bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular characterization of sub-frontal recurrent medulloblastomas reveals potential clinical relevance
Authors: Chen Zirong , Yang Huaitao , Wang Jiajia , Long Guoxian , Xi Qingsong , Chen Tao , He Yue , Zhang Bin , Wan Feng
Published: April 2023

Background

Single recurrence in the sub-frontal region after cerebellar medulloblastoma (MB) resection is rare and the underlying molecular characteristics have not been specifically addressed.

Methods

We summarized two such cases in our center. All five samples were molecularly profiled for their genome and transcriptome signatures.

Results

The recurrent tumors displayed genomic and transcriptomic divergence. Pathway analysis of recurrent tumors showed functional convergence in metabolism, cancer, neuroactive ligand–receptor interaction, and PI3K-AKT signaling pathways. Notably, the sub-frontal recurrent tumors had a much higher proportion (50–86%) of acquired driver mutations than that reported in other recurrent locations. The acquired putative driver genes in the sub-frontal recurrent tumors functionally enriched for chromatin remodeler-associated genes, such as KDM6B, SPEN, CHD4, and CHD7. Furthermore, the germline mutations of our cases showed a significant functional convergence in focal adhesion, cell adhesion molecules, and ECM–receptor interaction. Evolutionary analysis showed that the recurrence could be derived from a single primary tumor lineage or had an intermediate phylogenetic similarity to the matched primary one.

Conclusion

Rare single sub-frontal recurrent MBs presented specific mutation signatures that might be related to the under-dose radiation. Particular attention should be paid to optimally covering the sub-frontal cribriform plate during postoperative radiotherapy targeting.
Effects of esketamine on postoperative rebound pain in patients undergoing unilateral total knee arthroplasty: a single-center, randomized, double-blind, placebo-controlled trial protocol
Authors: Zhu Youzhuang , Li Qun , Liu Guilin , Sheng Fang , Zhang Xiaotian , Jiang Lili , Li Shaona , He Jianshuai , Zou Zhijin , Zhang Baobo , Wang Changyao , Jiang Xin , Zhao Yang
Published: April 2023

Introduction

Rebound pain, transient and acute postoperative pain after the disappearance of regional block anesthesia, has been a concern in recent years. Insufficient preemptive analgesia and hyperalgesia induced by regional block are the main mechanisms. At present, the evidence for the treatment of rebound pain is limited. The esketamine, as an antagonist of the N-methyl-D-aspartate receptor, has been proven to prevent hyperalgesia. Therefore, this trial aims to evaluate the impact of esketamine on postoperative rebound pain in patients undergoing total knee arthroplasty.

Methods/design

This study is a single-center, prospective, double-blind, randomized, placebo-controlled trial. Participants who plan to undergo total knee arthroplasty will be randomly assigned to the esketamine group (N = 178) and placebo group (N = 178) in a ratio of 1:1. This trial aims to evaluate the impact of esketamine on postoperative rebound pain in patients undergoing total knee arthroplasty. The primary outcome of this trial is the incidence of rebound pain within 12 h after the operation in the esketamine group and the placebo group. The secondary outcome will be to compare (1) the incidence of rebound pain 24 h after the operation; (2) the time to enter the pain cycle for the first time within 24 h after the procedure; (3) the first time of rebound pain occurred within 24 h after surgery; (4) the modified rebound pain score; (5) NRS score under rest and exercise at different time points; (6) the cumulative opioid consumption at different time points; (7) patient’s prognosis and knee joint function evaluation; (8) blood glucose and cortisol concentration; (9) patient’s satisfaction score; (10) adverse reactions and adverse events.

Discussion

The effect of ketamine on preventing postoperative rebound pain is contradictory and uncertain. The affinity of esketamine to the N-methyl-D-aspartate receptor is about four times higher than levo-ketamine, the analgesic effect is 3 times higher than levo-ketamine, and there are fewer adverse mental reactions. To our knowledge, there is no randomized controlled trial to verify the impact of esketamine on postoperative rebound pain in patients undergoing total knee arthroplasty. Therefore, this trial is expected to fill an important gap in relevant fields and provide novel evidence for individualized pain management.

Clinical Trial Registration

http://www.chictr.org.cn, identifier ChiCTR2300069044.
Integrating media content analysis, reception analysis, and media effects studies
Authors: Schmälzle Ralf , Huskey Richard
Published: April 2023

Every day, the world of media is at our fingertips, whether it is watching movies, listening to the radio, or browsing online media. On average, people spend over 8 h per day consuming messages from the mass media, amounting to a total lifetime dose of more than 20 years in which conceptual content stimulates our brains. Effects from this flood of information range from short-term attention bursts (e.g., by breaking news features or viral ‘memes’) to life-long memories (e.g., of one’s favorite childhood movie), and from micro-level impacts on an individual’s memory, attitudes, and behaviors to macro-level effects on nations or generations. The modern study of media’s influence on society dates back to the 1940s. This body of mass communication scholarship has largely asked, “what is media’s effect on the individual?” Around the time of the cognitive revolution, media psychologists began to ask, “what cognitive processes are involved in media processing?” More recently, neuroimaging researchers started using real-life media as stimuli to examine perception and cognition under more natural conditions. Such research asks: “what can media tell us about brain function?” With some exceptions, these bodies of scholarship often talk past each other. An integration offers new insights into the neurocognitive mechanisms through which media affect single individuals and entire audiences. However, this endeavor faces the same challenges as all interdisciplinary approaches: Researchers with different backgrounds have different levels of expertise, goals, and foci. For instance, neuroimaging researchers label media stimuli as “naturalistic” although they are in many ways rather artificial. Similarly, media experts are typically unfamiliar with the brain. Neither media creators nor neuroscientifically oriented researchers approach media effects from a social scientific perspective, which is the domain of yet another species. In this article, we provide an overview of approaches and traditions to studying media, and we review the emerging literature that aims to connect these streams. We introduce an organizing scheme that connects the causal paths from media content → brain responses → media effects and discuss network control theory as a promising framework to integrate media content, reception, and effects analyses.
Machine learning for the prediction of cognitive impairment in older adults
Authors: Li Wanyue , Zeng Li , Yuan Shiqi , Shang Yaru , Zhuang Weisheng , Chen Zhuoming , Lyu Jun
Published: April 2023

Objective

The purpose of this study was to develop and validate a predictive model of cognitive impairment in older adults based on a novel machine learning (ML) algorithm.

Methods

The complete data of 2,226 participants aged 60–80 years were extracted from the 2011–2014 National Health and Nutrition Examination Survey database. Cognitive abilities were assessed using a composite cognitive functioning score (Z-score) calculated using a correlation test among the Consortium to Establish a Registry for Alzheimer's Disease Word Learning and Delayed Recall tests, Animal Fluency Test, and the Digit Symbol Substitution Test. Thirteen demographic characteristics and risk factors associated with cognitive impairment were considered: age, sex, race, body mass index (BMI), drink, smoke, direct HDL-cholesterol level, stroke history, dietary inflammatory index (DII), glycated hemoglobin (HbA1c), Patient Health Questionnaire-9 (PHQ-9) score, sleep duration, and albumin level. Feature selection is performed using the Boruta algorithm. Model building is performed using ten-fold cross-validation, machine learning (ML) algorithms such as generalized linear model (GLM), random forest (RF), support vector machine (SVM), artificial neural network (ANN), and stochastic gradient boosting (SGB). The performance of these models was evaluated in terms of discriminatory power and clinical application.

Results

The study ultimately included 2,226 older adults for analysis, of whom 384 (17.25%) had cognitive impairment. After random assignment, 1,559 and 667 older adults were included in the training and test sets, respectively. A total of 10 variables such as age, race, BMI, direct HDL-cholesterol level, stroke history, DII, HbA1c, PHQ-9 score, sleep duration, and albumin level were selected to construct the model. GLM, RF, SVM, ANN, and SGB were established to obtain the area under the working characteristic curve of the test set subjects 0.779, 0.754, 0.726, 0.776, and 0.754. Among all models, the GLM model had the best predictive performance in terms of discriminatory power and clinical application.

Conclusions

ML models can be a reliable tool to predict the occurrence of cognitive impairment in older adults. This study used machine learning methods to develop and validate a well performing risk prediction model for the development of cognitive impairment in the elderly.
Integrating CT-based radiomic model with clinical features improves long-term prognostication in high-risk prostate cancer
Authors: Ching Jerry C. F. , Lam Saikit , Lam Cody C. H. , Lui Angie O. Y. , Kwong Joanne C. K. , Lo Anson Y. H. , Chan Jason W. H. , Cai Jing , Leung W. S. , Lee Shara W. Y.
Published: April 2023

Objective

High-risk prostate cancer (PCa) is often treated by prostate-only radiotherapy (PORT) owing to its favourable toxicity profile compared to whole-pelvic radiotherapy. Unfortunately, more than 50% patients still developed disease progression following PORT. Conventional clinical factors may be unable to identify at-risk subgroups in the era of precision medicine. In this study, we aimed to investigate the prognostic value of pre-treatment planning computed tomography (pCT)-based radiomic features and clinical attributes to predict 5-year progression-free survival (PFS) in high-risk PCa patients following PORT.

Materials and methods

A total of 176 biopsy-confirmed PCa patients who were treated at the Hong Kong Princess Margaret Hospital were retrospectively screened for eligibility. Clinical data and pCT of one hundred eligible high-risk PCa patients were analysed. Radiomic features were extracted from the gross-tumour-volume (GTV) with and without applying Laplacian-of-Gaussian (LoG) filter. The entire patient cohort was temporally stratified into a training and an independent validation cohort in a ratio of 3:1. Radiomics (R), clinical (C) and radiomic-clinical (RC) combined models were developed by Ridge regression through 5-fold cross-validation with 100 iterations on the training cohort. A model score was calculated for each model based on the included features. Model classification performance on 5-year PFS was evaluated in the independent validation cohort by average area-under-curve (AUC) of receiver-operating-characteristics (ROC) curve and precision-recall curve (PRC). Delong’s test was used for model comparison.

Results

The RC combined model which contains 6 predictive features (tumour flatness, root-mean-square on fine LoG-filtered image, prostate-specific antigen serum concentration, Gleason score, Roach score and GTV volume) was the best-performing model (AUC = 0.797, 95%CI = 0.768-0.826), which significantly outperformed the R-model (AUC = 0.795, 95%CI = 0.774-0.816) and C-model (AUC = 0.625, 95%CI = 0.585-0.665) in the independent validation cohort. Besides, only the RC model score significantly classified patients in both cohorts into progression and progression-free groups regarding their 5-year PFS (p< 0.05).

Conclusion

Combining pCT-based radiomic and clinical attributes provided superior prognostication value regarding 5-year PFS in high-risk PCa patients following PORT. A large multi-centre study will potentially aid clinicians in implementing personalised treatment for this vulnerable subgroup in the future.
Identification of a prognostic signature and ENTR1 as a prognostic biomarker for colorectal mucinous adenocarcinoma
Authors: Huang An , Shi Jingyi , Sun Zhuang , Yang Yong , Gao Zhaoya , Gu Jin
Published: April 2023

Background

Mucinous adenocarcinoma (MAC) is a unique clinicopathological colorectal cancer (CRC) type that has been recognized as a separate entity from non-mucinous adenocarcinoma (NMAC), with distinct clinical, pathologic, and molecular characteristics. We aimed to construct prognostic signatures and identifying candidate biomarkers for patients with MAC.

Methods

Differential expression analysis, weighted correlation network analysis (WGCNA), and least absolute shrinkage and selection operator (LASSO)-Cox regression model were used to identify hub genes and construct a prognostic signature based on RNA sequencing data from TCGA datasets. The Kaplan-Meier survival curve, gene set enrichment analysis (GSEA), cell stemness, and immune infiltration were analyzed. Biomarker expression in MAC and corresponding normal tissues from patients operated in 2020 was validated using immunohistochemistry.

Results

We constructed a prognostic signature based on ten hub genes. Patients in the high-risk group had significantly worse overall survival (OS) than patients in the low-risk group (p < 0.0001). We also found that ENTR1 was closely associated with OS (p = 0.016). ENTR1 expression was significantly positively correlated with cell stemness of MAC (p < 0.0001) and CD8+ T cell infiltration (p = 0.01), whereas it was negatively associated with stromal scores (p = 0.03). Finally, the higher expression of ENTR1 in MAC tissues than in normal tissues was validated.

Conclusion

We established the first MAC prognostic signature, and determined that ENTR1 could serve as a prognostic marker for MAC.
Systematic review of the perioperative immunotherapy in patients with non-small cell lung cancer: evidence mapping and synthesis
Authors: Ni Yunfeng , Lei Jie , Huang Wan , Wang Jian , Guo Haihua , Lv Feng , Kang Shuhong , Lan Ke , Jiang Tao
Published: April 2023

Objectives

This study aimed to use evidence mapping to provide an overview of immune checkpoint inhibitors (ICIs) as perioperative treatments for non-small cell lung cancer (NSCLC) and to identify areas of this field where future research is most urgently needed.

Methods

Multiple databases (PubMed, EMBASE, Cochrane Library, and Web of Science) were searched to identify clinical trials published up to November 2021 that examined the effect of perioperative ICIs for perioperative treatment of NSCLC. Study design, sample size, patient characteristics, therapeutic regimens, clinical stages, short-term and long-term therapeutic outcomes, surgery associated parameters, and therapeutic safety were examined.

Results

We included 66 trials (3564 patients) and used evidence mapping to characterize the available data. For surgery associated outcomes, sixty-two studies (2480 patients) provided complete information regarding the use of surgery after neoadjuvant immunotherapy and data on R0 resection were available in 42 studies (1680 patients); for short-term clinical outcomes, 57 studies (1842 patients) evaluated pathologic complete response (pCR) after neoadjuvant immunotherapy and most of included studies achieved pCR in the range of 30 to 40%; for long-term clinical outcomes, 15 studies (1932 patients) reported DFS, with a median range of 17.9-53.6 months; and only a few studies reported the safety profiles of perioperative immunotherapies.

Conclusion

Our evidence mapping systematically summarized the results of all clinical trials and studies that examined ICIs as perioperative treatments for NSCLC. The results indicated more studies that evaluate long-term patient outcomes are needed to provide a stronger foundation for the use of these treatments.
Construction of an interferon regulatory factors-related risk model for predicting prognosis, immune microenvironment and immunotherapy in clear cell renal cell carcinoma
Authors: Pan Hao , Lu Wei , Zhang Mengyuan , Liu Chengxiao
Published: April 2023

Background

Interferon regulatory factors (IRFs) played complex and essential roles in progression, prognosis, and immune microenvironment in clear cell renal cell carcinoma (ccRCC). The purpose of this study was to construct a novel IRFs-related risk model to predict prognosis, tumor microenvironment (TME) and immunotherapy response in ccRCC.

Methods

Multi-omics analysis of IRFs in ccRCC was performed based on bulk RNA sequencing and single cell RNA sequencing data. According to the expression profiles of IRFs, the ccRCC samples were clustered by non-negative matrix factorization (NMF) algorithm. Then, least absolute shrinkage and selection operator (LASSO) and Cox regression analyses were applied to construct a risk model to predict prognosis, immune cells infiltration, immunotherapy response and targeted drug sensitivity in ccRCC. Furthermore, a nomogram comprising the risk model and clinical characteristics was established.

Results

Two molecular subtypes with different prognosis, clinical characteristics and infiltration levels of immune cells were identified in ccRCC. The IRFs-related risk model was developed as an independent prognostic indicator in the TCGA-KIRC cohort and validated in the E-MTAB-1980 cohort. The overall survival of patients in the low-risk group was better than that in the high-risk group. The risk model was superior to clinical characteristics and the ClearCode34 model in predicting the prognosis. In addition, a nomogram was developed to improve the clinical utility of the risk model. Moreover, the high-risk group had higher infiltration levels of CD8+ T cell, macrophages, T follicular helper cells and T helper (Th1) cells and activity score of type I IFN response but lower infiltration levels of mast cells and activity score of type II IFN response. Cancer immunity cycle showed that the immune activity score of most steps was remarkably higher in the high-risk group. TIDE scores indicated that patients in the low-risk group were more likely responsive to immunotherapy. Patients in different risk groups showed diverse drug sensitivity to axitinib, sorafenib, gefitinib, erlotinib, dasatinib and rapamycin.

Conclusions

In brief, a robust and effective risk model was developed to predict prognosis, TME characteristics and responses to immunotherapy and targeted drugs in ccRCC, which might provide new insights into personalized and precise therapeutic strategies.
Primary tumor resection in colorectal cancer patients with unresectable distant metastases: a minireview
Authors: Bai Junge , Yang Ming , Liu Zheng , Efetov Sergey , Kayaalp Cuneyt , Dulskas Audrius , Shaw Darcy , Wang Xishan
Published: April 2023

Colorectal cancer (CRC) is the second most common cause of cancer-related death among both men and women worldwide and the third most common cancer overall. About 20% of patients diagnosed with CRC were discovered to have distant metastatic lesions, the majority of which were located in the liver. For the optimum treatment of CRC patients with hepatic metastases, interventional radiologists, medical oncologists, and surgeons must all collaborate. The surgical excision of the primary tumor is an important part of CRC treatment since it has been found to be curative in cases of CRC with minimal metastases. However, given the evidence to date was gathered from retrospective data, there is still controversy over the effectiveness of primary tumor resection (PTR) in improving the median overall survival (OS) and quality of life. Patients who have hepatic metastases make up a very tiny fraction of those who are candidates for resection. With a focus on the PTR, this minireview attempted to review the current advancements in the treatment options for hepatic colorectal metastatic illness. This evaluation also included information on PTR’s risks when performed on individuals with stage IV CRC.
Multiple functions and regulatory network of miR-150 in B lymphocyte-related diseases
Authors: Hu Yue-Zi , Li Qiao , Wang Peng-Fei , Li Xue-Ping , Hu Zhao-Lan
Published: April 2023

MicroRNAs (miRNAs) play vital roles in the post-transcriptional regulation of gene expression. Previous studies have shown that miR-150 is a crucial regulator of B cell proliferation, differentiation, metabolism, and apoptosis. miR-150 regulates the immune homeostasis during the development of obesity and is aberrantly expressed in multiple B-cell-related malignant tumors. Additionally, the altered expression of MIR-150 is a diagnostic biomarker of various autoimmune diseases. Furthermore, exosome-derived miR-150 is considered as prognostic tool in B cell lymphoma, autoimmune diseases and immune-mediated disorders, suggesting miR-150 plays a vital role in disease onset and progression. In this review, we summarized the miR-150-dependent regulation of B cell function in B cell-related immune diseases.
Breast cancer diagnosis using the fast learning network algorithm
Authors: Albadr Musatafa Abbas Abbood , Ayob Masri , Tiun Sabrina , AL-Dhief Fahad Taha , Arram Anas , Khalaf Sura
Published: April 2023

The use of machine learning (ML) and data mining algorithms in the diagnosis of breast cancer (BC) has recently received a lot of attention. The majority of these efforts, however, still require improvement since either they were not statistically evaluated or they were evaluated using insufficient assessment metrics, or both. One of the most recent and effective ML algorithms, fast learning network (FLN), may be seen as a reputable and efficient approach for classifying data; however, it has not been applied to the problem of BC diagnosis. Therefore, this study proposes the FLN algorithm in order to improve the accuracy of the BC diagnosis. The FLN algorithm has the capability to a) eliminate overfitting, b) solve the issues of both binary and multiclass classification, and c) perform like a kernel-based support vector machine with a structure of the neural network. In this study, two BC databases (Wisconsin Breast Cancer Database (WBCD) and Wisconsin Diagnostic Breast Cancer (WDBC)) were used to assess the performance of the FLN algorithm. The results of the experiment demonstrated the great performance of the suggested FLN method, which achieved an average of accuracy 98.37%, precision 95.94%, recall 99.40%, F-measure 97.64%, G-mean 97.65%, MCC 96.44%, and specificity 97.85% using the WBCD, as well as achieved an average of accuracy 96.88%, precision 94.84%, recall 96.81%, F-measure 95.80%, G-mean 95.81%, MCC 93.35%, and specificity 96.96% using the WDBC database. This suggests that the FLN algorithm is a reliable classifier for diagnosing BC and may be useful for resolving other application-related problems in the healthcare sector.
The emerging nanomedicine-based technology for non-small cell lung cancer immunotherapy: how far are we from an effective treatment
Authors: Peng Lei , Xu Quan , Yin Sui , Zhang Ye , Wu Hao , Liu Yangchun , Chen Liru , Hu Yeji , Yuan Jun , Peng Kai , Lin Qin
Published: April 2023

Non-small cell lung cancer (NSCLC) is a prominent etiology of cancer-related mortality. The heterogeneous nature of this disease impedes its accurate diagnosis and efficacious treatment. Consequently, constant advancements in research are imperative in order to comprehend its intricate nature. In addition to currently available therapies, the utilization of nanotechnology presents an opportunity to enhance the clinical outcomes of NSCLC patients. Notably, the burgeoning knowledge of the interaction between the immune system and cancer itself paves the way for developing novel, emerging immunotherapies for treating NSCLC in the early stages of the disease. It is believed that with the novel engineering avenues of nanomedicine, there is a possibility to overcome the inherent limitations derived from conventional and emerging treatments, such as off-site drug cytotoxicity, drug resistance, and administration methods. Combining nanotechnology with the convergence points of current therapies could open up new avenues for meeting the unmet needs of NSCLC treatment.
ER predicts poor prognosis in male lung squamous cell cancer of stage IIIA-N2 disease after sequential adjuvant chemoradiotherapy
Authors: Yang Xue , Wang Lili , Jin Xiangfeng , Xu Rongjian , Yu Zhuang , Li Hongmei , Lu Haijun , An Ning
Published: April 2023

Introduction

The efficacy of postoperative radiotherapy (PORT) is still unclear in non-small cell lung cancer (NSCLC) patients with pIIIA-N2 disease. Estrogen receptor (ER) was proven significantly associated with poor clinical outcome of male lung squamous cell cancer (LUSC) after R0 resection in our previous study.

Methods

A total of 124 male pIIIA-N2 LUSC patients who completed four cycles of adjuvant chemotherapy and PORT after complete resection were eligible for enrollment in this study from October 2016 to December 2021. ER expression was evaluated using immunohistochemistry assay.

Results

The median follow-up was 29.7 months. Among 124 patients, 46 (37.1%) were ER positive (stained tumor cells≥1%), and the rest 78 (62.9%) were ER negative. Eleven clinical factors considered in this study were well balanced between ER+ and ER- groups. ER expression significantly predicted a poor prognosis in disease-free survival (DFS, HR=2.507; 95% CI: 1.629-3.857; log-rank p=1.60×10-5). The 3-year DFS rates were 37.8% with ER- vs. 5.7% with ER+, with median DFS 25.9 vs. 12.6 months, respectively. The significant prognostic advantage in ER- patients was also observed in overall survival (OS), local recurrence free survival (LRFS), and distant metastasis free survival (DMFS). The 3-year OS rates were 59.7% with ER- vs. 48.2% with ER+ (HR, 1.859; 95% CI: 1.132-3.053; log-rank p=0.013), the 3-year LRFS rates were 44.1% vs. 15.3% (HR=2.616; 95% CI: 1.685-4.061; log-rank p=8.80×10-6), and the 3-year DMFS rates were 45.3% vs. 31.8% (HR=1.628; 95% CI: 1.019-2.601; log-rank p=0.039). Cox regression analyses indicated that ER status was the only significant factor for DFS (p=2.940×10-5), OS (p=0.014), LRFS (p=1.825×10-5) and DMFS (p=0.041) among other 11 clinical factors.

Conclusions

PORT might be more beneficial for ER negative LUSCs in male, and the examination of ER status might be helpful in identifying patients suitable for PORT.
Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls
Authors: Grandt Caine Lucas , Brackmann Lara Kim , Poplawski Alicia , Schwarz Heike , Marini Federico , Hankeln Thomas , Galetzka Danuta , Zahnreich Sebastian , Mirsch Johanna , Spix Claudia , Blettner Maria , Schmidberger Heinz , Marron Manuela
Published: April 2023

Introduction

Long non-coding ribonucleic acids (lncRNAs) are involved in the cellular damage response following exposure to ionizing radiation as applied in radiotherapy. However, the role of lncRNAs in radiation response concerning intrinsic susceptibility to late effects of radiation exposure has not been examined in general or in long-term survivors of childhood cancer with and without potentially radiotherapy-related second primary cancers, in particular.

Methods

Primary skin fibroblasts (n=52 each) of long-term childhood cancer survivors with a first primary cancer only (N1), at least one second primary neoplasm (N2+), as well as tumor-free controls (N0) from the KiKme case-control study were matched by sex, age, and additionally by year of diagnosis and entity of the first primary cancer. Fibroblasts were exposed to 0.05 and 2 Gray (Gy) X-rays. Differentially expressed lncRNAs were identified with and without interaction terms for donor group and dose. Weighted co-expression networks of lncRNA and mRNA were constructed using WGCNA. Resulting gene sets (modules) were correlated to the radiation doses and analyzed for biological function.

Results

After irradiation with 0.05Gy, few lncRNAs were differentially expressed (N0: AC004801.4; N1: PCCA-DT, AF129075.3, LINC00691, AL158206.1; N2+: LINC02315). In reaction to 2 Gy, the number of differentially expressed lncRNAs was higher (N0: 152, N1: 169, N2+: 146). After 2 Gy, AL109976.1 and AL158206.1 were prominently upregulated in all donor groups. The co-expression analysis identified two modules containing lncRNAs that were associated with 2 Gy (module1: 102 mRNAs and 4 lncRNAs: AL158206.1, AL109976.1, AC092171.5, TYMSOS, associated with p53-mediated reaction to DNA damage; module2: 390 mRNAs, 7 lncRNAs: AC004943.2, AC012073.1, AC026401.3, AC092718.4, MIR31HG, STXBP5-AS1, TMPO-AS1, associated with cell cycle regulation).

Discussion

For the first time, we identified the lncRNAs AL158206.1 and AL109976.1 as involved in the radiation response in primary fibroblasts by differential expression analysis. The co-expression analysis revealed a role of these lncRNAs in the DNA damage response and cell cycle regulation post-IR. These transcripts may be targets in cancer therapy against radiosensitivity, as well as provide grounds for the identification of at-risk patients for immediate adverse reactions in healthy tissues. With this work we deliver a broad basis and new leads for the examination of lncRNAs in the radiation response.
An anoikis-related gene signature predicts prognosis and reveals immune infiltration in hepatocellular carcinoma
Authors: Chen Yang , Lin Qiao-xin , Xu Yi-ting , Qian Fang-jing , Lin Chen-jing , Zhao Wen-ya , Huang Jing-ren , Tian Ling , Gu Dian-na
Published: April 2023

Background

Hepatocellular carcinoma (HCC) is a global health burden with poor prognosis. Anoikis, a novel programmed cell death, has a close interaction with metastasis and progression of cancer. In this study, we aimed to construct a novel bioinformatics model for evaluating the prognosis of HCC based on anoikis-related gene signatures as well as exploring the potential mechanisms.

Materials and methods

We downloaded the RNA expression profiles and clinical data of liver hepatocellular carcinoma from TCGA database, ICGC database and GEO database. DEG analysis was performed using TCGA and verified in the GEO database. The anoikis-related risk score was developed via univariate Cox regression, LASSO Cox regression and multivariate Cox regression, which was then used to categorize patients into high- and low-risk groups. Then GO and KEGG enrichment analyses were performed to investigate the function between the two groups. CIBERSORT was used for determining the fractions of 22 immune cell types, while the ssGSEA analyses was used to estimate the differential immune cell infiltrations and related pathways. The “pRRophetic” R package was applied to predict the sensitivity of administering chemotherapeutic and targeted drugs.

Results

A total of 49 anoikis-related DEGs in HCC were detected and 3 genes (EZH2, KIF18A and NQO1) were selected out to build a prognostic model. Furthermore, GO and KEGG functional enrichment analyses indicated that the difference in overall survival between risk groups was closely related to cell cycle pathway. Notably, further analyses found the frequency of tumor mutations, immune infiltration level and expression of immune checkpoints were significantly different between the two risk groups, and the results of the immunotherapy cohort showed that patients in the high-risk group have a better immune response. Additionally, the high-risk group was found to have higher sensitivity to 5-fluorouracil, doxorubicin and gemcitabine.

Conclusion

The novel signature of 3 anoikis-related genes (EZH2, KIF18A and NQO1) can predict the prognosis of patients with HCC, and provide a revealing insight into personalized treatments in HCC.
IDO1 and inflammatory neovascularization: bringing new blood to tumor-promoting inflammation
Authors: Muller Alexander J. , Mondal Arpita , Dey Souvik , Prendergast George C.
Published: April 2023

In parallel with the genetic and epigenetic changes that accumulate in tumor cells, chronic tumor-promoting inflammation establishes a local microenvironment that fosters the development of malignancy. While knowledge of the specific factors that distinguish tumor-promoting from non-tumor-promoting inflammation remains inchoate, nevertheless, as highlighted in this series on the ‘Hallmarks of Cancer’, it is clear that tumor-promoting inflammation is essential to neoplasia and metastatic progression making identification of specific factors critical. Studies of immunometabolism and inflamometabolism have revealed a role for the tryptophan catabolizing enzyme IDO1 as a core element in tumor-promoting inflammation. At one level, IDO1 expression promotes immune tolerance to tumor antigens, thereby helping tumors evade adaptive immune control. Additionally, recent findings indicate that IDO1 also promotes tumor neovascularization by subverting local innate immunity. This newly recognized function for IDO1 is mediated by a unique myeloid cell population termed IDVCs (IDO1-dependent vascularizing cells). Initially identified in metastatic lesions, IDVCs may exert broader effects on pathologic neovascularization in various disease settings. Mechanistically, induction of IDO1 expression in IDVCs by the inflammatory cytokine IFNγ blocks the antagonistic effect of IFNγ on neovascularization by stimulating the expression of IL6, a powerful pro-angiogenic cytokine. By contributing to vascular access, this newly ascribed function for IDO1 aligns with its involvement in other cancer hallmark functionalities, (tumor-promoting inflammation, immune escape, altered cellular metabolism, metastasis), which may stem from an underlying role in normal physiological functions such as wound healing and pregnancy. Understanding the nuances of how IDO1 involvement in these cancer hallmark functionalities varies between different tumor settings will be crucial to the future development of successful IDO1-directed therapies.
Bibliometric analysis of ferroptosis: a comprehensive evaluation of its contribution to cancer immunity and immunotherapy
Authors: Wang Zhen , Zhang Hui , Wang Li , Ma Zhen , Cui Yu’ang , Fu Haitian , Yu Chunjing
Published: April 2023

Background

In the past 5 years, ferroptosis-associated cancer immunity has been attracted significant research interest.

Objective

This study was performed to identify and analyze the global output trend for ferroptosis in cancer immunity.

Methods

Relevant studies were retrieved from the Web of Science Core Collection on Feb 10th, 2023. The VOSviewer and Histcite softwares were utilized to perform the visual bibliometric and deep mining analyses.

Results

A total of 694 studies (530 articles (76.4%) and 164 (23.6%) review articles) were retrieved from the Web of Science Core Collection for visualization analyses. The top 3 key keywords were ferroptosis, prognosis and immunotherapy. The top 30 local citation score (LCS) authors were all collaborators of Zou Weiping. Deep mining of 51 nanoparticle-related articles showed that BIOMATERIALS was the most popular journal. The primary goal of gene signatures related to ferroptosis and cancer immunity was to establish prognostic predictions.

Conclusion

There has been a significant increase in ferroptosis-associated immune publications in the recent 3 years. The key research hotspots include mechanisms, prediction and therapeutic outcomes. The most influential article was from the Zou Weiping’s group, which proposed that system xc-mediated ferroptosis is induced by CD8(+) T cell-secreted IFNγ after PD-L1 blockage for immunotherapy. The frontier of research in the field of ferroptosis-associated immune is the study on nanoparticle and gene signature The limitation of this bibliometric study is that publications on this topic are few.
Immunosuppressant drugs and quality-of-life outcomes in kidney transplant recipients: An international cohort study (EU-TRAIN)
Authors: Girardin François R. , Nicolet Anna , Bestard Oriol , Lefaucheur Carmen , Budde Klemens , Halleck Fabian , Brouard Sophie , Giral Magali , Gourraud Pierre-Antoine , Horcholle Béatrice , Villard Jean , Marti Joachim , Loupy Alexandre
Published: April 2023

Introduction: Patient-Reported Outcomes (PRO) integrate a wide range of holistic dimensions that arenot captured within clinical outcomes. Particularly, from induction treatment to maintenance therapy, patient quality-of-life (QoL) of kidney transplant recipients have been sparsely investigated in international settings.

Methods: In a prospective, multi-centric cohort study, including nine transplant centers in four countries, we explored the QoL during the year following transplantation using validated elicitation instruments (EQ-5D-3L index with VAS) in a population of kidney transplant patients receiving immunosuppressive therapies. Calcineurin inhibitors (tacrolimus and ciclosporin), IMPD inhibitor (mycophenolate mofetil), and mTOR inhibitors (everolimus and sirolimus) were the standard-of-care (SOC) medications, together with tapering glucocorticoid therapy. We used EQ-5D and VAS data as QoL measures alongside descriptive statistics at inclusion, per country and hospital center. We computed the proportions of patients with different immunosuppressive therapy patterns, and using bivariate and multivariate analyses, assessed the variations of EQ-5D and VAS between baseline (i.e., inclusion Month 0) and follow up visits (Month 12).

Results: Among 542 kidney transplant patients included and followed from November 2018 to June 2021, 491 filled at least one QoL questionnaire at least at baseline (Month 0). The majority of patients in all countries received tacrolimus and mycophenolate mofetil, ranging from 90.0% in Switzerland and Spain to 95.8% in Germany. At M12, a significant proportion of patients switched immunosuppressive drugs, with proportion varying from 20% in Germany to 40% in Spain and Switzerland. At visit M12, patients who kept SOC therapy had higher EQ-5D (by 8 percentage points, p < 0.05) and VAS (by 4 percentage points, p < 0.1) scores than switchers. VAS scores were generally lower than EQ-5D (mean 0.68 [0.5–0.8] vs. 0.85 [0.8–1]).

Discussion: Although overall a positive trend in QoL was observed, the formal analyses did not show any significant improvements in EQ-5D scores or VAS. Only when the effect of a therapy use was separated from the effect of switching, the VAS score was significantly worse for switchers during the follow up period, irrespective of the therapy type. If adjusted for patient characteristics and medical history (e.g., gender, BMI, eGRF, history of diabetes), VAS and EQ-5D delivered sound PRO measures for QoL assessments during the year following renal transplantation.
SARS-CoV-2 infection dysregulates the expression of clinically relevant drug metabolizing enzymes in Vero E6 cells and membrane transporters in human lung tissues
Authors: Nwabufo Chukwunonso K. , Hoque Md. Tozammel , Yip Lily , Khara Maliha , Mubareka Samira , Pollanen Michael S. , Bendayan Reina
Published: April 2023

SARS-CoV-2-mediated interactions with drug metabolizing enzymes and membrane transporters (DMETs) in different tissues, especially lung, the main affected organ may limit the clinical efficacy and safety profile of promising COVID-19 drugs. Herein, we investigated whether SARS-CoV-2 infection could dysregulate the expression of 25 clinically relevant DMETs in Vero E6 cells and postmortem lung tissues from COVID-19 patients. Also, we assessed the role of 2 inflammatory and 4 regulatory proteins in modulating the dysregulation of DMETs in human lung tissues. We showed for the first time that SARS-CoV-2 infection dysregulates CYP3A4 and UGT1A1 at the mRNA level, as well as P-gp and MRP1 at the protein level, in Vero E6 cells and postmortem human lung tissues, respectively. We observed that at the cellular level, DMETs could potentially be dysregulated by SARS-CoV-2-associated inflammatory response and lung injury. We uncovered the pulmonary cellular localization of CYP1A2, CYP2C8, CYP2C9, and CYP2D6, as well as ENT1 and ENT2 in human lung tissues, and observed that the presence of inflammatory cells is the major driving force for the discrepancy in the localization of DMETs between COVID-19 and control human lung tissues. Because alveolar epithelial cells and lymphocytes are both sites of SARS-CoV-2 infection and localization of DMETs, we recommend further investigation of the pulmonary pharmacokinetic profile of current COVID-19 drug dosing regimen to improve clinical outcomes.
Suvorexant, an FDA-approved dual orexin receptor antagonist, reduces oxycodone self-administration and conditioned reinstatement in male and female rats
Authors: Illenberger Jessica M. , Flores-Ramirez Francisco J. , Matzeu Alessandra , Mason Barbara J. , Martin-Fardon Rémi
Published: April 2023

Background: The Department of Health and Human Services reports that prescription pain reliever (e.g., oxycodone) misuse was initiated by 4,400 Americans each day in 2019. Amid the opioid crisis, effective strategies to prevent and treat prescription opioid use disorder (OUD) are pressing. In preclinical models, the orexin system is recruited by drugs of abuse, and blockade of orexin receptors (OX receptors) prevents drug-seeking behavior. The present study sought to determine whether repurposing suvorexant (SUV), a dual OX receptor antagonist marketed for the treatment of insomnia, can treat two features of prescription OUD: exaggerated consumption and relapse.

Methods: Male and female Wistar rats were trained to self-administer oxycodone (0.15 mg/kg, i. v., 8 h/day) in the presence of a contextual/discriminative stimulus (SD) and the ability of SUV (0–20 mg/kg, p. o.) to decrease oxycodone self-administration was tested. After self-administration testing, the rats underwent extinction training, after which we tested the ability of SUV (0 and 20 mg/kg, p. o.) to prevent reinstatement of oxycodone seeking elicited by the SD.

Results: The rats acquired oxycodone self-administration and intake was correlated with the signs of physical opioid withdrawal. Additionally, females self-administered approximately twice as much oxycodone as males. Although SUV had no overall effect on oxycodone self-administration, scrutiny of the 8-h time-course revealed that 20 mg/kg SUV decreased oxycodone self-administration during the first hour in males and females. The oxycodone SD elicited strong reinstatement of oxycodone-seeking behavior that was significantly more robust in females. Suvorexant blocked oxycodone seeking in males and reduced it in females.

Conclusions: These results support the targeting of OX receptors for the treatment for prescription OUD and repurposing SUV as pharmacotherapy for OUD.
When we shouldn’t borrow information from an existing network of trials for planning a new trial
Authors: Ye Fangshu , Wang Chong , O’Connor Annette M.
Published: April 2023

Introduction: To achieve higher power or increased precision for a new trial, methods based on updating network meta-analysis (NMA) have been proposed by researchers. However, this approach could potentially lead to misinterpreted results and misstated conclusions. This work aims to investigate the potential inflation of type I error risk when a new trial is conducted only when, based on a p-value of the comparison in the existing network, a “promising” difference between two treatments is noticed.

Methods: We use simulations to evaluate the scenarios of interest. In particular, a new trial is to be conducted independently or depending on the results from previous NMA in various scenarios. Three analysis methods are applied to each simulation scenario: with the existing network, sequential analysis and without the existing network.

Results: For the scenario that the new trial will be conducted only when a promising finding (p-value <5%) is indicated by the existing network, the type I error risk increased dramatically (38.5% in our example data) when analyzed with the existing network and sequential analysis. The type I error is controlled at 5% when analyzing the new trial without the existing network.

Conclusion: If the intention is to combine a trial result with an existing network of evidence, or if it is expected that the trial will eventually be included in a network meta-analysis, then the decision that a new trial is performed should not depend on a statistically “promising” finding indicated by the existing network.
Therapeutic effects of Crataegus monogyna inhibitors against breast cancer
Authors: Basavarajappa Girish Meravanige , Rehman Abdur , Shiroorkar Predeepkumar Narayanappa , Sreeharsha Nagaraja , Anwer Md. Khalid , Aloufi Bandar
Published: April 2023

Breast cancer is a silent killer disorder among women and a serious economic burden in healthcare management. Every 19 s, a woman is diagnosed with breast cancer, and every 74 s, a woman worldwide passes away from the disease. Despite the increase in progressive research, advanced treatment approaches, and preventive measures, breast cancer rates continue to increase. This study provides a combination of data mining, network pharmacology, and docking analysis that surely could revolutionize cancer treatment by exploiting prestigious phytochemicals. Crataegus monogyna is a small, rounded deciduous tree with glossy, deeply lobed leaves and flat sprays of cream flowers, followed by dark red berries in autumn. Various studies demonstrated that C. monogyna is therapeutically effective against breast cancer. However, the particular molecular mechanism is still unknown. This study is credited for locating bioactive substances, metabolic pathways, and target genes for breast cancer treatment. According to the current investigation, which examined compound–target genes–pathway networks, it was found that the bioactive compounds of C. monogyna may operate as a viable solution against breast cancer by altering the target genes implicated in the disease pathogenesis. The expression level of target genes was analyzed using GSE36295 microarray data. Docking analysis and molecular dynamic simulation studies further strengthened the current findings by validating the effective activity of the bioactive compounds against putative target genes. In summary, we propose that six key compounds, luteolin, apigenin, quercetin, kaempferol, ursolic acid, and oleanolic acid, contributed to the development of breast cancer by affecting the MMP9 and PPARG proteins. Integration of network pharmacology and bioinformatics revealed C. monogyna’s multitarget pharmacological mechanisms against breast cancer. This study provides convincing evidence that C. monogyna might partially alleviate breast cancer and ultimately lays a foundation for further experimental research on the anti-breast cancer activity of C. monogyna.