Changes In Signatures Research Articles

Characterization of mesenchymal stem cells in pre-B acute lymphoblastic leukemia.

Components of the bone marrow microenvironment (BMM) have been shown to mediate the way in which leukemia develops, progresses and responds to treatment. Increasing evidence shows that leukemic cells hijack the BMM, altering its functioning and establishing leukemia-supportive interactions with stromal and immune cells. While previous work has highlighted functional defects in the mesenchymal stem cell (MSC) population from the BMM of acute leukemias, thorough characterization and molecular profiling of MSCs in pre-B cell acute lymphoblastic leukemia (B-ALL), the most common cancer in children, has not been conducted. Here, we investigated the cellular and transcriptome profiles of MSCs isolated from the BMM of an immunocompetent BCR-ABL1+ model of B-ALL. Leukemia-associated MSCs exhibited reduced self-renewal capacity in vitro and significant changes in numerous molecular signatures, including upregulation of inflammatory signaling pathways. Additionally, we found downregulation of genes involved in extracellular matrix organization and osteoblastogenesis in leukemia-associated MSCs. This study provides cellular and molecular insights into the role of MSCs during B-ALL progression.

Integrative systems immunology uncovers molecular networks of the cell cycle that stratify COVID-19 severity.

Several perturbations in the number of peripheral blood leukocytes, such as neutrophilia and lymphopenia associated with Coronavirus disease 2019 (COVID-19) severity, point to systemic molecular cell cycle alterations during severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the landscape of cell cycle alterations in COVID-19 remains primarily unexplored. Here, we performed an integrative systems immunology analysis of publicly available proteome and transcriptome data to characterize global changes in the cell cycle signature of COVID-19 patients. We found significantly enriched cell cycle-associated gene co-expression modules and an interconnected network of cell cycle-associated differentially expressed proteins (DEPs) and genes (DEGs) by integrating the molecular data of 1469 individuals (981 SARS-CoV-2 infected patients and 488 controls [either healthy controls or individuals with other respiratory illnesses]). Among these DEPs and DEGs are several cyclins, cell division cycles, cyclin-dependent kinases, and mini-chromosome maintenanceproteins. COVID-19 patients partially shared the expression pattern of some cell cycle-associated genes with other respiratory illnesses but exhibited some specific differential features. Notably, the cell cycle signature predominated in the patients' blood leukocytes (B, T, and natural killercells) and was associated with COVID-19 severity and disease trajectories. These results provide a unique global understanding of distinct alterations in cell cycle-associated molecules in COVID-19 patients, suggesting new putative pathways for therapeutic intervention.

Comparison of transcriptome profiles between medulloblastoma primary and recurrent tumors uncovers novel variance effects in relapses

Nowadays medulloblastoma (MB) tumors can be treated with risk-stratified approaches with up to 80% success rate. However, disease relapses occur in approximately 30% of patients and successful salvage treatment strategies at relapse remain scarce. Acquired copy number changes or TP53 mutations are known to occur frequently in relapses, while methylation profiles usually remain highly similar to those of the matching primary tumors, indicating that in general molecular subgrouping does not change during the course of the disease. In the current study, we have used RNA sequencing data to analyze the transcriptome profiles of 43 primary-relapse MB pairs in order to identify specific molecular features of relapses within various tumor groups. Gene variance analysis between primary and relapse samples demonstrated the impact of age in SHH-MB: the changes in gene expression relapse profiles were more pronounced in the younger patients (< 10 years old), which were also associated with increased DNA aberrations and somatic mutations at relapse probably driving this effect. For Group 3/4 MB transcriptome data analysis uncovered clear sets of genes either active or decreased at relapse that are significantly associated with survival, thus could be potential predictive markers. In addition, deconvolution analysis of bulk transcriptome data identified progression-associated differences in cell type enrichment. The proportion of undifferentiated progenitors increased in SHH-MB relapses with a concomitant decrease of differentiated neuron-like cells, while in Group 3/4 MB relapses cell cycle activity increases and differentiated neuron-like cells proportion decreases as well. Thus, our findings uncovered significant transcriptome changes in the molecular signatures of relapsed MB and could be potentially useful for further clinical purposes.

Wolf in sheep's clothing - Oral proliferative verrucous leukoplakia: Progression with longitudinal molecular insights

BackgroundOral proliferative verrucous leukoplakia (OPVL) is a chronic form of oral leukoplakia that progresses to a multifocal disease with confluent, exophytic and proliferative features. The clinical differential diagnosis for OPVL includes frictional keratosis, leukoplakia, chronic hyperplastic candidiasis, squamous papilloma, verrucous hyperplasia, verrucous carcinoma and squamous cell carcinoma. In this study, we aimed to delineate the dynamic changes in molecular signature during OPVL progression. We compare to a cohort of oral cavity keratinizing squamous cell carcinoma (OSCC) patients covering the spectrum of verrucous carcinoma to invasive squamous cell carcinoma including cytologically bland cuniculatum variant. MethodsSamples from a large OPVL lesion that exhibited a histopathologic continuum of OPVL progression. ResultsCanonical hotspot TERT promoter mutations were identified in all patients. TERT C228T was dominant and mutually exclusive with TERT C250T. In patients with TERT C250T, there was concurrent PI3 point mutation. TP53 mutations were also consistently found (8/10). At the protein level, p53 was abnormal, with loss of function and gain of function. ConclusionsOPVL is a pathology that shows proximity to the gene expression profile of OSCC, highlighting signatures in common that can be important targets for drug treatment, as well as in the development of diagnostic and prognostic strategies for this disease.

Phenotype- and species-specific skin proteomic signatures for incision-induced pain in humans and mice

BackgroundAcute pain after surgery is common and often leads to chronic post-surgical pain, but neither treatment nor prevention is currently sufficient. We hypothesised that specific protein networks (protein-protein interactions) are relevant for pain after surgery in humans and mice. MethodsStandardised surgical incisions were performed in male human volunteers and male mice. Quantitative and qualitative sensory phenotyping were combined with unbiased quantitative mass spectrometry-based proteomics and protein network theory. The primary outcomes were skin protein signature changes in humans and phenotype-specific protein-protein interaction analysis 24 h after incision. Secondary outcomes were interspecies comparison of protein regulation as well as protein-protein interactions after incision and validation of selected proteins in human skin by immunofluorescence. ResultsSkin biopsies in 21 human volunteers revealed 119/1569 regulated proteins 24 h after incision. Protein-protein interaction analysis delineated remarkable differences between subjects with small (low responders, n=12) and large incision-related hyperalgesic areas (high responders, n=7), a phenotype most predictive of developing chronic post-surgical pain. Whereas low responders predominantly showed an anti-inflammatory protein signature, high responders exhibited signatures associated with a distinct proteolytic environment and persistent inflammation. Compared to humans, skin biopsies in mice habored even more regulated proteins (435/1871) 24 h after incision with limited overlap between species as assessed by proteome dynamics and PPI. Immunohistochemistry confirmed the expression of high priority candidates in human skin biopsies. ConclusionsProteome profiling of human skin after incision revealed protein-protein interactions correlated with pain and hyperalgesia, which may be of potential significance for preventing chronic post-surgical pain. Importantly, protein-protein interactions were differentially modulated in mice compared to humans opening new avenues for successful translational research.

Multi-Path Attention Inverse Discrimination Network for Offline Signature Verification

Signature verification, which is a method to distinguish the authenticity of signature images, is a biometric verification technique that can effectively reduce the risk of forged signatures in financial, legal, and other business environments. However, compared with ordinary images, signature images have the following characteristics: First, the strokes are slim, i.e., there is less effective information. Second, the signature changes slightly with the time, place, and mood of the signer, i.e., it has high intraclass differences. These challenges lead to the low accuracy of the existing methods based on convolutional neural networks (CNN). This study proposes an end-to-end multi-path attention inverse discrimination network that focuses on the signature stroke parts to extract features by reversing the foreground and background of signature images, which effectively solves the problem of little effective information. To solve the problem of high intraclass variability of signature images, we add multi-path attention modules between discriminative streams and inverse streams to enhance the discriminative features of signature images. Moreover, a multi-path discrimination loss function is proposed, which does not require the feature representation of the samples with the same class label to be infinitely close, as long as the gap between inter-class distance and the intra-class distance is bigger than the set classification threshold, which radically resolves the problem of high intra-class difference of signature images. In addition, this loss can also spur the network to explore the detailed information on the stroke parts, such as the crossing, thickness, and connection of strokes. We respectively tested on CEDAR, BHSig-Bengali, BHSig-Hindi, and GPDS Synthetic datasets with accuracies of 100%, 96.24%, 93.86%, and 83.72%, which are more accurate than existing signature verification methods. This is more helpful to the task of signature authentication in justice and finance.

Fertilizers disrupt the electric feel of flowers

Electricity is literally all around us. As humans, we generate weak electric fields whenever we move our muscles; spiders use static electricity in the air to fly across great distances; and geckos use static in their sticky feet to scale vertical walls with ease. Since everything has an electric field, we can imagine that this fundamental force of nature plays an important role in many ecological interactions. Among insects, bumblebees are known to alter the static electricity of flowers to communicate with members of their hive; the positive charge that collects on their tiny hairs alters the electric field around a visited flower for ∼100 s, communicating to the next bee that buzzes by that the nectar and pollen rewards from that flower have already been exhausted. Ellard Hunting and colleagues from University of Bristol, UK, and the Woods Hole Oceanographic Institution, USA, set out to test whether the application of agricultural sprays alters the electric field of flowers and whether bumblebees can detect these disruptions.The pervasive use of chemicals in agriculture is a substantial source of pollution. But besides chemical toxicity, little is known about how agrochemicals otherwise affect plant–pollinator interactions. Hunting and colleagues observed that bumblebees tend to hover around chemically treated flowers and decide not to land. To investigate the cause of this avoidance behaviour, the researchers developed a computational model for how the application of agricultural sprays may alter floral electric fields up to 4 cm from the flower. Their model considered how the presence of droplets on the flower's surface and localized increases in humidity from a spray application might impact the flower's electric field.Next, the researchers studied the effect of common agricultural fertilizers on flower features that bees recognize. To see if fertilizer sprays change the way bees see flowers, the researchers determined what wavelengths of light are reflected from droplets with and without fertilizers added. To study whether fertilizer sprays change the way flowers smell, they measured how much effort the bees put into feeding when offered sugar water laced with fertilizer compared with just sugar water. Lastly, to visualize the electric fields surrounding various blooms, the scientists sprayed charged coloured powder particles onto the centre of ragwort flowers and observed how the powder distributed across the surfaces. Although the fertilizers did not affect how bees see or smell flowers, the chemicals did alter the electric field around each bloom for several minutes.Next, Hunting and colleagues tested whether the adverse effects of spray applications persist over time. To do this, they planted electrodes into the cut stems of potted lavender and Texas bluebell plants and recorded the electrical current streaming down the stems in response to different spray applications. While a water spray caused a change in current that only lasted 30–60 s, a spray containing the fertilizer caused a consistent change in current that lasted up to 16 min. A spray with another common agricultural chemical – the pesticide Imidacloprid – induced a change in current that lasted up to 25 mins. Even subsequent water sprays, simulating rain, produced prolonged changes in the plant stem's electrical signature, suggesting that this effect can endure even after a single application of fertilizer.Finally, the researchers observed wild bumblebees foraging on cut flowers with artificially applied electric fields to mimic the effect of fertilizers. They pierced lavender stems with metal electrodes, placed them in glass jars of tap water, and attached a 13 V battery to produce an electric current in the plant. By recording 2 h videos and counting the number of bumblebees that approached versus those that landed on the lavender, the team showed that bumblebees somehow sense weird electricity as they approach a flower and land less as a result, serving as a healthy reminder that as humans we affect our environments in ways we can't even sense.

Hyperspectral mapping of nanoscale photophysics and degradation processes in hybrid perovskite at the single grain level.

With solar cells reaching 26.1% certified efficiency, hybrid perovskites are now the most efficient thin film photovoltaic material. Though substantial effort has focussed on synthesis approaches and device architectures to further improve perovskite-based solar cells, more work is needed to correlate physical properties of the underlying film structure with device performance. Here, using cathodoluminescence microscopy coupled with unsupervised machine learning, we quantify how nanoscale heterogeneity globally builds up within a large morphological grain of hybrid perovskite when exposed to extrinsic stimuli such as charge accumulation from electron beams or milder environmental factors like humidity. The converged electron-beam excitation allows us to map PbI2 and the emergence of other intermediate phases with high spatial and energy resolution. In contrast with recent reports of hybrid perovskite cathodoluminescence, we observe no significant change in the PbI2 signatures, even after high-energy electron beam excitation. In fact, we can exploit the stable PbI2 signatures to quantitatively map how hybrid perovskites degrade. Moreover, we show how our methodology allows disentangling of the photophysics associated with photon recycling and band-edge emission with sub-micron resolution using a fundamental understanding of electron interactions in hybrid perovskites.

Effect of short-term use of FFP2 (N95) masks on the salivary metabolome of young healthy volunteers: a pilot study.

The use of face masks has become an integral part of public life in the post-pandemic era. However, the understanding of the effect of wearing masks on physiology remains incomplete and is required for informing public health policies. For the first time, we report the effects of wearing FFP2 masks on the metabolic composition of saliva, a proximal matrix to breath, along with cardiopulmonary parameters. Un-induced saliva was collected from young (31.2 ± 6.3 years) healthy volunteers (n = 10) before and after wearing FFP2 (N95) masks for 30 minutes and analyzed using GCMS. The results showed that such short-term mask use did not cause any significant change in heart rate, pulse rate or SpO2. Three independent data normalization approaches were used to analyze the changes in metabolomic signature. The individuality of the overall salivary metabotype was found to be unaffected by mask use. However, a trend of an increase in the salivary abundance of L-fucose, 5-aminovaleric acid, putrescine and phloretic acid was indicated irrespective of the method of data normalization. Quantitative analysis confirmed increases in concentrations of these metabolites in saliva of paired samples amid high inter-individual variability. The results showed that while there was no significant change in measured physiological parameters and individual salivary metabotypes, mask use was associated with correlated changes in these metabolites plausibly originating from altered microbial metabolic activity. These results might also explain the change in odour perception reported to be associated with mask use. Potential implications of these changes on mucosal health and immunity warrants further investigation to evolve more prudent mask use policies.

Viable FA based bacterial cells as sustainable solution for corrosion prevention in RC structures

Reinforcement corrosion is one of the biggest challenges faced by the construction industry, with billions of dollars spent on corrosion remediation and prevention. Recently, microbially induced calcium carbonate precipitation (MICCP) has been considered a novel method in corrosion mitigation of reinforced concrete (RC) structures. In the current investigation, fly ash (FA) based inoculum for construction industry was developed and tested for cell viability to define the shelf life of the carrier product. The results indicated that FA-based inoculum possessed a shelf life of 180 days with an effective cell count required to induce MICCP in reinforced concrete. FA-based inoculum was immobilized in fresh concrete supplemented with nutrients to study the corrosion mitigation potential. The prepared specimens were cured for 28 days and then subjected to impressed current-induced chloride corrosion. For corrosion assessment, well established electrochemical technique and a newly emerged electromechanical impedance (EMI) technique were employed separately on different RC specimens. In the electrochemical technique, open circuit potential (OCP), corrosion potential (Ecorr), corrosion current density (Icorr) were obtained over the test exposure; whereas in EMI technique, admittance signatures were acquired for the entire testing duration at an interval of 7 days. Further to examine the changes in admittance signatures, root mean square deviation (RMSD) was used to quantify the corrosion process. Results indicated that Icorr and RMSD were linearly increasing over the test exposure. The results clearly prove that the FA-based carrier material can be effectively used for the corrosion prevention and the emerging EMI technique can efficiently monitor the corrosion process.

Disease progression promotes changes in adipose tissue signatures in type 2 diabetic (db/db) mice: The potential pathophysiological role of batokines

Unlike the white adipose tissue (WAT) which mainly stores excess energy as fat, brown adipose tissue (BAT) has become physiologically important and therapeutically relevant for its prominent role in regulating energy metabolism. The current study makes use of an established animal model of type 2 diabetes (T2D) db/db mice to determine the effect of the disease progression on adipose tissue morphology and gene regulatory signatures. Results showed that WAT and BAT from db/db mice display a hypertrophied phenotype that is consistent with increased expression of the pro-inflammatory cytokine, tumor necrosis factor-alpha (Tnf-α). Moreover, BAT from both db/db and non-diabetic db/+ control mice displayed an age-related impairment in glucose homeostasis, inflammatory profile, and thermogenic regulation, as demonstrated by reduced expression of genes like glucose transporter (Glut-4), adiponectin (AdipoQ), and uncoupling protein 1 (Ucp-1). Importantly, gene expression of the batokines regulating sympathetic neurite outgrowth and vascularization, including bone morphogenic protein 8b (Bmp8b), fibroblast growth factor 21 (Fgf-21), neuregulin 4 (Nrg-4) were altered in BAT from db/db mice. Likewise, gene expression of meteorin-like (Metrnl), growth differentiation factor 15 (Gdt-15), and C-X-C motif chemokine-14 (Cxcl-14) regulating pro- and anti-inflammation were altered. This data provides some new insights into the pathophysiological mechanisms involved in BAT hypertrophy (or whitening) and the disturbances of batokines during the development and progression of T2D. However, these are only preliminary results as additional experiments are necessary to confirm these findings in other experimental models of T2D.

Automated Identification of Valid Model Networks Using Model-Based Systems Engineering

To handle increasing complexity in product development, model-based systems engineering (MBSE) approaches are well suited, in which the technical system is represented in a system model. To efficiently test requirements, domain models are integrated into the system model. For each purpose (e.g., battery lifetime calculation), there are typically several models at several fidelity levels. Since the model signatures (i.e., necessary inputs for the models and their outputs) differ depending on the fidelity level, not all models can be used in any development phase. In addition, due to the different model signatures, not all models can be combined arbitrarily to model networks. Currently, valid model networks in system models must be determined in a time-consuming, manual process. Therefore, this paper presents an approach that automates this task via the implementation of an algorithm that analyzes a system model and the model signatures and automatically returns all valid model networks. When input parameters, models or their signatures change, the algorithm updates automatically, and the user receives the valid model network without any manual effort. The approach is demonstrated with the running example of battery system development.

Regional mutational signature activities in cancer genomes.

Cancer genomes harbor a catalog of somatic mutations. The type and genomic context of these mutations depend on their causes and allow their attribution to particular mutational signatures. Previous work has shown that mutational signature activities change over the course of tumor development, but investigations of genomic region variability in mutational signatures have been limited. Here, we expand upon this work by constructing regional profiles of mutational signature activities over 2,203 whole genomes across 25 tumor types, using data aggregated by the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium. We present GenomeTrackSig as an extension to the TrackSig R package to construct regional signature profiles using optimal segmentation and the expectation-maximization (EM) algorithm. We find that 426 genomes from 20 tumor types display at least one change in mutational signature activities (changepoint), and 306 genomes contain at least one of 54 recurrent changepoints shared by seven or more genomes of the same tumor type. Five recurrent changepoint locations are shared by multiple tumor types. Within these regions, the particular signature changes are often consistent across samples of the same type and some, but not all, are characterized by signatures associated with subclonal expansion. The changepoints we found cannot strictly be explained by gene density, mutation density, or cell-of-origin chromatin state. We hypothesize that they reflect a confluence of factors including evolutionary timing of mutational processes, regional differences in somatic mutation rate, large-scale changes in chromatin state that may be tissue type-specific, and changes in chromatin accessibility during subclonal expansion. These results provide insight into the regional effects of DNA damage and repair processes, and may help us localize genomic and epigenomic changes that occur during cancer development.

Inhibition of calcium‐dependent phospholipase A2 improves blood‐brain barrier integrity in ApoE4 carrying mice

AbstractBackgroundBlood‐brain barrier (BBB) is essential for neural health and function. Degradation of BBB is observed in Alzheimer’s disease (AD) and is more pronounced in individuals carrying the apolipoprotein E4 (ApoE4) allele, which is a major genetic risk factor for AD. ApoE4 increases the activation of calcium‐dependent phospholipase A2 (cPLA2), which is linked to BBB function. Here, we asked if cPLA2 inhibition in ApoE4 carrying mice could repair BBB integrity and if the changes could be observed in vivo by dynamic contrast‐enhanced MRI (DCE‐MRI).Method16‐month‐old ApoE4 targeted replacement (ApoE4‐TR) mice were divided into a control group treated with vehicle (n=4) and an experimental group treated with a cPLA2 inhibitor ASB‐14780 (n=4). All imaging was performed using a 7T MRI scanner. DCE‐MRI protocol involved acquisition of baseline images (5min), mice receiving a bolus of gadolinium diethylenetriaminepentaacetic acid (Gd‐DTPA, 0.3mmol/kg, i.v.)) and followed by post‐bolus scans for 20min. Regions of interest (ROIs), such as the hippocampus and isocortex, were manually defined using T2‐weighted (FSE) anatomical scans in ImageJ. Volume transfer constants (KTrans) of the contrast agent uptake were calculated for each subject from the dynamic DCE‐MRI scan using the Patlak model on the Rocketship software (MATLAB).ResultKTrans values for the isocortex and the hippocampus were calculated for two animals from the control group and three animals from the experimental group. The mean KTrans value in the hippocampus region was 60% lower for the mice treated with cPLA2 inhibitor than controls (p=0.056), 0.0459 ± 0.0168 min‐1 and 0.117 ± 0.030 min‐1 respectively. Similarly, the mean KTrans value in the isocortex for the treated mice was 50% lower than the controls (p=0.89), 0.0554 ± 0.018 min‐1 and 0.110 ± 0.028 min‐1 respectively.ConclusionWe observed that cPLA2 inhibition decreased KTrans values implying increased BBB function. Thus, cPLA2 inhibition can be a possible therapeutic path towards reversing some of the damage to the brain due to AD. Currently, we are validating this observation with larger sample sizes and by analyzing the brains of these mice for changes in molecular signatures of BBB.

Equipment for Monitoring Synchronous Generators Condition through External Magnetic Field Waveforms

This paper presents an equipment for monitoring synchronous generators condition through characteristics of the time derivative of the external magnetic field. The developed monitoring methodology allows the identification of established or incipient faults, by detecting changes in the magnetic signature of the synchronous generator. In this methodology, the measurement of signals outside the machine gives this equipment a non-invasive characteristic, allowing its monitoring without interfering or disturbing its operation. The developed system includes the specification of magnetic field sensors, signal measurement and processing equipment, as well as software for analysis and monitoring. The validation of the methodology used in this system was carried out through the analysis of experimental data, presenting efficient results in the detection of electrical and mechanical faults in synchronous generators of an experimental test bench and a hydroelectric power plant. As a result, the commercial specification of this equipment was obtained and two units were implemented in a hydroelectric power plant to monitor 305 MVA synchronous generators.

MRI signatures of Brain Age in the Alzheimer’s disease continuum

AbstractBackgroundAge is the biggest risk factor for Alzheimer’s disease (AD). Substantial efforts to extract age signatures from magnetic resonance imaging (MRI) of the brain have achieved impressive accuracy and demonstrated these signatures were altered by neurological disorders including AD. In this work, we develop a deep learning model to characterize brain age signatures and examine their variation over the AD continuum.MethodA 3D deep ResNet model was implemented to learn the structural signatures of brain age in predicting the chronological age of the participants. The model was trained on 7372 T1‐weighted MRI scans from a combined lifespan cohort of 5848 cognitively normal participants (age: 8‐ 95 yrs) using a 10‐fold cross validation procedure. The model was then applied to the independent ADNI cohort (N=1175, 50‐98 yrs) to examine MRI derived brain age signatures variation in the AD continuum. The difference (∆age) between model predicted age and chronological age was used as the independent variable for group comparison using univariate ANCOVA tests, controlling for sex, education, and APOE4 gene dose, among five clinical groups: normal control (NC), normal to MCI converters (NC‐MCI), stable MCI (MCIs), MCI to AD converters (MCI‐AD), and AD patients.ResultThe ResNet model achieved an MAE=3.76 yrs and R2=0.93 across 10 folds in the lifespan cohort. In the baseline data of the ADNI cohort, model derived ∆age increased along the AD continuum as expected: NC (‐1.2yrs) &lt; NC‐MCI (‐0.7yrs) &lt; MCIs (‐0.3yrs) &lt; MCI‐AD (0.7yrs) &lt;AD (1.5yrs) (F=11.24, p&lt;0.0001). Post‐hoc pairwise comparison results are summarized in Table 1/Figure 2. Although the difference between NC and NC‐MCI did not reach significance (p=0.24) for the baseline data, comparison between the two groups using data from all visits was significant (p=0.0009), suggesting more subtle differences.ConclusionA ResNet model was developed that captures the MRI signatures of brain age with high accuracy in age prediction. The model detected group level differences along the AD continuum in the expected direction. Subtle changes in brain signatures were observable in normal participants who later developed cognitive impairment. Our technique provides a novel approach to investigate the relationship between aging and AD.

Non-growth inhibitory doses of dimethyl sulfoxide alter gene expression and epigenetic pattern of bacteria.

Although dimethyl sulfoxide (DMSO) is a widely used solvent in scientific research, drug screening settings, and biomedical applications, its solvent (vehicle) effects on biological processes are overlooked. Using Escherichia coli as a model, we aimed to investigate and evaluate the effects of low-dose DMSO-driven changes in bacterial cells in a comprehensive and multifaceted manner by combining Fourier transform infrared spectroscopy analyses, analytical cell-biology approaches, and high-throughput sequencing. Here, we show that the non-toxic (1.0 and 2.5%, v/v) DMSO doses reduce the cellular levels of reactive oxygen species, change the cellular nucleic acid content and DNA topology, affect the global 5-methylcytosine pattern of the genome, and modulate gene transcription. These results indicate that even at non-toxic concentrations, DMSO is not inert: it can alter validity by changing or masking the assessed activity of the analyte. Besides, this manuscript does not only highlight that the low, non-toxic solvent doses of DMSO impinge on biological processes, including genome structure and function, but also, the high-throughput sequence data obtained during the study offer a platform for future research to elucidate the mechanism of epigenetically regulated genes in bacteria. KEY POINTS: •A clear-cut differentiation between the low-dose DMSO-treated and -untreated bacteria by PCA and LDA. •Drastic alterations in the DNA topology and nucleic acids of DMSO-treated bacteria. •Changes in transcriptome and epigenetic signatures with the low-dose DMSO.

Changes in organic molecular marker signatures in soils amended with biochar during a three-year experiment with maize on a Fluvisol

Abstract Biochar is widely used as a soil amendment to improve soil properties and as a tool to absorb net carbon from the atmosphere. In this study we determined the signatures of organic molecular markers in soil following the incorporation of 5 and 10 t/ha biochar in a Fluvisol, cultivated with maize at the experimental field of the ISSAPP “N. Poushkarov” institute in Bulgaria. The n-alkane distribution in the biochar treated soils was uni- or bimodal maximizing at n-C17 alkane, n-C18 or C18 branched alkanes, i.e. there was an imprint of biomass burning, e.g. from the biochar due to predominance of short chain (&lt; C20) homologues and increased microbial activity (presence of branched alkanes). This is also confirmed by the values for the average chain length (ACL) of n-alkanes which indicated prevalence of homologues of shorter chain (20–21 C atoms) in the variants of longer biochar residence time. There was evidence of trans-13-docosenamide, which originated from biochar. Fatty acids and fatty alcohols distributions also implicate microbial contribution to soil organic matter (SOM), supporting the suggestion that biochar addition can improve soil microbiological status.

EMT-like Activation in CLL Provides Novel Therapeutic Target

Introduction: There is growing interest in the role of Epithelial to Mesenchymal Transition (EMT) regulators in immune cell development, but the functional role of EMT in B-cell biology and transformation remains obscured. The outcomes of the "classical" EMT activation of epithelial cells are known; committed migratory cells do not divide and become resistant to apoptotic stimuli. Importantly, EMT supports migratory cells' "stem cell-like" properties, allowing differentiation into more than one cell type and/or terminal differentiation and senescence. Chronic lymphocytic leukaemia (CLL) cells engage with antigen and microenvironment stimuli in tissue sites that lead to proliferation, followed by their egress from the tissue sites into the peripheral blood. This lifecycle implies functional changes altering CLL cell movement. Here we show EMT-like activation in CLL that correlates with disease progression and transformation. We identified a targetable candidate and show that it can be inhibited by small molecule ligands. Results: Our analysis of available expression datasets showed the expression of various EMT factors in healthy B cells. The single-cell analysis of lymph nodes confirms strong EMT-like activation in healthy B-cells (GSE159929), confirming the idea that genes involved in classical EMT would be expressed differently depending on the stage of B-cell differentiation. The following GENEVESTIGATOR analysis of B cell malignancies highlighted high EMT-like activation in CLL cases. However, differential expression (DE) analysis of peripheral blood (PB) samples from 44 CLL patients and 24 healthy B-cell donors identified six EMT factors aberrantly expressed in CLL cells compared to healthy B cells indicating significant changes in CLL EMT-like activation. At the transcription level, ZEB1 expression was higher and ZEB2 expression lower in PB CLL cells. The main stimulatory events in CLL cells appear restricted to affected tissue sites, primarily in lymph nodes (LN) where CLL cells migrate to reactivate and proliferate. Further, EMT factor protein expression was confirmed in CLL LN tissue microarrays. Strikingly, transformation into a more aggressive form (Richter syndrome) strongly correlates with an increase in ZEB2 but not ZEB1 protein expression. Interestingly, analysis of the published transcriptome data set of CLL cells co-cultured with nurse-like cells shows an increase in ZEB2 and a decrease in ZEB1 expression after 14 days (GSE13811). An apparent reliance of the EMT-like activation in CLL on the environmental stimuli has been demonstrated in CLL cells stimulated with BCR activation (anti-IgM) or mitogen (PMA), implying protection from cell death and activation of migration. Additionally, we observed higher S100A4 expression in CLL cells compared to mature B-cells from healthy individuals. Previously it has been shown that this calcium-dependent protein can control cell movement by direct interaction with non-muscle myosin and via regulation of stress fibre formation, thus facilitating cellular protrusions and increasing cell migration and invasion. Our analysis has shown the S100A4 positive correlation with CLL markers of poor prognosis, Zap70 and CD38. The S100A4 knockdown with siRNA dramatically impeded CLL migration in trans-well assay (Figure 1). Biochemical inhibitor screening for disruption of S100A4 interaction with myosin II identified several promising leads active in the low micromolar range in both biochemical and cell assays. Conclusions: Our findings improve the understanding of CLL pathobiology. Normally, healthy naïve B cells give rise to multiple B-cell subtypes with specific functions and locations. EMT-like activation likely contributes to B-cell development at different stages of differentiation and B-cell malignant transformation. Our investigation shows that the EMT-like activation is dysregulated in CLL cells compared to healthy B cells. The EMT expression signature changes upon B-cell receptor stimulation. These results suggest that targeting some of the aberrantly expressed EMT components such as S100A4 in CLL can be exploited, prolonging remission by, for example, impeding CLL returning to the tissue sites after an egress due to the treatment with Ibrutinib depriving these cells of vital microenvironmental support. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

PLX51107 Enhances the Anti-Tumor Activity of Targeted Therapy in Chronic Lymphocytic Leukemia When Combined with Venetoclax

Background: The development of drugs targeting BTK and BCL2 have dramatically improved the therapeutic landscape in chronic lymphocytic leukemia (CLL). However, resistance to these agents have been reported due to non-recurrent changes in oncogenic pathways and gene expression signatures. The bromodomain and extra terminal (BET) family proteins (BRD2, BRD3, BRD4 and BRDT) are epigenetic reader proteins that recognize acetylated lysine residues in histones. They play a critical role in mediating gene transcription and have been considered as highly promising targets in several diseases including cancer. Of these, the BRD4 protein is highly enriched in super enhancers and regulate gene transcription of relevant oncogenes such as MYC, CDK genes, cyclin-D1, BCL2 and MCL-1. BRD4 inhibitors (BRD4i) block the transcription of these key oncogenes through the displacement of BRDs and other epigenetic modifiers from chromatin. In this study, we investigated the preclinical activity of BRD4i PLX51107, and their cooperative role with BCL2 inhibitor Venetoclax in CLL. Methods: 56 primary CLL cells were isolated via histopaque-1077 (Sigma-Aldrich, St Louis MO) from peripheral blood apheresis samples from consenting adults using Roswell Park Comprehensive Cancer Center protocol CIC-01-16. Peripheral blood mononuclear cells (PBMC) were seeded at 3 x106/mL in a 384 or 6 well tissue culture plates and exposed to different doses of PLX51107 (1-20uM) as a single agent or in combination with Venetoclax (1-100nM) for 48 and 72hrs (Selleck Chemicals, Houston TX). Cell viability was assessed using Cell Titer-glo (Promega, Madison WI) with all data being normalized to untreated controls. Synergy was calculated using Calcusyn (Cambridge, UK) software to determine Coefficient of Synergy (CI) values. Anti-tumor effect was also analyzed by induction of apoptosis using Annexin-V/PI staining by flow cytometry at 72hrs. Cells pellets were saved for western blotting to determine expression of BRD4 members and different members of the B-cell receptor, NF-kB pathway as also the BCL-2 family of proteins. Bcl-2 family profiling was performed via Milliplex Bcl-2 family protein panels 1 and 2 to look at overall changes in Bcl-2 family expression. Results: Single agent exposure to PLX51107 displayed time and dose dependent induction of apoptosis of CLL cells (Figure 1a). Next, we examined the interaction between the PLX51107 and Venetoclax. In 72hr exposure the combination of PLX51107 with Venetoclax with an ATM deletion was synergistic in 4 of 8 samples and 4 of 7 samples with p53 deletion. Annexin/PI staining yielded apoptotic cell death in the single agent and combination exposure with Venetoclax. Western blotting showed a modulation of both BRD4 proteins as well as Bcl-2 family member proteins (Figure 1b). Bcl-2 family profiling via Milliplex panels demonstrated the ratio of Bcl-2/Bcl x/L was much higher in samples with a high Venetoclax IC50 (136/1) compared to Venetoclax low IC50 (54/1). (Figure 1) -A) Samples with p53 deletion and corresponding synergy. (B) BCL2 family protein expression of CLL sample 214c. Conclusions: Our data indicates that a) PLX51107 has an antitumor effect in CLL cells; b) the combinational treatment of Venetoclax with PLX51107 highly improved the apoptotic effect of single agent treatments. A better understanding of the key signaling pathways for CLL cells' proliferation and survival impacted by BRD4i in combination with Venetoclax would provide a proof-of-concept rationale for studies validating BRD4i as epigenetic approach to target BCR signaling in CLL. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal