Differential Alterations Research Articles

Contribution of differential alteration in oxidative stress and anti-oxidation related molecular signals to toxicity difference between atrazine and its main metabolites in nematodes

As a widely used herbicide, atrazine and its two main metabolites of deethylatrazine (DEA) and deisopropylatrazine (DIA) pose an exposure risk for both human beings and animals in the environment. In this study, Caenorhabditis elegans was selected as an in vivo model to compare the toxicity between atrazine and its main metabolites. Upon exposure from the larval stage L1 to adult day 3, both DEA and DIA showed less toxicity on locomotion and reproduction compared with atrazine at concentration of 0.001, 0.01 0.1 and 1 mg/L for parental generation. In addition, exposure to DEA and DIA at concentration of 0.1 mg/L also induced less transgenerational toxicity on locomotion than exposure to atrazine for both parental generation and offspring of F1–F4. Accordingly, exposure to DEA and DIA caused less ROS production and alteration in the expression of some genes (mev-1, gas-1, and clk-1) governing oxidative stress compared to atrazine. Meanwhile, DEA and DIA lead to less increase in expression of superoxide dismutase genes (sod-2 and sod-3) and SOD-3::GFP than atrazine. Moreover, atrazine and its two main metabolites differentially activated the daf-16 encoding FOXO transcriptional factor in insulin signaling pathway during the control of downstream target of SOD-3. Overall, our results highlighted the important role of oxidative stress and anti-oxidation related molecular signals in mediating toxicity of atrazine, DEA and DIA, which provided a novel explanation for the different toxicity between atrazine and its main metabolites.

A comparative proteomics analysis of four contact allergens in THP-1 cells shows distinct alterations in key metabolic pathways

Allergic contact dermatitis (ACD) is the predominant form of immunotoxicity in humans. The sensitizing potential of chemicals can be assessed in vitro. However, a better mechanistic understanding could improve the current OECD-validated test battery. The aim of this study was to get insights into toxicity mechanisms of four contact allergens, p-benzoquinone (BQ), 2,4-dinitrochlorobenzene (DNCB), p-nitrobenzyl bromide (NBB) and NiSO4, by analyzing differential proteome alterations in THP-1 cells using two common proteomics workflows, stable isotope labeling by amino acids in cell culture (SILAC) and label-free quantification (LFQ). Here, SILAC was found to deliver more robust results. Overall, the four allergens induced similar responses in THP-1 cells, which underwent profound metabolic reprogramming, including a striking upregulation of the TCA cycle accompanied by pronounced induction of the Nrf2 oxidative stress response pathway. The magnitude of induction varied between the allergens with DNCB and NBB being most potent. A considerable overlap between transcriptome-based signatures of the GARD assay and the proteins identified in our study was found. When comparing the results of this study to a previous proteomics study in human primary monocyte-derived dendritic cells, we found a rather low share in regulated proteins. However, on pathway level, the overlap was high, indicating that affected pathways rather than single proteins are more eligible to investigate proteomic changes induced by contact allergens. Overall, this study confirms the potential of proteomics to obtain a profound mechanistic understanding, which may help improving existing in vitro assays for skin sensitization.

Analysis of heroin effects on calcium channels in rat cardiomyocytes based on transcriptomics and metabolomics.

Heroin can cause damage to many human organs, possibly leading to different types of arrhythmias and abnormal electrophysiological function of the heart muscle and the steady state of calcium-ion channels. We explored cardiomyocytes treated with heroin and the effect on calcium-ion channels. Transcriptomics and metabolomics were used to screen for differential genes and metabolite alterations after heroin administration to jointly analyze the effect of heroin on calcium channels in cardiomyocytes. Cardiomyocytes from primary neonatal rats were cultured in vitro and were treated with different concentrations of heroin to observe the changes in morphology and spontaneous beat frequency and rhythm by a patch clamp technique. Transcriptomic studies selected a total of 1,432 differentially expressed genes, 941 upregulated and 491 downregulated genes in rat cardiomyocytes from the control and drug intervention groups. Gene Ontology functional enrichment showed that 1,432 differential genes selected by the two groups were mainly involved in the regulation of the multicellular organismal process, response to external stimulus, myofibril, inflammatory response, muscle system process, cardiac muscle contraction, etc. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that these genes were mainly concentrated in cardiac muscle contraction, osteoclast differentiation, adrenergic signaling in cardiomyocytes, dilated cardiomyopathy, hypertrophic cardiomyopathy, and other important pathways. Metabolomic testing further suggested that cardiomyocyte metabolism was severely affected after heroin intervention. After the treatment with heroin, the L-type calcium channel current I-V curve was up-shifted, the peak value was significantly lower than that of the control group, action potential duration 90 was significantly increased in the action potential, resting potential negative value was lowered, and action potential amplitude was significantly decreased in cardiomyocytes. In this study, heroin could cause morphological changes in primary cardiomyocytes of neonatal rats and electrophysiological function. Heroin can cause myocardial contraction and calcium channel abnormalities, damage the myocardium, and change the action potential and L-type calcium channel.

Modifying functional brain networks in focal epilepsy by manual visceral-osteopathic stimulation of the vagus nerve at the abdomen.

Non-invasive transcutaneous vagus nerve stimulation elicits similar therapeutic effects as invasive vagus nerve stimulation, offering a potential treatment alternative for a wide range of diseases, including epilepsy. Here, we present a novel, non-invasive stimulation of the vagus nerve, which is performed manually viscero-osteopathically on the abdomen (voVNS). We explore the impact of short-term voVNS on various local and global characteristics of EEG-derived, large-scale evolving functional brain networks from a group of 20 subjects with and without epilepsy. We observe differential voVNS-mediated alterations of these characteristics that can be interpreted as a reconfiguration and modification of networks and their stability and robustness properties. Clearly, future studies are necessary to assess the impact of such a non-pharmaceutical intervention on clinical decision-making in the treatment of epilepsy. However, our findings may add to the current discussion on the importance of the gut-brain axis in health and disease. Clinical Trial Registration: https://drks.de/search/en/trial/DRKS00029914, identifier DRKS00029914.

Variability of extracellular vesicle release during storage of red blood cell concentrates is associated with differential membrane alterations, including loss of cholesterol-enriched domains.

Transfusion of red blood cell concentrates is the most common medical procedure to treat anaemia. However, their storage is associated with development of storage lesions, including the release of extracellular vesicles. These vesicles affect in vivo viability and functionality of transfused red blood cells and appear responsible for adverse post-transfusional complications. However, the biogenesis and release mechanisms are not fully understood. We here addressed this issue by comparing the kinetics and extents of extracellular vesicle release as well as red blood cell metabolic, oxidative and membrane alterations upon storage in 38 concentrates. We showed that extracellular vesicle abundance increased exponentially during storage. The 38 concentrates contained on average 7 × 1012 extracellular vesicles at 6weeks (w) but displayed a ∼40-fold variability. These concentrates were subsequently classified into 3 cohorts based on their vesiculation rate. The variability in extracellular vesicle release was not associated with a differential red blood cell ATP content or with increased oxidative stress (in the form of reactive oxygen species, methaemoglobin and band3 integrity) but rather with red blood cell membrane modifications, i.e., cytoskeleton membrane occupancy, lateral heterogeneity in lipid domains and transversal asymmetry. Indeed, no changes were noticed in the low vesiculation group until 6w while the medium and the high vesiculation groups exhibited a decrease in spectrin membrane occupancy between 3 and 6w and an increase of sphingomyelin-enriched domain abundance from 5w and of phosphatidylserine surface exposure from 8w. Moreover, each vesiculation group showed a decrease of cholesterol-enriched domains associated with a cholesterol content increase in extracellular vesicles but at different storage time points. This observation suggested that cholesterol-enriched domains could represent a starting point for vesiculation. Altogether, our data reveal for the first time that the differential extent of extracellular vesicle release in red blood cell concentrates did not simply result from preparation method, storage conditions or technical issues but was linked to membrane alterations.

Maternal Intake of Either Fructose or the Artificial Sweetener Acesulfame-K Results in Differential and Sex-Specific Alterations in Markers of Skin Inflammation and Wound Healing Responsiveness in Mouse Offspring: A Pilot Study.

Growing evidence has demonstrated that maternal artificial sweetener (AS) consumption may not be a beneficial alternative when compared to sugar-sweetened beverages and potentially leads to metabolic dysfunction in adult offspring. Compromised skin integrity and wound healing associated with type 2 diabetes can lead to complications such as diabetic pressure injury (PI). In this context, the skin plays an important role in the maintenance of metabolic homeostasis, yet there is limited information on the influence of sugar- or AS-sweetened beverages during pregnancy on developmental programming and offspring skin homeostasis. This study examined the impact of maternal fructose or acesulfame-k consumption on offspring wound healing. Female C57Bl/6 mice received a chow diet ad libitum with either water (CD), fructose (FR; 34.7 mM fructose), or AS (AS; 12.5 mM Acesulfame-K) throughout pregnancy and lactation. PIs were induced in offspring at 9 weeks of age (n = 6/sex/diet). PIs and healthy skin biopsies were collected for later analysis. Maternal AS intake increased skin inflammatory markers in healthy biopsies while an FR diet increased Tgfb expression, and both diets induced subtle changes in inflammatory markers post-wound inducement in a sex-specific manner. Furthermore, a maternal FR diet had a significant effect on pressure wound severity and early wound healing delay, while AS maternal diet had a sex-specific effect on the course of the healing process. This study demonstrates the need for a better understanding of developmental programming as a mediator of later-life skin integrity and wound responsiveness.

Single-cell analysis reveals dysregulated inflammatory response in peripheral blood immunity in patients with acute respiratory distress syndrome.

Introduction: Acute respiratory distress syndrome (ARDS) remains a major clinical challenge for patients in intensive care units. Determining the differential mechanisms underlying ARDS with different etiologies is a key goal to improve the effectiveness of ARDS therapy. Despite growing evidence that different immune cell types are involved in ARDS, the role of altered immune cell subpopulations in disease progression is unelucidated. Methods: In this study, we combined scRNA-seq and bulk-level sequencing to analyze the transcriptomes of peripheral blood mononuclear cells from healthy volunteers and patients with septic ARDS (sep-ARDS) and pneumonic ARDS (PNE-ARDS). Results: Our data revealed differential alterations at the cellular and molecular levels and within biological signaling pathways in ARDS with different etiologies. The dynamics of neutrophils, macrophages (Macs), classical dendritic cells (cDCs), myeloid-derived suppressive cells (MDSCs), and CD8+ T cells varied significantly among groups of different samples, with neutrophils and cDCs at higher, and Macs at significantly lower, amounts in the patients with sep-ARDS. Furthermore, MDSCs were highly enriched only in the sep-ARDS patients, whereas a higher abundance of CD8+ T cells was observed in patients with PNE-ARDS. In addition, these cell subpopulations were found to be significantly involved in apoptosis, inflammatory, and immune-related pathways. In particular, a significant enhancement of the oxidative stress response was observed in the neutrophil subpopulation. Conclusion: Our study shows that the composition of cells involved in the main peripheral circulation differs in patients with ARDS with different etiologies. Studying the role and mechanism of action of these cells during ARDS will provide new opportunities for the treatment of this condition.

Searching for biomarkers in the fluidity of mental ill-health.

Searching for biomarkers in the fluidity of mental ill-health.

Expression of MCMs in Endometrial Cancer and its Biological Correlation Analysis.

Minichromosome maintenance (MCM) has been demonstrated to be involved in tumorigenesis and pathogenesis of many cancer types. However, the role of MCMs in endometrial cancer (EC) has not been elucidated. We first employed GEPIA, cBioPortal, and R software to perform the differential expression analysis, survival analysis, and gene alteration analysis of the MCMs family. Then, GSE17025 and GSE63678 datasets and CTPAC were used to verify the mRNA and protein expression levels of MCM4. In addition, the internal mechanism of the MCM4 was investigated by comparing MCM4 expression-correlated differentially expressed genes (DEGs) from GEPIA and MCM4-interacted genes from STRING. Last, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to identify MCM4-related biological processes. Compared with normal tissues, only MCM2 and MCM4 expression were significantly upregulated in EC tissues. High expression of MCM4 was related to worse clinicopathological features and poor prognosis in EC cohorts. Additionally, a certain degree of gene alterations in the MCM2-7 gene was observed. By comparing MCM4 expression-correlated DEGs and MCM4- interacted genes, six genes were obtained: SSRP1, ORC1, GINS1, CDK2, DBF4 and GINS3. Functional enrichment analysis suggested that MCM4 may be involved in regulating the biological processes of DNA replication and the p53 signaling pathway. This was the first comprehensive study to disclose the biological effects of MCMs in EC, indicating that MCM4 could be used as a new prognostic biomarker and potential therapeutic target for EC.

MP20-10 ENZALUTAMIDE INCREASES PROSTATE CANCER (PCa) CELL INVASION YET DECREASES BLADDER CANCER (BCa) CELL INVASION VIA DIFFERENTIALLY REGULATING THE AR/circRNA-ARC1/miR-125b-2-3p OR MiR-4736/PPARγ/MMP-9 SIGNALS

You have accessJournal of UrologyCME1 Apr 2023MP20-10 ENZALUTAMIDE INCREASES PROSTATE CANCER (PCa) CELL INVASION YET DECREASES BLADDER CANCER (BCa) CELL INVASION VIA DIFFERENTIALLY REGULATING THE AR/circRNA-ARC1/miR-125b-2-3p OR MiR-4736/PPARγ/MMP-9 SIGNALS Gang Deng, Yixi Hu, Yin Sun, Jean Joseph, Shuyuan Yeh, Edward M. Messing, and Chawnshang Chang Gang DengGang Deng More articles by this author , Yixi HuYixi Hu More articles by this author , Yin SunYin Sun More articles by this author , Jean JosephJean Joseph More articles by this author , Shuyuan YehShuyuan Yeh More articles by this author , Edward M. MessingEdward M. Messing More articles by this author , and Chawnshang ChangChawnshang Chang More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003245.10AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Androgen-deprivation therapy (ADT) is a standard treatment to prevent and shrink PCa growing. However, some patients undergoing ADT may finally develop to hormone-insensitive PCa. The underlying mechanisms haven't been fully elucidated. Here we found ADT-Enz led to increased PCa cell invasion, yet decreased BCa cell invasion. Our goal is to 1.reveal mechanisms of Enz induced hormone-insensitive PCa and find a potential combination therapy. 2. reveal mechanisms of ADT role in BCa and provide an evidence of applying ADT in BCa. METHODS: The human PCa and BCa cells: C4-2, CWR22Rv1, T24 and TCC-SUP were used. Lentiviral plasmids were used to generate gene engineering tools. qPCR and Western blot were used to detect gene expressions. Invasion assay were applied to determine cancer cell invasion capability. Protein-DNA binding complexes were detected by Chromatin immunoprecipitation (ChIP) assays. PPARGC1B/PDK1 3′UTR regions were cloned into the psiCHECKTM-2 vector to assay the miRNA functions. Preclinical mouse PCa model was used to evaluate the anti-cancer efficacy of Enz and circRNA-ARC1 blockage. RESULTS: Mechanistic dissection revealed that suppressing androgens/AR signals could result in differential alterations of the selective circular RNAs (circRNAs) as a result of differential endogenous AR transcription. A negative autoregulation in PCa, yet a positive autoregulation in BCa, as a result of differential binding of AR to different androgen-response elements (AREs) and a discriminating histone H3K4 methylation. Further mechanistic studies indicated that AR-encoded circRNA-ARC1 might sponge the availability of the miR-125b-2-3p and/or miR-4736 to impact the metastasis-related PPARγ/MMP-9 signals. The preclinical mouse model confirms in vitro cell lines data, showing that Enz treatment could increase PCa metastasis, which can be suppressed after iknockdown of circRNA-ARC1. Together, these results demonstrate that antiandrogen therapy with Enz treatment may differentially lead to promoting PCa cell invasion, yet decreasing BCa cell invasion. CONCLUSIONS: Our study is the first to reveal ADT-Enz treatment can promote PCa Cell Invasion yet decrease BCa cell Invasion via differentially regulating the AR/circRNA-ARC1/miR-125b-2-3p or MiR-4736/PPARγ/MMP-9 Signals. Furthermore, our findings may help in development of novel therapeutic approaches to increase the Enz efficacy with less adverse effects in patients with PCa, and providing an evidence of applying ADT in BCa. Source of Funding: This work was partially supported by URMC Urology Department Research fund and George H. Whipple Professorship Endowment © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e279 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Gang Deng More articles by this author Yixi Hu More articles by this author Yin Sun More articles by this author Jean Joseph More articles by this author Shuyuan Yeh More articles by this author Edward M. Messing More articles by this author Chawnshang Chang More articles by this author Expand All Advertisement PDF downloadLoading ...

Bioinformatics gene analysis of potential biomarkers and therapeutic targets of osteoarthritis associated myelodysplastic syndrome.

Objective: Osteoarthritis (OA) and Myelodysplastic syndrome (MDS) are diseases caused by the same immune disorder with unclear etiology and many similarities in clinical manifestations; however, the specific mechanisms between osteoarthritis and myelodysplastic syndrome are unclear. Methods: The expression profile microarrays of osteoarthritis and myelodysplastic syndrome were searched in the GEO database, the intersection of their differential genes was taken, Venn diagrams were constructed to find common pathogenic genes, bioinformatics analysis signaling pathway analysis was performed on the obtained genes, and protein-protein interaction networks were constructed to find hub genes in order to establish diagnostic models for each disease and explore the immune infiltration of hub genes. Results: 52 co-pathogenic genes were screened for association with immune regulation, immune response, and inflammation. The mean area under the receiver operating characteristic (ROC) for all 10 genes used for co-causal diagnosis ranged from 0.71-0.81. Immune cell infiltration analysis in the myelodysplastic syndrome subgroup showed that the relative numbers of Macrophages M1, B cells memory, and T cells CD4 memory resting in the myelodysplastic syndrome group were significantly different from the normal group, however, in the osteoarthritis subgroup the relative numbers of Mast cells resting in the osteoarthritis subgroup was significantly different from the normal group. Conclusion: There are common pathogenic genes in osteoarthritis and myelodysplastic syndrome, which in turn mediate differential alterations in related signaling pathways and immune cells, affecting the high prevalence of osteoarthritis and myelodysplastic syndrome and the two disease phenomena.

Regional superficial amygdala resting-state functional connectivity in adults infers childhood maltreatment severity.

Childhood maltreatment (CM) is a potential risk factor for some neuropsychiatric disorders in adulthood (e.g. depression and anxiety) and alters trajectories of brain development. Accumulating evidence suggests that functional connectivity of the limbic system, especially the amygdala, is highly associated with childhood maltreatment, although not all studies have found this. These inconsistent results may be due to differential alterations of amygdala resting-state functional connectivity (rsFC) following childhood maltreatment. Our aim was to investigate the relationship between the rsFC of amygdala subregions and CM severity, as well as to develop a stable rsFC-based model for inferring the severity of CM. In this study, we employed the Childhood Trauma Questionnaire (CTQ) to assess CM severity in each individual. We explored the relationship between the rsFC of amygdala subregions (i.e. centromedial -CMA, basolateral -BLA, superficial-SFA amygdala) and CM experience in a discovery dataset of n=110 healthy Chinese participants by linear multiple regression analysis. Subsequent dimensional and categorical approach were performed to elucidate the relationship between rsFCs and CM severity and CM subtypes, respectively. A support vector regression model was then conducted to validate the associations between rsFCs and total CTQ scores. Moreover, we also verified the model into another independent replication dataset (n=38). Our findings suggested that childhood maltreatment was negatively associated with rsFC between the right superficial amygdala and perigenual anterior cingulate cortex (pgACC)/postcentral gyrus (PCG) but not the other two amygdala subregions. Moreover, SFA-pgACC coupling was more associated with physical neglect whereas the SFA-PCG was more related to emotional neglect. In addition, supervised machine learning confirmed that using these two rsFCs as predictors could stably estimate continuous maltreatment severity in both discovery and replication datasets. The current study supports that the rsFCs of superficial amygdala are related to childhood maltreatment and which may be a potential biomarker for the effects of childhood maltreatment-related psychiatric disorders (i.e. depression and anxiety).

Abstract P2-26-06: Association between CK+/CD45+ circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) alterations in advanced breast cancer patients

Abstract Background: Circulating tumor cells (CTCs) in breast cancer (BC) are commonly defined as epithelial cells (EPCAM and cytokeratin (CK) positive), lacking the universal blood cell marker CD45. Nonetheless, CTCs expressing both CK and CD45 (= dual-positive, DP cells) can be observed in the blood of cancer patients. Early evidence suggests that DP cells might derive from the fusion of tumor cells and macrophages, and we have previously demonstrated that they present aberrant genomes and are associated with worse prognosis in BC [1,2]. Here, to further investigate the mechanisms/pathways underlying their presence, we analyzed the association between DP cells and circulating tumor DNA (ctDNA) alterations. Methods: Blood samples were collected from patients with advanced BC (aBC), before starting a new line of therapy. All patients were enrolled in a prospective clinical trial. For CTC and DP cells analysis, 7.5 ml of blood collected in CellSave® tubes was processed with the FDA-approved CellSearch® platform (positivity cutoffs were ≥1 cell for DPcells and ≥5 cells for CTCs). For ctDNA analysis, plasma was collected from Streck stabilizing tubes and analyzed with the Guardant360™ NGS platform for the detection of somatic single nucleotide variants (SNVs), insertions/deletions (indels), gene fusions/rearrangements and copy number variations (CNVs), which were then classified into pathways based on previously defined profiles generated on the Cancer Genome Atlas database (RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Associations between ctDNA-detected gene alterations and circulating cell types were analyzed through chi square test, while mutant allele frequency (MAF) and number of detected alterations (NDA) were tested by Mann Whitney test. Results: We analyzed blood samples from 169 patients with luminal-like (n=80), HER2+ (n=34) and triple-negative (n=52) aBC. DPcells were detected in 85 patients (50.3 %, range 0-53), of which 40 (47 %) were CTC-positive and 45 (53%) CTC-negative. Somatic ctDNA alterations were detected in all analyzed samples. In the overall population, the presence of ≥1 DPcell was associated with SNVs in the cell cycle pathway (p = 0.043), a numerically higher incidence was also observed for CNVs in this pathway. SNVs and CNVs in the cell cycle pathway were associated with CTCs ≥ 5 as well (p = 0.005 and p = 0.003, respectively). Moreover, associations with CTCs ≥ 5 were observed for RTK SNVs and CNVs (p = 0.041 and p = 0.046, respectively), PI3K SNVs and CNVs (p = 0.006 and p = 0.007, respectively), MYC SNVs and CNVs (p = 0.042). No associations were observed in terms of MAF and NDA. In the luminal-like subgroup an association was highlighted for CNVs in the cell cycle pathway, p = 0.038. CTCs ≥ 5 were associated with PI3K SNVs (p = 0.031). In the triple-negative subgroup DPcells were associated with SNVs in the RAF pathway (p = 0.041), whereas CTCs ≥ 5 were associated with PI3K SNVs and CNVs (p = 0.044 and p = 0.024, respectively) and RTK SNVs (p = 0.008). In the HER2 positive subgroup, a higher MAF and number of detected SNVs was observed for samples with ≥1 DPcell (p = 0.0286 and p = 0.0099, respectively). Conclusions: The study analyzed ctDNA features associated with canonical and CK+/CD45+ CTCs, showing differential gene alteration profiles. Cell cycle pathway SNVs were common in both CTC populations, while other pathways (RTK, PI3K, MYC and RAF) were significantly altered in a mutually exclusive pattern. These results suggest that DPcells might have a different biological meaning compared to canonical CTCs. More studies need to be conducted to better characterize this understudied CTC subpopulation and understand their specific contribution to cancer progression.

Abnormal cerebellum connectivity patterns related to motor subtypes of Parkinson’s disease

Cerebellar dysfunction may substantially contribute to the clinical symptoms of Parkinson’s disease (PD). The role of cerebellar subregions in tremors and gait disturbances in PD remains unknown. To investigate alterations in cerebellar subregion volumes and functional connectivity (FC), as well as FC between the dentate nucleus (DN) and ventral lateral posterior nucleus (VLp) of the thalamus, which are potentially involved in different PD motor subtypes. We conducted morphometric and resting-state functional connectivity analyses in various cerebellar subregions in 22 tremor-dominant (TD)-PD and 35 postural instability gait difficulty dominant (PIGD)-PD patients and 38 sex- and age-matched healthy controls (HCs). The volume and FC alterations in various cerebellar subregions and the neural correlates of these changes with the clinical severity scores were investigated. The PIGD-PD group showed greater FC between the right motor cerebellum (CBMm) and left postcentral gyrus than the HC group, and a higher FC was associated with less severe PIGD symptoms. In contrast, the TD-PD group had decreased FC between the right DN and left VLp compared with the PIGD-PD and HC groups, and lower FC was associated with worse TD symptoms. Furthermore, the PIGD-PD group had higher FC between the left DN and left inferior temporal gyrus than the TD-PD group. Morphometric analysis revealed that the TD-PD group showed a significantly higher volume of left CBMm than the HC group. Our findings point to differential alteration patterns in cerebellar subregions and offer a new perspective on the pathophysiology of motor subtypes of PD.

Demultiplexing Ig repertoires by parallel mRNA/DNA sequencing shows major differential alterations in severe COVID-19

To understand the fine differential elements that can lead to or prevent acute respiratory distress syndrome (ARDS) in COVID-19 patients, it is crucial to investigate the immune response architecture. We herein dissected the multiple layers of B cell responses by flow cytometry and Ig repertoire analysis from acute phase to recovery. Flow cytometry with FlowSOM analysis showed major changes associated with COVID-19 inflammation such as an increase of double-negative B-cells and ongoing plasma cell differentiation. This paralleled COVID-19-driven expansion of two disconnected B-cell repertoires. Demultiplexing successive DNA and RNA Ig repertoire patterns characterized an early expansion of IgG1 clonotypes with atypically long and uncharged CDR3, the abundance of this inflammatory repertoire being correlated with ARDS and likely pejorative. A superimposed convergent response included convergent anti-SARS-CoV-2 clonotypes. It featured progressively increasing somatic hypermutation together with normal-length or short CDR3 and it persisted until a quiescent memory B-cell stage after recovery.

Impact of genome and epigenome on intratumor heterogeneity in colorectal cancer

Impact of genome and epigenome on intratumor heterogeneity in colorectal cancer

Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations

BackgroundRhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood.ResultsWe report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato.ConclusionsOur study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.

Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulation

BackgroundMolecular characterisation of hepatocellular carcinoma (HCC) is central to the development of novel therapeutic strategies for the disease. We have previously demonstrated mutagenic consequences of Long-Interspersed Nuclear Element-1 (LINE1s/L1) retrotransposition. However, the role of L1 in HCC, besides somatic mutagenesis, is not well understood.MethodsWe analysed L1 expression in the TCGA-HCC RNAseq dataset (n = 372) and explored potential relationships between L1 expression and clinical features. The findings were confirmed by immunohistochemical (IHC) analysis of an independent human HCC cohort (n = 48) and functional mechanisms explored using in vitro and in vivo model systems.ResultsWe observed positive associations between L1 and activated TGFβ-signalling, TP53 mutation, alpha-fetoprotein and tumour invasion. IHC confirmed a positive association between pSMAD3, a surrogate for TGFβ-signalling status, and L1 ORF1p (P < 0.0001, n = 32). Experimental modulation of L1 ORF1p levels revealed an influence of L1 ORF1p on key hepatocarcinogenesis-related pathways. Reduction in cell migration and invasive capacity was observed upon L1 ORF1 knockdown, both in vitro and in vivo. In particular, L1 ORF1p increased PIN1 cytoplasmic localisation. Blocking PIN1 activity abrogated L1 ORF1p-induced NF-κB-mediated inflammatory response genes while further activated TGFβ-signalling confirming differential alteration of PIN1 activity in cellular compartments by L1 ORF1p.DiscussionOur data demonstrate a causal link between L1 ORF1p and key oncogenic pathways mediated by PIN1, presenting a novel therapeutic avenue.

Serrapeptase impairs biofilm, wall, and phospho-homeostasis of resistant and susceptible Staphylococcus aureus

Staphylococcus aureus biofilms are implicated in hospital infections due to elevated antibiotic and host immune system resistance. Molecular components of cell wall including amyloid proteins, peptidoglycans (PGs), and lipoteichoic acid (LTA) are crucial for biofilm formation and tolerance of methicillin-resistant S. aureus (MRSA). Significance of alkaline phosphatases (ALPs) for biofilm formation has been recorded. Serrapeptase (SPT), a protease of Serratia marcescens, possesses antimicrobial properties similar or superior to those of many antibiotics. In the present study, SPT anti-biofilm activity was demonstrated against S. aureus (ATCC 25923, methicillin-susceptible strain, methicillin-susceptible S. aureus (MSSA)) and MRSA (ST80), with IC50 values of 0.67 μg/mL and 7.70 μg/mL, respectively. SPT affected bacterial viability, causing a maximum inhibition of − 46% and − 27%, respectively. Decreased PGs content at [SPT] ≥ 0.5 μg/mL and ≥ 8 μg/mL was verified for MSSA and MRSA, respectively. In MSSA, LTA levels decreased significantly (up to − 40%) at lower SPT doses but increased at the highest dose of 2 μg/mL, a counter to spectacularly increased cellular and secreted LTA levels in MRSA. SPT also reduced amyloids of both strains. Additionally, intracellular ALP activity decreased in both MSSA and MRSA (up to − 85% and − 89%, respectively), while extracellular activity increased up to + 482% in MSSA and + 267% in MRSA. Altered levels of DING proteins, which are involved in phosphate metabolism, in SPT-treated bacteria, were also demonstrated here, implying impaired phosphorus homeostasis. The differential alterations in the studied molecular aspects underline the differences between MSSA and MRSA and offer new insights in the treatment of resistant bacterial biofilms.Key points• SPT inhibits biofilm formation in methicillin-resistant and methicillin-susceptible S. aureus.• SPT treatment decreases bacterial viability, ALP activity, and cell wall composition.• SPT-treated bacteria present altered levels of phosphate-related DING proteins.Graphical

Rare earth element signature modifications induced by differential acid alteration of rocks in the Iberian Pyrite Belt

The efficient use of REE as tracers of weathering processes requires further data acquisition to establish robust connections between mechanisms, mineral assemblages and REE concentration patterns. Here, results are provided corresponding to rocks from four locations in the Iberian Pyrite Belt that were altered with different intensity by sulfuric fluids. The acidic alteration was mild (pH 5–7) in Calañas and El Villar, while strong (pH below 3 to 5) in Quebrantahuesos and Tharsis. The main REE reservoir before alteration were phyllosilicates (and plagioclase/feldspar in El Villar only). Mild alteration generated mainly kaolinite while illite and some plagioclase/feldspar were preserved. Mildly altered rocks approximately preserved the relative REE concentrations of their precursors, interpreted as indicating a low fluid/rock ratio environment where binding sites in minerals outnumbered those in fluids. Strong acid alteration produced alunite, jarosite, beudantite and goethite, with partial illite preservation. Where illite and/or goethite were major minerals, this alteration generated REE patterns enriched in light REE over heavy REE or did not modify the relative REE concentrations of the original rock. However, samples where REE concentrations were controlled by alunite or jarosite had LREE > > HREE. In alunite the maximum concentration corresponded to Nd and Sm. In jarosite concentrations decreased from La to Lu, except that a positive Eu anomaly was preserved from the precursor. These REE concentration patterns are interpreted as due to crystallographic factors, controlled by the best fit of REE with charge 3+ in the 12-fold coordination site of K in jarosite and alunite. This site is larger in jarosite and fits La best, whereas the smaller site in alunite best fits Nd and Sm. Goethite REE signature is variable, perhaps due to two formation routes, (1) silicates ➔ goethite and (2) silicates ➔ jarosite ➔ goethite. Our interpretations of REE concentration in alunite, jarosite and goethite are novel and provide new routes to further develop REE as tracers of acid alteration processes.