ceRNAR: An R package for identification and analysis of ceRNA-miRNA triplets.

Competitive endogenous RNA (ceRNA) represents a novel mechanism of gene regulation that controls several biological and pathological processes. Recently, an increasing number of in silico methods have been developed to accelerate the identification of such regulatory events. However, there is still a need for a tool supporting the hypothesis that ceRNA regulatory events only occur at specific miRNA expression levels. To this end, we present an R package, ceRNAR, which allows identification and analysis of ceRNA-miRNA triplets via integration of miRNA and RNA expression data. The ceRNAR package integrates three main steps: (i) identification of ceRNA pairs based on a rank-based correlation between pairs that considers the impact of miRNA and a running sum correlation statistic, (ii) sample clustering based on gene-gene correlation by circular binary segmentation, and (iii) peak merging to identify the most relevant sample patterns. In addition, ceRNAR also provides downstream analyses of identified ceRNA-miRNA triplets, including network analysis, functional annotation, survival analysis, external validation, and integration of different tools. The performance of our proposed approach was validated through simulation studies of different scenarios. Compared with several published tools, ceRNAR was able to identify true ceRNA triplets with high sensitivity, low false-positive rates, and acceptable running time. In real data applications, the ceRNAs common to two lung cancer datasets were identified in both datasets. The bridging miRNA for one of these, the ceRNA for MAP4K3, was identified by ceRNAR as hsa-let-7c-5p. Since similar cancer subtypes do share some biological patterns, these results demonstrated that our proposed algorithm was able to identify potential ceRNA targets in real patients. In summary, ceRNAR offers a novel algorithm and a comprehensive pipeline to identify and analyze ceRNA regulation. The package is implemented in R and is available on GitHub (https://github.com/ywhsiao/ceRNAR).

Using proteomic profiling to characterize protein signatures of different thymoma subtypes.

BACKGROUND: Histology is a traditional way to classify subtypes of thymoma, because of low cost and convenience. Yet, due to the diverse morphology of thymoma, this method increases the complexity of histopathologic classification, and requires experienced experts to perform correct diagnosis. Therefore, in this study, we developed an alternative method by identifying protein biomarkers in order to assist clinical practitioners to make right classification of thymoma subtypes. METHODS: In total, 204 differentially expressed proteins in three subtypes of thymoma, AB, B2, and B3, were identified using mass spectrometry. Pathway analysis showed that the differentially expressed proteins in the three subtypes were involved in activation-related, signaling transduction-related and complement system-related pathways. To predict the subtypes of thymoma using the identified protein signatures, a support vector machine algorithm was used. Leave-one-out cross validation methods and receiver operating characteristic analysis were used to evaluate the predictive performance. RESULTS: The mean accuracy rates were > 80% and areas under the curve were ≧0.93 across these three subtypes. Especially, subtype B3 had the highest accuracy rate (96%) and subtype AB had the greatest area under the curve (0.99). One of the differentially expressed proteins COL17A2 was further validated using immunohistochemistry. CONCLUSIONS: In summary, we identified specific protein signatures for accurately classifying subtypes of thymoma, which could facilitate accurate diagnosis of thymoma patients.

Early Allogeneic Transplantation Favorably Influences the Outcome of Pediatric Acute Myeloid Leukemia-A Retrospective Study in a Single Center Over 2 Decades.

BACKGROUND: Transplantation advancements offer the potential for improving the prognosis of patients with acute myeloid leukemia (AML). Controversies surrounding indications and timing persist. We focused on identifying prognostic factors and exploring the advantages of early transplantation. PATIENTS AND METHODS: We studied 102 pediatric patients with AML (February 1999-August 2022), using Cox regression to analyze survival and hematopoietic cell transplantation (HCT) outcomes and Kaplan-Meier curves to assess HCT timing's impact on prognosis. RESULTS: "Treatment in First Complete Remission [CR1]: Chemotherapy" showed increased risk in multivariate and univariate Cox regression analyses, whereas "HCT during the study period" displayed divergent outcomes. Focusing on transplanted patients, "Treatment in CR1: Chemotherapy" still correlated with higher mortality risk. These findings emphasize the pivotal role of the treatment strategy adopted in CR1 on overall survival rather than HCT alone. Donor cytomegalovirus (CMV) positivity is also related to reduced mortality risk. Kaplan-Meier analysis supported superior 5-year survival rates with "HCT" compared with "chemotherapy" in CR1. In the 3-arm analysis, "HCT in CR1" demonstrated better 5-year overall survival (OS) and 5-year disease-free survival (DFS) compared with "Never HCT," whereas "HCT in CR2" had the least favorable prognosis (5-year OS: 79.2% vs 57.1% vs 50%, P = .056; 5-year DFS: 73.6% vs 55.2% vs 0%, P = .000). CONCLUSION: Our study highlights the benefits of transplantation during CR1 on prognosis. However, when contemplating CR1 transplantation recommendations, evaluation of various factors, such as the patient's clinical state, relapse risk, transplant-related mortality, CMV status, and other pertinent considerations, is vital. Comprehensive case discussions with patients and families are demanded in optimizing treatment.

Blinatumomab in Children with MRD-Positive B-Cell Precursor Acute Lymphoblastic Leukemia: A Report of 11 Cases.

Background/Objectives: Relapsed B-cell acute lymphoblastic leukemia (B-ALL) remains an unresolved matter of concern regarding adverse outcomes. This case study aimed to evaluate the effectiveness of blinatumomab, with or without door lymphocyte infusion (DLI), in treating measurable residual disease (MRD)-positive B-ALL. Methods: All patients who received blinatumomab salvage therapy were included in this study. Eleven patients were included in the study. All patients were evaluated for MRD-negativity. Results: Before starting blinatumomab therapy, seven patients tested positive for MRD, three tested negative, and one had refractory disease. Hematopoietic cell transplantation (HCT) was reserved for five patients with persistent MRD. Six patients became MRD-negative and subsequent HCT was not performed. Only two patients relapsed; one patient died of relapse, and the other one received carfilzomib-based therapy and was MRD-negative thereafter. Nine patients were MRD-negative at a median follow-up of 28 months (15-52 months). Two of three MRD-positive post-transplant patients remained in complete molecular remission after preemptive DLI at the last follow-up date. In the first salvage, blinatumomab may achieve complete remission and bridging to HCT in pediatric patients with end-of-induction MRD-positive B-cell precursor ALL. Conclusions: The decision on how to treat post-transplant relapse continues to affect survival outcomes. Blinatumomab combined with DLI may extend the armamentarium of release options for high-risk pediatric patients. This approach is encouraging for high-risk ALL patients who are MRD-positive post-transplantation.

Outcome of Tocilizumab Treatment in Febrile Neutropenic Children with Severe Sepsis/Septic Shock in a Single-Center Retrospective Case Series.

PURPOSE: To assess the efficacy of an IL-6 blockade with tocilizumab on treatment outcome of severe sepsis/septic shock in children with febrile neutropenia. METHODS: We performed a retrospective study of febrile neutropenic patients younger than 18 years old who developed severe sepsis/septic shock at a single medical center between November 2022 and October 2023. RESULTS: Seven patients with febrile neutropenia complicated with severe sepsis/septic shock were identified. Four of seven patients received tocilizumab in addition to standard of care. The median IL-6 level before administration of tocilizumab was 14,147 pg/mL (range: 672-30,509 pg/mL). All four patients successfully recovered from severe sepsis/septic shock. Three of seven patients received standard of care without tocilizumab. IL-6 levels were checked intwo2 patients, with a median of 1514.5 (range: 838-2191). Only one of three (33%) patients without tocilizumab therapy made a full recovery from severe sepsis/septic shock. The mortality rate was higher in patients without tocilizumab therapy compared to patients with tocilizumab therapy (67% vs. 0%). CONCLUSIONS: Administration of tocilizumab reduced mortality of severe sepsis/septic shock in children with febrile neutropenia. However, it warrants confirmation with a larger number of patients and a longer follow-up.

Immersive Virtual Reality to Distract From Pain in Children Treated With L-asparaginase by Intramuscular Injection.

Background Treatment-related pain and discomfort are two of the most common manifestations in children with acute lymphoblastic leukemia (ALL). Patients with ALL are usually treated with L-asparaginase (L-ASP) by intramuscular injection. Children receiving L-ASP chemotherapy must bear adverse reactions such as pain caused by intramuscular injections. The use of virtual reality (VR) distraction technology could be a non-pharmacological intervention to bolster patients' comfort and decrease anxiety and procedure-related pain within hospital settings. Methodology The study explored the potential benefits of VR as a psychological intervention to induce positive emotions and reduce pain levels in participants receiving L-ASP injections. Participants in the study had the opportunity to select a nature theme of their choosing during their treatment session. The study provided a noninvasive solution that promoted relaxation to reduce anxiety by shifting an individual's mood positively during treatment. The objective was met by measuring participants' mood and pain levels before and after the VR experience and participant satisfaction with the use of the technology. This mixed-methods study of children aged six to 18 received L-ASP between April 2021 and March 2022, using a Numerical Rating Scale (NRS) with sheer numbers ranging from 0 (no pain) to 10 (extreme or most pain possible). Semi-structured interviews were conducted to collect new data and explore participants' thoughts and beliefs about a particular topic. A total of 14 patients participated. Descriptive statistics and content analysis are used to describe the data analyzed. VR is an enjoyable distraction intervention for managing treatment-related pain in ALL with intramuscular chemotherapy. Results Eight of 14 patients found a reduction in perceived pain after wearing VR. During the intervention implementation, the primary caregivers felt that the patient's pain perception was more positive when using the virtual reality device, and there was less resistance and less crying. Conclusions This study describes changes and experiences associated with pain and physical discomfort in children with ALL receiving intramuscular chemotherapy. This teaching model is applied to developing medical personnel, providing information about the disease and daily care, and educating the participants' family members. This study may expand the usage of VR applications so that more patients can benefit from them.

Aloe vera gel for prevention of chemotherapy-induced hyperpigmentation: Four case reports.

RATIONALE: This study aimed to evaluate the efficacy of topical application of Aloe vera gel in preventing chemotherapy-induced hyperpigmentation (CIH). CIH is a common side effect of chemotherapy that causes skin irritation, redness, and itching. Aloe vera has been studied for its potential use in treating radiation-induced dermatitis, which may help alleviate some of the symptoms associated with this condition. PATIENT CONCERNS: In this study, 4 children requiring curative chemotherapy were prospectively enrolled and treated with Aloe vera gel. DIAGNOSIS: Acute skin reactions were monitored and classified according to the Common Terminology Criteria for Adverse Events Grading Scale. INTERVENTIONS: Patients were asked to use the gel on one-half of the body field twice daily from the beginning of treatment until 4 weeks after the completion of chemotherapy, with no medication to be used on the other half. OUTCOMES: The results indicate that applying Aloe vera gel may reduce the visibility of hyperpigmentation at subsequent time points. The most important observation was that the continued application of Aloe vera gel 4 weeks after the completion of chemotherapy was effective in reducing the grading of CIH. LESSONS: These effects highlight the potential of Aloe vera gel as a topical onconutraceutical treatment for CIH.

Race-Specific Genetic Profiles of Homologous Recombination Deficiency in Multiple Cancers.

Homologous recombination deficiency (HRD) has been used to predict both cancer prognosis and the response to DNA-damaging therapies in many cancer types. HRD has diverse manifestations in different cancers and even in different populations. Many screening strategies have been designed for detecting the sensitivity of a patient's HRD status to targeted therapies. However, these approaches suffer from low sensitivity, and are not specific to each cancer type and population group. Therefore, identifying race-specific and targetable HRD-related genes is of clinical importance. Here, we conducted analyses using genomic sequencing data that was generated by the Pan-Cancer Atlas. Collapsing non-synonymous variants with functional damage to HRD-related genes, we analyzed the association between these genes and race within cancer types using the optimal sequencing kernel association test (SKAT-O). We have identified race-specific mutational patterns of curated HRD-related genes across cancers. Overall, more significant mutation sites were found in ATM, BRCA2, POLE, and TOP2B in both the 'White' and 'Asian' populations, whereas PTEN, EGFG, and RIF1 mutations were observed in both the 'White' and 'African American/Black' populations. Furthermore, supported by pathogenic tendency databases and previous reports, in the 'African American/Black' population, several associations, including BLM with breast invasive carcinoma, ERCC5 with ovarian serous cystadenocarcinoma, as well as PTEN with stomach adenocarcinoma, were newly described here. Although several HRD-related genes are common across cancers, many of them were found to be specific to race. Further studies, using a larger cohort of diverse populations, are necessary to identify HRD-related genes that are specific to race, for guiding gene testing methods.

A risk prediction model of gene signatures in ovarian cancer through bagging of GA-XGBoost models.

Introduction: Ovarian cancer (OC) is one of the most frequent gynecologic cancers among women, and high-accuracy risk prediction techniques are essential to effectively select the best intervention strategies and clinical management for OC patients at different risk levels. Current risk prediction models used in OC have low sensitivity, and few of them are able to identify OC patients at high risk of mortality, which would both optimize the treatment of high-risk patients and prevent unnecessary medical intervention in those at low risk. Objectives: To this end, we have developed a bagging-based algorithm with GA-XGBoost models that predicts the risk of death from OC using gene expression profiles. Methods: Four gene expression datasets from public sources were used as training (n = 1) or validation (n = 3) sets. The performance of our proposed algorithm was compared with fine-tuning and other existing methods. Moreover, the biological function of selected genetic features was further interpreted, and the response to a panel of approved drugs was predicted for different risk levels. Results: The proposed algorithm showed good sensitivity (74-100%) in the validation sets, compared with two simple models whose sensitivity only reached 47% and 60%. The prognostic gene signature used in this study was highly connected to AKT, a key component of the PI3K/AKT/mTOR signaling pathway, which influences the tumorigenesis, proliferation, and progression of OC. Conclusion: These findings demonstrated an improvement in the sensitivity of risk classification of OC patients with our risk prediction models compared with other methods. Ongoing effort is needed to validate the outcomes of this approach for precise clinical treatment.

RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow.

RNA-Seq analysis has revolutionized researchers' understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the underlying biological impact of transcription. RNA-Seq analysis requires multiple processing steps and huge computational capabilities. There are many well-developed R packages for individual steps; however, there are few R/Bioconductor packages that integrate existing software tools into a comprehensive RNA-Seq analysis and provide fundamental end-to-end results in pure R environment so that researchers can quickly and easily get fundamental information in big sequencing data. To address this need, we have developed the open source R/Bioconductor package, RNASeqR. It allows users to run an automated RNA-Seq analysis with only six steps, producing essential tabular and graphical results for further biological interpretation. The features of RNASeqR include: six-step analysis, comprehensive visualization, background execution version, and the integration of both R and command-line software. RNASeqR provides fast, light-weight, and easy-to-run RNA-Seq analysis pipeline in pure R environment. It allows users to efficiently utilize popular software tools, including both R/Bioconductor and command-line tools, without predefining the resources or environments. RNASeqR is freely available for Linux and macOS operating systems from Bioconductor (https://bioconductor.org/packages/release/bioc/html/RNASeqR.html).

Rare variants discovery by extensive whole-genome sequencing of the Han Chinese population in Taiwan: Applications to cardiovascular medicine.

Introduction: A population-specific genomic reference is important for research and clinical practice, yet it remains unavailable for Han Chinese (HC) in Taiwan. Objectives: We report the first whole genome sequencing (WGS) database of HC (1000 Taiwanese genome (1KTW-WGS)) and demonstrate several applications to cardiovascular medicine. Methods: Whole genomes of 997 HC were sequenced to at least 30X depth. A total of 20,117 relatively healthy HC individuals were genotyped using a customized Axiom GWAS array. We performed a genome-wide genotype imputation technique using IMPUTE2. Results: We identified 26.7 million single-nucleotide variants (SNVs) and 4.2 million insertions-deletions. Of the SNVs, 16.1% were novel relative to dbSNP (build 152), and 34.2% were novel relative to gnomAD. A total of 18,450 healthy HC individuals were genotyped using a customized Genome-Wide Association Study (GWAS) array. We identified hypertension-associated variants and developed a hypertension prediction model based on the correlation between the WGS data and GWAS data (combined clinical and genetic models, AUC 0.887), and also identified 3 novel hyperlipidemia-associated variants. Each individual carried an average of 16.42 (SD = 3.72) disease-causing variants. Additionally, we established an online SCN5A (an important cardiac gene) database that can be used to explore racial differences. Finally, pharmacogenetics studies identified HC population-specific SNVs in genes (CYP2C9 and VKORC1) involved in drug metabolism and blood clotting. Conclusion: This research demonstrates the benefits of constructing a population-specific genomic reference database for precision medicine.

Tumor-Infiltrating Leukocyte Composition and Prognostic Power in Hepatitis B- and Hepatitis C-Related Hepatocellular Carcinomas.

BACKGROUND: Tumor-infiltrating leukocytes (TILs) are immune cells surrounding tumor cells, and several studies have shown that TILs are potential survival predictors in different cancers. However, few studies have dissected the differences between hepatitis B- and hepatitis C-related hepatocellular carcinoma (HBV-HCC and HCV-HCC). Therefore, we aimed to determine whether the abundance and composition of TILs are potential predictors for survival outcomes in HCC and which TILs are the most significant predictors. METHODS: Two bioinformatics algorithms, ESTIMATE and CIBERSORT, were utilized to analyze the gene expression profiles from 6 datasets, from which the abundance of corresponding TILs was inferred. The ESTIMATE algorithm examined the overall abundance of TILs, whereas the CIBERSORT algorithm reported the relative abundance of 22 different TILs. Both HBV-HCC and HCV-HCC were analyzed. RESULTS: The results indicated that the total abundance of TILs was higher in non-tumor tissue regardless of the HCC type. Alternatively, the specific TILs associated with overall survival (OS) and recurrence-free survival (RFS) varied between subtypes. For example, in HBV-HCC, plasma cells (hazard ratio [HR] = 1.05; 95% CI 1.00-1.10; p = 0.034) and activated dendritic cells (HR = 1.08; 95% CI 1.01-1.17; p = 0.03) were significantly associated with OS, whereas in HCV-HCC, monocytes (HR = 1.21) were significantly associated with OS. Furthermore, for RFS, CD8+ T cells (HR = 0.98) and M0 macrophages (HR = 1.02) were potential biomarkers in HBV-HCC, whereas neutrophils (HR = 1.01) were an independent predictor in HCV-HCC. Lastly, in both HBV-HCC and HCV-HCC, CD8+ T cells (HR = 0.97) and activated dendritic cells (HR = 1.09) had a significant association with OS, while γ delta T cells (HR = 1.04), monocytes (HR = 1.05), M0 macrophages (HR = 1.04), M1 macrophages (HR = 1.02), and activated dendritic cells (HR = 1.15) were highly associated with RFS. Conclusions: These findings demonstrated that TILs are potential survival predictors in HCC and different kinds of TILs are observed according to the virus type. Therefore, further investigations are warranted to elucidate the role of TILs in HCC, which may improve immunotherapy outcomes.

Clinicopathologic Characterization of GREB1-rearranged Uterine Sarcomas With Variable Sex-Cord Differentiation.

Uterine mesenchymal tumors are genetically heterogenous; those with uniform cytomorphology, best exemplified by endometrial stromal tumors, often contain various fusion genes. Novel fusions involving ESR1 and GREB1, key factors in sex hormone pathways, have been implicated in rare uterine mesenchymal tumors. Particularly, the fusions between 5'-ESR1/GREB1 and 3'-NCOA2/NCOA3 were recently identified in 4 uterine tumors resembling ovarian sex-cord tumor (UTROSCT). By RNA sequencing, pathology review, and FISH screening, we identified 4 uterine sarcomas harboring rearranged GREB1, including GREB1-NCOA2 and the novel GREB1-NR4A3, GREB1-SS18, and GREB1-NCOA1, validated by RT-PCR and/or FISH. They occurred in the myometrium of postmenopausal women and were pathologically similar despite minor differences. Tumor cells were generally uniform and epithelioid, with vesicular nuclei and distinct to prominent nucleoli. Growth patterns included solid sheets, trabeculae/cords, nests, and fascicles. Only 1 tumor showed small foci of definitive sex-cord components featuring well-formed tubules, retiform structures, Leydig-like cells, and lipid-laden cells and exhibiting convincing immunoreactivity to sex-cord markers (calretinin, α-inhibin, and Melan-A). In contrast, all the 4 classic UTROSCT we collected occurred in premenopausal patients, consisted predominantly of unequivocal sex-cord elements, prominently expressed multiple sex-cord markers, and harbored ESR1-NCOA3 fusion. Combined with previously reported cases, GREB1-rearranged tumors involved significantly older women (P=0.001), tended to be larger and more mitotically active, showed more variable and often inconspicuous sex-cord differentiation, and appeared to behave more aggressively than ESR1-rearranged UTROSCT. Therefore, these 2 groups of tumors might deserve separate consideration, despite some overlapping features and the possibility of belonging to the same disease spectrum.

Dual immuno-renal targeting of 7-benzylidenenaltrexone alleviates lupus nephritis via FcγRIIB and HO-1.

Known as a selective δ1 opioid receptor (DOR1) antagonist, the 7-benzylidenenaltrexone (BNTX) is also a DOR1-independent immunosuppressant with unknown mechanisms. Here we investigated if BNTX could be beneficial for diseased MRL/lpr lupus mice. We treated mice with 0.5, 2, 5 or 10 mg/kg/day of BNTX for 2 weeks. At as low as 2 mg/kg/day, BNTX significantly improved splenomegaly and lymphadenopathy. Notably, B cell numbers, particularly autoreactive plasma cells, were preferentially reduced; moreover, BNTX enhanced surface expression of FcγRIIB, an immune complex (IC)-dependent apoptotic trigger of B cells. Consequently, serum autoantibody concentrations were significantly decreased, leading to diminished glomerular IC deposition and renal fibrosis, thereby improving proteinuria. Microarray and pathway analyses revealed heme oxygenase-1 (HO-1) and p38 MAPK as key mediators of BNTX-induced upregulation of FcγRIIB. Moreover, HO-1 expression was also induced by BNTX via p38 MAPK at renal proximal tubules to further cytoprotection. Taken together, we demonstrate that BNTX can alleviate lupus nephritis by reducing autoreactive B cells via FcγRIIB and by augmenting renal protection via HO-1. Accordingly, we propose a new strategy to treat lupus nephritis via such a dual immuno-renal targeting using either a single agent or combined agents to simultaneously deplete B cells and enhance renal protection. KEY MESSAGES: 7-Benzylidenenaltrexone (BNTX) alleviates lupus nephritis in diseased MRL/lpr mice. BNTX reduces autoreactive plasma cell numbers and serum autoantibody titers. BNTX upregulates FcγRIIB levels via p38 MAPK and HO-1 to reduce B cell numbers. Reduction of immune complex deposition and fibrosis by BNTX improves proteinuria. BNTX induces HO-1 via p38 MAPK to enhance protection of renal proximal tubules.

A standardized herbal extract mitigates tumor inflammation and augments chemotherapy effect of docetaxel in prostate cancer.

Activation of the NFκB pathway is often associated with advanced cancer and has thus been regarded as a rational therapeutic target. Wedelia chinensis is rich in luteolin, apigenin, and wedelolactone that act synergistically to suppress androgen receptor activity in prostate cancer. Interestingly, our evaluation of a standardized Wedelia chinensis herbal extract (WCE) concluded its efficacy on hormone-refractory prostate cancer through systemic mechanisms. Oral administration of WCE significantly attenuated tumor growth and metastasis in orthotopic PC-3 and DU145 xenografts. Genome-wide transcriptome analysis of these tumors revealed that WCE suppressed the expression of IKKα/ß phosphorylation and downstream cytokines/chemokines, e.g., IL6, CXCL1, and CXCL8. Through restraining the cytokines expression, WCE reduced tumor-elicited infiltration of myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages (TAMs) and endothelial cells into the tumors, therefore inhibiting angiogenesis, tumor growth, and metastasis. In MDSCs, WCE also reduced STAT3 activation, downregulated S100A8 expression and prevented their expansion. Use of WCE in combination with docetaxel significantly suppressed docetaxel-induced NFκB activation, boosted the therapeutic effect and reduced the systemic toxicity caused by docetaxel monotherapy. These data suggest that a standardized preparation of Wedelia chinensis extract improved prostate cancer therapy through immunomodulation and has potential application as an adjuvant agent for castration-resistant prostate cancer.