bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geometric constraint of mechanosensing in bone marrow stromal cell cultures prevents stiffness-induced differentiation
Authors: Hernandez-Miranda M , Xu D , Johnston DA , Browne M , Cook RB , Sengers BG , Evans ND 
Published: October 2023

ABSTRACTExtracellular matrix (ECM) stiffness is fundamental in cell division, movement and differentiation. The stiffness that cells sense is determined not only by the elastic modulus of the ECM material, but also by ECM geometry and cell density. We hypothesised that these factors would influence cell-traction-induced matrix deformations and cellular differentiation in bone marrow stromal cells (BMSCs). To achieve this, we cultivated BMSCs on polyacrylamide hydrogels that varied in elastic modulus and geometry and measured cell spreading, cell-imparted matrix-deformations and differentiation. At low cell density BMSCs spread to a greater extent on stiff compared to soft hydrogels, or on thin compared to thick hydrogels. Cell-imparted matrix deformations were greater on soft compared to stiff hydrogels or thick compared to thin hydrogels. There were no significant differences in osteogenic differentiation relative to hydrogel elastic modulus and thickness. However, increased cell density and/or prolonged culture significantly reduced matrix deformations on soft hydrogels to levels similar to those on stiff substrates. This suggests that at high cell densities cell traction-induced matrix displacements are reduced by both neighbouring cells and the constraint imposed by an underlying stiff support. This may explain observations of the lack of difference in osteogenic differentiation as a function of stiffness.
Deciphering Cell-types and Gene Signatures Associated with Disease Activity in Rheumatoid Arthritis using Single Cell RNA-sequencing
Authors: Binvignat M. , Miao B. Y. , Wibrand C. , Yang M.M. , Rychkov D. , Flynn E. , Nititham J. , Tamaki W. , Khan U. , Carvidi A. , Krueger M. , Niemi E. , Sun Y. , Fragiadakis G. , Sellam J. , Mariotti-Ferrandiz E. , Klatzmann D. , Gross A. , Ye J. , Butte A. J. , Criswell L.A , Nakamura M. , Sirota M. 
Published: October 2023

AbstractObjectiveSingle cell profiling of synovial tissue has previously identified gene signatures associated with rheumatoid arthritis (RA) pathophysiology, but synovial tissue is difficult to obtain. This study leverages single cell sequencing of peripheral blood mononuclear cells (PBMCs) from patients with RA and matched healthy controls to identify disease relevant cell subsets and cell type specific signatures of disease.MethodsSingle-cell RNA sequencing (scRNAseq) was performed on peripheral blood mononuclear cells (PBMCs) from 18 RA patients and 18 matched controls, accounting for age, gender, race, and ethnicity). Samples were processed using standard CellRanger and Scanpy pipelines, pseudobulk differential gene expression analysis was performed using DESeq2, and cell-cell communication analysis using CellChat.ResultsWe identified 18 distinct PBMC subsets, including a novel IFITM3+ monocyte subset. CD4+ T effector memory cells were increased in patients with moderate to high disease activity (DAS28-CRP ≥ 3.2), while non-classical monocytes were decreased in patients with low disease activity or remission (DAS28-CRP < 3.2). Differential gene expression analysis identified RA-associated genes in IFITM3+ and non-classical monocyte subsets, and downregulation of pro-inflammatory genes in the Vδ subset. Additionally, we identified gene signatures associated with disease activity, characterized by upregulation of pro-inflammatory genesTNF, JUN, EGR1, IFIT2, MAFB, G0S2, and downregulation ofHLA-DQB1, HLA-DRB5, TNFSF13B. Notably, cell-cell communication analysis revealed upregulation of immune-associated signaling pathways, including VISTA, in patients with RA.ConclusionsWe provide a novel single-cell transcriptomics dataset of PBMCs from patients with RA, and identify insights into the systemic cellular and molecular mechanisms underlying RA disease activity.
RNA structure modulates Cas13 activity and enables mismatch detection
Authors: Kimchi Ofer , Larsen Benjamin B. , Dunkley Owen R. S. , te Velthuis Aartjan J.W. , Myhrvold Cameron 
Published: October 2023

AbstractThe RNA-targeting CRISPR nuclease Cas13 has emerged as a powerful tool for applications ranging from nucleic acid detection to transcriptome engineering and RNA imaging1–6. Cas13 is activated by the hybridization of a CRISPR RNA (crRNA) to a complementary single-stranded RNA (ssRNA) protospacer in a target RNA1,7. Though Cas13 is not activated by double-stranded RNA (dsRNA)in vitro, it paradoxically demonstrates robust RNA targeting in environments where the vast majority of RNAs are highly structured2,8. Understanding Cas13’s mechanism of binding and activation will be key to improving its ability to detect and perturb RNA; however, the mechanism by which Cas13 binds structured RNAs remains unknown9. Here, we systematically probe the mechanism of LwaCas13a activation in response to RNA structure perturbations using a massively multiplexed screen. We find that there are two distinct sequence-independent modes by which secondary structure affects Cas13 activity: structure in the protospacer region competes with the crRNA and can be disrupted via a strand-displacement mechanism, while structure in the region 3’ to the protospacer has an allosteric inhibitory effect. We leverage the kinetic nature of the strand displacement process to improve Cas13-based RNA detection, enhancing mismatch discrimination by up to 50-fold and enabling sequence-agnostic mutation identification at low (<1%) allele frequencies. Our work sets a new standard for CRISPR-based nucleic acid detection and will enable intelligent and secondary-structure-guided target selection while also expanding the range of RNAs available for targeting with Cas13.
Epigenetic field defect discriminates normal tissues from healthy and tumor-bearing kidneys
Authors: Serth Jurgen , Reese Christel , Hubscher Tatyana , Hill Bastian , Klintschar Michael , Hennenlotter Jorg , Kuczyk Markus Antonius 
Published: October 2023

AbstractBackgroundThe detection of alterations in DNA methylation (DNAm) in normal human tissues may provide molecular insights for cancer development, the estimation of personal cancer risk, and a basis for early diagnosis of malignancies to reduce cancer lethality. Thus, whether DNAm allows discrimination between healthy normal and normal tumor-adjacent renal tissues is an important question.MethodsDNAm of loci in the LINE1 repetitive sequence andANKRD34B, NHLH2, TBR1, andZIC1was measured in a total of 493 tissue samples representing 342 normal autopsy and 151 histopathological normal tumor-adjacent renal tissues by pyro-sequencing a total of 22 CpG sites.ResultsUnsupervised k-means clustering demonstrated a significant imbalance of tissue samples in three stable tissue clusters. Random forest classification demonstrated discrimination of normal and normal tumor-adjacent renal tissues with a median area under the ROC curve of 0.81 (p=2.7×10−9, diagnostic odds ratio 10.4). Variable importance analysis revealed CpG sites in LINE1 andANKRD34Bas the most important model contributors.ConclusionsDNAm alterations in normal tissues allow detection of renal cancer with high diagnostic efficiency, defining a DNAm field effect in the kidney. The methylation signature may serve as a basis for an epigenetic DNAm clock permitting estimation of individual renal cancer risk.
The developmental trajectory of1H-MRS brain metabolites from childhood to adulthood
Authors: Thomson Alice R. , Hwa Hannah , Pasanta Duanghathai , Hopwood Benjamin , Powell Helen J. , Lawrence Ross , Garcia Tabuenca Zeus , Arichi Tomoki , Edden Richard A. E. , Chai Xiaoqian , Puts Nicolaas A. 
Published: October 2023

AbstractHuman brain development is ongoing throughout childhood, with for example myelination of nerve fibres and refinement of synaptic connections continuing until early adulthood.1H-Magnetic Resonance Spectroscopy (1H-MRS)can be used to quantify the concentrations of endogenous metabolites (e.g., glutamate and γ-aminobutyric acid (GABA)) in the human brain in vivo and so can provide valuable, tractable insight into the biochemical processes that support postnatal neurodevelopment. This can feasibly provide new insight into and aid management of neurodevelopmental disorders by providing chemical markers of atypical development. This study aims to characterize the normative developmental trajectory of various brain metabolites, as measured by1H-MRS from a midline posterior parietal voxel. We find significant non-linear trajectories for GABA+, Glx, tNAA and tCr concentrations. Glx and GABA+ concentrations steeply decrease across childhood. tNAA concentrations are relatively stable in childhood but gradually decrease from early adulthood, while tCr concentrations increase from childhood to early adulthood. tCho was the only metabolite to have a strictly linear association with age. Trajectories likely reflect fundamental neurodevelopmental processes (including local circuit refinement) which occur from childhood to early adulthood and can be associated with cognitive development; we find GABA+ concentrations significantly positively correlate with recognition memory scores across post-natal development.
Rapid threat assessment in theDrosophilathermosensory system
Authors: Jouandet Genevieve C. , Alpert Michael H. , Simões José Miguel , Suhendra Richard , Frank Dominic D. , Levy Joshua I. , Para Alessia , Kath William L. , Gallio Marco 
Published: October 2023

SUMMARYNeurons that participate in sensory processing often display “ON” responses, i.e. fire transiently at the onset of a stimulus. ON transients are widespread, perhaps universal to sensory coding, yet their function is not always well-understood. Here, we show that ON responses in theDrosophilathermosensory system extrapolate the trajectory of temperature change, priming escape behavior if unsafe thermal conditions are imminent. First, we show that second-order thermosensory projection neurons (TPN-IIIs) and their Lateral Horn targets (TLHONs), display ON responses to thermal stimuli, independent of direction of change (heating or cooling) and of absolute temperature. Instead, they track the rate of temperature change, with TLHONs firing exclusively to rapid changes (>0.2°C/sec). Next, we use connectomics to track TLHON’s output to descending neurons that control walking and escape, and modeling and genetic silencing to demonstrate how ON transients can flexibly amplify aversive responses to small thermal change. Our results suggest that, across sensory systems, ON transients may represent a general mechanism to systematically anticipate and respond to salient or dangerous conditions.
HERV activation segregates ME/CFS from fibromyalgia while defining a novel nosologic entity
Authors: Giménez-Orenga Karen , Martín-Martínez Eva , Nathanson Lubov , Oltra Elisa 
Published: October 2023

AbstractResearch of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Fibromyalgia (FM), two acquired chronic illnesses affecting mainly females, has failed to ascertain their frequent co-appearance and etiology. Despite prior detection of human endogenous retrovirus (HERV) activation in these diseases, the potential biomarker value of HERV expression profiles for their diagnosis, and the relationship of HERV expression profiles with patient immune systems and symptoms had remained unexplored. By using HERV-V3 high-density microarrays (including over 350k HERV elements and more than 1500 immune-related genes) to interrogate the transcriptomes of peripheral blood mononuclear cells from female patients diagnosed with ME/CFS, FM or both, and matched healthy controls (n=43), this study fills this gap of knowledge. Hierarchical clustering of HERV expression profiles strikingly allowed perfect participant assignment into four distinct groups: ME/CFS, FM, co-diagnosed, or healthy, pointing at a potent biomarker value of HERV expression profiles to differentiate between these hard-to-diagnose chronic syndromes. Differentially expressed HERV-immune-gene modules revealed unique profiles for each of the four study groups and highlighting decreased γδ T cells, and increased plasma and resting CD4 memory T cells, correlating with patient symptom severity in ME/CFS. Moreover, activation of HERV sequences coincided with enrichment of binding sequences targeted by transcription factors which recruit SETDB1 and TRIM28, two known epigenetic silencers of HERV, in ME/CFS, offering a mechanistic explanation for the findings. Unexpectedly, HERV expression profiles appeared minimally affected in co-diagnosed patients denoting a new nosological entity with low epigenetic impact, a seemingly relevant aspect for the diagnosis and treatment of this prevalent group of patients.
Humans and a subterranean rodent have contrasting biological rhythms
Authors: Appenzeller Otto , Qualls Clifford , Bromage Tim 
Published: October 2023

AbstractHere we show that naked mole rats (NMR’s) have an extraordinary survival advantage. We base this statement on a spectral analysis of the time series of measured intervals in teeth of 3 species (NMR’s, Killer Whale, and Modern Humans). We used Fourier decomposition to analyze the variability of these intervals. We find these animals go through their long life without any of the age-associated diseases seen in humans such as osteoporosis or cancer and they show no signs of muscle atrophy or slowing of mobility. Global warming will delay its effects on these animals whereas for humans it is a clear and present danger.
Microfluidics-free single-cell genomics reveals complex central-peripheral immune crosstalk in the mouse brain during peripheral inflammation
Authors: Boles Jake Sondag , Uriarte Huarte Oihane , Tansey Malú Gámez 
Published: October 2023

AbstractInflammation is a realized detriment to brain health in a growing number of neurological diseases, but querying neuroinflammation in its cellular complexity remains a challenge. This manuscript aims to provide a reliable and accessible strategy for examining the brain’s immune system. We compare the efficacy of cell isolation methods in producing ample and pure immune samples from mouse brains. Then, with the high-input single-cell genomics platform PIPseq, we generate a rich neuroimmune dataset containing microglia and many peripheral immune populations. To demonstrate this strategy’s utility, we interrogate the well-established model of LPS-induced neuroinflammation with single-cell resolution. We demonstrate the activation of crosstalk between microglia and peripheral phagocytes and highlight the unique contributions of microglia and peripheral immune cells to neuroinflammation. Our approach enables the high-depth evaluation of inflammation in longstanding rodent models of neurological disease to reveal novel insight into the contributions of the immune system to brain health.
FMNL2 regulates actin for ER and mitochondria distribution in oocyte meiosis
Authors: Pan Meng-Hao , Pan Zhen-Nan , Sun Ming-Hong , Li Xiao-Han , Ju Jia-Qian , Luo Shi-Ming , Ou Xiang-Hong , Sun Shao-Chen 
Published: October 2023

AbstractDuring mammalian oocyte meiosis, spindle migration and asymmetric cytokinesis are unique steps for the successful polar body extrusion. The asymmetry defects of oocytes will lead to the failure of fertilization and embryo implantation. In present study we reported that an actin nucleating factor formin-like 2 (FMNL2) played critical roles in the regulation of spindle migration and organelle distribution. Our results showed that FMNL2 mainly localized at the oocyte cortex and periphery of spindle. Depletion of FMNL2 led to the failure of polar body extrusion and large polar bodies in oocytes. Live-cell imaging revealed that the spindle failed to migrate to the oocyte cortex, which caused polar body formation defects, and this might be due to the decreased polymerization of cytoplasmic actin by FMNL2 depletion. Furthermore, mass spectrometry analysis indicated that FMNL2 was associated with mitochondria and endoplasmic reticulum-related proteins, and FMNL2 depletion disrupted the function and distribution of mitochondria and endoplasmic reticulum, showing with decreased mitochondrial membrane potential and the occurrence of endoplasmic reticulum stress. Microinjecting Fmnl2-EGFP mRNA into FMNL2-depleted oocytes significantly rescued these defects. Thus, our results indicate that FMNL2 is essential for the actin assembly, which further involves into meiotic spindle migration and ER/mitochondria functions in mouse oocytes.
A Novel Interaction Between Aquaporin 1 and Caspase-3 in Pulmonary Arterial Smooth Muscle Cells
Authors: Niedermeyer Shannon , Yun Xin , Trujillo Marielena , Andrade Manuella Ribas , Kolb Todd , Suresh Karthik , Damarla Mahendra , Shimoda Larissa A. 
Published: October 2023

AbstractPulmonary arterial hypertension (PAH) is a disease in which remodeling of the precapillary pulmonary vasculature leads to hyperplasia and hypertrophy of the muscular vascular wall, and the formation of vaso-occlusive lesions. These pathologic changes are predominantly due to abnormal proliferation and migration of pulmonary arterial smooth muscle cells (PASMCs), enhanced cellular functions that have been linked to increases in the cell membrane protein aquaporin-1 (AQP1). However, the mechanisms underlying increased AQP1 abundance have not been fully elucidated. Here we present data that establishes a novel interaction between AQP1 and the proteolytic enzyme caspase-3.In silicoanalysis of the AQP1 protein reveals two caspase-3 cleavage sites on its c-terminal tail, proximal to known ubiquitin sites. Using biotin proximity ligase techniques, we establish that AQP1 and caspase-3 interact in both HEK293A cells and rat PASMCs. Furthermore, we demonstrate that AQP1 levels increase and decrease with enhanced caspase-3 activity and inhibition respectively. Ultimately, further work characterizing this interaction could provide the foundation for novel PAH therapeutics.
Beta-Validation of a Non-Invasive Method for Simultaneous Detection of Early-Stage Female-Specific Cancers
Authors: Ramamoorthy Sudhakar , Sundaramoorthy Saranya , Gupta Ankur , Siddiqui Zaved , Sagar Ganga , Rao Kanury V.S. , Saquib Najmuddin , Mohan Surapeni Krishna 
Published: October 2023

ABSTRACTObjectivesIn this report, we assessed the accuracy of our previously developed method for simultaneous diagnosis of the four female cancers of the Breast, Endometrium, Cervix, and Ovary, in a clinical set-up with blinded protocol.Materials and MethodsOur test protocol combined global serum metabolome profiling wherein data was analyzed with machine learning algorithms to extract metabolite signatures that correlated with early-stage cancers. High-resolution mass spectrometry was employed to profile the serum metabolome and the resulting data were subjected to a pre-processing pipeline to obtain the data set. The data was then analyzed using artificial intelligence algorithms to identify early-stage cancer metabolic signatures.ResultsOverall, a total of 1000 blinded samples were analyzed by generating the serum metabolome profiles, followed by sequential algorithms for cancer detection and multiclass cancer type identification. Of these 1000 samples, 797 were identified as cancer positive, while, 203 samples were identified as cancer-negative. The multiclass algorithm was then applied to the 797 cancer-positive samples, to distinguish between samples that were from patients with either endometrial, breast, cervical, or ovarian cancer. After completion of the analysis, the sample code was broken to estimate the accuracy of the results. Concerning the identification of samples that were cancer-positive, the sensitivity obtained was 99.6% whereas the specificity was 100%. For the second stage of analysis which involves ‘tissue of origin’, all 107 breast cancer samples were correctly identified without any false calls. The accuracy for identification of cervical and ovarian cancers was between 95-96% for each, whereas 91% for endometrial cancer.ConclusionsOur present study validates the performance of our method for the early-stage detection of female-specific cancers in a clinical setting. Importantly, the algorithms for cancer detection and ‘tissue of origin’ prediction, which were initially trained using samples from Caucasian patients, retained the accuracy on samples from Indian women patients. This suggests that the performance of these algorithms was minimally influenced by variables such as ethnicity and race. Present results, therefore, also underscore the potential clinical utility of our method for early-stage diagnosis of cancers that are specific to females.
Hs-CRP is associated with Heart Failure Hospitalization in Patients with MAFLD and Normal LVEF Undergoing Coronary Angiography
Authors: Zhou Xiao-Dong , Chen Qin-Fen , Targher Giovanni , Byrne Christopher D. , Shapiro Michael D. , Tian Na , Xiao Tie , Sung Ki-Chul , Lip Gregory Y. H. , Zheng Ming-Hua 
Published: October 2023

AbstractBackgroundSystemic chronic inflammation plays a role in the pathophysiology of both heart failure with preserved ejection fraction (HFpEF) and metabolic dysfunction-associated fatty liver disease (MAFLD).AimThis study aimed to investigate whether serum high-sensitivity C-reactive protein (hs-CRP) levels were associated with the future risk of heart failure (HF) hospitalization in patients with MAFLD and a normal left ventricular ejection fraction (LVEF).MethodsThe study enrolled consecutive individuals with MAFLD and normal LVEF who underwent coronary angiography for suspected coronary heart disease. The study population was subdivided into non-HF, pre-HFpEF, and HFpEF groups at baseline. The study outcome was the first hospitalization for HF.ResultsIn 10,019 middle-aged individuals (mean age 63.3±10.6 years; 38.5% female), the prevalence rates of HFpEF and pre-HFpEF were 34.2% and 34.5%, with a median serum hs-CRP level of 4.5 mg/L (IQR: 1.9-10 mg/L) and 5.0 mg/L (IQR: 2.1-10.1 mg/L), respectively. Serum hs-CRP levels were significantly higher in the pre-HFpEF and HFpEF groups than in the non-HF group. HF hospitalizations occurred in 1942 (19.4%) patients over a median of 3.2 years, with rates of 3.7% in non-HF, 20.8% in pre-HFpEF, and 32.1% in HFpEF, respectively. Cox regression analyses showed that patients in the highest hs-CRP level quartile had a ∼4.5-fold increased risk of being hospitalized for HF compared to those in the lowest hs-CRP level quartile (adjusted-Hazard Ratio 4.42, 95% CI 3.72-5.25).ConclusionsThere was a high prevalence of baseline pre-HFpEF and HFpEF in subjects with MAFLD. There was an increased risk of HF hospitalization in those with elevated hs-CRP levels.