bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxidative Stress-Related lncRNAs Are Potential Biomarkers for Predicting Prognosis and Immune Responses in Patients With LUAD
Authors: Sun Xinti , Huang Xingqi , Sun Xiaojuan , Chen Si , Zhang Zeyang , Yu Yao , Zhang Peng
Published: June 2022

Lung adenocarcinoma is increasingly harmful to society and individuals as cancer with an inferior prognosis and insensitive to chemotherapy. Previous studies have demonstrated that oxidative stress and lncRNAs play a vital role in many biological processes. Therefore, we explored the role of lncRNAs associated with oxidative stress in the prognosis and survival of LUAD patients. We examined the expression profiles of lncRNAs and oxidative stress genes in this study. A prognosis prediction model and a nomogram were built based on oxidative stress-related lncRNAs. Functional and drug sensitivity analyses were also performed depending on oxidative stress-related lncRNA signature. Moreover, we investigated the relationship between immune response and immunotherapy. The results showed that a risk scoring model based on 16 critical oxidative stress lncRNAs was able to distinguish the clinical status of LUAD and better predict the prognosis and survival. Additionally, the model demonstrated a close correlation with the tumor immune system, and these key lncRNAs also revealed the relationship between LUAD and chemotherapeutic drug sensitivity. Our work aims to provide new perspectives and new ideas for the treatment and management of LUAD.
Pharmacogenetics of Praziquantel Metabolism: Evaluating the Cytochrome P450 Genes of Zimbabwean Patients During a Schistosomiasis Treatment
Authors: Zdesenko Grace , Mduluza Takafira , Mutapi Francisca
Published: June 2022

Schistosomiasis is a parasitic disease infecting over 236 million people annually, with the majority affected residing on the African continent. Control of this disease is reliant on the drug praziquantel (PZQ), with treatment success dependent on an individual reaching PZQ concentrations lethal to schistosomes. Despite the complete reliance on PZQ to treat schistosomiasis in Africa, the characterization of the pharmacogenetics associated with PZQ metabolism in African populations has been sparse. We aimed to characterize genetic variation in the drug-metabolising cytochrome P450 enzymes (CYPs) and determine the association between each variant and the efficacy of PZQ treatment in Zimbabwean patients exposed to Schistosoma haematobium infection. Genomic DNA from blood samples of 114 case-control Zimbabweans infected with schistosomes were sequenced using the CYP1A2, CYP2C9, CYP2C19, CYP2D6, CYP3A4, and CYP3A5 genes as targets. Bioinformatic tools were used to identify and predict functional effects of detected single nucleotide polymorphisms (SNPs). A random forest (RF) model was then used to assess SNPs most predictive of PZQ efficacy, with a misclassification rate of 29%. SNPs were detected across all six genes, with 70 SNPs identified and multiple functional changes to the CYP enzymes predicted. Only four SNPs were significantly associated with PZQ efficacy using χ2 tests, with rs951840747 (OR: 3.61, p = 0.01) in the CYP1A2 gene having the highest odds of an individual possessing this SNP clearing infection, and rs6976017 (OR: 2.19, p = 0.045) of CYP3A5 determined to be the most predictive of PZQ efficacy via the RF. Only the rs28371702 (CC) genotype (OR: 2.36, p = 0.024) of CYP2D6 was significantly associated with an unsuccessful PZQ treatment. This study adds to the genomic characterization of the diverse populations in Africa and identifies variants relevant to other pharmacogenetic studies crucial for the development and usage of drugs in these populations.
Transcriptomic Analysis of Dysregulated Genes of the nDNA-mtDNA Axis in a Mouse Model of Dilated Cardiomyopathy
Authors: Ziemann Mark , Wu Wei , Deng Xiu-Ling , Du Xiao-Jun
Published: June 2022

Background: Mitochondrial dysfunction is implicated in the development of cardiomyopathy and heart failure. Transcription of mitochondrial DNA (mtDNA) encoded genes and subsequent protein synthesis are tightly regulated by nuclear DNA (nDNA) encoded proteins forming the nDNA-mtDNA axis. The scale of abnormalities in this axis in dilated cardiomyopathy (DCM) is unclear. We previously demonstrated, in a mouse DCM model with cardiac Mst1 overexpression, extensive downregulation of mitochondrial genes and mitochondrial dysfunction. Using the pre-acquired transcriptome sequencing database, we studied expression of gene sets of the nDNA-mtDNA axis.

Methods: Using RNA-sequencing data from DCM hearts of mice at early and severe disease stages, transcriptome was performed for dysregulated nDNA-encoded gene sets that govern mtDNA transcription and in situ protein synthesis. To validate gene data, expression of a panel of proteins was determined by immunoblotting.

Results: Relative to littermate controls, DCM hearts showed significant downregulation of all mtDNA encoded mRNAs, as well as mtDNA transcriptional activators. Downregulation was also evident for gene sets of mt-rRNA processing, aminoacyl-tRNA synthases, and mitoribosome subunits for in situ protein synthesis. Multiple downregulated genes belong to mitochondrial protein-importing machinery indicating compromised importing of proteins for mtDNA transcription and translation. Diverse changes were genes of mtRNA-binding proteins that govern maturation and stability of mtDNA-derived RNAs. Expression of mtDNA replicome genes was largely unchanged. These changes were similarly observed in mouse hearts at early and severe stages of DCM.

Conclusion: Transcriptome revealed in our DCM model dysregulation of multiple gene sets of the nDNA-mtDNA axis, that is, expected to interfere with mtDNA transcription and in situ protein synthesis. Dysfunction of the nDNA-mtDNA axis might contribute to mitochondrial dysfunction and ultimately development of DCM.
Liver Kinase B1 Regulates Remodeling of the Tumor Microenvironment in Triple-Negative Breast Cancer
Authors: King Connor T. , Matossian Margarite D. , Savoie Jonathan J. , Nguyen Khoa , Wright Maryl K. , Byrne C. Ethan , Elliott Steven , Burks Hope E. , Bratton Melyssa R. , Pashos Nicholas C. , Bunnell Bruce A. , Burow Matthew E. , Collins-Burow Bridgette M. , Martin Elizabeth C.
Published: June 2022

Liver kinase B1 (LKB1) is a potent tumor suppressor that regulates cellular energy balance and metabolism as an upstream kinase of the AMP-activated protein kinase (AMPK) pathway. LKB1 regulates cancer cell invasion and metastasis in multiple cancer types, including breast cancer. In this study, we evaluated LKB1’s role as a regulator of the tumor microenvironment (TME). This was achieved by seeding the MDA-MB-231-LKB1 overexpressing cell line onto adipose and tumor scaffolds, followed by the evaluation of tumor matrix-induced tumorigenesis and metastasis. Results demonstrated that the presence of tumor matrix enhanced tumorigenesis in both MDA-MB-231 and MDA-MB-231-LKB1 cell lines. Metastasis was increased in both MDA-MB-231 and -LKB1 cells seeded on the tumor scaffold. Endpoint analysis of tumor and adipose scaffolds revealed LKB1-mediated tumor microenvironment remodeling as evident through altered matrix protein production. The proteomic analysis determined that LKB1 overexpression preferentially decreased all major and minor fibril collagens (collagens I, III, V, and XI). In addition, proteins observed to be absent in tumor scaffolds in the LKB1 overexpressing cell line included those associated with the adipose matrix (COL6A2) and regulators of adipogenesis (IL17RB and IGFBP4), suggesting a role for LKB1 in tumor-mediated adipogenesis. Histological analysis of MDA-MB-231-LKB1-seeded tumors demonstrated decreased total fibril collagen and indicated decreased stromal cell presence. In accordance with this, in vitro condition medium studies demonstrated that the MDA-MB-231-LKB1 secretome inhibited adipogenesis of adipose-derived stem cells. Taken together, these data demonstrate a role for LKB1 in regulating the tumor microenvironment through fibril matrix remodeling and suppression of adipogenesis.
Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions
Authors: Hiromoto Takeshi , Ikura Teikichi , Honjo Eijiro , Blaber Michael , Kuroki Ryota , Tamada Taro
Published: June 2022

Protein crystals are generally fragile and sensitive to subtle changes such as pH, ionic strength, and/or temperature in their crystallization mother liquor. Here, using T4 phage lysozyme as a model protein, the three-dimensional rigidification of protein crystals was conducted by introducing disulfide cross-links between neighboring molecules in the crystal. The effect of cross-linking on the stability of the crystals was evaluated by microscopic observation and X-ray diffraction. When soaking the obtained cross-linked crystals into a precipitant-free solution, the crystals held their shape without dissolution and diffracted to approximately 1.1 Å resolution, comparable to that of the non-cross-linked crystals. Such cross-linked crystals maintained their diffraction even when immersed in other solutions with pH values from 4 to 10, indicating that the disulfide cross-linking made the packing contacts enforced and resulted in some mechanical strength in response to changes in the preservation conditions. Furthermore, the cross-linked crystals gained stability to permit soaking into solutions containing high concentrations of organic solvents. The results suggest the possibility of obtaining protein crystals for effective drug screening by introducing appropriate cross-linked disulfide bonds.
Gene Expression Data for Investigating Glaucoma Treatment Options and Pharmacology in the Anterior Segment, State-of-the-Art and Future Directions
Authors: Fuellen Georg , Jünemann Anselm
Published: June 2022

Glaucoma treatment options as well as its etiology are far from understood. Gene expression (transcriptomics) data of the anterior segment of the eye can help by elucidating the molecular-mechanistic underpinnings, and we present an up-to-date description and discussion of what gene expression data are publicly available, and for which purposes these can be used. We feature the few resources covering all segments of the eye, and we then specifically focus on the anterior segment, and provide an extensive list of the Gene Expression Omnibus data that may be useful. We also feature single-cell data of relevance, particularly three datasets from tissues of relevance to aqueous humor outflow. We describe how the data have been used by researchers, by following up resource citations and data re-analyses. We discuss datasets and analyses pertaining to fibrosis following glaucoma surgery, and to glaucoma resulting from the use of steroids. We conclude by pointing out the current lack and underutilization of ocular gene expression data, and how the state of the art is expected to improve in the future.
Low Transforming Growth Factor-β Pathway Activity in Cervical Adenocarcinomas
Authors: Marvin Dieuwke L. , Spaans Vivian M. , de Kroon Cor D. , Slieker Roderick C. , Khelil Maryam , ten Dijke Peter , Ritsma Laila , Jordanova Ekaterina S.
Published: June 2022

Cervical cancer is the fourth most common cancer in women worldwide. Squamous cell carcinoma (SCC) and adenocarcinoma (AC) are the most common histological types, with AC patients having worse prognosis. Over the last two decades, incidence rates of AC have increased, highlighting the importance of further understanding AC tumorigenesis, and the need to investigate new treatment options. The cytokine TGF-β functions as a tumour suppressor in healthy tissue. However, in tumour cells this suppressive function can be overcome. Therefore there is an increasing interest in using TGF-β inhibitors in the treatment of cancer. Here, we hypothesize that TGF-β plays a different role in SCC and AC. Analysis of RNA-seq data from the TCGA, using a TGF-β response signature, resulted in separate clustering of the two subtypes. We further investigated the expression of TGF-β-signalling related proteins (TβR1/2, SMAD4, pSMAD2, PAI-1, αvβ6 and MMP2/9) in a cohort of 62 AC patients. Low TβR2 and SMAD4 expression was associated with worse survival in AC patients and interestingly, high PAI-1 and αvβ6 expression was also correlated with worse survival. Similar correlations of TβR2, PAI-1 and αvβ6 with clinical parameters were found in previously reported SCC analyses. However, when comparing expression levels between SCC and AC patient samples, pSMAD2, SMAD4, PAI-1 and αvβ6 showed lower expression in AC compared to SCC. Because of the low expression of core TβR1/2, (p-)SMAD2 and SMAD4 proteins and the correlation with worse prognosis, TGF-β pathway most likely leads to tumour inhibitory effects in AC and therefore the use of TGF-β inhibitors would not be recommended. However, given the correlation of PAI-1 and αvβ6 with poor prognosis, the use of TGF- β inhibitors might be of interest in SCC and in the subsets of AC patients with high expression of these TGF-β associated proteins.
Up-Regulation of TRIM32 Associated With the Poor Prognosis of Acute Myeloid Leukemia by Integrated Bioinformatics Analysis With External Validation
Authors: Xu Xiaoyan , Qi Jiaqian , Yang Jingyi , Pan Tingting , Han Haohao , Yang Meng , Han Yue
Published: June 2022

Background

Acute myeloid leukemia (AML) is a malignant and molecularly heterogeneous disease. It is essential to clarify the molecular mechanisms of AML and develop targeted treatment strategies to improve patient prognosis.

Methods

AML mRNA expression data and survival status were extracted from TCGA and GEO databases (GSE37642, GSE76009, GSE16432, GSE12417, GSE71014). Weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis were performed. Functional enrichment analysis and protein-protein interaction (PPI) network were used to screen out hub genes. In addition, we validated the expression levels of hub genes as well as the prognostic value and externally validated TRIM32 with clinical data from our center. AML cell lines transfected with TRIM32 shRNA were also established to detect the proliferation in vitro.

Results

A total of 2192 AML patients from TCGA and GEO datasets were included in this study and 20 differentially co-expressed genes were screened by WGCNA and differential gene expression analysis methods. These genes were mainly enriched in phospholipid metabolic processes (biological processes, BP), secretory granule membranes (cellular components, CC), and protein serine/threonine kinase activity (molecular functions, MF). In addition, the protein-protein interaction (PPI) network contains 15 nodes and 15 edges and 10 hub genes (TLE1, GLI2, HDAC9, MICALL2, DOCK1, PDPN, RAB27B, SIX3, TRIM32 and TBX1) were identified. The expression of 10 central genes, except TLE1, was associated with survival status in AML patients (p<0.05). High expression of TRIM32 was tightly associated with poor relapse-free survival (RFS) and overall survival (OS) in AML patients, which was verified in the bone marrow samples from our center. In vitro, knockdown of TRIM32 can inhibit the proliferation of AML cell lines.

Conclusion

TRIM32 was associated with the progression and prognosis of AML patients and could be a potential therapeutic target and biomarker for AML in the future.
Platelet Activation in High D-Dimer Plasma Plays a Role in Acquired Resistance to Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Patients with Mutant Lung Adenocarcinoma
Authors: Lee Meng-Jung , Weng Chih-Ming , Chao Wei , Fang Yueh-Fu , Chung Fu-Tsai , Lin Chien-Huang , Kuo Han-Pin
Published: June 2022

Objective

Platelet activation and adhesion to cancer cells increase the release of multiple factors that contribute to EMT and chemoresistance. Elevated levels of D-dimer have been associated with poor clinical outcomes in lung cancer. Platelets in high D-dimer plasma may be activated and implicated in acquired resistance to EGFR TKI in advanced lung adenocarcinoma with mutant EGFR.

Materials and Methods

Clinical responsive rate (RR), progression-free survival (PFS), and overall survival (OS) were prospectively measured in treatment-naïve lung adenocarcinoma patients with activation mutation. Plasma or platelets from patients with high or low D-dimer level were obtained to investigate the cytotoxic effects of TKIs on mutant cancer cells, and the mechanistic pathways were also explored.

Results

Patients with high D-dimer had worse RR, PFS, and OS. High D-dimer plasma induced resistance to gefitinib, erlotinib, afatinib, or osimertinib in EGFR mutant lung cancer cells. Depletion of platelets in high D-dimer plasma reversed the resistance to TKI. Platelets of high D-dimer plasma had higher adherence capacity to cancer cells, and induced EGFR and Akt activation as well as EMT through Src activation. Inhibition of platelet adherence or activation of Src or Akt conquered the resistance to TKI. The acquired resistance to TKI by high D-dimer plasma was less attributed to secondary gene mutation.

Conclusion

Increased platelet activation in the high D-dimer plasma may contribute to first-line acquired EGFR TKI resistance. Thus, therapeutic strategy against platelet activation in patients with high D-dimer levels may improve the efficacy of first-line treatment with EGFR TKI.
Targeting ALK in Neuroendocrine Tumors of the Lung
Authors: Akhoundova Dilara , Haberecker Martina , Fritsch Ralph , Höller Sylvia , Kiessling Michael K. , Rechsteiner Markus , Rüschoff Jan H. , Curioni-Fontecedro Alessandra
Published: June 2022

Background

Anaplastic lymphoma kinase (ALK) rearrangements are known oncogenic drivers in non-small cell lung cancer (NSCLC). Few case reports described the occurrence of such rearrangements in large cell neuroendocrine carcinomas (LCNECs) of the lung without information on clinical responses to ALK tyrosine kinase inhibitors (TKIs) in these cases. Currently, neuroendocrine tumors of the lungs are not screened for ALK rearrangements.

Methods

To illustrate the clinical impact of molecular characterization in LCNECs, we report the disease course in three patients with ALK-rearranged metastatic LCNEC from our clinical routine, as well as their treatment response to ALK TKIs (index cases). To gain insight into the prevalence of ALK rearrangements in neuroendocrine tumors of the lung, we analyzed a retrospective cohort of 436 tumor biopsies including LCNEC (n = 61), small cell lung cancer (SCLC) (n = 206), typical (n = 91) and atypical (n = 69) carcinoids, and mixed histology (n = 9) for the presence of ALK rearrangements using a sequential diagnostic algorithm. ALK immunohistochemistry (IHC) was evaluable in 362 cases; fluorescence in situ hybridization (FISH) was evaluable in 28 out of the 35 IHC-positive cases, followed by next-generation sequencing (NGS) that was available in 12 cases.

Results

Within the retrospective cohort, ALK IHC was positive in 35 out of 362 (9.7%) evaluable samples. FISH was positive in 3 out of the 28 (10.7%) evaluable cases: 2 with atypical carcinoids and 1 with LCNEC. Additionally, the 3 index cases showed positive ALK IHC, which was confirmed by NGS. Within the retrospective cohort, NGS confirmed the presence of an ALK genomic rearrangement in one FISH-positive atypical carcinoid where material was sufficient for sequencing. Two out of three patients with metastatic ALK-rearranged LCNEC received up-front treatment with the ALK TKI alectinib and showed rapid tumor response at all metastatic sites, including multiple brain metastases.

Conclusions

ALK rearrangements represent rare but targetable oncogenic driver alterations in LCNEC. Contrarily to NSCLC, the detection of ALK rearrangements in neuroendocrine tumors of the lung is challenging, since ALK IHC can lead to false-positive results and therefore needs confirmation by FISH or NGS. Up-front comprehensive molecular profiling with NGS should be performed in metastatic LCNEC in order not to miss actionable genomic alterations.
H3K27M Mutation Doesn’t Mean Worse Prognosis in Old Patients
Authors: Hu Xiao Mu , Nie Xiao yu , Xu Kai lun , Wang Yin , Tang Feng , Du Zun guo , Xiong Ji
Published: June 2022

Objective

Diffuse midline glioma (DMG), H3K27 altered is a new entity that has become widely recognized. However, studies concerning DMG in adult patients remain rare. We did a retrospective study covering the largest amount of patients to date to analyze the clinicopathological characteristics of diffuse glioma in midline structures of the adult.

Methods

We reviewed 108 cases of adult DMG, collected their clinical data, and pathological results including H3K27 mutation. Summarized their features and the connection with overall survival in different age groups.

Results

Among 108 cases, 79 tumors were located at the thalamus. 38 patients had H3K27M mutation, whose average age was 35.7 years. The median overall survival of H3K27M-mutant gliomas and the 70 H3K27M wild-type gliomas were both 17 months. For young patients (age ≤ 35), The median survival time of the H3K27M-mutant was 18 months, while that of the H3K27M wild-type was 37 months. For older patients (age>35), the median survival time of the H3K27M-mutant was 16 months, while that of the H3K27M wild-type was 13 months. Other clinicopathological factors including sex, tumor location, the approach of surgery, histological grade, ATRX, and P53 were statistically irrelevant to prognosis.

Conclusion

The DMG in adults mainly occurred in the thalamus. H3K27M mutations tend to happen more frequently in young adults, and this genetic alteration results in a worse outcome only in young patients (≤35). For old patients, age is the only independent prognostic factor. Patients who underwent different surgical operations including biopsy, subtotal resection, and total resection had similar prognoses.
Predicting Tumor Mutational Burden From Lung Adenocarcinoma Histopathological Images Using Deep Learning
Authors: Niu Yi , Wang Lixia , Zhang Xiaojie , Han Yu , Yang Chunjie , Bai Henan , Huang Kaimei , Ren Changjing , Tian Geng , Yin Shengjie , Zhao Yan , Wang Ying , Shi Xiaoli , Zhang Minghui
Published: June 2022

Tumor mutation burden (TMB) is an important biomarker for tumor immunotherapy. It plays an important role in the clinical treatment process, but the gold standard measurement of TMB is based on whole exome sequencing (WES). WES cannot be done in most hospitals due to its high cost, long turnaround times and operational complexity. To seek out a better method to evaluate TMB, we divided the patients with lung adenocarcinoma (LUAD) in TCGA into two groups according to the TMB value, then analyzed the differences of clinical characteristics and gene expression between the two groups. We further explored the possibility of using histopathological images to predict TMB status, and developed a deep learning model to predict TMB based on histopathological images of LUAD. In the 5-fold cross-validation, the area under the receiver operating characteristic (ROC) curve (AUC) of the model was 0.64. This study showed that it is possible to use deep learning to predict genomic features from histopathological images, though the prediction accuracy was relatively low. The study opens up a new way to explore the relationship between genes and phenotypes.
Early Feasibility Assessment: A Method for Accurately Predicting Biotherapeutic Dosing to Inform Early Drug Discovery Decisions
Authors: Marcantonio Diana H. , Matteson Andrew , Presler Marc , Burke John M. , Hagen David R. , Hua Fei , Apgar Joshua F.
Published: June 2022

The application of model-informed drug discovery and development (MID3) approaches in the early stages of drug discovery can help determine feasibility of drugging a target, prioritize between targets, or define optimal drug properties for a target product profile (TPP). However, applying MID3 in early discovery can be challenging due to the lack of pharmacokinetic (PK) and pharmacodynamic (PD) data at this stage. Early Feasibility Assessment (EFA) is the application of mechanistic PKPD models, built from first principles, and parameterized by data that is readily available early in drug discovery to make effective dose predictions. This manuscript demonstrates the ability of EFA to make accurate predictions of clinical effective doses for nine approved biotherapeutics and outlines the potential of extending this approach to novel therapeutics to impact early drug discovery decisions.
New Hypoglycemic Drugs: Combination Drugs and Targets Discovery
Authors: Ni Xiayun , Zhang Lei , Feng Xiaojun , Tang Liqin
Published: June 2022

New hypoglycemic drugs, including glucagon-like peptide 1 receptor agonists (GLP-1RA), dipeptidyl peptidase-4 inhibitors (DPP-4i) and sodium-glucose cotransporter 2 inhibitors (SGLT-2i), which brings more options for the treatment of type 2 diabetes (T2DM). They are generally well tolerated, although caution is required in rare cases. Clinical trials have show good glycemic control with combination therapy with new hypoglycemic drugs in prediabetes and T2DM (mostly traditional stepwise therapy), but early combination therapy appears to have faster, more, and longer-lasting benefits. With the widespread clinical application of oral semaglutide, it is time to develop combinations drugs containing new hypoglycemic drugs, especially SGLT-2i and/or GLP-1RA, to control the risk of prediabetes and newly diagnosed T2DM and its cardiovascular complications, while improving patient compliance. Clinical and preclinical studies support that SGLT-2i exerts its protective effect on heart failure through indirect and direct effects. How this comprehensive protective effect regulates the dynamic changes of heart genes needs further study. We provide ideas for the development of heart failure drugs from the perspective of “clinical drug-mechanism-intensive disease treatment.” This will help to accelerate the development of heart failure drugs, and to some extent guide the use of heart failure drugs.
Impact of SLCO1B1*5 on Flucloxacillin and Co-Amoxiclav–Related Liver Injury
Authors: Alshabeeb Mohammad , Alomar Fadhel A. , Khan Amjad
Published: June 2022

Background: Idiosyncratic drug-induced liver injury (DILI) is a serious uncommon disease that may develop as a result of the intake of certain drugs such as the antimicrobials flucloxacillin and co-amoxiclav. The reported cases showed significant associations between DILI and various human leukocyte (HLA) markers. The solute carrier organic anion transporter 1B1 (SLCO1B1), a non-HLA candidate gene, was previously reported as a risk factor for liver injury induced by rifampin and methimazole. This study presumed that SLCO1B1 may play a general role in the DILI susceptibility and therefore investigated the association of rs4149056 (SLCO1B1*5, T521C) polymorphism with flucloxacillin- and co-amoxiclav–induced liver injury.

Methodology: We recruited 155 and 165 DILI cases of white ancestral origin from various European countries but mainly from the United Kingdom owing to flucloxacillin and co-amoxiclav, respectively. Only adult patients (≥18 years) who were diagnosed with liver injury and who showed i) clinical jaundice or bilirubin >2x the upper limit of normal (ULN), ii) alanine aminotransferase (ALT) >5x ULN or iii) alkaline phosphatase (ALP) >2x ULN and bilirubin > ULN were selected. The population reference sample (POPRES), a European control group (n = 282), was used in comparison with the investigated cases. TaqMan SNP genotyping custom assay designed by Applied Biosystems was used to genotype both DILI cohorts for SLCO1B1 polymorphism (rs4149056). Allelic discrimination analysis was performed using a step one real-time PCR machine. Genotype differences between cases and controls were examined using Fisher’s exact test. GraphPad Prism version 5.0 was used to determine the p-value, odds ratio, and 95% confidence interval. Compliance of the control group with Hardy–Weinberg equilibrium was proven using a web-based calculator available at https://wpcalc.com/en/equilibrium-hardy-weinberg/.

Results: A small number of cases failed genotyping in each cohort. Thus, only 149 flucloxacillin and 162 co-amoxiclav DILI cases were analyzed. Genotyping of both DILI cohorts did not show evidence of association with the variant rs4149056 (T521C) (OR = 0.71, 95% CI = 0.46–1.12; p = 0.17 for flucloxacillin cases and OR = 0.87, 95% CI = 0.56–1.33; p = 0.58 for co-amoxiclav), although slightly lower frequency (22.8%) of positive flucloxacillin cases was noticed than that of POPRES controls (29.4%).

Conclusion: Carriage of the examined allele SLCO1B1*5 is not considered a risk factor for flucloxacillin DILI or co-amoxiclav DILI as presumed. Testing a different allele (SLCO1B1*1B) and another family member gene (SLCO1B3) may still be needed to provide a clearer role of SLCO1B drug transporters in DILI development–related to the chosen antimicrobials.
Cuscuta chinensis Lam. Protects Against Light-Induced Retinal Degeneration: Therapeutic Implications for Photoreceptor Degenerative Disorders
Authors: Wu Hanhan , Zhu Beijing , Li Daijin , Xu Jing , Chang Jie , Du Xiaoye , Cui Jingang , Zhang Ning , Zhang Teng , Chen Yu
Published: June 2022

Cuscuta chinensis Lam. (CCL) is a medicinal herb widely used in traditional Chinese medicine for the treatment of ophthalmic diseases, including age-dependent vision-threatening retinal degenerative disorders that involve irreversible loss of the first-order retinal neurons, photoreceptors. However, evidence is lacking if CCL is pharmacologically active at protecting against loss of photoreceptors and photoreceptor degeneration-associated retinal structural and functional impairment. The current study thus evaluates the potential photoreceptor protective effects of CCL to better support its clinical applications in the prevention and treatment of photoreceptor degenerative diseases. Non-invasive full-retinal optical coherence tomography, electroretinography, histological examination, immunohistochemistry and real-time qPCR analysis were performed to assess the retinal protective effects of CCL in light-exposed BALB/c mice characterized by photooxidative stress-mediated photoreceptor loss and associated retinal morphological and functional impairment. The results showed that CCL treatment protected against light-induced degeneration of the photoreceptor structure and deterioration of the retinal function. Furthermore, CCL treatment increased the retinal expression of rhodopsin, S-opsin and M-opsin, supporting the protective effects of CCL in both rod and cone photoreceptors. CCL treatment suppressed photoreceptor cell death in the light-exposed retinas. The morphological integrity of the second-order retinal neurons was also preserved as a result of CCL treatment. In addition, CCL treatment attenuated light-induced reactive müller gliosis, microglial activation and inflammation in the retina. In conclusion, the current work demonstrates for the first time that CCL protects against photooxidative stress-mediated degeneration of photoreceptors and associated disturbance of structural, functional and immune homeostasis of the retina. The findings here thus provide novel experimental evidence supporting the clinical application of CCL in the prevention and treatment photoreceptor degenerative diseases.
Integrated Lipidomics and Metabolomics Study of Four Chemically Induced Mouse Models of Acute Intrahepatic Cholestasis
Authors: Li Weiwei , Chen Hui , Qian Yihan , Wang Shouchuan , Luo Zichen , Shan Jinjun , Kong Xiaoni , Gao Yueqiu
Published: June 2022

Lithocholic acid (LCA), alpha-naphthyl isothiocyanate (ANIT), 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC), and ethinyl estradiol (EE) are four commonly used chemicals for the construction of acute intrahepatic cholestasis. In order to better understand the mechanisms of acute cholestasis caused by these chemicals, the metabolic characteristics of each model were summarized using lipidomics and metabolomics techniques. The results showed that the bile acid profile was altered in all models. The lipid metabolism phenotype of the LCA group was most similar to that of primary biliary cirrhosis (PBC) patients. The ANIT group and the DDC group had similar metabolic disorder characteristics, which were speculated to be related to hepatocyte necrosis and inflammatory pathway activation. The metabolic profile of the EE group was different from other models, suggesting that estrogen-induced cholestasis had its special mechanism. Ceramide and acylcarnitine accumulation was observed in all model groups, indicating that acute cholestasis was closely related to mitochondrial dysfunction. With a deeper understanding of the mechanism of acute intrahepatic cholestasis, this study also provided a reference for the selection of appropriate chemicals for cholestatic liver disease models.
Cardioprotective Effect of Rheum turkestanicum Against Doxorubicin-Induced Toxicity in Rats
Authors: Hosseini Azar , Safari Mohammad-Kazem , Rajabian Arezoo , Boroumand-Noughabi Samaneh , Eid Ali H. , Al Dhaheri Yusra , Gumpricht Eric , Sahebkar Amirhossein
Published: June 2022

Background: Doxorubicin as an anti-cancer drug causes cardiotoxicity, limiting its tolerability and use. The mechanism of toxicity is due to free radical production and cardiomyocytes injury. This research evaluated Rheum turkestanicum (R.turkestanicum) extract against doxorubicin cardiotoxicity due to its considerable in vitro antioxidant activity.

Methods: Male Wistar rats received 2.5 mg/kg doxorubicin intraperitoneally every other day for 2 weeks to create an accumulative dose. R. turkestanicum was administrated at a dose of 100 and 300 mg/kg intraperitoneally from the second week for 7 days. On the 15th day, the animals were anesthetized and blood was collected from cardiac tissue for evaluation of alanine aminotransferase (ALT), cardiac muscle creatinine kinase (CK-MB), troponin T (cTn-T), lactate dehydrogenase (LDH), and B-type natriuretic peptide brain natriuretic peptide. A cardiac homogenate was also collected to determine superoxide dismutase (SOD), catalase Catalase Activity, malondialdehyde (MDA), and thiols. Histopathology was also performed.

Results: Doxorubicin increased all cardiac enzymes and malondialdehyde, correlating with a reduction in SOD, catalase, and thiols. Histopathology revealed extracellular edema, moderate congestion, and hemorrhage of foci. In contrast, administration of R. turkestanicum ameliorated these doxorubicin-induced pathophysiological changes.

Conclusion: This study revealed that the extract ameliorated doxorubicin-induced cardiac toxicity via modulation of oxidative stress-related pathways. Liquid chromatography-mass spectrometry analysis of R. turkestanicum indicated several components with potent pharmacological properties.
Antidepressant Effects of NSAIDs in Rodent Models of Depression—A Systematic Review
Authors: Bay-Richter Cecilie , Wegener Gregers
Published: June 2022

In recent years much focus has been on neuroimmune mechanisms of depression. As a consequence, many preclinical and clinical trials have been performed examining potential antidepressant effects of several anti-inflammatory drugs. The results of such trials have been varied. With the current manuscript we wished to elucidate the effects of non-steroidal anti-inflammatory drugs (NSAIDs) on depressive-like behaviour in rodent models of depression by performing a systematic review of the available literature. We performed a systematic literature search in PubMed for rodent models of depression where NSAIDs were administered and a validated measure of depressive-like behaviour was applied. 858 studies were initially identified and screened using Covidence systematic review software. Of these 36 met the inclusion criteria and were included. The extracted articles contained data from both rat and mouse studies but primarily male animals were used. Several depression models were applied and 17 different NSAIDs were tested for antidepressant effects. Our results suggest that stress models are the best choice when examining antidepressant effects of NSAIDs. Furthermore, we found that rat models provide a more homogenous response than mouse models. Intriguingly, the use of female animals was only reported in three studies and these failed to find antidepressant effects of NSAIDs. This should be explored further. When comparing the different classes of NSAIDs, selective COX-2 inhibitors were shown to provide the most stable antidepressant effect compared to non-selective COX-inhibitors. Suggested mechanisms behind the antidepressant effects were attenuation of neuroinflammation, HPA-axis dysregulation and altered monoamine expression.
Neuroprotective Effect of Taohong Siwu Decoction on Cerebral Ischemia/Reperfusion Injury via Mitophagy-NLRP3 Inflammasome Pathway
Authors: Ji Zhao-Jie , Shi Yun , Li Xing , Hou Rui , Yang Yu , Liu Zhu-Qing , Duan Xian-Chun , Liu Qing , Chen Wei-Dong , Peng Dai-Yin
Published: June 2022

Objective: Globally, cerebral ischemia has been shown to be the second leading cause of death. Our previous studies have shown that Taohong Siwu Decoction (THSWD) exhibits obvious neuroprotective effects on cerebral ischemia/reperfusion (I/R) injury (CIRI). In this study, we further explored the modulatory effect of THSWD on mitochondrial autophagy in CIRI and the relationship between modulatory effect and NLRP3 inflammatory vesicle activation, so as to further explain the mechanism of neuroprotective effect of THSWD.

Methods: Middle cerebral artery occlusion reperfusion (MCAO/R) model in rats was built to simulate I/R. Adult male SD rats (220–270 g) were randomly divided into the following four groups: the sham group, the MCAO/R group, the MCAO/R + THSWD group, and the MCAO/R + THSWD + Mitochondrial division inhibitor 1 (Mdivi-1) group. Neurological defect scores were used to evaluate neurological function. 2,3,5-Triphenyltetrazolium chloride (TTC) staining was conducted to measure cerebral infarct volume. Nissl staining, H&E staining and TUNEL staining were executed to detect ischemic cortical neuronal cell viability and apoptosis. Electron microscopy was used to observe the ultrastructural changes of mitochondria. Total Reactive Oxygen Species (ROS) in tissue were measured by fluorescence spectrophotometry, and the activation status of microglia was evaluated by Iba-1/CD16 immunofluorescence staining. The levels of mitophagy-related proteins (LC3, Parkin, PINK1), NLRP3 inflammasome-related proteins (NLRP3, ASC, Pro-caspase-1, Cleaved-caspase-1), and inflammatory cytokines (Pro-IL-18, Pro-IL-1β, IL-18, IL-1β) were evaluated by western blotting.

Results: The studies showed that THSWD treatment alleviated cerebral infarction and neurological deficiencies. THSWD upregulated the expressions of autophagy markers (LC3-II/LC3-I and Beclin1) mitochondrial autophagy markers (Parkin and PINK1) after CIRI. Furthermore, THSWD treatment attenuated microglia activation and damage to mitochondrial structures, thereby reducing ROS production and NLRP3 inflammasome activation. In contrast, the mitochondrial autophagy inhibitor Mdivi-1 inhibited the above beneficial effects of THSWD.

Conclusions: THSWD exhibits neuroprotective effects against MCAO/R in rats by enhancing mitochondrial autophagy and reducing NLRP3 inflammasome activation.
Trends of Dispensed Opioids in Catalonia, Spain, 2007–19: A Population-Based Cohort Study of Over 5 Million Individuals
Authors: Xie Junqing , Strauss Victoria Y. , Collins Gary S. , Khalid Sara , Delmestri Antonella , Turkiewicz Aleksandra , Englund Martin , Tadrous Mina , Reyes Carlen , Prieto-Alhambra Daniel
Published: June 2022

Objective: To characterize the trend of opioid use (number of users, dispensations and oral morphine milligram equivalents) in Catalonia (Spain).

Design, setting, and participants: This population-based cohort study included all individuals aged 18 years or older, registered in the Information System for Research in Primary Care (SIDIAP), which covers >75% of the population in Catalonia, Spain, from 1 January 2007, to 31 December 2019.

Main exposure and outcomes: The exposures were all commercialized opioids and their combinations (ATC-codes): codeine, tramadol, oxycodone, tapentadol, fentanyl, morphine, and other opioids (dihydrocodeine, hydromorphone, dextropropoxyphene, buprenorphine, pethidine, pentazocine). The main outcomes were the annual figures per 1,000 individuals of 1) opioid users, 2) dispensations, and 3) oral morphine milligram equivalents (MME). Results were stratified separately by opioid types, age (5-year age groups), sex (male or female), living area (rural or urban), and socioeconomic status (from least, U1, to most deprived, U5). The overall trends were quantified using the percentage change (PC) between 2007 and 2019.

Results: Among 4,656,197 and 4,798,114 residents from 2007 to 2019, the number of opioid users, dispensations and morphine milligram equivalents per 1,000 individuals increased 12% (percentage change: 95% confidence interval (CI) 11.9–12.3%), 105% (95% confidence interval 83%–126%) and 339% (95% CI 289%–390%) respectively. Tramadol represented the majority of opioid use in 2019 (61, 59, and 54% of opioid users, dispensations, and total MME, respectively). Individuals aged 80 years or over reported the sharpest increase regarding opioid users (PC: 162%), dispensations (PC: 424%), and MME (PC: 830%). Strong opioids were increasingly prescribed for non-cancer pains over the years.

Conclusion: Despite the modest increase of opioid users, opioid dispensations and MME increased substantially, particularly in the older population. In addition, strong opioids were incrementally indicated for non-cancer pains over the years. These findings suggest a transition of opioid prescriptions from intermittent to chronic and weak to strong and call for more rigorous opioid stewardship.
The Role of Gastrointestinal Microbiota in Functional Dyspepsia: A Review
Authors: Zhou Li , Zeng Yi , Zhang Hongxing , Ma Yan
Published: June 2022

Functional dyspepsia is a clinically common functional gastrointestinal disorder with a high prevalence, high impact and high consumption of medical resources. The microbiota in the gastrointestinal tract is a large number of families and is one of the most complex microbial reservoirs in the human body. An increasing number of studies have confirmed the close association between dysbiosis of the gastrointestinal microbiota and the occurrence and progression of functional dyspepsia. Therefore, we reviewed the role of dysbiosis of the gastrointestinal microbiota,H. pyloriinfection and gastrointestinal microbiota metabolites in functional dyspepsia, focusing on the possible mechanisms by which dysbiosis of the gastrointestinal microbiota contributes to the pathogenesis of functional dyspepsia. Several studies have confirmed that dysbiosis of the gastrointestinal microbiota may cause the occurrence and progression of functional dyspepsia by disrupting the biological barrier of the intestinal mucosa, by disturbing the immune function of the intestinal mucosa, or by causing dysregulation of the microbial-gut-brain axis. Probiotics and antibiotics have also been chosen to treat functional dyspepsia in clinical studies and have shown some improvement in the clinical symptoms. However, more studies are needed to explore and confirm the relationship between dysbiosis of the gastrointestinal microbiota and the occurrence and progression of functional dyspepsia, and more clinical studies are needed to confirm the therapeutic efficacy of microbiota modulation for functional dyspepsia.
Agroclimatic Metrics for the Main Stone Fruit Producing Areas in Spain in Current and Future Climate Change Scenarios: Implications From an Adaptive Point of View
Authors: Egea Jose A. , Caro Manuel , García-Brunton Jesús , Gambín Jesús , Egea José , Ruiz David
Published: June 2022

Stone fruit production has enormous economic importance in Spain. Cultivation locations for these fruit species (i.e., peach, apricot, plum, and sweet cherry) cover wide and climatically diverse geographical areas within the country. Climate change is already producing an increase in average temperatures with special intensity in certain areas like the Mediterranean ones. These changes lead to a decrease in the accumulated chill, which can have a profound impact on the phenology ofPrunusspecies like stone fruits due to, e.g., difficulties to cover the chilling requirements to break endodormancy, the occurrence of late frost events, or abnormal early high temperatures. All these factors can severely affect fruit production and quality and therefore provoke very negative consequences from the socio-economic point of view in the incumbent regions. Thus, characterization of current cultivation areas in terms of agroclimatic variables (e.g., chill and heat accumulation and probabilities of frost and early abnormal heat events), based on data from 270 weather stations for the past 20 years, is carried out in this work to produce an informative picture of the current situation. Besides, future climatic projections from different global climate models (data retrieved from the Meteorological State Agency of Spain—AEMET) up to 2065 for two Representative Concentration Pathway scenarios (i.e., RCP4.5 and RCP8.5) are also analyzed. Using the current situation as a baseline and considering the future scenarios, information on the current and future adaptive suitability of the different species/cultivars to the different growing areas can be inferred. This information could be the basis of a decision support tool to help the different stakeholders to take optimal decisions regarding current and future stone fruit or other temperate species cultivation in Spain.
Identification of Abietane-Type Diterpenoids and Phenolic Acids Biosynthesis Genes in Salvia apiana Jepson Through Full-Length Transcriptomic and Metabolomic Profiling
Authors: Hu Jiadong , Wang Feiyan , Liang Fengying , Wu Ziding , Jiang Rui , Li Jinxing , Chen Junfeng , Qiu Shi , Wang Jing , Zhang Yuchen , Li Qing , Chen Wansheng
Published: June 2022

Salvia apiana (S. apiana) Jepson is a medicinal plant that is frequently used by the Chumash Indians in southern California as a diaphoretic, calmative, diuretic, or antimicrobial agent. Abietane-type diterpenoids (ATDs) and phenolic acids (PAs) are the main bioactive ingredients in S. apiana. However, few studies have looked into the biosynthesis of ATDs and PAs in S. apiana. In this study, using metabolic profiling focused on the ATDs and PAs in the roots and leaves of S. apiana, we found a distinctive metabolic feature with all-around accumulation of ATDs, but absence of salvianolic acid B. To identify the candidate genes involved in these biosynthesis pathways, full-length transcriptome was performed by PacBio single-molecule real-time (SMRT) sequencing. A total of 50 and 40 unigenes were predicted to be involved in ATDs and PAs biosynthesis, respectively. Further transcriptional profile using Illumina HiSeq sequencing showed that the transcriptional variations of these pathways were consistent with the accumulation patterns of corresponding metabolites. A plant kingdom-wide phylogenetic analysis of cytochromes (CYPs) identified two CYP76AK and two CYP76AH subfamily genes that might contribute for the specific ATDs biosynthesis in S. apiana. We also noticed that the clade VII laccase gene family was significantly expanded in Salvia miltiorrhiza compared with that of S. apiana, indicating their involvements in the formation of salvianolic acid B. In conclusion, our results will enable the further understanding of ATDs and PAs biosynthesis in S. apiana and Salvia genus.