes. While its role in tumor progression is well-established, its specific contribution to stomach adenocarcinoma (STAD) remains elusive. This study seeks to explore the clinical and pathological relevance of ALKBH1, its impact on the tumor immune microenvironment, and its potential for precision oncology in STAD.

METHODS

We adopted a comprehensive multi-omics approach to identify ALKBH1 as an potential diagnostic biomarker for STAD, demonstrating its association with advanced clinical stages and reduced overall survival rates. Our analysis involved the utilization of publicly available datasets from GEO and TCGA. We identified differentially expressed genes in STAD and scrutinized their relationships with immune gene expression, overall survival, tumor stage, gene mutation profiles, and infiltrating immune cells. Moreover, we employed spatial transcriptomics to investigate ALKBH1 expression across distinct regions of STAD. Additionally, we conducted spatial transcriptomic and single-cell RNA-sequencing analyses to elucidate the correlation between ALKBH1 expression and immune cell populations. Our findings were validated through immunohistochemistry and bioinformatics on 60 STAD patient samples.

RESULTS

Our study unveiled crucial gene regulators in STAD linked with genetic variations, deletions, and the tumor microenvironment. Mutations in these regulators demonstrated a positive association with distinct immune cell populations across six immune datasets, exerting a substantial influence on immune cell infiltration in STAD. Furthermore, we established a connection between elevated ALKBH1 expression and macrophage infiltration in STAD. Pharmacogenomic analysis of gastric cancer cell lines further indicated that ALKBH1 inactivation correlated with heightened sensitivity to specific small-molecule drugs.

CONCLUSION

In conclusion, our study highlights the potential role of ALKBH1 alterations in the advancement of STAD, shedding light on novel diagnostic and prognostic applications of ALKBH1 in this context. We underscore the significance of ALKBH1 within the tumor immune microenvironment, suggesting its utility as a precision medicine tool and for drug screening in the management of STAD.

Kinetic isotope effect study of N-6 methyladenosine chemical demethylation in bicarbonate-activated peroxide system

N-6 methyladenosine is the most abundant nucleic acid modification in eukaryotes and plays a crucial role in gene regulation. The AlkB family of alpha-ketoglutarate-dependent dioxygenases is responsible for nucleic acid demethylation. Recent studies have discovered that a chemical demethylation system using hydrogen peroxide and ammonium bicarbonate can effectively demethylate nucleic acids. The addition of ferrous ammonium sulfate boosts the oxidation rate by forming a Fenton reagent with hydrogen peroxide. However, the specific mechanism and key steps of this process remain unclear. In this study, we investigate the influence of ferrous ammonium sulfate concentration on the kinetic isotope effect (KIE) of the chemical demethylation system using LC-MS. As the concentration of ferrous ions increases, the observed KIE decreases from 1.377 ± 0.020 to 1.120 ± 0.016, indicating a combination of the primary isotope effect and inverse α-secondary isotope effect with the ion pairing effect. We propose that the initial hydrogen extraction is the rate-limiting step and observe a tight transition state structure in the formation of the hm6A process through the analysis of KIE trends. The concentration-dependent KIE provides a novel perspective on the mechanism of chemical demethylation and offers a chemical model for enzyme-catalyzed demethylation.

RNA modification: mechanisms and therapeutic targets

RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.

ERβ1 Sensitizes and ERβ2 Desensitizes ERα-Positive Breast Cancer Cells to the Inhibitory Effects of Tamoxifen, Fulvestrant and Their Combination with All-Trans Retinoic Acid

Adjuvant endocrine therapy (AET) is the treatment of choice for early-stage estrogen receptor alpha (ERα)-positive breast cancer (BC). However, almost 40% of tamoxifen-treated cases display no response or a partial response to AET, thus increasing the need for new treatment options and strong predictors of the therapeutic response of patients at high risk of relapse. In addition to ERα, BC research has focused on ERβ1 and ERβ2 (isoforms of ERβ), the second ER isotype. At present, the impact of ERβ isoforms on ERα-positive BC prognosis and treatment remains elusive. In the present study, we established clones of MCF7 cells constitutively expressing human ERβ1 or ERβ2 and investigated their role in the response of MCF7 cells to antiestrogens [4-hydroxytamoxifen (OHΤ) and fulvestrant (ICI182,780)] and retinoids [all-trans retinoic acid (ATRA)]. We show that, compared to MCF7 cells, MCF7-ERβ1 and MCF7-ERβ2 cells were sensitized and desensitized, respectively, to the antiproliferative effect of the antiestrogens, ATRA and their combination and to the cytocidal effect of the combination of OHT and ATRA. Analysis of the global transcriptional changes upon OHT-ATRA combinatorial treatment revealed uniquely regulated genes associated with anticancer effects in MCF7-ERβ1 cells and cancer-promoting effects in MCF7-ERβ2 cells. Our data are favorable to ERβ1 being a marker of responsiveness and ERβ2 being a marker of resistance of MCF7 cells to antiestrogens alone and in combination with ATRA.

Downregulated PRNP Facilitates Cell Proliferation and Invasion and Has Effect on the Immune Regulation in Ovarian Cancer

Background. Ovarian cancer (OC) seriously threatens women’s life. Ferroptosis plays an essential role in the initiation and development of OC. However, more molecular targets and mechanisms for ferroptosis in OC remain to be further elucidated. Methods. Several OC datasets were integrated in this study and three candidate genes including PRNP were further screened out as the ferroptosis-related gene which was differentially expressed in OC. Then, comprehensive evaluations concerning gene expression, clinical implication, in vitro validation of expression and functional experiments, prediction of downstream molecules and related signal pathways, and immune-modulating function were performed. Results. PRNP was the only downregulated ferroptosis-related gene with prognostic value for OC patients. The decreased mRNA and protein expression was verified in OC tissues and cell lines. PRNP was significantly correlated with cancer stages, primary therapy outcomes, and age in OC patients. Moreover, we found that overexpression of PRNP inhibited the proliferation, migration, and invasion ability of OC cells through in vitro experiments. PRNP was enriched to the Ras signaling pathway. PRNP expression was positively correlated with the infiltration of immune cells, such as mast cells, T effector memory cells, plasmacytoid DC cells, NK cells, and eosinophils. In addition, the association of PRNP with other immune signatures was also found. Conclusion. This study demonstrated for the first time showed that ferroptosis-related gene PRNP exerted a tumor suppressive role in OC and the aberrant expression and function of PRNP making it a potential novel biomarker for OC diagnosis, prognosis, and response to immunotherapies.