bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data
Authors: Hafstað Völundur , Häkkinen Jari , Persson Helena
Published: September 2023

Background

In cancer, genomic rearrangements can create fusion genes that either combine protein-coding sequences from two different partner genes or place one gene under the control of the promoter of another gene. These fusion genes can act as oncogenic drivers in tumor development and several fusions involving kinases have been successfully exploited as drug targets. Expressed fusions can be identified in RNA sequencing (RNA-Seq) data, but fusion prediction software often has a high fraction of false positive fusion transcript predictions. This is problematic for both research and clinical applications.

Results

We describe a method for validation of fusion transcripts detected by RNA-Seq in matched whole-genome sequencing (WGS) data. Our pipeline uses discordant read pairs to identify supported fusion events and analyzes soft-clipped read alignments to determine genomic breakpoints. We have tested it on matched RNA-Seq and WGS data for both tumors and cancer cell lines and show that it can be used to validate both new predicted gene fusions and experimentally validated fusion events. It was considerably faster and more sensitive than using BreakDancer and Manta, software that is instead designed to detect many different types of structural variants on a genome-wide scale.

Conclusions

We have developed a fast and very sensitive pipeline for validation of gene fusions detected by RNA-Seq in matched WGS data. It can be used to identify high-quality gene fusions for further bioinformatic and experimental studies, including validation of genomic breakpoints and studies of the mechanisms that generate fusions. In a clinical setting, it could help find expressed gene fusions for personalized therapy.
Identification and characterization of SCCmec typing with psm-mec positivity in staphylococci from patients with coagulase-negative staphylococci peritoneal dialysis-related peritonitis
Authors: Zhou Jun , Yang Chuishun , Lei Wenjuan , Xu Man , Cai Xingli , Yuan Wanqiong , Lin Hua
Published: September 2023

Background

Peritonitis is the most important complication of peritoneal dialysis (PD) and coagulase-negative staphylococci (CNS) are a frequent cause of dialysis-related infections. The association between SCCmec typing with psm-mec positivity in staphylococci and PD-related infections has not been identified. We aim to investigate the molecular epidemiology of CNS isolated from PD-peritonitis in a single Chinese center, focusing on the genetic determinants conferring methicillin resistance.

Methods

We collected 10 genetically unrelated CNS isolates from 10 patients with CNS PD-related peritonitis. The patients were divided into two groups based on the results of MIC to oxacillin: the methicillin-resistant CNS (MRCNS) and methicillin-sensitive CNS (MSCNS) groups. The biofilm formation group (BFG) and the non-biofilm formation group (NBFG) were used as the control groups. Phenotypic and molecular methods were used to analyze SCCmec types I, II and III, associated genes and biofilm formation and the existence of psm-mec. The demographic data and clinical indicators were collected.

Results

Ten CNS PD-related peritonitis patients were enrolled for this study. There were 6 MRCNS and 4 MRCNS isolates. SCCmec types were fully determined in 10 isolates. Seven staphylococci (70%) carried SCCmec, of which 4 isolates carried single SCCmec type I (40%) and 3 isolates had multiple SCCmec elements (I + III). Of the 6 MRCNS isolates, 3 carried SCCmec type I (50%) and 2 isolates carried SCCmec type I + III (33.3%). A high diversity of ccr types, mec complexes and ccr-mec complex combinations was identified among the 10 CNS isolates. The psm-mec gene was detected in 2/10 (20%) CNS isolates. There was no mutation in the psm-mec gene.

Conclusions

The majority of isolates were hospital-associated isolates. Furthermore, 2 psm-mec positive isolates were MRCNS in the NBFG. The PD patients frequent exposure to hospital would be the main risk factor. The presence of the psm-mec signal in the spectra of the MRCNS tested here demonstrates the presence of certain SCCmec cassettes that convey methicillin resistance.
Timely support for promoting mental wellbeing among families with young children –an interview study exploring the experiences of multi-professional practitioners in Finland
Authors: Viklund Emilia W. E. , Forsman Anna K. , Nordmyr Johanna
Published: September 2023

Background

Childhood is a critical period for promoting mental wellbeing and previous research suggests that various family-focused mental health promotion and early prevention initiatives are effective. The aim of the study was to explore Finnish health and social care practitioners’ views and experiences of mental health promotion practice targeting families with young children.

Methods

Individual semi-structured interviews with 14 practitioners representing various municipal services, faith-based and third sector organizations were conducted in 2021 and analysed using thematic analysis.

Results

Various challenges and opportunities for supporting mental health related to both structural features of the health and social care landscape and the varying needs of families were identified. The lack of resources as well as the social stigma associated with mental health problems and with public welfare services, hindered proactive work approaches and timely support. However, low-threshold initiatives and adapted information to families as well as further training about mental health for practitioners together with multi-professional collaboration and teamwork were suggested as potential enablers for mental health promotion.

Conclusions

The study highlights the importance of reaching families in a timely manner in order to promote mental wellbeing and prevent mental health problems. The findings, bringing to the fore the practitioners’ own experiences and views, suggest how current practice could be developed in order to safeguard mental health and wellbeing for all families with young children. The practitioners’ views and experiences are key components when building future sustainable and proactive health and social care services.
Remote evaluation of sleep to enhance understanding of early dementia due to Alzheimer’s Disease (RESTED-AD): an observational cohort study protocol
Authors: Blackman Jonathan , Morrison Hamish Duncan , Gabb Victoria , Biswas Bijetri , Li Haoxuan , Turner Nicholas , Jolly Amy , Trender William , Hampshire Adam , Whone Alan , Coulthard Elizabeth
Published: September 2023

Background

Sleep and circadian rhythm disorders are well recognised in both AD (Alzheimer’s Disease) dementia and MCI-AD (Mild Cognitive Impairment due to Alzheimer’s Disease). Such abnormalities include insomnia, excessive daytime sleepiness, decreased sleep efficiency, increased sleep fragmentation and sundowning.

Enhancing understanding of sleep abnormalities may unveil targets for intervention in sleep, a promising approach given hypotheses that sleep disorders may exacerbate AD pathological progression and represent a contributory factor toward impaired cognitive performance and worse quality of life. This may also permit early diagnosis of AD pathology, widely acknowledged as a pre-requisite for future disease-modifying therapies.

This study aims to bridge the divide between in-laboratory polysomnographic studies which allow for rich characterisation of sleep but in an unnatural setting, and naturalistic studies typically approximating sleep through use of non-EEG wearable devices. It is also designed to record sleep patterns over a 2 month duration sufficient to capture both infradian rhythm and compensatory responses following suboptimal sleep. Finally, it harnesses an extensively phenotyped population including with AD blood biomarkers.

Its principal aims are to improve characterisation of sleep and biological rhythms in individuals with AD, particularly focusing on micro-architectural measures of sleep, compensatory responses to suboptimal sleep and the relationship between sleep parameters, biological rhythms and cognitive performance.

Methods/design

This observational cohort study has two arms (AD-MCI / mild AD dementia and aged-matched healthy adults). Each participant undergoes a baseline visit for collection of demographic, physiological and neuropsychological information utilising validated questionnaires. The main study period involves 7 nights of home-based multi-channel EEG sleep recording nested within an 8-week study period involving continuous wrist-worn actigraphy, sleep diaries and regular brief cognitive tests. Measurement of sleep parameters will be at home thereby obtaining a real-world, naturalistic dataset. Cognitive testing will be repeated at 6 months to stratify participants by longitudinal disease progression.

Discussion

This study will generate new insights particularly in micro-architectural measures of sleep, circadian patterns and compensatory sleep responses in a population with and without AD neurodegenerative change. It aims to enhance standards of remotely based sleep research through use of a well-phenotyped population and advanced sleep measurement technology.
Small molecule targeting of the p38/Mk2 stress signaling pathways to improve cancer treatment
Authors: Alimbetov D. , Umbayev B. , Tsoy A. , Begimbetova D. , Davis T. , Kipling D. , Askarova Sh.
Published: September 2023

Purpose

Although a long-term goal of cancer therapy always has been the development of agents that selectively destroy cancer cells, more recent trends have been to seek secondary agents that sensitize cancer cells to existing treatment regimens. In this regard, the present study explored the possibility of using small molecule inhibitors of p38MAPK/MK2 stress signaling pathways as potential agents to enhance the sensitivity of cancer cells with abrogated G1 checkpoint to the DNA damaging agent etoposide by specifically targeting the DNA damage-induced G2 cell cycle checkpoint.

Methods

We have applied CCK8 and FACS-based viability assays and cell cycle analysis to investigate the effect of small molecules SB203580 and MK2.III on the sensitivity of small cell lung cancer cells (SCLC) that lack the G1 checkpoint to the DNA damaging agent Etoposide when used in combination. We have also assessed the effectiveness of combination chemotherapy on tumor xenograft suppression with etoposide and MK2.III in immunosuppressed mice. In addition, additional CCK8 cell viability analysis of the MDA-MB-231 breast cancer cell line, and SW620, and SW480 colorectal cancer cell lines was performed.

Results

Results suggest that etoposide produces a profound effect on the cell cycle profile of cells in a manner that is consistent with the degree of cell viability that is seen using the viable cell assay. Results of the co-treatment experiments revealed that the p38/MK2 kinase inhibitors SB203580 and MK2.III both enhanced the DNA-damaging effects of etoposide on NCI-H69 cell viability in vitro. Results revealed that in vivo MK2.III was able to act as a chemosensitizer when used in combination with etoposide making NCI-H69 lung cancer cells sensitive to chemotherapeutic drug by 45% compared to single usage of the drug. We also report that MK2.III sensitizes metastatic cell lines SW-620 and MDA-MB-231 to etoposide but does not increase the sensitivity of non-metastasizing SW-480 colorectal cells to DNA damaging agent in vitro.

Conclusion

Findings reported in this study provide evidence that specific inhibitors of MK2 may indeed improve overall cancer therapy; however, their effectiveness depends on cell types.
LINC00955 suppresses colorectal cancer growth by acting as a molecular scaffold of TRIM25 and Sp1 to Inhibit DNMT3B-mediated methylation of the PHIP promoter
Authors: Ren Ganglin , Li Hongyan , Hong Dan , Hu Fangyu , Jin Rongjia , Wu Shuang , Sun Wenhao , Jin Honglei , Zhao Lingling , Zhang Xiaodong , Liu Dongxiang , Huang Chuanshu , Huang Haishan
Published: September 2023

Background

Long non-coding RNAs play an important role in the development of colorectal cancer (CRC), while many CRC-related lncRNAs have not yet been identified.

Methods

The relationship between the expression of LINC00955 (Long Intergenic Non-protein Coding RNA 955) and the prognosis of colorectal cancer patients was analyzed using the sequencing results of the TCGA database. LINC00955 expression levels were measured using qRT-PCR. The anti-proliferative activity of LINC00955 was evaluated using CRC cell lines in vitro and xenograft models in nude mice in vivo. The interaction of TRIM25-Sp1-DNMT3B-PHIP-CDK2 was analyzed by western blotting, protein degradation experiment, luciferase, RNA-IP, RNA pull-down assays and immunohistochemically analysis. The biological roles of LINC00955, tripartite motif containing 25 (TRIM25), Sp1 transcription factor (Sp1), DNA methyltransferase 3 beta (DNMT3B), pleckstrin homology domain interacting protein (PHIP), cyclin dependent kinase 2 (CDK2) in colorectal cancer cells were analyzed using ATP assays, Soft agar experiments and EdU assays.

Results

The present study showed that LINC00955 is downregulated in CRC tissues, and such downregulation is associated with poor prognosis of CRC patients. We found that LINC00955 can inhibit CRC cell growth both in vitro and in vivo. Evaluation of its mechanism of action showed that LINC00955 acts as a scaffold molecule that directly promotes the binding of TRIM25 to Sp1, and promotes ubiquitination and degradation of Sp1, thereby attenuating transcription and expression of DNMT3B. DNMT3B inhibition results in hypomethylation of the PHIP promoter, in turn increasing PHIP transcription and promoting ubiquitination and degradation of CDK2, ultimately leading to G0/G1 growth arrest and inhibition of CRC cell growth.

Conclusions

These findings indicate that downregulation of LINC00955 in CRC cells promotes tumor growth through the TRIM25/Sp1/DNMT3B/PHIP/CDK2 regulatory axis, suggesting that LINC00955 may be a potential target for the therapy of CRC.
Influences on treatment-seeking and antibiotic use for common illnesses in eastern China
Authors: Zhang Tingting , Lin Hanyi , Zhao Xinping , Wang Wei , Yan Fei , Lambert Helen
Published: September 2023

Background

Antibiotic resistance rates remain high in China where antibiotics are widely used for common illnesses. This study aimed to investigate the influences on people’s decisions on treatment and antibiotic use for common illnesses in eastern China.

Methods

Semi-structured interviews were conducted with 29 patients recruited through convenience sampling between July 2020 and January 2021 in one hospital in County A in Zhejiang Province, and one hospital and one village clinic in County B in Jiangsu Province, respectively. All interviews were audio-recorded, transcribed verbatim and thematically analysed. This study is nested in a larger interdisciplinary mixed method project and we also compared our qualitative findings with quantitative results from a household survey conducted as part of this wider project.

Results

Participants’ decisions about treatment-seeking and antibiotic use for common illnesses were found to be influenced by four interactive domains. (i) Self-evaluation of illness severity: Participants tend to self-treat minor conditions with ordinary medicines first and do not resort to antibiotics unless the condition worsens or is considered inflammation- related. Visiting healthcare facilities is seen as the final option. (ii) Access to and trust in care: These treatment-seeking practices are also associated with the perception, in contrast with retail pharmacies, hospitals provide professional and trustworthy care but are difficult to access, and hence require visiting only for severe illness. (iii) Prior experience: previous medical treatment and experiences of self-medication also influence participants’ treatment decisions including the use of antibiotics. (iv) Medication characteristics: Participants view antibiotics as powerful medicines with harms and risks, requiring consumers to carefully trade off benefits and harms before use.

Conclusions

People’s treatment decisions in relation to antibiotic use in eastern China are influenced by an interplay of lay conceptual models of illnesses and antibiotics and broader organisational, social, and contextual factors. Interventions focusing on individual education to incorporate biomedical knowledge into lay understandings, and reducing situational and social incentives for self-medicating with antibiotics by strengthening access to quality professional care, would be helpful in promoting antibiotic stewardship.
Identifying the sociodemographic and work-related factors related to workers’ daily physical activity using a decision tree approach
Authors: Biswas Aviroop , Chen Cynthia , Dobson Kathleen G. , Prince Stephanie A. , Shahidi Faraz Vahid , Smith Peter M. , Fuller Daniel
Published: September 2023

Background

The social and behavioural factors related to physical activity among adults are well known. Despite the overlapping nature of these factors, few studies have examined how multiple predictors of physical activity interact. This study aimed to identify the relative importance of multiple interacting sociodemographic and work-related factors associated with the daily physical activity patterns of a population-based sample of workers.

Methods

Sociodemographic, work, screen time, and health variables were obtained from five, repeated cross-sectional cohorts of workers from the Canadian Health Measures Survey (2007 to 2017). Classification and Regression Tree (CART) modelling was used to identify the discriminators associated with six daily physical activity patterns. The performance of the CART approach was compared to a stepwise multinomial logistic regression model.

Results

Among the 8,909 workers analysed, the most important CART discriminators of daily physical activity patterns were age, job skill, and physical strength requirements of the job. Other important factors included participants’ sex, educational attainment, fruit/vegetable intake, industry, work hours, marital status, having a child living at home, computer time, and household income. The CART tree had moderate classification accuracy and performed marginally better than the stepwise multinomial logistic regression model.

Conclusion

Age and work-related factors–particularly job skill, and physical strength requirements at work–appeared as the most important factors related to physical activity attainment, and differed based on sex, work hours, and industry. Delineating the hierarchy of factors associated with daily physical activity may assist in targeting preventive strategies aimed at promoting physical activity in workers.
The impact of boarding schools on the development of cognitive and non-cognitive abilities in adolescents
Authors: Chang Fang , Huo Yanan , Zhang Songyan , Zeng Hang , Tang Bin
Published: September 2023

Background

Since China adopted a policy to eliminate rural learning centers, boarding has become an important feature of the current rural student community. However, there is a lack of consensus on the impact of boarding schools on students' cognitive and non-cognitive development. This study investigates the effect of boarding schools on the development of cognitive and non-cognitive abilities of junior high school students in rural northwest China.

Methods

Using a sample of 5,660 seventh-grade students from 160 rural junior high schools across 19 counties, we identify a causal relationship between boarding and student abilities with the instrumental variables (IV) approach.

Results

The results suggest that boarding positively influences memory and attention, while it has no significant effect on other cognitive abilities such as reasoning, transcription speed, and accuracy. Furthermore, we find no significant association between boarding and the development of non-cognitive skills.

Conclusions

Given the widespread prevalence of boarding schools in rural regions, our study highlights the growing importance of improving school management to promote the development of students’ cognitive abilities and integrating the development of non-cognitive or social-emotional abilities into students’ daily routines.
Assessment of clinical and radiographic efficiency of manual and pediatric rotary file systems in primary root canal preparation: a randomized controlled clinical trial
Authors: Hadwa Shimaa M. , Ghouraba Rehab F. , Kabbash Ibrahim A. , EL-Desouky Shaimaa S.
Published: September 2023

Introduction

The success of primary teeth pulpectomy is strongly reliant on instrumentation techniques and their impact on obturation quality & postoperative pain. Recently, pediatric rotary file systems have been implemented.

Aim

to compare two pediatric rotary file systems (Kedo-S-Square & Fanta AF™ Baby) with manual K-files concerning obturation quality, instrumentation time, and postoperative pain in root canal preparation of primary molars using cone beam computed tomography (CBCT).

Methods

A randomized clinical trial was conducted with the trial registration number (TRN: NCT05619796 and date of registration: (17/11/2022) on sixty primary lower 2nd molars in healthy children aged 4–7 years. Molars were assigned randomly to three groups (n = 20). Group-I and -II were prepared with Kedo-S-Square & Fanta AF™Baby rotary systems respectively while group-III was prepared with a manual K-file. Instrumentation time was recorded using a stopwatch. CBCT was used to assess obturation quality immediately & recorded as optimal, underfilled, or overfilled. Postoperative pain was evaluated at 6, 12, 24, 48 h-time intervals using a four-point pain intensity scale. Statistical analysis was performed for the collected data.

Results

Among the three groups, group-I revealed a greater number of optimally filled teeth (85%) & less instrumentation time (74.75 s) followed by group-II & manual-K file group (p < 0.05). The hand K-file group had significantly more postoperative pain than the two rotary groups (p < 0.05).

Conclusion

the tested rotary file systems resulted in better obturation quality, less instrumentation time, and less postoperative pain compared to manual-K files during primary teeth pulpectomy.
Localization and distribution of goose astrovirus 2 antigens in different tissues at different times
Authors: Wei Feng , Jiang Xiaoning , He Dalin , Diao Youxiang , Tang Yi
Published: September 2023

Goose astrovirus 2 (GAstV-2) causes visceral gout in goslings and has resulted in significant economic losses in the goose industry of China since its outbreak in 2017. To further investigate the distribution and localization of GAstV-2 in different tissues at different times, a monoclonal antibody (mAb)-based immunohistochemical (IHC) assay was developed to detect GAstV-2. A total of 80 1-day-old healthy goslings were inoculated with GAstV-2 via the oral (n = 40) and intramuscular routes (n = 40). GAstV-2 in the tissues of interest was detected using the established IHC assay. The results showed that positive signals were detected in most tissues at 1 day post-infection (dpi). Viral antigens were mainly distributed in the cytoplasm, and the staining intensity was higher in the renal tubular epithelial cells than in other cells. Taken together, our data demonstrated that GAstV-2 has a broad tissue tropism and primarily targets the kidneys. These results are likely to provide a scientific basis for further elucidation of the pathogenesis of GAstV-2.
Hemolysis, icterus and lipemia interfere with the determination of two oxidative stress biomarkers in canine serum
Authors: Perez-Montero B. , Fermin-Rodriguez M. L. , Miro G. , de Juan L. , Cruz-Lopez F.
Published: September 2023

Background

Oxidative stress has been proven to play a role in numerous human and canine diseases. Among the biomarkers of oxidative stress, Thiobarbituric Acid Reactive Substances (TBARS) and Total Antioxidant Status (TAS) are two of the most widely used. Preanalytical factors are crucial for obtaining accurate results in these assays. Hemolysis, icterus and lipemia (HIL) are common sources of preanalytical errors in the laboratory; however, limited information is available regarding the considerations for canine specimens. Therefore, the objective of this study was to evaluate the potential interferences of HIL in the determination of TBARS and TAS in canine serum.

Methods

Solutions of pooled canine serum samples were prepared by adding increasing concentrations of hemolysate, bilirubin and a synthetic lipid emulsion. TBARS and TAS were determined, and biases from the control value caused by the interfering substances were calculated.

Results

Hemolysis, icterus and lipemia induced significant interferences on TBARS and TAS, albeit to varying degrees depending on the specific biomarker and interfering substance. TBARS appeared to be more susceptible to interferences in this study. Slight hemolysis, moderate icterus and slight lipemia caused notable deviations in TBARS values, surpassing the acceptable threshold for interference. TAS assay was also affected by HIL, although to a lesser extent compared to TBARS. Significant biases from TAS control value were observed when icterus was moderate, and when hemolysis and lipemia were more pronounced.

Conclusions

In light of our results, we conclude that hemolyzed, icteric and lipemic specimens are not suitable for TBARS and TAS determination in canine serum. Our findings hold considerable practical utility, as a simple visual inspection would be sufficient for identifying and excluding such specimens.
Biomechanical and clinical research of Isobar semi-rigid stabilization devices for lumbar degenerative diseases: a systematic review
Authors: Guan Jianbin , Liu Tao , Yu Xing , Li Wenhao , Feng Ningning , Jiang Guozheng , Zhao He , Yang Yongdong
Published: September 2023

While lumbar spinal fusion using rigid rods is a prevalent surgical technique, it can lead to complications such as adjacent segment disease (ASDis). Dynamic stabilization devices serve to maintain physiological spinal motion and alleviate painful stress, yet they are accompanied by a substantial incidence of construct failure and subsequent reoperation. Compared to traditional rigid devices, Isobar TTL semi-rigid stabilization devices demonstrate equivalent stiffness and effective stabilization capabilities. Furthermore, when contrasted with dynamic stabilization techniques, semi-rigid stabilization offers improved load distribution, a broader range of motion within the fixed segment, and reduced mechanical failure rates. This paper will review and evaluate the clinical and biomechanical performance of Isobar TTL semi-rigid stabilization devices. A literature search using the PubMed, EMBASE, CNKI, Wanfang, VIP, and Cochrane Library databases identified studies that met the eligibility criteria. Twenty-eight clinical studies and nine biomechanical studies were included in this systematic review. The VAS, the ODI, and Japanese Orthopedic Association scoring improved significantly in most studies. UCLA grading scale, Pfirrmann grading, and modified Pfirrmann grading of the upper adjacent segments improved significantly in most studies. The occurrence rate of ASD was low. In biomechanical studies, Isobar TTL demonstrated a superior load sharing distribution, a larger fixed segment range of motion, and reduced stress at the rod–screw/screw–bone interfaces compared with titanium rods. While findings from mechanical studies provided promising results, the clinical studies exhibited low methodological quality. As a result, the available evidence does not possess sufficient strength to substantiate superior outcomes with Isobar semi-rigid system in comparison to titanium rods. To establish more conclusive conclusions, further investigations incorporating improved protocols, larger sample sizes, and extended follow-up durations are warranted.
Dominoes with interlocking consequences triggered by zinc: involvement of microelement-stimulated MSC-derived exosomes in senile osteogenesis and osteoclast dialogue
Authors: Yin Shi , Lin Sihan , Xu Jingyi , Yang Guangzheng , Chen Hongyan , Jiang Xinquan
Published: September 2023

As societal aging intensifies, senile osteoporosis has become a global public health concern. Bone microdamage is mainly caused by processes such as enhancing osteoclast activity or reducing bone formation by osteoblast-lineage cells. Compared with young individuals, extracellular vesicles derived from senescent bone marrow mesenchymal stem cells(BMSCs) increase the transient differentiation of bone marrow monocytes (BMMs) to osteoclasts, ultimately leading to osteoporosis and metal implant failure. To address this daunting problem, an exosome-targeted orthopedic implant composed of a nutrient coating was developed. A high-zinc atmosphere used as a local microenvironmental cue not only could inhibit the bone resorption by inhibiting osteoclasts but also could induce the reprogramming of senile osteogenesis and osteoclast dialogue by exosome modification. Bidirectional regulation of intercellular communication via cargoes, including microRNAs carried by exosomes, was detected. Loss- and gain-of-function experiments demonstrated that the key regulator miR-146b-5p regulates the protein kinase B/mammalian target of rapamycin pathway by targeting the catalytic subunit gene of PI3K–PIK3CB. In vivo evaluation using a naturally-aged osteoporotic rat femoral defect model further confirmed that a nutrient coating substantially augments cancellous bone remodeling and osseointegration by regulating local BMMs differentiation. Altogether, this study not only reveals the close link between senescent stem cell communication and age-related osteoporosis but also provides a novel orthopedic implant for elderly patients with exosome modulation capability.
Analysis of proteome and post-translational modifications of 2-hydroxyisobutyrylation reveals the glycolysis pathway in oral adenoid cystic carcinoma
Authors: Chen Sining , Li Dandan , Zeng Zhipeng , Zhang Wei , Xie Hongliang , Tang Jianming , Liao Shengyou , Cai Wanxia , Liu Fanna , Tang Donge , Dai Yong
Published: September 2023

Purpose

Oral adenoid cystic carcinoma (OACC) has high rates of both local–regional recurrence and distant metastasis. The objective of this study is to investigate the impact of Khib on OACC and its potential as a targeted therapeutic intervention.

Experimental design

We investigated the DEPs (differentially expressed proteins) and DHMPs between OACC-T and OACC-N using LC–MS/MS-based quantitative proteomics and using several bioinformatics methods, including GO enrichment analysis, KEGG pathway analysis, subcellular localization prediction, MEA (motif enrichment analysis), and PPI (protein–protein interaction networks) to illustrate how Khib modification interfere with OACC evolution.

Results

Compared OACC-tumor samples (OACC-T) with the adjacent normal samples (OACC-N), there were 3243 of the DEPs and 2011 Khib sites were identified on 764 proteins (DHMPs). DEPs and DHMPs were strongly associated to glycolysis pathway. GAPDH of K254, ENO of K228, and PGK1 of K323 were modified by Khib in OACC-T. Khib may increase the catalytic efficiency to promote glycolysis pathway and favor OACC progression.

Conclusions and clinical relevance

Khib may play a significant role in the mechanism of OACC progression by influencing the enzyme activity of the glycolysis pathway. These findings may provide new therapeutic options of OACC.
Portal vein thrombosis after cetuximab and 5-fluorouracil therapy in a patient with advanced colon cancer and decompensated cirrhosis: a case report and review of the literature
Authors: Liu Fangyu , Xu Yongmei , Yang Guowang , Guo Yuhong , Nian Jiayun
Published: September 2023

Background

Treatment options for advanced colon cancer are mainly combinations of chemotherapy and targeted drugs. However, poor physical health and medication intolerance limit the choice of anticancer drugs. Colon cancer with cirrhosis is a particular patient group that poses a challenge to clinical treatment.

Case presentation

This article presents a case of a patient in the decompensated stage of cirrhosis who was diagnosed with advanced colon cancer. The initial presentation was a nodule on his navel named the Sister Mary Joseph’s nodule, which was later confirmed by biopsy and PET-CT as one of the metastases of colon cancer. The patient was treated with cetuximab and 5-fluorouracil at a below-guideline dose; however, portal vein thrombosis developed and led to death. This entire process, from diagnosis to death, occurred within a span of three months.

Conclusion

Cancers with cirrhosis are a special group that deserves more attention. There is no unified treatment guideline for these patients, especially those with extrahepatic primary tumors. We should be more cautious when choosing treatment for such patients in the future. Both chemotherapy and targeted treatment may potentially induce portal vein thrombosis, which appears to have a higher incidence and worse prognosis than cancers without cirrhosis.
Matched analysis of circulating selenium with the breast cancer selenotranscriptome: a multicentre prospective study
Authors: Demircan Kamil , Bengtsson Ylva , Chillon Thilo Samson , Vallon-Christersson Johan , Sun Qian , Larsson Christer , Malmberg Martin , Saal Lao H. , Rydén Lisa , Borg Åke , Manjer Jonas , Schomburg Lutz
Published: September 2023

Introduction

Low serum selenium and altered tumour RNA expression of certain selenoproteins are associated with a poor breast cancer prognosis. Selenoprotein expression stringently depends on selenium availability, hence circulating selenium may interact with tumour selenoprotein expression. However, there is no matched analysis to date.

Methods

This study included 1453 patients with newly diagnosed breast cancer from the multicentric prospective Sweden Cancerome Analysis Network – Breast study. Total serum selenium, selenoprotein P and glutathione peroxidase 3 were analysed at time of diagnosis. Bulk RNA-sequencing was conducted in matched tumour tissues. Fully adjusted Cox regression models with an interaction term were employed to detect dose-dependent interactions of circulating selenium with the associations of tumour selenoprotein mRNA expression and mortality.

Results

237 deaths were recorded within ~ 9 years follow-up. All three serum selenium biomarkers correlated positively (p < 0.001). All selenoproteins except for GPX6 were expressed in tumour tissues. Single cell RNA-sequencing revealed a heterogeneous expression pattern in the tumour microenvironment. Circulating selenium correlated positively with tumour SELENOW and SELENON expression (p < 0.001). In fully adjusted models, the associations of DIO1, DIO3 and SELENOM with mortality were dose-dependently modified by serum selenium (p < 0.001, p = 0.020, p = 0.038, respectively). With increasing selenium, DIO1 and SELENOM associated with lower, whereas DIO3 expression associated with higher mortality. Association of DIO1 with lower mortality was only apparent in patients with high selenium [above median (70.36 µg/L)], and the HR (95%CI) for one-unit increase in log(FPKM + 1) was 0.70 (0.50–0.98).

Conclusions

This first unbiased analysis of serum selenium with the breast cancer selenotranscriptome identified an effect-modification of selenium on the associations of DIO1, SELENOM, and DIO3 with prognosis. Selenium substitution in patients with DIO1-expressing tumours merits consideration to improve survival.
LncRNA AC142119.1 facilitates the progression of neuroblastoma by epigenetically initiating the transcription of MYCN
Authors: Yang Rui , Liu Nanjing , Li Ting , Liu Fangjie , Zhang Jun , Zhao Hui , Zou Lin , He Xiaoyan
Published: September 2023

Background

Oncogene MYCN is closely related with malignant progression and poor prognosis of neuroblastoma (NB). Recently, long non-coding RNAs (lncRNAs) have been recognized as crucial regulators in various cancers. However, whether lncRNAs contribute to the overexpression of MYCN in NB is unclear.

Methods

Microarray analysis were applied to analyze the differentially expressed lncRNAs between MYCN-amplified and MYCN-non-amplified NB cell lines. Bioinformatic analyses were utilized to identify lncRNAs nearby MYCN locus. qRT-PCR was used to detect the expression level of lncRNA AC142119.1 in NB cell lines and tissues. Gain- and loss-of-function assays were conducted to investigate the biological effect of AC142119.1 in NB. Fluorescence in situ hybridization, RNA pull-down, RNA immunoprecipitation, mass spectrometry, RNA electrophoretic mobility shift, chromatin immunoprecipitation and chromatin isolation by RNA purification assays were performed to validate the interaction between AC142119.1 and WDR5 protein as well as MYCN promoter.

Results

AC142119.1 was significantly elevated in NB tissues with MYCN amplification, advanced INSS stage and high risk, and associated with poor survival of NB patients. Moreover, enforced expression of AC142119.1 reinforced the proliferation of NB cells in vitro and in vivo. Additionally, AC142119.1 specifically recruited WDR5 protein to interact with MYCN promoter, further initiating the transcription of MYCN and accelerating NB progression.

Conclusions

We identified a novel lncRNA AC142119.1, which promoted the progression of NB through epigenetically initiating the transcription of MYCN via interacting with both WDR5 protein and the promoter of MYCN, indicating that AC142119.1 might be a potential diagnostic biomarker and therapeutic target for NB.
Biologic switching patterns among children with non-systemic juvenile idiopathic arthritis
Authors: Pedersen Mia Lindegaard , Neve-Græsbøll Amalie , Herlin Troels , Glerup Mia
Published: September 2023

Background

In juvenile idiopathic arthritis (JIA) clinical remission is unattainable in some patients despite modern biologic disease-modifying antirheumatic drugs (bDMARD) therapy and switching bDMARD is required. The best choice of second-line bDMARD remains unclear. This retrospective observational study aims to describe the pattern, timing, frequency, and reasons for bDMARD switching among children diagnosed with non-systemic JIA.

Methods

Patients were identified by combining unique personal identification numbers, the International Code of Diagnosis (ICD10) for JIA and biologic therapy. Clinical characteristics were collected retrospectively from the electronic medical records. Included were 200 children diagnosed with non-systemic JIA initiating their first biologic drug between January 1st, 2012, and March 1st, 2021. We compared characteristics of non-switchers vs switchers and early switchers (≤ 6 months) vs late switchers (> 6 months).

Results

The median age at diagnosis was 7.7 years. We found that 37% switched to a different bDMARD after a median age of 6.3 years after diagnosis. In total, and 17.5% of patients switched at least twice, while 6% switched three or more times. The most common reason for switching was inefficacy (57%) followed by injection/infusion reactions (15%) and uveitis (13%). 77% were late switchers, and switched primarily due to inefficacy. All patients started a tumor necrosis factor inhibitor (TNFi) as initial bDMARD (Etanercept (ETN): 49.5%, other TNFis: 50.5%). The patients who started ETN as first-line bDMARD were more likely to be switchers compared to those who started another TNFi.

Conclusion

During a median 6.3-year follow-up biologic switching was observed in more than one third, primarily due to inefficacy.
LncRNA CCAT1 facilitates the progression of gastric cancer via PTBP1-mediated glycolysis enhancement
Authors: Zhang Cong , Wang Huixia , Liu Qingwei , Dai Suli , Tian Guo , Wei Xintong , Li Xiaoya , Zhao Lianmei , Shan Baoen
Published: September 2023

Background

Gastric cancer (GC) is one of the most prevalent malignant tumors of the digestive system. As a hallmark of cancer, energy-related metabolic reprogramming is manipulated by multiple factors, including long non-coding RNAs (lncRNAs). Notably, lncRNA CCAT1 has been identified as a crucial regulator in tumor progression. Nevertheless, the precise molecular mechanisms underlying the involvement of CCAT1 in metabolic reprogramming of GC remain unclear.

Methods

Gain- and loss-of-function experiments were performed to evaluate the roles of CCAT1 in tumorigenesis and glycolysis of GC. Bioinformatics analyses and mechanistic experiments, such as mass spectrometry (MS), RNA-pulldown, and RNA immunoprecipitation (RIP), were employed to reveal the potential interacting protein of CCAT1 and elucidate the regulatory mechanism of CCAT1 in GC glycolysis. Moreover, the nude mice xenograft assay was used to evaluate the effect of CCAT1 on GC cells in vivo.

Results

In this study, we identified that CCAT1 expression was significantly elevated in the tissues and plasma exosomes of GC patients, as well as GC cell lines. Functional experiments showed that the knockdown of CCAT1 resulted in a substantial decrease in the proliferation, migration and invasion of GC cells both in vitro and in vivo through decreasing the expression of glycolytic enzymes and glycolytic rate. Conversely, overexpression of CCAT1 exhibited contrasting effects. Mechanistically, CCAT1 interacted with PTBP1 and effectively maintained its stability by inhibiting the ubiquitin-mediated degradation process. As a critical splicing factor, PTBP1 facilitated the transition from PKM1 to PKM2, thereby augmenting the glycolytic activity of GC cells and ultimately fostering the progression of GC.

Conclusions

Our findings demonstrate that CCAT1 plays a significant role in promoting the proliferation, migration, and invasion of GC cells through the PTBP1/PKM2/glycolysis pathway, thus suggesting CCAT1’s potential as a biomarker and therapeutic target for GC.
Histone crotonylation of peripheral blood mononuclear cells is a potential biomarker for diagnosis of colorectal cancer
Authors: Hou Jia-Yi , Li Ning , Wang Jie , Gao Li-Juan , Chang Jia-Song , Cao Ji-Min
Published: September 2023

Background

Blood-based tests have public appeal in screening cancers due to their minimally invasive nature, ability to integrate with other routine blood tests, and high compliance. This study aimed to investigate whether certain epigenetic modulation of peripheral blood mononuclear cells (PBMCs) could be a biomarker of colorectal cancer (CRC).

Results

Western blotting of histones in the PBMCs from 40 colorectal cancer patients and 40 healthy controls was performed to identify the crotonylation sites of proteins. The correlation of crotonylation with tumor staging and diagnostic efficacy were analyzed. Crotonylation of H2BK12 (H2BK12cr) was identified significantly upregulated in the PBMCs of CRC patients compared to healthy controls, and were closely related to distant metastasis (P = 0.0478) and late TNM stage (P = 0.0201). Receiver operator characteristic curve (ROC) analysis demonstrated that the area under curve (AUC) of H2BK12cr was 0.8488, the sensitivity was 70%, and the specificity was 92.5%. The H2BK12cr parameter significantly increased the diagnostic effectiveness of CRC compared with the commercial carcinoembryonic antigen assays.

Conclusions

The H2BK12cr level in PBMCs of CRC patients has a potential to be a biomarker for distinguishing CRC patients from healthy controls with the advantages of easy operation and high diagnostic efficacy.
Long-term effects of vitamin D supplementation and maintaining sufficient vitamin D on knee osteoarthritis over 5 years
Authors: Wang Zhiqiang , Zhu Zhaohua , Pan Feng , Zheng Shuang , Parameswaran Venkat , Blizzard Leigh , Ding Changhai , Antony Benny
Published: September 2023

Objectives

This study aimed to investigate the long-term effect of vitamin D supplementation compared to placebo over 5 years in participants with knee osteoarthritis (OA). We also aimed to describe the effect of maintaining sufficient serum vitamin D levels over five years in knee OA.

Methods

Participants (n = 173) from the Hobart centre of the Vitamin D Effects on Osteoarthritis (VIDEO) trial were extensively followed up 3 years after the cessation of 2-year investigational treatment. Participants were classified as maintaining sufficient vitamin D (n = 79) and not maintaining sufficient vitamin D (n = 61) groups.

Results

There was no significant difference in change in the knee symptoms, depression, and serum levels of IL6 and hs-CRP between both comparisons after 3 years of cessation of the clinical trial. However, among participants who reported no knee surgery (KS), there was a significant improvement in WOMAC function (β: − 83.7, 95% CI: − 167.3, 0) and depression scores (β: − 1.3, 95% CI: − 2.3, − 0.2) in vitamin D group compared to the placebo group. Similarly, those who maintained adequate vitamin D levels over 5 years had significantly less WOMAC knee pain (β: − 33.9, 95% CI: − 65.7, − 2) and physical dysfunction (β: − 105.5, 95% CI: − 198.2, − 12.8) than participants with vitamin D deficiency over 5 years.

Conclusion

Vitamin D supplementation over 2 years or maintaining vitamin D sufficiency for 5 years was not associated with statistically significant differences in change in knee symptom scores over 5 years. However, among participants who did not report KS, 2-year vitamin D supplementation and maintaining sufficient vitamin D was linked to modest improvements in knee symptoms and depression scores in knee OA.
METTL3 exerts synergistic effects on m6A methylation and histone modification to regulate the function of VGF in lung adenocarcinoma
Authors: Shi Kesong , Sa Rula , Dou Le , Wu Yuan , Dong Zhiqiang , Fu Xinyao , Yu Haiquan
Published: September 2023

Background

Multiple genetic and epigenetic regulatory mechanisms play a vital role in tumorigenesis and development. Understanding the interplay between different epigenetic modifications and its contribution to transcriptional regulation in cancer is essential for precision medicine. Here, we aimed to investigate the interplay between N6-methyladenosine (m6A) modifications and histone modifications in lung adenocarcinoma (LUAD).

Results

Based on the data from public databases, including chromatin property data (ATAC-seq, DNase-seq), methylated RNA immunoprecipitation sequencing (MeRIP-seq), and gene expression data (RNA-seq), a m6A-related differentially expressed gene nerve growth factor inducible (VGF) was identified between LUAD tissues and normal lung tissues. VGF was significantly highly expressed in LUAD tissues and cells, and was associated with a worse prognosis for LUAD, silencing of VGF inhibited the malignant phenotype of LUAD cells by inactivating the PI3K/AKT/mTOR pathway. Through the weighted correlation network analysis (WGCNA) and integration of TCGA-LUAD RNA-seq and m6A methyltransferase METTL3-knockdown RNA-seq data, a significant positive correlation between METTL3 and VGF was observed. By using the MeRIP-qPCR and dual-luciferase reporter assays, we demonstrated that METTL3 knockdown decreased m6A modification level of VGF coding sequences in LUAD cells, the colorimetric m6A quantification assay also showed that METTL3 knockdown significantly decreased global m6A modification level in LUAD cells. Interestingly, we found that METTL3 knockdown also reduced VGF expression by increasing H3K36me3 modification at the VGF promoter. Further research revealed that METTL3 knockdown upregulated the expression of histone methylase SETD2, the major H3K36me3 methyltransferase, by methylating the m6A site in the 3'UTR of SETD2 mRNA in LUAD cells.

Conclusions

Overall, our results reveal that the expression of VGF in LUAD cells is regulated spatio-temporally by METTL3 through both transcriptional (via histone modifications) and post-transcriptional (via m6A modifications) mechanisms. The synergistic effect of these multiple epigenetic mechanisms provides new opportunities for the diagnosis and precision treatment of tumors.