bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Learning-driven Automatic Nuclei Segmentation of Label-free Live Cell Chromatin-sensitive Partial Wave Spectroscopic Microscopy Imaging
Authors: Alom MD Shahin , Daneshkhah Ali , Acosta Nicolas , Anthony Nick , Liwag Emily Pujadas , Backman Vadim , Gaire Sunil Kumar 
Published: August 2024

AbstractChromatin-sensitive Partial Wave Spectroscopic (csPWS) microscopy offers a non-invasive glimpse into the mass density distribution of cellular structures at the nanoscale, leveraging the spectroscopic information. Such capability allows us to analyze the chromatin structure and organization and the global transcriptional state of the cell nuclei for the study of its role in carcinogenesis. Accurate segmentation of the nuclei in csPWS microscopy images is an essential step in isolating them for further analysis. However, manual segmentation is error-prone, biased, time-consuming, and laborious, resulting in disrupted nuclear boundaries with partial or over-segmentation. Here, we present an innovative deep-learning-driven approach to automate the accurate nuclei segmentation of label-free live cell csPWS microscopy imaging data. Our approach, csPWS-seg, harnesses the Convolutional Neural Networks-based U-Net model with an attention mechanism to automate the accurate cell nuclei segmentation of csPWS microscopy images. We leveraged the structural, physical, and biological differences between the cytoplasm, nucleus, and nuclear periphery to construct three distinct csPWS feature images for nucleus segmentation. Using these images of HCT116 cells, csPWS-seg achieved superior performance with a median Intersection over Union (IoU) of 0.80 and a Dice Similarity Coefficient (DSC) score of 0.88. The csPWS-seg overcame the segmentation performance over the baseline U-Net model and another attention-based model, SE-U-Net, marking a significant improvement in segmentation accuracy. Further, we analyzed the performance of our proposed model with four loss functions: binary cross-entropy loss, focal loss, dice loss, and Jaccard loss. The csPWS-seg with focal loss provided the best results compared to other loss functions. The automatic and accurate nuclei segmentation offered by the csPWS-seg not only automates, accelerates, and streamlines csPWS data analysis but also enhances the reliability of subsequent chromatin analysis research, paving the way for more accurate diagnostics, treatment, and understanding of cellular mechanisms for carcinogenesis.
Characterizing the role of exosomal miRNAs in metastasis
Authors: Agrawal Piyush , Olgun Gulden , Singh Arashdeep , Gopalan Vishaka , Hannenhalli idhar 
Published: August 2024

AbstractBackgroundExosomal microRNAs (exomiRs), transported via exosomes, play a pivotal role in intercellular communication. In cancer, exomiRs influence tumor progression by regulating key cellular processes such as proliferation, angiogenesis, and metastasis. Their role in mediating communication between cancer cells and the tumor microenvironment highlights their significance as potential diagnostic and therapeutic targets.MethodologyIn this study, we aimed to characterize the role of exomiRs in influencing the pre-metastatic niche (PMN). Across 7 tumor types, including 4 cell lines and three tumors, we extracted high confidence exomiRs (Log FC >= 2 in exosomes relative to control) and their targets (experimentally identified and targeted by at least 2 exomiRs). Subsequently, we identified enriched pathways and selected the top 100 high-confidence exomiR targets based on the frequency of their appearance in the enriched pathways. These top 100 targets were consistently used throughout the analysis.ResultsCancer cell line and tumor derived ExomiRs have significantly higher GC content relative to genomic background. Pathway enriched among the top exomiR targets included general cancer-associated processes such as “wound healing” and “regulation of epithelial cell proliferation”, as well as cancer-specific processes, such as “regulation of angiogenesis in kidney” (KIRC), “ossification” in lung (LUAD), and “positive regulation of cytokine production” in pancreatic cancer (PAAD). Similarly, ‘Pathways in cancer’ and ‘MicroRNAs in cancer’ ranked among the top 10 enriched KEGG pathways in all cancer types. ExomiR targets were not only enriched for cancer-specific tumor suppressor genes (TSG) but are also downregulated in pre-metastatic niche formed in lungs compared to normal lung. Motif analysis shows high similarity among motifs identified from exomiRs across cancer types. Our analysis recapitulates exomiRs associated with M2 macrophage differentiation and chemoresistance such as miR-21 and miR-222-3p, regulating signaling pathways such as PTEN/PI3/Akt, NF-κB, etc. Cox regression indicated that exomiR targets are significantly associated with overall survival of patients in TCGA. Lastly, a Support Vector Machine (SVM) model using exomiR target gene expression classified responders and non-responders to neoadjuvant chemotherapy with an AUROC of 0.96 (in LUAD), higher than other previously reported gene signatures.ConclusionOur study characterizes the pivotal role of exomiRs in shaping the PMN in diverse cancers, underscoring their diagnostic and therapeutic potential.
Lipid A phosphoethanolamine transferase-mediated site-selective modifications show association with colistin resistance phenotypes and fitness
Authors: Schumann A. , Gaballa A. , Yang H. , Vu D. , Ernst RK. , Wiedmann M. 
Published: August 2024

ABSTRACTGenes encoding lipid A modifying phosphoethanolamine transferases (PETs) are genetically diverse and can confer resistance to colistin and antimicrobial peptides. To better understand the functional diversity of PETs, we characterized three canonical mobile colistin resistance (mcr) alleles (mcr-1,-3,-9), one intrinsicpet(eptA), and twomcr-like genes (petB,petC). Using an isogenic expression system, we show thatmcr-1andmcr-3are phenotypically similar by conferring colistin resistance with lower fitness costs.mcr-9, which is phylogenetically closely related tomcr-3, andeptAonly provide fitness advantages in the presence of sub-inhibitory concentrations of colistin and significantly reduce fitness in media only. PET-B and PET-C were phenotypically distinct from bonafide PETs; neither conferred colistin resistance or caused considerable fitness cost inEscherichia coli. Strikingly, we found for the first time that different PETs selectively modify different phosphates of lipid A - MCR-1, MCR-3, and PET-C selectively modify the 4’-phosphate, while MCR-9 and EptA modify the 1-phosphate. 4’-phosphate modifications facilitated by MCR-1 and -3 are associated with high levels of colistin resistance and low toxicity. Our results suggest that PETs have a wide phenotypic diversity and that high level colistin resistance is associated with specific lipid A modification patterns that has been largely unexplored thus far.IMPORTANCERising levels of resistance to increasing numbers of antimicrobials has led to the revival of last resort antibiotic colistin. Unfortunately, resistance to colistin is also spreading in the form ofmcrgenes, making it essential to (i) improve identification of resistant bacteria to allow clinicians to prescribe effective drug regimens and (ii) develop new combination therapies effective at targeting resistant bacteria. Our results demonstrate that PETs, including MCR variants, are site-selective inE. coli, with site-selectivity correlating with the level of resistance and fitness costs conferred by certain PETs. Site-selectivity associated with a given PET may not only help predict colistin resistance phenotypes, but may also provide an avenue to (i) improved drug regimens and (ii) development of new combination therapies to better combat colistin resistant bacteria.
Proliferative events ameliorate DNA damage accumulation without affecting function in hematopoietic stem cells
Authors: Mehatre Shubham Haribhau , Agrawal Harsh , Roy Irene Mariam , Schouteden Sarah , Khurana Satish 
Published: August 2024

AbstractUpon aging, HSCs show functional decline with increased proliferation, myeloid skewing, and poor engraftment efficiency. Accumulation of DNA damage has been causally linked with this phenomenon, with the debatable role of proliferative events. In this study, we sought to enquire the effect of increased hematopoietic stem cell (HSC) proliferation during the lifetime on the hematopoietic aging in mice. Multiple rounds of blood withdrawals were performed between two to twelve months of adult life to maintain higher proliferation rate in HSC population. Our experiments showed little effect of increased proliferation rate on age-associated functional decline in hematopoietic system. However, we noted a decrease in the double strand breaks (DSBs) accumulated with age in mice that underwent serial bleeding regimen. Analysis of single-cell sequencing data from mouse and human HSPCs showed enrichment of DNA damage response pathways confirmed by increased expression of the genes involved. Importantly, we demonstrate that the induction of HSC proliferation in aged mice is sufficient to decrease the load of DSBs. Hence, our results show that proliferative events during lifetime might aid in clearing age-associated DSBs. While these DNA damages might not be directly linked with the functional decline, proliferation induced clearance can have clinical implications.
Transcriptomic analysis and high throughput functional characterization of human induced pluripotent stem cell derived sensory neurons
Authors: Truong Vincent , Brougher Jackson , Strassmaier Tim , Lu Irene , George Dale , Price Theodore J. , Obergrussberger Alison , Randolph Aaron , Haedo Rodolfo J. , Fertig Niels , Walsh Patrick 
Published: August 2024

AbstractPeripheral sensory neurons are a primary effector in pain neurotransmission, and have become a useful cellular model for the study of pain. While rodent tissue has historically served as a source of these neurons, it has become increasingly clear that pain mechanisms in rodents and humans are substantially divergent. Sensory neurons harvested from cadaveric human tissue serve as a superior translational model for studying pain mechanisms, however their relative paucity limits their widespread utility. Theoretically, sensory neurons manufactured from human pluripotent stem cells (hPSCs) could help bridge this translational gap given their relative abundance and potential similarity to primary human tissue. However, hPSC-derived sensory neurons manufactured with the most common methodologies correlate poorly to human tissue both transcriptionally and functionally. In the present work, we compare a novel population of hPSC-derived sensory neurons to previously published datasets and find this novel population to more closely resemble human primary dorsal root ganglia transcriptionally. Furthermore, we evaluate the heterogeneity of this novel population via single nucleus RNA sequencing and find it resembles specific nociceptor and mechanoreceptor subsets found in vivo. Finally, we assay the functionality of this population with high throughput automated patch clamp electrophysiology with respect to voltage-gated sodium (Nav) and potassium channels (Kv), and ligand-gated ionotropic GABA and P2X receptors. Overall, we find this population of hPSC-derived sensory neurons to be of relatively high fidelity, and suitable for interrogating numerous potential pain targets on a fully humanized platform.
Rearrangement of 3D genome organization in breast cancer epithelial - mesenchymal transition and metastasis organotropism
Authors: Das Priyojit , San Martin Rebeca , Hong Tian , McCord Rachel Patton 
Published: August 2024

ABSTRACTBreast cancer cells exhibit organotropism during metastasis, showing preferential homing to certain organs such as bone, lung, liver, and brain. One potential explanation for this organotropic behavior is that cancer cells gain properties that enable thriving in certain microenvironments. Such specific metastatic traits may arise from gene regulation at the primary tumor site. Spatial genome organization plays a crucial role in oncogenic transformation and progression, but the extent to which chromosome architecture contributes to organ-specific metastatic traits is unclear. This work characterizes chromosome architecture changes associated with organotropic metastatic traits. By comparing a collection of genomic data from different subtypes of localized and lung metastatic breast cancer cells with both normal and cancerous lung cells, we find important trends of genomic reorganization. The most striking differences in 3D genome compartments segregate cell types according to their epithelial vs. mesenchymal status. This EMT compartment signature occurs at genomic regions distinct from transcription-defined EMT signatures, suggesting a separate layer of regulation. Specifically querying organotropism, we find 3D genome changes consistent with adaptations needed to survive in a new microenvironment, with lung metastatic breast cells exhibiting compartment switch signatures that shift the genome architecture to a lung cell-like conformation and brain metastatic prostate cancer cells showing compartment shifts toward a brain-like state. TCGA patient data reveals gene expression changes concordant with these organ-permissive compartment changes. These results suggest that genome architecture provides an additional level of cell fate specification informing organotropism and enabling survival at the metastatic site.SIGNIFICANCEComputational analysis of a cohort of cancer cell lines reveals 3D genome spatial compartment changes are associated with transitions in cancer cell state that favor metastasis (EMT) and enable survival in a new organ context.
Proteomic profiling of UV damage repair patches uncovers histone chaperones with central functions in chromatin repair
Authors: Plessier Alexandre , Chansard Audrey , Petit Eliane , Ducassou Julia Novion , Couté Yohann , Polo Sophie E. 
Published: August 2024

SUMMARYDNA damage compromises not only genome stability but also the integrity of the chromatin template, which plays a central role in controlling cell identity. Our understanding of chromatin repair mechanisms is very incomplete. To bridge this knowledge gap, here we devise a novel proteomic strategy to characterize dynamic changes in the chromatin landscape during the repair of UV-induced DNA lesions in human cells, in a quantitative, unbiased and time-resolved manner. Thus, we identify the histone chaperones DNAJC9 and MCM2 as central players in chromatin repair. We demonstrate that DNAJC9 and MCM2 are independently recruited to sites of UV damage repair. DNAJC9 provides new H3-H4 histones to CAF-1 and HIRA chaperones for deposition into chromatin and also stimulates old H3-H4 histone recovery. DNAJC9 cooperates with MCM2 to coordinate old and new histone dynamics during UV damage repair. Together, our proteomic dataset provides a molecular framework for further dissecting epigenome maintenance mechanisms.
Understanding the Global Spread of Artemisinin Resistance: Insights from over 100KPlasmodium falciparumSamples
Authors: Balmer Andrew J. , White Nina F. D. , Ünlü Eyyüb S. , Lee Chiyun , Pearson Richard D. , Almagro-Garcia Jacob , Ariani Cristina V. 
Published: August 2024

AbstractArtemisinin partial resistance (ART-R) inPlasmodium falciparumis one of the most pressing threats to global malaria control. Over the last two decades, ART-R has spread widely across Southeast Asia, compromising public health strategies and hindering elimination efforts. As of 2024, ART-R has now emerged in East Africa, with the potential to dramatically increase human mortality in the region. Mitigating the spread of ART-R requires detailed genomic surveillance of point mutations in thekelch13gene, the primary determinant of resistance to artemisinin derivatives. Although extensive surveillance data on these markers is available, it is distributed across many literature studies and open databases. In this literature review, we aggregate publicly available spatiotemporal data for 112,933P. falciparumsamples between 1980 – 2023 into a single resource, providing the most comprehensive overview ofkelch13markers to date. By synthesising insights from these samples over a global scale, we outline the history and current status ofkelch13mutations associated with ART-R, with particular reference to their emergence in Southeast Asia and recent emergence in East and Northeast Africa. Concerningly, we find their recent increases in frequency in these areas of Africa are comparable to those observed in Southeast Asia 10-15 years ago. We review several factors that may influence the spread of ART-R going forwards, such as fitness costs, treatment strategies, and local epidemiological dynamics, before articulating possible scenarios on how resistance may spread in Africa in coming years. In summary, this review provides a unified, comprehensive account of how the situation of ART-R has unfolded globally so far, highlighting insights both for researchers in the field and public health bodies which aim to reduce its negative effects. More broadly, we highlight the critical role genomic surveillance has had, and will continue to have in combating the spread of ART-R.
Host-Guest binding free energies à la carte: an automated OneOPES protocol
Authors: Febrer Martinez Pedro , Rizzi Valerio , Aureli Simone , Gervasio Francesco Luigi 
Published: August 2024

AbstractEstimating absolute binding free energies from molecular simulations is a key step in computer-aided drug design pipelines, but agreement between computational results and experiments is still very inconsistent. Both the accuracy of the computational model and the quality of the statistical sampling contribute to this discrepancy, yet disentangling the two remains a challenge. In this study, we present an automated protocol based on OneOPES, an enhanced sampling method that exploits replica exchange and can accelerate several collective variables, to address the sampling problem. We apply this protocol to 37 host-guest systems. The simplicity of setting up the simulations and of producing well-converged binding free energy estimates without the need to optimize simulation parameters provides a reliable solution to the sampling problem. This, in turn, allows for a systematic force field comparison and ranking according to the correlation between simulations and experiments, which can inform the selection of an appropriate model. The protocol can be readily adapted to test more force field combinations and study more complex protein-ligand systems, where the choice of an appropriate physical model is often based on heuristic considerations rather than a systematic optimization.
In vivocontribution ofCyp24a1promoter vitamin D response elements
Authors: Meyer Mark B. , Lee Seong Min , Towne Jordan M. , Cichanski Shannon R. , Kaufmann Martin , Jones Glenville , Pike J. Wesley 
Published: August 2024

AbstractCYP24A1 is a multifunctional, P450 mitochondrial 24-hydroxylase enzyme that is responsible for catabolism of the most active vitamin D hormone (calcitriol, 1,25(OH)2D3), its precursor (calcifediol, 25(OH)D3), and numerous other vitamin D metabolites at the 23- and 24-carbon positions. In the kidney,Cyp24a1is induced by 1,25(OH)2D3, induced by FGF23, and potently suppressed by PTH to tightly control the circulating blood levels of 1,25(OH)2D3. This gene is believed to be under the control of a pair of classic promoter proximal (PRO) vitamin D response elements (VDREs) that are aided by distal, downstream (DS) containing enhancers that we identified more recently. The DS1 enhancer cluster was found to respond to PTH and FGF23 actions in a kidney-specific manner. The DS2 enhancer cluster was found to assist in the response of 1,25(OH)2D3in kidney, as well as other target tissues. Despite this knowledge, thein vivocontribution of the PRO VDREs to gene expression, what drivesCyp24a1basal expression in the kidney, how FGF23 activatesCyp24a1, and importantly, how PTH suppressesCyp24a1, all remain unknown. Here in this study, we utilize homology directed CRISPR to mutate one or both VDREs in the PRO region of theCyp24a1genein vivoin the mouse to address these questions. We found that the VDRE (VDRE1) more proximal to the to the transcriptional start site (TSS) is the dominant VDRE of the pair and mutation of both VDREs leads to a dramatic loss of VDR, a reduction ofCyp24a1gene expression in the kidney, and a near elimination of 1,25(OH)2D3induction in the intestine. FGF23 induction ofCyp24a1was reduced with mutation of the PRO VDREs, however, co-treatment of 1,25(OH)2D3and FGF23 synergistically increasedCyp24a1expression even with the loss of the PRO VDREs. PTH suppression ofCyp24a1gene expression was unchanged with PRO VDRE mutations, despite a minor reduction in total pCREB occupancy. Finally, VDR occupancy was dramatically reduced across the DS enhancers in theCyp24a1locus after the PRO VDREs mutation. Taken together, our data suggest a cooperative relationship between the DS and PRO enhancers in the regulation ofCyp24a1by 1,25(OH)2D3and FGF23, and despite the overall reduction of CREB on the genome it appeared that suppression either does not rely on CREB or that the PRO VDREs are unconnected to PTH suppression altogether. These studies point to the DS1 region as a basal switch forCyp24a1expression and help further define the interconnected genomic control of these hormones on vitamin D catabolism.
Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
Authors: Petersen Rachel M. , Vockley Christopher M. , Lea Amanda J. 
Published: August 2024

ABSTRACTA major goal in evolutionary biology and biomedicine is to understand the complex interactions between genetic variants, the epigenome, and gene expression. However, the causal relationships between these factors remain poorly understood. mSTARR-seq, a methylation-sensitive massively parallel reporter assay, is capable of identifying methylation-dependent regulatory activity at many thousands of genomic regions simultaneously, and allows for the testing of causal relationships between DNA methylation and gene expression on a region-by-region basis. Here, we developed a multiplexed mSTARR-seq protocol to assay naturally occurring human genetic variation from 25 individuals sampled from 10 localities in Europe and Africa. We identified 6,957 regulatory elements in either the unmethylated or methylated state, and this set was enriched for enhancer and promoter annotations, as expected. The expression of 58% of these regulatory elements was modulated by methylation, which was generally associated with decreased RNA expression. Within our set of regulatory elements, we used allele-specific expression analyses to identify 8,020 sites with genetic effects on gene regulation; further, we found that 42.3% of these genetic effects varied between methylated and unmethylated states. Sites exhibiting methylation-dependent genetic effects were enriched for GWAS and EWAS annotations, implicating them in human disease. Compared to datasets that assay DNA from a single European individual, our multiplexed assay uncovers dramatically more genetic effects and methylation-dependent genetic effects, highlighting the importance of including diverse individuals in assays which aim to understand gene regulatory processes.