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Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression.

ABSTRACT: Non-small cell lung cancer is often diagnosed at advanced stages, and many patients are still treated with classical chemotherapy. The unselective nature of chemotherapy often results in severe myelosuppression. Previous studies showed that protein-coding mutations could not fully explain the predisposition to myelosuppression. Here, we investigate the possible role of enhancer mutations in myelosuppression susceptibility. We produced transcriptome and promoter-interaction maps (using HiCap) of three blood stem-like cell lines treated with carboplatin or gemcitabine. Taking advantage of publicly available enhancer datasets, we validated HiCap results in silico and in living cells using epigenetic CRISPR technology. We also developed a network approach for interactome analysis and detection of differentially interacting genes. Differential interaction analysis provided additional information on relevant genes and pathways for myelosuppression compared with differential gene expression analysis at the bulk level. Moreover, we showed that enhancers of differentially interacting genes are highly enriched for variants associated with differing levels of myelosuppression. Altogether, our work represents a prominent example of integrative transcriptome and gene regulatory datasets analysis for the functional annotation of noncoding mutations.

SUBMITTER: Zhigulev A

PROVIDER: S-EPMC10796589 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression.

Zhigulev Artemy A Norberg Zandra Z Cordier Julie J Spalinskas Rapolas R Bassereh Hassan H Björn Niclas N Pradhananga Sailendra S Gréen Henrik H Sahlén Pelin P

Life science alliance 20240116 3

Non-small cell lung cancer is often diagnosed at advanced stages, and many patients are still treated with classical chemotherapy. The unselective nature of chemotherapy often results in severe myelosuppression. Previous studies showed that protein-coding mutations could not fully explain the predisposition to myelosuppression. Here, we investigate the possible role of enhancer mutations in myelosuppression susceptibility. We produced transcriptome and promoter-interaction maps (using HiCap) of ...[more]

PMID: 38228368

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Project description:Patients with advanced cancer often undergo myelosuppression after receiving chemotherapy. However, severe myelosuppression results in treatment delay, and some can even be life-threatening. At present, cancer patients undergoing chemotherapy urgently need effective intervention strategies to prevent myelosuppression. Fortunately, ginsenoside Rg3 has shown promise as an anti-myelosuppression agent. Therefore, this study was conducted to evaluate the effectiveness of ginsenoside Rg3 in preventing chemotherapy-induced myelosuppression in cancer patients. The PubMed, Cochrane Library, EMBASE, China National Knowledge Infrastructure (CNKI), Weipu (VIP), and Wanfang databases were searched in this study. A total of 18 trials which reported on 2,222 subjects were identified. All trials concerning the use of ginsenoside Rg3 for the prevention of chemotherapy-induced myelosuppression (the decline of leukocyte, hemoglobin, platelet, and neutrophil counts) were randomized-controlled trials. Dichotomous data were expressed as odds ratio (OR) with their respective 95% confidence intervals (CI). The Cochrane evidence-based medicine systematic evaluation was used to evaluate the methodological quality of the included trials. The Review Manager 5.3 and Stata 12.0 software were used to perform the statistical analyses. The trial sequential analysis (TSA) was used to evaluate information size and prevention benefits. The results revealed obvious ginsenoside Rg3-induced improvement in the leukocyte (OR, 0.46; 95% CI, 0.37-0.55), hemoglobin (OR, 0.64; 95% CI, 0.53-0.77), platelet (OR, 0.60; 95% CI, 0.48-0.75) and neutrophil (OR, 0.62; 95% CI, 0.43-0.90) counts at toxic grades I-IV, and leukocyte (OR, 0.39; 95% CI, 0.28-0.54) counts at toxic grades III-IV. The sensitivity analysis revealed that the results were robust. The Egger's test indicated that there was no publication bias in the results. Overall, this study suggested that ginsenoside Rg3 is beneficial for alleviating the chemotherapy-induced decrease in leukocyte, hemoglobin, platelet, and neutrophil counts. However, the confirmation of the ginsenoside Rg3 can be recommended for myelosuppression patients was limited due to poor methodological quality. Thus, more rigorously designed randomized-controlled trials (RCTs) are required to assess the efficacy of ginsenoside Rg3 for myelosuppression.

Project description:BackgroundShenmai injection (SMI), a traditional Chinese medicine (TCM) injection prepared from Red ginseng and Ophiopogon japonicus, is widely used in clinics to treat chemotherapy-induced myelosuppression. Similar to other TCM injections, SMI contains a high amount of carbohydrates (fructose, sucrose, and maltose) in addition to the bioactive substances, specifically ginsenosides (Rg1, Re, and Rb1). To date, the role of these carbohydrates in the hematopoietic function of SMI remains unclear.PurposeWe aimed to investigate the hematopoietic effects and potential mechanisms of SMI and its components, focusing on the carbohydrates present in SMI.Experimental design/methodsFirst, we evaluated the hematopoietic effect of SMI on 5-fluorouracil (5-FU)-induced myelotoxicity in a tumor-bearing mouse model. Then we prepared mixtures of ginsenosides and carbohydrates according to their proportions in SMI and evaluated their hematopoietic function in mice with 5-FU-induced myelosuppression. Finally, hematopoiesis-related molecular networks were built based on RNA sequencing (RNA-seq) of the bone marrow stromal cells (BMSCs), and the potential mechanisms of carbohydrates and ginsenosides were evaluated.ResultsSMI attenuated 5-FU-induced myelotoxicity in tumor-bearing mice. Both ginsenosides and carbohydrates increased the bone marrow nucleated cell (BMNC) count and improved the bone marrow morphology in myelosuppressive mice; they promoted the proliferation of BMSCs derived from those myelosuppressive mice. Bioinformatics analyses revealed ECM-receptor interaction, Hippo signaling, and Wnt signaling are common pathways regulated by both ginsenosides and carbohydrates; Gstt1, Gstp2, Gsta4 and Oplah in Glutathione metabolism pathway and Cd19, Cd79a, and Cd79b in B cell receptor pathway are uniquely regulated genes related to carbohydrates but not ginsenosides.ConclusionsCarbohydrates may collaborate with ginsenosides and contribute to the hematopoietic function of SMI. Carbohydrates could be considered as a bioactive component in this TCM injection.

Project description:ObjectiveMyelosuppression is the most common adverse reaction of chemotherapy, which seriously affects the course of treatment. Zusanli (ST36) acupoint injection with dexamethasone has achieved good clinical efficacy in China. This study aimed to systematically evaluate the efficacy of ST36 acupoint injection with dexamethasone in the treatment of chemotherapy-induced myelosuppression (CIM).MethodsRandomized controlled trials of CIM treated with ST36 acupoint injection with dexamethasone were retrieved from eight electronic databases. We used the Cochrane Collaboration tool to assess the risk of bias. Excel 2010 was used to establish a database for information extraction, and RevMan 5.3.0 software was used to analyze the included test data. GRADE profiler 3.6 software was used to grade the quality of evidence for the outcome indicators of the study.ResultsA total of 17 studies involving 1177 patients were included in this meta-analysis. The results showed that, compared with conventional western medicine (CWM), ST36 acupoint injection with dexamethasone could significantly improve the clinical total effective rate [RR=1.95, 95% CI (1.53, 2.49), P <0.00001] and increase white blood cell (WBC) (MD=1.38, 95% CI (0.74, 2.01), P<0.0001) and hemoglobin (Hb) levels [MD=3.89, 95% CI (1.57, 6.20), P=0.001]. In addition, ST36 acupoint injection with dexamethasone can shorten recovery time of myelosuppression [MD=-3.94, 95% CI (-4.97 to -2.91), P<0.00001] and improve Karnofsky performance status [MD=10.7, 95% CI (1.36, 20.05), P=0.02<0.05]. However, there was no significant difference among ST36 acupoint injection with dexamethasone and CWM in platelet (PLT) elevation [MD=4.61, 95% CI (-10.14, 19.35), P=0.54].ConclusionThis study found that ST36 acupoint injection with dexamethasone had a positive effect on CIM. However, more studies with well-designed, large sample size, strict randomization, and clear descriptions about detection and reporting processes are needed in the future to further confirm the efficacy of ST36 acupoint injection with dexamethasone in the treatment of CIM.Systematic review registrationhttps://www.crd.york.ac.uk/, identifier CRD42021223979.

Project description:Purpose: Develop and validate an accessible prediction model using machine learning (ML) to predict the risk of chemotherapy-induced myelosuppression (CIM) in children with Wilms' tumor (WT) before chemotherapy is administered, enabling early preventive management. Methods: A total of 1433 chemotherapy cycles in 437 children with WT who received chemotherapy in our hospital from January 2009 to March 2022 were retrospectively analyzed. Demographic data, clinicopathological characteristics, hematology and blood biochemistry baseline results, and medication information were collected. Six ML algorithms were used to construct prediction models, and the predictive efficacy of these models was evaluated to select the best model to predict the risk of grade ≥ 2 CIM in children with WT. A series of methods, such as the area under the receiver operating characteristic curve (AUROC), the calibration curve, and the decision curve analysis (DCA) were used to test the model's accuracy, discrimination, and clinical practicability. Results: Grade ≥ 2 CIM occurred in 58.5% (839/1433) of chemotherapy cycles. Based on the results of the training and validation cohorts, we finally identified that the extreme gradient boosting (XGB) model has the best predictive efficiency and stability, with an AUROC of up to 0.981 in the training set and up to 0.896 in the test set. In addition, the calibration curve and the DCA showed that the XGB model had the best discrimination and clinical practicability. The variables were ranked according to the feature importance, and the five variables contributing the most to the model were hemoglobin (Hgb), white blood cell count (WBC), alkaline phosphatase, coadministration of highly toxic chemotherapy drugs, and albumin. Conclusions: The incidence of grade ≥ 2 CIM was not low in children with WT, which needs attention. The XGB model was developed to predict the risk of grade ≥ 2 CIM in children with WT for the first time. The model has good predictive performance and stability and has the potential to be translated into clinical applications. Based on this modeling and application approach, the extension of CIM prediction models to other pediatric malignancies could be expected.

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Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression.

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Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression.

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