Separate Assays Research Articles

GPR137-RAB8A activation promotes ovarian cancer development via the Hedgehog pathway

BackgroundOvarian cancer (OC) progression is one of the commonest cause of female cancer death. While treatments in clinic includes primary surgery and targeted chemotherapy, curative and survival trends in OC have not significantly improved. Thus, further investigation of the mechanisms regarding OC carcinogenesis and discovery of novel targets is of great importance.MethodsHuman ovarian tissue specimens, RNA sequencing, GEPIA database and bioinformatics analyses were used to analyze the gene correlation, and to identify and validate potential downstream candidates. The biological effects of GPR137-RAB8A-Hedgehog(HH) were investigated using in vitro and in vivo models and methods including qRT-PCR, RNA stability assay, RNA immunoprecipitation assay, GLI-luciferase reporter assay, nucleo-cytoplasmic separation assay, membrane-cytoplasmic separation assay, western blot, co-immunoprecipitation, immunofluorescence staining, cell counting kit-8 assay, wound healing assay, matrigel invasion assay, colony formation assay, xenografts assay, in situ transplantation tumor model of ovarian cancer in nude mice, and immunohistochemistry staining.ResultsGPR137 expression was significantly higher in collected clinical OC tissues, compared with the adjacent normal tissues. Consistently, suppression of GPR137 inhibited human SK-OV-3 and A2780 OC cell proliferation, migration, invasion, and colony formation, whereas overexpression of GPR137 in human OC HO8910 cell exerted the opposite effects on cell biological behaviors. Mechanistically, RAB8A was identified as a downstream target of GPR137, and GPR137 promotes RAB8A expression by promoting RAB8A mRNA stability. By RNA-sequencing and experiments in vitro using multiple ovarian cancer cell models as well as in vivo using subcutaneous xenografts assay and in situ transplantation ovarian cancer model in nude mice, we further demonstrated that RAB8A positively mediated OC progression through activating HH signaling pathway by disassociating the protein–protein complex formation of GLI and SuFu (Suppressor of Fused), which reciprocally enhanced GPR137 activity, forming a regulation loop between HH signaling and GPR137.ConclusionsCollectively, this study depicts the role of GPR137-RAB8A-HH cascade in the development of OC, deepening our understanding of tumor biomechanics regarding OC progression and providing novel targets for OC therapy in future.

Structural and molecular properties of mumps virus inclusion bodies.

Viral RNA synthesis of mononegaviruses occurs in cytoplasmic membraneless organelles called inclusion bodies (IBs). Here, we report that IBs of mumps virus (MuV), which is the causative agent of mumps and belongs to the family Paramyxoviridae, displayed liquid organelle properties formed by liquid-liquid phase separation. Super-resolution microscopic analysis of MuV IBs demonstrated that nucleocapsid and phospho (P)-proteins formed a cage-like structure and that the viral polymerase adopted a reticular pattern and colocalized with viral RNAs. In addition, we characterized host RNAs localized in MuV IBs by a spatial transcriptome analysis, and found that RNAs containing G-quadruplex motif sequences (G4-RNAs) were concentrated. An in vitro phase separation assay showed that the G4-RNAs interacted with the P protein and enhanced condensation in P droplets. Together, our data show that MuV generates IBs with a characteristic cage-like structure and host G4-RNAs play an important role in forming MuV IBs.

Actin polymerization counteracts prewetting of N-WASP on supported lipid bilayers

Cortical condensates, transient punctate-like structures rich in actin and the actin nucleation pathway member Neural Wiskott-Aldrich syndrome protein (N-WASP), form during activation of the actin cortex in the Caenorhabditis elegans oocyte. Their emergence and spontaneous dissolution is linked to a phase separation process driven by chemical kinetics. However, the mechanisms that drive the onset of cortical condensate formation near membranes remain unexplored. Here, using a reconstituted phase separation assay of cortical condensate proteins, we demonstrate that the key component, N-WASP, can collectively undergo surface condensation on supported lipid bilayers via a prewetting transition. Actin partitions into the condensates, where it polymerizes and counteracts the N-WASP prewetting transition. Taken together, the dynamics of condensate-assisted cortex formation appear to be controlled by a balance between surface-assisted condensate formation and polymer-driven condensate dissolution. This opens perspectives for understanding how the formation of complex intracellular structures is affected and controlled by phase separation.

A reinvestigation of cognitive styles in sticklebacks: decision success varies with behavioral type.

The "cognitive styles" hypothesis suggests that individual differences in behavior are associated with variation in cognitive performance via underlying speed-accuracy trade-offs. While this is supported, in part, by a growing body of evidence, some studies did not find the expected relationships between behavioral type and cognitive performance. In some cases, this may reflect methodological limitations rather than the absence of a true relationship. The physical design of the testing arena and the number of choices offered in an assay can hinder our ability to detect inter-individual differences in cognitive performance. Here, we re-investigated the cognitive styles hypothesis in threespine stickleback (Gasterosteus aculeatus), adapting the maze design of a previous study which found no cost to decision success by faster (bolder) individuals. We used a similar design but increased the size of the maze and incorporated an additional choice in the form of a third maze arm. We found, in accordance with cognitive style expectations, that individuals who were consistently slower to emerge from the start chamber made fewer errors than fish that emerged faster. Activity in an open field test, however, did not show evidence of a relationship with decision success, possibly due to the low number of repeated observations per fish in this separate assay. Our results provide further empirical support for the cognitive styles hypothesis and highlight important methodological aspects to consider in studies of inter-individual differences in cognition.

An investigation of personality in the Creek Chub, Semotilus atromaculatus

AbstractIntraspecific variation in personality traits is increasingly recognized as an important driver of ecological processes, particularly within the context of species invasions. However, relatively few studies have investigated personality in native fauna with more localized dispersal patterns, and information regarding the existence of personality in stream fishes native to the southeastern US is particularly lacking. In this study, we investigated personality in a native and widespread minnow species, the Creek Chub (Semotilus atromaculatus). Because of its piscivorous diet, use of its nests by nest-associating minnows, and its role as a colonizer of intermittent streams, the Creek Chub is an appropriate species for investigating the broad importance of personality-dependent processes to stream communities. We identified personality traits by estimating the repeatability of sociability, boldness, exploration, and activity in two separate behavioral assays and interpreted correlations between traits as evidence of behavioral syndromes. We did not detect repeatability for measures of sociability, possibly due to predatory interactions within this species. However, boldness, exploration, and activity were significantly repeatable and positively correlated, pointing to the existence of a bold-exploratory-active syndrome in this species. Larger individuals tended to be less active, and, despite a relatively small sample size, we detected significant differences between source populations for measures of boldness. This is the first study to identify the existence of a behavioral syndrome in Creek Chub and points to the importance of considering the role of personality in ecological processes involving native fauna.

Proteins and noncoding RNAs that promote homologous chromosome recognition and pairing in fission yeast meiosis undergo condensate formation invitro.

Pairing of homologous chromosomes during meiosis is crucial for successful sexual reproduction. Previous studies have shown that the fission yeast sme2 RNA, a meiosis-specific long noncoding RNA (lncRNA), accumulates at the sme2 locus and plays a key role in mediating robust pairing during meiosis. Several RNA-binding proteins accumulate at the sme2 and other lncRNA gene loci in conjunction with the lncRNAs transcribed from these loci. These lncRNA-protein complexes form condensates that exhibit phase separation properties on chromosomes and are necessary for robust pairing of homologous chromosomes. To further understand the mechanisms by which phase separation affects homologous chromosome pairing, we conducted an invitro phase separation assay with the sme2 RNA-associated proteins (Smps) and RNAs. Our findings reveal that one of the Smps, Seb1, forms condensates resembling phase separation; the observed number and size of these condensates increase upon the addition of another Smp, Rhn1, and purified RNAs. Additionally, we have found that RNAs protect Smp condensates from treatment with 1,6-hexanediol. The Smp condensates containing different types of RNA display distinct FRAP profiles, and the Smp condensates containing the same type of RNA tend to fuse together more readily than those containing different types of RNAs. Collectively, these results indicate that the specific RNA species within condensates modulate their physical properties, potentially enabling the formation of regional RNA-Smp condensates with distinct characteristics that facilitate homologous chromosome pairing.

Cardiac myosin-binding protein-C: assessing fragmentation patterns to differentiate between forms of myocardial injury

Abstract Background Cardiac myosin-binding protein-C (cMyC) is a novel biomarker of myocardial injury. We hypothesize that fragmentation of cMyC differs according to aetiology of myocardial injury. Assessing the fragmentation pattern of the protein may aid diagnosis of these conditions. Purpose This work represents an examination of cMyC fragmentation in human serum, and studies its utility in differentiating between forms of myocardial injury. Methods Patients who were admitted to a hospital during October-November 2023 with acute myocardial injury were recruited. Acute myocardial injury was defined as a dynamic troponin rise above the 99th centile (Abbott Alinity: cTnI>34ng/L male, cTnI >16ng/L female). Following collection, samples were left at room temperature for 30 minutes and then centrifuged. Serum was separated for cMyC measurement, frozen in liquid nitrogen and stored at -80 °C. Recruited patients were followed up during their inpatient journey. Their final diagnosis was defined using the 4th universal definition of MI by two cardiologists, with a third cardiologist acting as adjudicator, if required. The serum samples were analysed using two separate electrochemiluminescence sandwich ELISA assays detecting different portions of cMyC. One assay formulated for total concentration of cMyC using high affinity mouse N-terminal monoclonal antibodies (mAb) targeting epitopes in close proximity (Limit of Detection (LoD) = 9.0ng/L). The other assay uses a N-terminal and a C-terminal mouse mAb which straddle the major proteolytic cleavage site of cMyC. This assay detects the intact (fuller-length) cMyC (LoD= 14.2ng/L). Both assays perform with good sensitivity, low variability and are capable of detecting cMyC at concentrations well below the 99th centile. Results 11 patient samples were collected with final diagnoses of; type 1 MI (STEMI n=3, NSTEMI n=4), type 4 MI (alcohol septal ablation n=1), acute myocardial injury (myocarditis n=2) and type 2 MI (chest sepsis with known coronary disease n=2). Figure one details the percentage of intact cMyC relative to total cMyC measured in serum for each patient, and is split into their adjudicated diagnosis. The bars display the median and interquartile range (IQR). Our findings suggest that the fragmentation pattern of cMyC could help differentiate between forms of myocardial injury. The ratio of intact: total cMyC was higher in the type 2 MI than any other condition. The results did not reach statistical significance (p = 0.06) due to the small sample size. Conclusions The fragmentation pattern of cMyC is dependent on the type of myocardial injury and could aid in the differentiation between type 2 MI and other forms of myocardial injury.Figure One

M6A-modified circXPO1 accelerates colorectal cancer progression via interaction with FMRP to promote WWC2 mRNA decay

BackgroundRecent evidence has demonstrated the vital roles of circular RNAs (circRNAs) in the progression of colorectal cancer (CRC); however, their functions and mechanisms in CRC need to be further explored. This study aimed to uncover the biological function of circXPO1 in CRC progression.MethodsCircXPO1 was identified by Sanger sequencing, RNase R, and actinomycin D treatment assays. Colony formation, scratch, transwell assays, and mouse xenograft models were adopted to evaluate CRC cell growth and metastasis in vitro and in vivo. Subcellular expression of circXPO1 was detected by FISH and nuclear-cytoplasmic separation assays. Molecular mechanisms were investigated by MeRIP, RIP, and RNA pull-down assays. Target molecular expression was detected by RT-qPCR, Western blotting and immunohistochemical staining.ResultscircXPO1 was up-regulated in CRC tissues and cells, which indicated a poor prognosis of CRC patients. circXPO1 deficiency delayed the growth, EMT, and metastasis of CRC cells. Mechanistical experiments indicated that down-regulation of ALKBH5 enhanced IGF2BP2-mediated m6A modification of circXPO1 to increase circXPO1 expression. Furthermore, circXPO1 interacted with FMRP to reduce the mRNA stability of WWC2, which consequently resulted in Hippo-YAP pathway activation. Rescue experiments suggested that WWC2 overexpression abrogated circXPO1-mediated malignant capacities of CRC cells. The in vivo growth and liver metastasis of CRC cells were restrained by circXPO1 depletion or WWC2 overexpression.Conclusionsm6A-modified circXPO1 by ALKBH5/IGF2BP2 axis destabilized WWC2 via interaction with FMRP to activate Hippo-YAP pathway, thereby facilitating CRC growth and metastasis. Targeting circXPO1 might be a potential therapeutic strategy for CRC.

Nuclear TOP1MT Confers Cisplatin Resistance via Pseudogene in HNSCC

Cisplatin resistance is one of the major causes of treatment failure in head and neck squamous cell carcinoma (HNSCC). There is an urgent need to uncover the underlying mechanism for developing effective treatment strategies. A quantitative proteomics assay was used to identify differential proteins in cisplatin-resistant cells. Mitochondrial topoisomerase I (TOP1MT) localization was determined using laser confocal microscopy and nucleocytoplasmic separation assay. Chromatin immunoprecipitation sequencing, dual-luciferase reporter assay, and RNA immunoprecipitation were used to identify the interaction between pseudogenes, miRNAs, and real genes. In vivo experiments verified the interaction between TOP1MT and pseudogenes on cisplatin resistance. TOP1MT was identified as a driving factor of cisplatin resistance in vitro, in vivo, and in HNSCC patients. Moreover, TOP1MT exceptionally translocated to the nucleus in cisplatin-resistant HNSCC cells in a signal peptide–dependent manner. Nuclear TOP1MT (nTOP1MT) transcriptionally regulated the mitochondrial functional pseudogene MTATP6P1, which bound to miR-137 and miR-491-5p as a competing endogenous RNA (ceRNA) and promoted the expression of MTATP6. An increase in MTATP6 enhanced mitochondrial oxidative phosphorylation (OXPHOS), which conferred cisplatin resistance in HNSCC. Our findings revealed that nTOP1MT transcriptionally activated MTAPT6P1 and increased MTATP6 expression via ceRNA, which facilitated OXPHOS and cisplatin resistance. These results provide novel insight for overcoming cisplatin resistance in HNSCC.

B-291 Validation of a Simple Qualitative Immunoassay for 21 Drugs of Abuse in Meconium on a Single Biochip Array

Abstract Background Drugs use during pregnancy is a major social and medical issue, which may lead to significant pre- and post-natal complications, such as preterm birth and newborn mortality. Exposed newborns may have long-term behavioral, cognitive, and developmental problems. Accurate detection of in utero drug exposure is crucial for timely medical intervention for the newborn and the mother. Meconium is the ‘gold standard' matrix for detection of drugs in newborn which reflects drug exposure during pregnancy. This study aims to develop and optimize a clinical assay for simultaneous screening of 21 drugs in meconium using a custom biochip array. Methods Custom biochip array (Randox Laboratories Ltd.) included 21 discrete test regions (DTRs) for amphetamine, methamphetamine, opioids/opiates (targeting morphine, oxymorphone, oxycodone, hydrocodone, 6-monoacetyl morphine, tramadol, buprenorphine, fentanyl, and methadone), phencyclidine (PCP), cocaine (targeting benzoylecgonine), benzodiazepines (targeting oxazepam, lorazepam, and clonazepam), zolpidem, barbiturates (targeting phenobarbital), ethyl glucuronide, methylphenidate, and marijuana metabolite (targeting Delta-9-Carboxy-Tetrahydrocannabinol [THC-COOH]). Patient samples were obtained from the residual meconium samples that had been previously used for other tests. Blank meconium samples were spiked at in-house cutoff, negative and positive assay control levels. All samples were extracted in specimen diluent using Biotage® Lysera and centrifuged. The supernatant was analyzed on a fully automated Randox Evidence+® Analyzer. A robotic arm pipetted 60 µL sample on to a biochip and then the analyzer performed a competitive chemiluminescent immunoassay. The results were generated as relative light units (RLUs). Results The sample results were determined to be “positive” or “negative” based on average RLU of cutoff controls for each analyte on an assay. The intra-assay (CV ≤ 15%) and inter-assay (CV ≤ 18%) precision was 100% agreement for positive and negative controls and there was no observed carryover for any of the analytes. The sample recovery was excellent with minimal to no matrix suppression for all analytes. Accuracy was performed by comparing spiked analyte results from Randox Evidence+® Analyzer with the expected results and all the spiked samples matched (positive or negative). When authentic patient or spiked results were compared with external laboratory test results, some discordant results were obtained. However, the discrepancies could be explained based on the different cutoffs (e.g., the Randox assay had lower cutoffs) or the known assay cross reactivities within the analytes of same class. These deviations did not affect clinical utility of the assay. Conclusions We validated a novel and simple qualitative chemiluminescent immunoassay in meconium using a custom biochip array. Unlike other routine screening/ELISA methods, which require separate assays for detection of similar drug targets, the custom biochip array offers a convenient, rapid and efficient method that utilizes only a single sample preparation for the screening of all 21 drug targets. Therefore, this technology has potential to be utilized as high-throughput screening assay. Like all qualitative assays, the limitation of this test is that all positive results will need to be assessed quantitatively for a definitive interpretation.

CircHIPK3 regulates cementoblast differentiation via the miR-10b-5p/DOHH/NF-κB axis

BackgroundIntact cementum is vital for tooth stability and health. Cementoblasts, which line the root surface, are responsible for cementum formation. Recent evidence suggests that circular RNAs (circRNAs) are involved in various cellular functions and may have clinical applications. Although circHIPK3 has been shown to participate in osteogenesis, its role in cementoblast differentiation and mineralization is not well understood. MethodsThe ring structure of circHIPK3 was confirmed using Sanger sequencing and an actinomycin D assay. Subcellular localization of circHIPK3 was assessed using a nucleus-cytoplasm separation assay. RT-qPCR was employed to analyze circHIPK3 expression during cementoblast differentiation and following TNF-α treatment. In vivo, periapical lesions were induced in mouse mandibular first molars to mimic an inflammatory environment, and circHIPK3 expression was evaluated. The interaction of the circHIPK3/miR-10b-5p/DOHH axis was explored through RNA pull-down assays, bioinformatics analysis, and dual-luciferase reporter assays. The effects on cementoblast differentiation and mineralization were assessed by measuring osteogenic markers, alkaline phosphatase (ALP) activity, ALP staining, and alizarin red S staining. ResultsCircHIPK3 was predominantly located in the cytoplasm of cementoblasts, and its expression was significantly upregulated during cementoblast differentiation. Knockdown of circHIPK3 inhibited cementoblast differentiation and mineralization, whereas its overexpression promoted these processes. Mechanistically, circHIPK3 upregulated DOHH expression by sponging miR-10b-5p, thereby enhancing cementoblast differentiation and mineralization. The NF-κB pathway was found to act downstream of the circHIPK3/miR-10b-5p/DOHH axis in these processes. Additionally, circHIPK3 expression was significantly downregulated in inflammatory environments both in vitro and in vivo. Forced overexpression of circHIPK3 mitigated the inhibitory effects of TNF-α on cementoblast differentiation and mineralization. ConclusionCircHIPK3 acts as a positive regulator of cementoblast differentiation and mineralization through the miR-10b-5p/DOHH/NF-κB axis, playing a crucial role in both normal and pathological cementogenesis.

Multiplexed Microfluidic Platform for Parallel Bacterial Chemotaxis Assays.

The sensing of and response to ambient chemical gradients by microorganisms via chemotaxis regulates many microbial processes fundamental to ecosystem function, human health, and disease. Microfluidics has emerged as an indispensable tool for the study of microbial chemotaxis, enabling precise, robust, and reproducible control of spatiotemporal chemical conditions. Previous techniques include combining laminar flow patterning and stop-flow diffusion to produce quasi-steady chemical gradients to directly probe single-cell responses or loading micro-wells to entice and ensnare chemotactic bacteria in quasi-steady chemical conditions. Such microfluidic approaches exemplify a trade-off between high spatiotemporal resolution of cell behavior and high-throughput screening of concentration-specific chemotactic responses. However, both aspects are necessary to disentangle how a diverse range of chemical compounds and concentrations mediate microbial processes such as nutrient uptake, reproduction, and chemorepulsion from toxins. Here, we present a protocol for the multiplexed chemotaxis device (MCD), a parallelized microfluidic platform for efficient, high-throughput, and high-resolution chemotaxis screening of swimming microbes across a range of chemical concentrations. The first layer of the two-layer polydimethylsiloxane (PDMS) device comprises a serial dilution network designed to produce five logarithmically diluted chemostimulus concentrations plus a control from a single chemical solution input. Laminar flow in the second device layer brings a cell suspension and buffer solution into contact with the chemostimuli solutions in each of six separate chemotaxis assays, in which microbial responses are imaged simultaneously over time. The MCD is produced via standard photography and soft lithography techniques and provides robust,repeatable chemostimulus concentrations across each assay in the device. This microfluidic platform provides a chemotaxis assay that blends high-throughput screening approaches with single-cell resolution to achieve a more comprehensive understanding of chemotaxis-mediated microbial processes. Key features • Microchannel master molds are fabricated using photolithography techniques in a clean room with a mask aligner to fabricate multilevel feature heights. • The microfluidic device is fabricated from PDMS using standard soft lithography replica molding from the master molds. • The resulting microchannel requires a one-time calibration of the driving inlet pressures, after which devices from the same master molds have robust performance. • The microfluidic platform is optimized and tested for measuring chemotaxis of swimming prokaryotes.

The value of net influx constant based on FDG PET/CT dynamic imaging in the differential diagnosis of metastatic from non-metastatic lymph nodes in lung cancer.

This study aims to evaluate the value of the dynamic and static quantitative metabolic parameters derived from 18F-fluorodeoxyglucose (FDG)-positron emission tomography/CT (PET/CT) in the differential diagnosis of metastatic from non-metastatic lymph nodes (LNs) in lung cancer and to validate them based on the results of a previous study. One hundred and twenty-one patients with lung nodules or masses detected on chest CT scan underwent 18F-FDG PET/CT dynamic + static imaging with informed consent. A retrospective collection of 126 LNs in 37 patients with lung cancer was pathologically confirmed. Static image analysis parameters include LN-SUVmax and LN-SUVmax/primary tumor SUVmax (LN-SUVmax/PT-SUVmax). Dynamic metabolic parameters including the net influx rate (Ki) and the surrogate of perfusion (K1) and of each LN were obtained by applying the irreversible two-tissue compartment model using in-house Matlab software. Ki/K1 was then calculated as a separate marker. Based on the pathological findings, we divided into a metastatic group and a non-metastatic group. The χ2 test was used to evaluate the agreement of the individual and combined diagnosis of each metabolic parameter with the gold standard. The receiver-operating characteristic (ROC) analysis was performed for each parameter to determine the diagnostic efficacy in differentiating non-metastatic from metastatic LNs with high FDG-avid. P < 0.05 was considered statistically significant. Among the 126 FDG-avid LNs confirmed by pathology, 70 LNs were metastatic, and 56 LNs were non-metastatic. For ROC analysis, in separate assays, the dynamic metabolic parameter Ki [sensitivity (SEN) of 84.30%, specificity (SPE) of 94.60%, accuracy of 88.89%, and AUC of 0.895] had a better diagnostic value than the static metabolic parameter SUVmax (SEN of 82.90%, SPE of 62.50%, accuracy of 74.60%, and AUC of 0.727) in differentiating between metastatic from non-metastatic LNs groups, respectively. In the combined diagnosis group, the combined SUVmax + Ki diagnosis had a better diagnostic value in the differential diagnosis of metastatic from non-metastatic LNs, with SEN, SPE, accuracy, and AUC of 84.3%, 94.6%, 88.89%, and 0.907, respectively. When the cutoff value of Ki was 0.022ml/g/min, it had a high diagnostic value in the differential diagnosis between metastasis and non-metastasis in FDG-avid LNs of lung cancer, especially in improving the specificity. The combination of SUVmax and Ki is expected to be a reliable metabolic parameter for N-staging of lung cancer.

CircRUNX2.2, highly expressed in Marek's disease tumor tissues, functions in cis to regulate parental gene RUNX2 expression

Marek's disease (MD), an immunosuppression disease induced by Marek's disease virus (MDV), is one of the significant diseases affecting the health and productive performance of poultry. The roles of circular RNAs (circRNAs) in MD development were poorly understood. In this study, we found a circRNA derived from exon 6 of RUNX family transcription factor 2 (RUNX2) gene, named circRUNX2.2, was highly expressed in chicken tumorous spleens (TS) induced by MDV. Through fluorescence in situ hybridization and nuclear-cytoplasmic separation assay, we determined circRUNX2.2 was mainly located in the nucleus. Knockout experiments confirmed that the flanking complementary sequences (RCMs) mediated its circularization. Gain of function assay and dual luciferase reporter gene assay revealed that circRUNX2.2 could promote the expression of RUNX2 via binding with its promoter region. RNA antisense purification assay and mass spectrometry assay showed circRUNX2.2 could recruit proteins such as CHD9 protein. Knocking down CHD9 expression decreased the expression of RUNX2 gene, which confirmed the positive regulation that circRUNX2.2 on RUNX2 expression was probably facilitated via recruiting CHD9 protein. Functional experiments showed that circRUNX2.2 promoted the proliferation of the MD lymphoma-derived chicken cell line, MDCC-MSB1, which confirmed the potential oncogenic role of circRNX2.2 in tumor development. In conclusion, we found that the RUNX2-derived circRUNX2.2 can positively regulate the transcription of the parental gene RUNX2 in a cis-acting manner. The high expression of circRUNX2.2 in MD tumor tissues indicated that it might mediate MD lymphoma progression.

Bidirectional modulation of negative emotional states by parallel genetically-distinct basolateral amygdala pathways to ventral striatum subregions.

Distinct basolateral amygdala (BLA) cell populations influence emotional responses in manners thought important for anxiety and anxiety disorders. The BLA contains numerous cell types which can broadcast information into structures that may elicit changes in emotional states and behaviors. BLA excitatory neurons can be divided into two main classes, one of which expresses Ppp1r1b (encoding protein phosphatase 1 regulatory inhibitor subunit 1B) which is downstream of the genes encoding the D1 and D2 dopamine receptors (drd1 and drd2 respectively). The role of drd1+ or drd2+ BLA neurons in learned and unlearned emotional responses is unknown. Here, we identified that the drd1+ and drd2+ BLA neuron populations form two parallel pathways for communication with the ventral striatum. These neurons arise from the basal nucleus of the BLA, innervate the entire space of the ventral striatum, and are capable of exciting ventral striatum neurons. Further, through three separate behavioral assays, we found that the drd1+ and drd2+ parallel pathways bidirectionally influence both learned and unlearned emotional states when they are activated or suppressed, and do so depending upon where they synapse in the ventral striatum - with unique contributions of drd1+ and drd2+ circuitry on negative emotional states. Overall, these results contribute to a model whereby parallel, genetically-distinct BLA to ventral striatum circuits inform emotional states in a projection-specific manner.

Potato spindle tuber viroid (PSTVd) loop 27 mutants promote cell-to-cell movement and phloem unloading of the wild type: Insights into RNA-based viroid interactions

Variations in infection progression with concurrent or prior infections by different viruses, viroids, or their strains are evident, but detailed investigations into viroid variant interactions are lacking. We studied potato spindle tuber viroid intermediate strain (PSTVd-I) to explore variant interactions. Two mutants, U177A/A182U (AU, replication- and trafficking-competent) and U178G/U179G (GG, replication-competent but trafficking-defective) on loop 27 increased cell-to-cell movement of wild-type (WT) PSTVd without affecting replication. In mixed infection assays, both mutants accelerated WT phloem unloading, while only AU promoted it in separate leaf assays, suggesting that enhancement of WT infection is not due to systemic signals. The mutants likely enhance WT infection due to their loop-specific functions, as evidenced by the lack of impact on WT infection seen with the distantly located G347U (UU) mutant. This study provides the first comprehensive analysis of viroid variant interactions, highlighting the prolonged phloem unloading process as a significant barrier to systemic spread.

Integrin αVβ1-activated PYK2 promotes the progression of non-small-cell lung cancer via the STAT3-VGF axis

BackgroundNon-small-cell lung cancer (NSCLC) accounts for 80–85% of all lung cancer and is the leading cause of cancer-related deaths globally. Although various treatment strategies have been introduced, the 5-year survival rate of patients with NSCLC is only 20–30%. Thus, it remains necessary to study the pathogenesis of NSCLC and develop new therapeutic drugs. Notably, PYK2 has been implicated in the progression of many tumors, including NSCLC, but its detailed mechanism remains unclear. In this study, we aimed to elucidate the mechanisms through which PYK2 promotes NSCLC progression.MethodsThe mRNA and protein levels of various molecules were measured using qRT-PCR, western blot (WB), and immunohistochemistry (IHC), respectively. We established stable PYK2 knockdown and overexpression cell lines, and CCK-8, EdU, and clonogenic assays; wound healing, transwell migration, and Matrigel invasion assays; and flow cytometry were employed to assess the phenotypes of tumor cells. Protein interactions were evaluated with co-immunoprecipitation (co-IP), immunofluorescence (IF)-based colocalization, and nucleocytoplasmic separation assays. RNA sequencing was performed to explore the transcriptional regulation mediated by PYK2. Secreted VGF levels were examined using ELISA. Dual-luciferase reporter system was used to detect transcriptional regulation site. PF4618433 (PYK2 inhibitor) and Stattic (STAT3 inhibitor) were used for rescue experiments. A public database was mined to analyze the effect of these molecules on NSCLC prognosis. To investigate the role of PYK2 in vivo, mouse xenograft models of lung carcinoma were established and examined.ResultsThe protein level of PYK2 was higher in human NSCLC tumors than in the adjacent normal tissue, and higher PYK2 expression was associated with poorer prognosis. PYK2 knockdown inhibited the proliferation and motility of tumor cells and caused G1-S arrest and cyclinD1 downregulation in A549 and H460 cells. Meanwhile, PYK2 overexpression had the opposite effect in H1299 cells. The siRNA-induced inhibition of integrins alpha V and beta 1 led to the downregulation of p-PYK2(Tyr402). Activated PYK2 could bind to STAT3 and enhance its phosphorylation at Tyr705, regulating the nuclear accumulation of p-STAT3(Tyr705). This further promoted the expression of VGF, as confirmed by RNA sequencing in a PYK2-overexpressing H1299 cell line and validated by rescue experiments. Two sites in promoter region of VGF gene were confirmed as binding sites of STAT3 by Dual-luciferase assay. Data from the TGCA database showed that VGF was related to the poor prognosis of NSCLC. IHC revealed higher p-PYK2(Tyr402) and VGF expression in lung tumors than in adjacent normal tissues. Moreover, both proteins showed higher levels in advanced TNM stages than earlier ones. A positive linear correlation existed between the IHC score of p-PYK2(Tyr402) and VGF. Knockdown of VGF inhibited tumor progression and reversed the tumor promoting effect of PYK2 overexpression in NSCLC cells. Finally, the mouse model exhibited enhanced tumor growth when PYK2 was overexpressed, while the inhibitors PF4618433 and Stattic could attenuate this effect.ConclusionsThe Integrin αVβ1-PYK2-STAT3-VGF axis promotes NSCLC development, and the PYK2 inhibitor PF4618433 and STAT3 inhibitor Stattic can reverse the pro-tumorigenic effect of high PYK2 expression in mouse models. Our findings provide insights into NSCLC progression and could guide potential therapeutic strategies against NSCLC with high PYK2 expression levels.

LINC01133 contributes to the malignant phenotypes of non-small cell lung cancer by targeting miR-30b-5p/FOXA1 pathway.

This study aimed to explore the mechanism of action of LINC01133 in non-small cell lung cancer. LINC01133 expression in NSCLC patient tissues and cells was detected by qRT-PCR. After transfecting siRNA-LINC01133 in NSCLC cells, the proliferation and invasive migration ability of the cells were assessed via CCK-8 and Transwell assay, respectively. The sublocalization of LINC01133 in NSCLC cells was analyzed by bioinformatics prediction and nucleoplasm separation assay and RNA-FISH assay. Analysis of the binding relationship between LINC01133, FOXA1 and miR-30b-5p was all through bioinformatics website analysis, dual-luciferase reporter and RNA Pulldown assay. Functional rescue experiments confirmed the character of miR-30b-5p and FOXA1 in LINC01133 regulating the NSCLC cells biological behavior. LINC01133 high expressions were found in NSCLC tissues and cells. siRNA-LINC01133 treatment inhibited NSCLC cells malignant behavior. Mechanistically: LINC01133 promoted FOXA1 expression through adsorption binding of miR-30b-5p. Knocking down miR-30b-5p expression or up-regulating FOXA1 expression was able to reverse siRNA-LINC01133 inhibitory effect of tumor cell malignant behavior. LINC01133 promoted FOX1 expression by competitively binding miR-30b-5p, which attenuated the targeting inhibitory effect of miR-30b-5p on FOXA1 and ultimately promoted proliferation and invasive migration of NSCLC cells.

Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer.

Mass spectrometry based targeted proteomics methods provide sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semi-stochastic sampling, or by empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific information on peptide detectability and quantification by mass spectrometry. To demonstrate the suitability of DIA data for selecting peptide targets, we reimplement a portion of an existing assay to measure 98 Alzheimer's disease proteins in cerebrospinal fluid (CSF). Peptides were selected from GPF-DIA based on signal intensity and reproducibility. The resulting SRM assay exhibits similar quantitative precision to published data, despite the inclusion of different peptides between the assays. This workflow enables development of new assays without additional up-front data acquisition, demonstrated here through generation of a separate assay for an unrelated set of proteins in CSF from the same dataset.

Characterization of Culturable Mycobiome of Newly Excavated Ancient Wooden Vessels from the Archeological Site of Viminacium, Serbia.

Two ancient wooden vessels, specifically a monoxyle (1st century BCE to 1st century CE) and shipwreck (15th to 17th century CE), were excavated in a well-preserved state east of the confluence of the old Mlava and the Danube rivers (Serbia). The vessels were found in the ground that used to be river sediment and were temporarily stored within the semi-underground exhibition space of Mammoth Park. As part of the pre-conservation investigations, the primary aim of the research presented was to characterize the culturable mycobiomes of two excavated wooden artifacts so that appropriate conservation procedures for alleviating post-excavation fungal infestation could be formulated. Utilizing culture-based methods, a total of 32 fungi from 15 genera were identified, mainly Ascomycota and to a lesser extent Mucoromycota sensu stricto. Soft-rot Ascomycota of genus Penicillium, followed by Aspergillus and Cephalotrichum species, were the most diverse of the isolated fungi. Out of a total of 38 isolates, screened on 7 biodegradation plate assays, 32 (84.21%) demonstrated at least one degradative property. Penicillium solitum had the highest deterioration potential, with a positive reaction in 5 separate plate assays. The obtained results further broaden the limited knowledge on the peculiarities of post-excavation soft-rot decay of archaeological wood and indicate the biochemical mechanisms at the root of post-excavation fungal deterioration.