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Motivation Predicting cell locations is important since with the understanding of cell locations, we may estimate the function of cells and their integration with the spatial environment. Thus, the DREAM challenge on single-cell transcriptomics required participants to predict the locations of single cells in the Drosophila embryo using single-cell transcriptomic data. Results We have developed over 50 pipelines by combining different ways of preprocessing the RNA-seq data, selecting the genes, predicting the cell locations and validating predicted cell locations, resulting in the winning methods which were ranked second in sub-challenge 1, first in sub-challenge 2 and third in sub-challenge 3. In this paper, we present an R package, SCTCwhatateam, which includes all the methods we developed and the Shiny web application to facilitate the research on single-cell spatial reconstruction. All the data and the example use cases are available in the Supplementary data. [ABSTRACT FROM AUTHOR]

An introduction is presented in which editors discusses various topics within the issue including recombinant human thyrotropin-aided radioiodine therapy, prognostic factors of differentiated carcinomas (DTC), and clinical significance of subcutaneous or intrastrap muscular recurrence.

Objective: Cancer is a leading cause of death globally, prompting numerous efforts to find effective treatments. HeLa cells, derived from Henrietta Lacks' cancerous squamous cells, have played a crucial role in cancer research due to their origin, resistance, and rapid growth. They are particularly useful for studying ways of cellular death triggering, or apoptosis, without an immune response. Thus, the objective of this paper was to review the latest publications on the subject of HeLa apoptosis so that a brief view to be available on the otherwise so extended subject. Methodology: To provide a concise review of the extensive research on this topic, a search was conducted using the phrase "HeLa cells apoptosis triggering" on PubMed. The articles that were published in English, in the last 6 years, presenting results sustained by valid morphological and chemical apoptotic changes present in cells, were selected and reviewed. A comprehensive table presenting the apoptotic mechanism exerted by each substance was made to assure a concise presentation of the results. Results: The reviewed studies have shown that many natural substances exhibit pro-apoptotic activity on malignant cells and can be used as chemotherapeutic agents. Some synthetic molecules were showed to have good results too. Important facts about these substances, their intervention site and metabolic modifications are presented in a concise form. The use of nano-carriers for targeted delivery was shown to increase their specificity towards cancerous cells. Conclusions: HeLa cells were a groundbreaking discovery that revolutionized scientific research. Although there is ongoing research towards cancer cures using HeLa cells, there are still many trials and considerations that need to be addressed. With the countless existing HeLa cell lines, the scientific possibilities for research are endless. [ABSTRACT FROM AUTHOR]

Extracellular matrix (ECM) is a kind of connective tissue in the cell microenvironment, which is of great significance to tissue development. ECM in muscle fiber niche consists of three layers: the epimysium, the perimysium, and the endomysium (basal lamina). These three layers of connective tissue structure can not only maintain the morphology of skeletal muscle, but also play an important role in the physiological functions of muscle cells, such as the transmission of mechanical force, the regeneration of muscle fiber, and the formation of neuromuscular junction. In this paper, detailed discussions are made for the structure and key components of ECM in skeletal muscle tissue, the role of ECM in skeletal muscle development, and the application of ECM in biomedical engineering. This review will provide the reader with a comprehensive overview of ECM, as well as a comprehensive understanding of the structure, physiological function, and application of ECM in skeletal muscle tissue. [ABSTRACT FROM AUTHOR]

Background: Emerging evidence suggests that microRNAs (miRNAs) play multiple roles in human cancers through regulating mRNAs and distinct pathways. This paper focused on the functions of miR-4429 in prostate cancer (PCa) progression and the molecules involved.Methods: Expression of miR-4429 in PCa tissues and cells was determined. Upregulation of miR-4429 was introduced in PCa cells to examine its role in the malignant behaviors of cells. The putative target mRNA of miR-4429 involved in PCa progression was predicted from a bioinformatic system and validated through luciferase assays. Overexpression of distal-less homeobox 1 (DLX1) was further induced in cells to validate its implication in miR-4429-mediated events. The activity of Wnt/β-catenin pathway was determined.Results: miR-4429 was poorly expressed in PCa tissues and cells. Artificial upregulation of miR-4429 significantly reduced proliferation, growth, invasion, migration and resistance to death of cancer cells and inactivated the Wnt/β-catenin pathway. DLX1 mRNA was found as a target of miR-4429. Upregulation of DLX1 restored the malignant behaviors of PCa cells which were initially suppressed by miR-4429, and it activated the Wnt/β-catenin pathway.Conclusion: Our study highlights that miR-4429 inhibits the growth of PCa cells by down-regulating DLX1 and inactivating the Wnt/β-catenin pathway. This finding may offer novel insights into PCa treatment. [ABSTRACT FROM AUTHOR]

As a newly discovered mechanosensitive ion channel protein, the piezo1 protein participates in the transmission of mechanical signals on the cell membrane and plays a vital role in mammalian biomechanics. Piezo1 has attracted widespread attention since it was discovered in 2010. In recent years, studies on piezo1 have gradually increased and deepened. In addition to the discovery that piezo1 is expressed in the respiratory, cardiovascular, gastrointestinal, and urinary systems, it is also stably expressed in cells such as mesenchymal stem cells (MSCs), osteoblasts, osteoclasts, chondrocytes, and nucleus pulposus cells that constitute vertebral bodies and intervertebral discs. They can all receive external mechanical stimulation through the piezo1 protein channel to affect cell proliferation, differentiation, migration, and apoptosis to promote the occurrence and development of lumbar degenerative diseases. Through reviewing the relevant literature of piezo1 in the abovementioned cells, this paper discusses the effect of piezo1 protein expression under mechanical stress stimuli on spinal degenerative disease, providing the molecular basis for the pathological mechanism of spinal degenerative disease and also a new basis, ideas, and methods for the prevention and treatment of this degenerative disease. [ABSTRACT FROM AUTHOR]

Background: Protein–protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. Most proteins perform their functions by interacting with other proteins, so predicting PPIs accurately is crucial for understanding cell physiology. Results: Recently, graph convolutional networks (GCNs) have been proposed to capture the graph structure information and generate representations for nodes in the graph. In our paper, we use GCNs to learn the position information of proteins in the PPIs networks graph, which can reflect the properties of proteins to some extent. Combining amino acid sequence information and position information makes a stronger representation for protein, which improves the accuracy of PPIs prediction. Conclusion: In previous research methods, most of them only used protein amino acid sequence as input information to make predictions, without considering the structural information of PPIs networks graph. We first time combine amino acid sequence information and position information to make representations for proteins. The experimental results indicate that our method has strong competitiveness compared with several sequence-based methods. [ABSTRACT FROM AUTHOR]

Elucidating the causal mechanisms responsible for disease can reveal potential therapeutic targets for pharmacological intervention and, accordingly, guide drug repositioning and discovery. In essence, the topology of a network can reveal the impact a drug candidate may have on a given biological state, leading the way for enhanced disease characterization and the design of advanced therapies. Network-based approaches, in particular, are highly suited for these purposes as they hold the capacity to identify the molecular mechanisms underlying disease. Here, we present drug2ways, a novel methodology that leverages multimodal causal networks for predicting drug candidates. Drug2ways implements an efficient algorithm which reasons over causal paths in large-scale biological networks to propose drug candidates for a given disease. We validate our approach using clinical trial information and demonstrate how drug2ways can be used for multiple applications to identify: i) single-target drug candidates, ii) candidates with polypharmacological properties that can optimize multiple targets, and iii) candidates for combination therapy. Finally, we make drug2ways available to the scientific community as a Python package that enables conducting these applications on multiple standard network formats. Author summary: At any given time, a large set of biomolecules are interacting in ways that give rise to the normal functioning of a cell. By representing biological interactions as networks, we can reconstruct the complex molecular mechanisms that govern the physiology of a cell. These networks can then be analyzed to understand where the system fails and how that can give rise to disease. Similarly, using computational methods, we can also enrich these networks with drugs, diseases and disease phenotypes to estimate how a drug, or a combination of drugs, would behave in a system and whether it can be used to treat or alleviate the symptoms of a disease. In this paper, we present drug2ways, a novel methodology designed for drug discovery applications, that exploits the information contained in a biological network comprising causal relations between drugs, proteins, and diseases. Employing these networks and an efficient algorithm, drugways2 traverses over the ensemble of paths between a drug and a disease to propose the drugs that are most likely to cure the disease based on the information contained in the network. We hypothesize that this ensemble of paths could be used to simulate the mechanism of action of a drug and the directionality inferred through these paths could be used as a proxy to identify drug candidates. Through several experiments, we demonstrate how drug2ways can be used to find novel ways of using existing drugs, identify drug candidates, optimize treatments by targeting multiple disease phenotypes, and propose combination therapies. Owing to the generalizability of the algorithm and the accompanying software, we ambition that drug2ways could be applied to a variety of biological networks to generate new hypotheses for drug discovery and a better understanding of their mechanisms of action. [ABSTRACT FROM AUTHOR]

The extensive literature dealing with the Golgi system emphasizes its role in protein secretion and modification, usually without specifying from which evolutionary ancient cell physiological necessity such secretion originated. Neither does it specify which functional requirements the secreted proteins must meet. From a reinterpretation of some classical and recent data gained mainly, but not exclusively, from (insect) endocrinology, the view emerged that the likely primordial function of the rough endoplasmic reticulum (RER)–Golgi complex in all eukaryotes was not the secretion of any type of protein but the removal of toxic excess Ca2+ from the cytoplasm. Such activity requires the concurrent secretion of large amounts of Ca2+-carrying/transporting proteins acting as a micro-conveyor belt system inside the RER–Golgi. Thus, (fitness increasing) protein secretion is subordinate to Ca2+ removal. Milk with its high content of protein and Ca2+ (60–90 mM vs. 100 nM in unstimulated mammary gland cells) is an extreme example. The sarco(endo)plasmatic reticulum Ca2+-ATPases (SERCAs) and SPCA1a Ca2+/Mn2+ transport ATPases are major players in Ca2+ removal through the Golgi. Both are blocked by the sesquiterpenoid thapsigargin. This strengthens the hypothesis (2014) that endogenous farnesol-like sesquiterpenoids (FLSs) may act as the long sought for but still unidentified agonist (s) for Ca2+-pumps in both the ER and Golgi. A second putative function also emerges. The fusion of both the incoming and outgoing transport vesicles, respectively, at the cis - and trans - side of Golgi stacks, with the membrane system requiring high flexibility and fast self-closing of the involved membranes. These properties may—possibly partially—be controlled by endogenous hydrophobic membrane "fluidizers" for which FLSs are prime candidates. A recent reexamination of unexplained classical data suggests that they are likely synthesized by the Golgi itself. This game-changing hypothesis is endorsed by several arguments and data, some of which date from 1964, that the insect corpus allatum (CA), which is the major production site of farnesol-esters, has active Golgi systems. Thus, in addition to secreting FLS, in particular juvenile hormone(s), it also secretes a protein(s) or peptide(s) with thus far unknown function. This paper suggests answers to various open questions in cell physiology and general endocrinology. [ABSTRACT FROM AUTHOR]

Benefiting from the developments of advanced optical microscopy techniques, the mysteries of biological functions at the cellular and subcellular levels have been continuously revealed. Stimulated Raman scattering (SRS) microscopy is a rapidly growing technique that has attracted broad attentions and become a powerful tool for biology and biomedicine, largely thanks to its chemical specificity, high sensitivity and fast image speed. This review paper introduces the principles of SRS, discusses the technical developments and implementations of SRS microscopy, then highlights and summarizes its applications on biological cellular machinery and finally shares our visions of potential breakthroughs in the future. [ABSTRACT FROM AUTHOR]

Chemokine-like factor-like MARVEL transmembrane domain containing member/chemokine-like factor superfamily member (CMTM/CKLFSF) including CKLF and CMTM -CMTM8 are a new family of proteins linking chemokines and transmembrane superfamilies. CMTM not only have broad chemotactic activities, but also associate with hematopoietic system, immune system, and tumor development and metastasis closely. CMTM proteins are involved in key biological processes of cancer development, which include activation and recycling of growth factor receptors, cell proliferation and metastasis, and regulation of the tumor immune microenvironment. This is a new focus of research on the relationship between CMTM and tumors, because CMTM4/CMTM6 can be considered as a regulator for programmed cell death ligand 1 (PD-L1). This paper reviews the role of CMTM family members on cancer, especially in tumor growth, metastasis and immune escape, summarize the latest findings on the relationship between CMTM and non-small cell lung cancer, and explores the potential clinical value of CMTM as a novel drug target or biomarker. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

Motivation Single cell RNA-Seq (scRNA-Seq) has broadened our understanding of cellular heterogeneity and provided valuable insights into cellular functions. Recent experimental strategies extend scRNA-Seq readouts to include additional features, including cell surface proteins and genomic perturbations. These 'feature barcoding' strategies rely on converting molecular and cellular features to unique sequence barcodes, which are then detected with the transcriptome. Results Here, we introduce FBA, a flexible and streamlined package to perform quality control, quantification, demultiplexing, multiplet detection, clustering and visualization of feature barcoding assays. Availabilityand implementation FBA is available on PyPi at https://pypi.org/project/fba and on GitHub at https://github.com/jlduan/fba. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Ventricular action potential is well-known because of its plateau phase with a spike-notch-dome morphology. As such, the morphology of action potential is necessary for ensuring a correct heart functioning. Any distraction from normal notch-dome morphology may trigger a circus movement reentry in the form of lethal ventricular fibrillation. When the epicardial action potential dome propagates from a site where it is maintained to regions where it has been lost, it gives rise to the proposed mechanism for the Brugada syndrome. Despite the impact of notch-dome dynamics on the heart function, no independent and explicit research has been performed on the simulation of notch-dome dynamics and morphology. In this paper, using a novel mathematical approach, a three-state variable model is proposed; we show that our proposed model not only can simulate morphology of action potential of ventricular cells but also can propose a biological reasonable tool for controlling of the morphology of action potential spike-notch-dome. We show that the processes of activation and inactivation of ionic gating variables (as positive or negative feedbacks on the voltage of cell membrane) and the ratio of their speeds (time constants) can be treated as a reasonable biological tool for simulating ventricular cell notch-dome. This finding may led to a new insight to the quantification of the health of a ventricular cell and may also propose a new drug therapy strategy for cardiac diseases. [ABSTRACT FROM AUTHOR]

Gastric precancerous lesions (GPLs) are an essential precursor in the occurrence and development of gastric cancer, known to be one of the most common and lethal cancers worldwide. Traditional Chinese medicine (TCM) has a positive prospect for the prevention and therapy of GPL owing to several advantages including a definite curative effect, fewer side effects compared to other treatments, multiple components, and holistic regulation. Despite these characteristic advantages, the mechanisms of TCM in treating GPL have not been fully elucidated. In this review, we summarize the current knowledge with respect to herbal formulations and the therapeutic mechanisms of TCM active ingredients for GPL. This paper elaborates on the mechanisms of TCM underlying the prevention and treatment of GPL, specifically those that are linked to anti-H. pylori, anti-inflammation, antiproliferation, proapoptotic, antioxidation, antiglycolytic, and antiangiogenesis effects. [ABSTRACT FROM AUTHOR]

MicroRNAs or miRNAs are a component of the non-coding RNAs family which is engaged in many cellular functions such as cell proliferation, apoptosis, gene expression, signaling pathways, angiogenesis, and etc. Endometriosis is a malignant gynecologic disorder occurring in women before menopausal age. Pathogenesis of this illness is still a discussion subject between the scientists but in our knowledge, microRNAs can be one of the possible involved factors. The purpose of this paper is to investigate the role of apoptotic activities of miRNAs in endometriosis. Accumulative evidence has demonstrated the role of cell proliferation, apoptosis, and invasion in the progression of these diseases. In this review, we looked into the specific role of apoptosis and its related genes and pathways in endometriosis and tied to present an explanation of how miRNAs can affect endometriosis by their apoptotic activities. What we found is that a great extent of miRNAs is involved in this illness and they are responsible for repressing apoptosis and progression of the disease. As a result, miRNAs have two different usages in endometriosis: biomarkers and potential therapeutic targets. In this review we gathered a great amount of evidence to inquire into the role of micro RNAs in inducing apoptosis and how this mechanism can be exerted for therapeutic purposes for endometriosis. [ABSTRACT FROM AUTHOR]

The endoplasmic reticulum (ER) is an organelle equipped with mechanisms for proper protein folding, trafficking, and degradation to maintain protein homeostasis in the secretory pathway. As a defense mechanism, perturbation of ER proteostasis by ER stress agents activates a cascade of signaling pathways from the ER to the nucleus known as unfolded protein response (UPR). The primary goal of UPR is to induce transcriptional and translational programs to restore ER homeostasis for cell survival. As such, defects in UPR signaling have been implicated as a key contributor to multiple diseases including metabolic diseases, degenerative diseases, inflammatory disorders, and cancer. Growing evidence support the critical role of ER stress in regulating the fate as well as the magnitude of the immune response. Moreover, the availability of multiple UPR pharmacological inhibitors raises the hope that targeting UPR can be a new strategy for immune modulation and immunotherapy of diseases. This paper reviews the principal mechanisms by which ER stress affects immune cell biology and function, with a focus of discussion on UPR-associated immunopathology and the development of potential ER stress-targeted therapeutics. [ABSTRACT FROM AUTHOR]

In vitro gametogenesis (IVG) might offer numerous research and clinical benefits. Some potential clinical applications of IVG, such as allowing opposite‐sex couples experiencing infertility to have genetically related children, have attracted support. Others, such as enabling same‐sex reproduction and solo reproduction, have attracted significantly more criticism. In this paper, we examine how different ethical principles might help us to draw lines and distinguish between ethically desirable and undesirable uses of IVG. We discuss the alleged distinction between therapeutic and non‐therapeutic uses of assisted reproduction in the context of IVG, and show how it is both problematic to apply in practice and theoretically dubious. We then discuss how the ethical principles of reproductive justice and beneficence apply to IVG for opposite‐sex reproduction, same‐sex reproduction, and solo reproduction. We suggest that these principles generate strong reasons for the use of IVG for opposite‐sex and same‐sex reproduction, but not for solo reproduction. [ABSTRACT FROM AUTHOR]

The article offers information on the special section focused on the special topics in biophotonics, photoacoustic tomography and fiber-based lasers and supercontinuum sources. It mentions that in biophysics and biology, optical sensing and manipulation of cells are the important part of the basic cell function.

Microglia are brain resident immune cells with multiple functions. However, little is known about microglia-vascular interactions. In a recent paper published in Nature Communications, Bisht et al. identify a signalling mechanism that attracts and maintains microglia at the capillary wall. Moreover, they show that microglia regulate capillary vascular tone, playing a more significant role in blood flow regulation than previously thought. [ABSTRACT FROM AUTHOR]

Cell membranes are flexible and often undergo large-scale morphological changes during processes like mitosis, protrusion and retraction, or vesicle fusion. Mathematical modeling of cell membranes depends on a representation of the free-form surface by discrete meshes. During morphological changes, these meshes must be adjusted under the minimization of the total free energy. Current methodology for meshing is limited in one of two ways: 1) Free energy-dependent methods have no restriction on the mesh geometry. The resulting irregular meshes cause artifacts in follow-up models of morphodynamics. 2) Geometry-dependent methods maintain mesh quality but violate the physics of free energy minimization. To fill this gap, we regulate mesh geometries via a free-energy-determined remeshing process: adding and removing mesh elements upon morphological changes based on barrier crossings in a double-barrier potential between neighboring vertices in the meshes. We test the method's robustness by reproducing the morphodynamics of red blood cells and vesicle fusions; and we demonstrate the method's adaptability by simulating the formation of filopodia, lamellipodia and invaginations. Finally, we use the method to study a mechanical decoupling effect of two connected membrane tethers that has been recently observed experimentally, but has not been mechanistically explained in the context of a complete membrane surface. We propose a biophysical model that strengthens the decoupling effect and broadens the original interpretation of the experiment. The method is developed in C/Matlab and distributed via https://github.com/DanuserLab/biophysicsModels. Author summary: Many cellular functions require morphological features such as tubulations, protrusions, and invaginations. These features emerge from membranes reshaped by curvature-inducing proteins, osmotic pressure, and other mechanical factors. To elucidate these morphodynamics mathematical models describing the relation between morphology, mechanics, and molecular compoisition are indispensable. The key to such models is discretizing the membrane. One popular discretization relies on meshing membranes into fully connected triangles. When necessary, the mesh configuration is updated via remeshing operations. These include adjusting the number of meshes, rearranging the mesh-to-mesh connectivity, and keeping the individual triangles nearly equilateral. Such flexibility and geometry is necessary accuracy wise. Current remeshing algorithms lack geometrical consistency or rely on user-defined rules that defy physical laws. Here, we propose a new algorithm that marries the needs for geometrical and physical accuracy in a double-barrier potential Vin. The two barriers confine the edges in the triangles to ensure their geometrical consistency. Large enough mechanical perturbations cause barrier crossings that trigger remeshing to restore the perturbed geometry. This physics-based algorithm is robust and more efficient than rule-based algorithms. We implement the algorithm to simulate distinct morphologies and to examine how lipid diffusion controls the mechanical coupling of distant locations on the membrane. [ABSTRACT FROM AUTHOR]

Objectives: Type 1 diabetes mellitus (T1DM) is a well-known autoimmune disease, characterized by β-cell destruction in pancreas islet cells, which results insulin deficiency and subsequent hyperglycemic sequelae. While there is screening for type 2 DM that leads to better glycemic control and outcome, the majority of T1DM patients are diagnosed when much of the pancreatic cells and their function are disturbed. The aim of this article is to present an overview of the effective factors in the positivity of Glutamic acid decarboxylase antibody)GADA(and identifying the high-risk individuals for T1DM. Methods: We searched English literature available at National Library of Medicine via PubMed, and Google Scholar through December 2020. Finally, 79 papers have been included in the study. Studies were summarized based on the number of positive autoantibodies and onset of T1DM over time and GADA correlation with different variables. Conclusions: GADA is an easy marker to measure that can be detected many months prior to the clinical presentation and remains positive even after early childhood. [ABSTRACT FROM AUTHOR]

Information transmission in cells occurs quite accurately even when concentration changes are “read” by individual binding sites. In this paper we study ligand number and site occupancy fluctuations when ligands diffuse and react going beyond the analyses that focus on their asymptotic decay. In this way we show that, for immobile binding sites, fluctuations in the number of bound molecules decay on a relatively fast scale before the asymptotic behavior kicks in. This result can explain the observed co-existence of highly fluctuating instantaneous transcriptional activities with accumulated mRNA concentrations that have relatively small noise levels. We also show that the initial stages of the decay in the bound molecule number fluctuations have one or two characteristic timescales depending on the concentration of free molecules. This transition can explain the changes in enzyme activity observed at the single molecule level. [ABSTRACT FROM AUTHOR]

The interaction between the immune system and the tumor matrix has a huge impact on the progression and treatment of cancer. This paper summarizes and discusses the crosstalk between T cells and cancer-associated fibroblasts (CAFs). CAFs can also produce inhibitors that counteract the function of T cells and promote tumor immune escape, while T cells can also engage in complex two-way interactions with CAFs through direct cell contact, the exchange of soluble factors such as cytokines, and the remodeling of the extracellular matrix. Precise targeted intervention can effectively reverse tumor-promoting crosstalk between T cells and CAFs, improve anti-tumor immune response, and provide a new perspective for cancer treatment. Therefore, it is important to deeply understand the mechanism of crosstalk between T cells and CAFs. This review aims to outline the underlying mechanisms of these interactions and discuss potential therapeutic strategies that may become fundamental tools in the treatment of cancer, especially hard-to-cure cancers. • CAFs regulate T cell infiltration and function through multiple pathways. • T cells modulate CAF functions through feedback mechanisms. • Crosstalk between CAFs and T cells reveals potential therapeutic targets. [ABSTRACT FROM AUTHOR]

Dynamic properties are essential for microtubule (MT) physiology. Current techniques for in vivo imaging of MTs present intrinsic limitations in elucidating the isotype-specific nuances of tubulins, which contribute to their versatile functions. Harnessing the power of the AlphaFold2 pipeline, we engineered a strategy for the minimally invasive fluorescence labeling of endogenous tubulin isotypes or those harboring missense mutations. We demonstrated that a specifically designed 16-amino acid linker, coupled with sfGFP11 from the split-sfGFP system and integration into the H1-S2 loop of tubulin, facilitated tubulin labeling without compromising MT dynamics, embryonic development, or ciliogenesis in Caenorhabditis elegans. Extending this technique to human cells and murine oocytes, we visualized MTs with the minimal background fluorescence and a pathogenic tubulin isoform with fidelity. The utility of our approach across biological contexts and species set an additional paradigm for studying tubulin dynamics and functional specificity, with implications for understanding tubulin-related diseases known as tubulinopathies. GFP-tagged tubulins have been widely used to monitor and visualize tubulin isotypes, but this is known to interfere with their cellular functions. This study describes a functional labeling strategy, guided by AlphaFold2 structural predictions, to label endogenous tubulins across diverse species while preserving functionality. [ABSTRACT FROM AUTHOR]

Mitochondria are crucial organelles responsible for energy generation in eukaryotic cells. Oxidative stress, calcium disorders, and mitochondrial DNA abnormalities can all cause mitochondrial dysfunction. It is now well documented that mitochondrial dysfunction significantly contributes to the pathogenesis of numerous illnesses. Hence, it is vital to investigate innovative treatment methods targeting mitochondrial dysfunction. Extracellular vesicles (EVs) are cell-derived nanovesicles that serve as intercellular messengers and are classified into small EVs (sEVs, < 200 nm) and large EVs (lEVs, > 200 nm) based on their sizes. It is worth noting that certain subtypes of EVs are rich in mitochondrial components (even structurally intact mitochondria) and possess the ability to transfer them or other contents including proteins and nucleic acids to recipient cells to modulate their mitochondrial function. Specifically, EVs can modulate target cell mitochondrial homeostasis as well as mitochondria-controlled apoptosis and ROS generation by delivering relevant substances. In addition, the artificial modification of EVs as delivery carriers for therapeutic goods targeting mitochondria is also a current research hotspot. In this article, we will focus on the ability of EVs to modulate the mitochondrial function of target cells, aiming to offer novel perspectives on therapeutic approaches for diverse conditions linked to mitochondrial dysfunction. [ABSTRACT FROM AUTHOR]

The Synaptotagmin-like mitochondrial-lipid binding protein (SMP) domain is found in a group of ER-resident lipid transfer proteins that are recruited to membrane contact sites (MCSs) by adaptors. Deciphering the molecular basis underlying the recruitment of SMP proteins to specific MCS sheds light not only on their cellular localization but also on their biological functions at these sites. Here we summarize recent advances in SMP domain-containing lipid transfer proteins, focusing on a recent study showing the localization, regulation and cellular function of a specific SMP protein named testis expressed protein 2 (Tex2). TMEM55, a potential PIP phosphatase on late endosome/lysosomal (LE/lys) membranes, was identified as an adaptor that enables the recruitment of Tex2 to ER- LE/lys MCS. In addition, we have summarized several important questions about the regulation and physiological functions of Tex2 that remained unanswered. [ABSTRACT FROM AUTHOR]

The article gives a brief description of geroprotection and rejuvenation methods known to date, presenting their main mechanisms and limitations. To overcome the main limitations of the process of rejuvenation, it is possible to use a process called "cell autocloning." The principle of the proposed method of rejuvenation is as follows: a periodic process of autocloning of the cell nucleus is initiated in the cellular genome with the formation of one unstable daughter copy and its subsequent self-elimination. In this case, the process of cell division stops in the phase of nuclei divergence without subsequent physical separation of the cell itself. This is especially important for postmitotic cells, where the looping of the "unidirectional" line of the ontogenesis program into a "ring" will mean their transition into renewable cells. The prototype for autocloning mechanisms could be the already known ways in which cells adapt to the increasing amount of their damage over time. These are polyploidy and asymmetric cell division, relying on which it is possible to obtain a renewable process of cell nuclei division, when only the original nucleus remains as a result of division. Although this is not a simple task, there are possible pathways to its solution using approaches that can suggest modern knowledge from the field of molecular and cell biology and genetics. The realization of such a goal will require a lot of work, but the expected result justifies it. [ABSTRACT FROM AUTHOR]

One of the main drivers of autism spectrum disorder is risk alleles within hundreds of genes, which may interact within shared but unknown protein complexes. Here we develop a scalable genome-editing-mediated approach to target 14 high-confidence autism risk genes within the mouse brain for proximity-based endogenous proteomics, achieving the identification of high-specificity spatial proteomes. The resulting native proximity proteomes are enriched for human genes dysregulated in the brain of autistic individuals, and reveal proximity interactions between proteins from high-confidence risk genes with those of lower-confidence that may provide new avenues to prioritize genetic risk. Importantly, the datasets are enriched for shared cellular functions and genetic interactions that may underlie the condition. We test this notion by spatial proteomics and CRISPR-based regulation of expression in two autism models, demonstrating functional interactions that modulate mechanisms of their dysregulation. Together, these results reveal native proteome networks in vivo relevant to autism, providing new inroads for understanding and manipulating the cellular drivers underpinning its etiology. Protein interactions are essential for neural signaling and often perturbed in brain conditions. Here, the authors developed a CRISPR-based chemical-genetic approach to identify endogenous proximity proteomes that inform mechanism and phenotypic rescue strategies in mouse models of autism. [ABSTRACT FROM AUTHOR]

Measurement of cellular resting membrane potential (RMP) is important in understanding ion channels and their role in regulation of cell function across a wide range of cell types. However, methods available for the measurement of RMP (including patch clamp, microelectrodes, and potential-sensitive fluorophores) are expensive, slow, open to operator bias, and often result in cell destruction. We present non-contact, label-free membrane potential estimation which uses dielectrophoresis to determine the cytoplasm conductivity slope as a function of medium conductivity. By comparing this to patch clamp data available in the literature, we have demonstratet the accuracy of this approach using seven different cell types, including primary suspension cells (red blood cells, platelets), cultured suspension cells (THP-1), primary adherent cells (chondrocytes, human umbilical mesenchymal stem cells), and adherent (HeLa) and suspension (Jurkat) cancer cell lines. Analysis of the effect of ion channel inhibitors suggests the effects of pharmaceutical agents (TEA on HeLa; DMSO and neuraminidase on red blood cells) can also be measured. Comparison with published values of membrane potential suggest that the differences between our estimates and values recorded by patch clamp are accurate to within published margins of error. The method is low-cost, non-destructive, operator-independent and label-free, and has previously been shown to allow cells to be recovered after measurement. [ABSTRACT FROM AUTHOR]

Development of resistance and tolerance to antifungal drugs in Candida albicans can compromise treatment of infections caused by this pathogenic yeast species. The uniquely expanded C. albicans TLO gene family is comprised of 14 paralogous genes which encode Med2, a subunit of the multiprotein Mediator complex which is involved in the global control of transcription. This study investigates the acquisition of fluconazole tolerance in a mutant in which the entire TLO gene family has been deleted. This phenotype was reversed to varying degrees upon reintroduction of representative members of the alpha- and beta-TLO clades (i.e. TLO1 and TLO2), but not by TLO11, a gamma-clade representative. Comparative RNA sequencing analysis revealed changes in the expression of genes involved in a range of cellular functions, including ergosterol biosynthesis, mitochondrial function, and redox homeostasis. This was supported by the results of mass spectrometry analysis, which revealed alterations in sterol composition of the mutant cell membrane. Our data suggest that members of the C. albicans TLO gene family are involved in the control of ergosterol biosynthesis and mitochondrial function and may play a role in the responses of C. albicans to azole antifungal agents. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are 18–25 nucleotides long, single-stranded, non-coding RNA molecules that regulate gene expression. They play a crucial role in maintaining normal cellular functions and homeostasis in organisms. Studies have shown that miR-124-3p is highly expressed in brain tissue and plays a significant role in nervous system development. It is also described as a tumor suppressor, regulating biological processes like cancer cell proliferation, apoptosis, migration, and invasion by controlling multiple downstream target genes. miR-124-3p has been found to be involved in the progression of various kidney diseases, including diabetic kidney disease, calcium oxalate kidney stones, acute kidney injury, lupus nephritis, and renal interstitial fibrosis. It mediates these processes through mechanisms like oxidative stress, inflammation, autophagy, and ferroptosis. To lay the foundation for future therapeutic strategies, this research group reviewed recent studies on the functional roles of miR-124-3p in renal diseases and the regulation of its downstream target genes. Additionally, the feasibility, limitations, and potential application of miR-124-3p as a diagnostic biomarker and therapeutic target were thoroughly investigated. [ABSTRACT FROM AUTHOR]

Signal processing by intracellular kinases controls near all biological processes but how signal pathway functions evolve with changed cellular context is poorly understood. Functional specificity of c-Jun N-terminal Kinases (JNK) are partly encoded by signal strength. Here we reveal that intracellular pH (pHi) is a significant component of the JNK network and defines signal response to specific stimuli. We show pHi regulates JNK activity in response to cell stress, with the relationship between pHi and JNK activity dependent on specific stimuli and upstream kinases activated. Using the optogenetic clustering tag CRY2, we show that an increase in pHi promotes the light-induced phase transition of ASK1 to augment JNK activation. While increased pHi similarly promoted CRY2-tagged JNK2 to form light-induced condensates, this attenuated JNK activity. Mathematical modelling of feedback signalling incorporating pHi and differential contributions by ASK1 and JNK2 condensates was sufficient to delineate signal responses to specific stimuli. Taking pHi and ASK1/JNK2 signal contributions into consideration may delineate oncogenic versus tumour suppressive JNK functions and cancer cell drug responses. The transduction of signals by c-Jun N-terminal kinases (JNK) is highly contextual and has diverse cell functions. Here, the authors reveal tiered kinases in the JNK pathway are regulated by intracellular pH with changed signaling outcomes. [ABSTRACT FROM AUTHOR]

Accurate chromosome segregation during cell division relies on coordinated actions of microtubule (MT)-based motor proteins in the mitotic spindle. Kinesin-14 motors play vital roles in spindle assembly and maintenance by crosslinking antiparallel MTs at the spindle midzone and anchoring spindle MTs' minus ends at the poles. In this study, we investigate the force generation and motility of the Kinesin-14 motors HSET and KlpA. Our findings reveal that both motors are non-processive, producing single load-dependent power strokes per MT encounter, with estimated load-free power strokes of ~30 and ~35 nm, respectively. Each homodimeric motor generates forces of ~0.5 pN, but when assembled in teams, they cooperate to generate forces of 1 pN or more. Notably, the cooperative activity among multiple motors leads to increased MT-sliding velocities. These results quantitatively elucidate the structure-function relationship of Kinesin-14 motors and underscore the significance of cooperative behavior in their cellular functions. This study reveals that Kinesin14 motors, HSET and KlpA, generate single load-dependent power strokes, producing forces of ~0.5 pN each. When working in teams, these motors achieve forces of 1 pN or more, enhancing MT-sliding velocities and highlighting their cooperative behaviour in cell division. [ABSTRACT FROM AUTHOR]

Simple Summary: Cancer is a difficult-to-cure disease with high worldwide incidence and mortality. Among the many changes observed in cancer cells and patient samples is altered glycosylation, a commonly observed modification of biomolecules such as proteins. These glycan structures can dictate protein function, and dysregulation of glycosylation can contribute to tumor migration and metastasis. Thus, manipulation of glycosylation states may be a novel approach to cancer treatment. One target of the well-known tumor suppressor p53 is FUCA1, encoding alpha-L-fucosidase, which plays a role in glycosylation, although the exact mechanism linking FUCA1 to cancer is unclear. Investigation into these glycosylation processes and the mechanisms linking the p53-FUCA1 axis to cancer development may provide new insights into this disease and suggest new drug targets for cancer therapies. Cancer is a difficult-to-cure disease with high worldwide incidence and mortality, in large part due to drug resistance and disease relapse. Glycosylation, which is a common modification of cellular biomolecules, was discovered decades ago and has been of interest in cancer research due to its ability to influence cellular function and to promote carcinogenesis. A variety of glycosylation types and structures regulate the function of biomolecules and are potential targets for investigating and treating cancer. The link between glycosylation and carcinogenesis has been more recently revealed by the role of p53 in energy metabolism, including the p53 target gene alpha-L-fucosidase 1 (FUCA1), which plays an essential role in fucosylation. In this review, we summarize roles of glycan structures and glycosylation-related enzymes to cancer development. The interplay between glycosylation and tumor microenvironmental factors is also discussed, together with involvement of glycosylation in well-characterized cancer-promoting mechanisms, such as the epidermal growth factor receptor (EGFR), phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) and p53-mediated pathways. Glycan structures also modulate cell–matrix interactions, cell–cell adhesion as well as cell migration and settlement, dysfunction of which can contribute to cancer. Thus, further investigation of the mechanistic relationships among glycosylation, related enzymes and cancer progression may provide insights into potential novel cancer treatments. [ABSTRACT FROM AUTHOR]

Simple Summary: Aquaporins (AQPs) have emerged as potential predictors of response to cancer therapy and as targets for increasing sensitivity to treatment. However, systemic therapeutic inhibition using pan-AQP or AQP-specific inhibitors has not been characterized for efficacy in treating breast cancer or as a component of combination treatment. We evaluated AQP inhibition using established AQP inhibitors in cytotoxicity and pharmacologic assays. This study identified AQPs as a targetable vulnerability in breast cancer. AQP inhibitors can increase therapeutic efficacy, both as single agents and in a combination therapy strategy, in treating breast cancer progression and metastasis. These results provide significant insights that support the future development of improved AQP inhibitors. AQPs contribute to breast cancer progression and metastasis. We previously found that genetic inhibition of Aqp7 reduces primary tumor burden and metastasis in breast cancer. In this study, we utilized two AQP inhibitors, Auphen and Z433927330, to evaluate the efficacy of therapeutic inhibition of AQPs in breast cancer treatment. The inhibitors were evaluated in breast cancer for both cytotoxicity and metabolic stability assays across both murine and human breast cancer cell lines. Both AQP inhibitors also affected the expression of other AQP transcripts and proteins, which demonstrates compensatory regulation between AQP family members. As a single agent, Auphen treatment in vivo extended overall survival but did not impact primary or metastatic tumor burden. However, Auphen treatment made cells more responsive to chemotherapy (doxorubicin) or endocrine treatment (tamoxifen, fulvestrant). In fact, treatment with Tamoxifen reduced overall AQP7 protein expression. RNA-seq of breast cancer cells treated with Auphen identified mitochondrial metabolism genes as impacted by Auphen and may contribute to reducing mammary tumor progression, lung metastasis, and increased therapeutic efficacy of endocrine therapy in breast cancer. Interestingly, we found that Auphen and tamoxifen cooperate to reduce breast cancer cell viability, which suggests that Auphen treatment makes the cells more susceptible to Tamoxifen. Together, this study highlights AQPs as therapeutic vulnerabilities of breast cancer metastasis that are promising and should be exploited. However, the pharmacologic results suggest additional chemical refinements and optimization of AQP inhibition are needed to make these AQP inhibitors appropriate to use for therapeutic benefit in overcoming endocrine therapy resistance. [ABSTRACT FROM AUTHOR]

The endosomal sorting complex required for transport (ESCRT) machinery is composed of an articulated architecture of proteins that assemble at multiple cellular sites. The ESCRT machinery is involved in pathways that are pivotal for the physiology of the cell, including vesicle transport, cell division, and membrane repair. The subunits of the ESCRT I complex are mainly responsible for anchoring the machinery to the action site. The ESCRT II subunits function to bridge and recruit the ESCRT III subunits. The latter are responsible for finalizing operations that, independently of the action site, involve the repair and fusion of membrane edges. In this review, we report on the data related to the activity of the ESCRT machinery at two sites: the nuclear membrane and the midbody and the bridge linking cells in the final stages of cytokinesis. In these contexts, the machinery plays a significant role for the protection of genome integrity by contributing to the control of the abscission checkpoint and to nuclear envelope reorganization and correlated resilience. Consistently, several studies show how the dysfunction of the ESCRT machinery causes genome damage and is a codriver of pathologies, such as laminopathies and cancer. [ABSTRACT FROM AUTHOR]

The skin is considered the most important organ system in mammals, and as the population ages, it is important to consider skin aging and anti-aging therapeutic strategies. Exposure of the skin to various insults induces significant changes throughout our lives, differentiating the skin of a young adult from that of an older adult. These changes are caused by a combination of intrinsic and extrinsic aging. We report the interactions between skin aging and its metabolism, showing that the network is due to several factors. For example, iron is an important nutrient for humans, but its level increases with aging, inducing deleterious effects on cellular functions. Recently, it was discovered that ferroptosis, or iron-dependent cell death, is linked to aging and skin diseases. The pursuit of new molecular targets for ferroptosis has recently attracted attention. Prevention of ferroptosis is an effective therapeutic strategy for the treatment of diseases, especially in old age. However, the pathological and biological mechanisms underlying ferroptosis are still not fully understood, especially in skin diseases such as melanoma and autoimmune diseases. Only a few basic studies on regulated cell death exist, and the challenge is to turn the studies into clinical applications. [ABSTRACT FROM AUTHOR]

In multicellular organisms, stem cells are impacted by microenvironmental resources such as nutrient availability and oxygen tension for their survival, growth, and differentiation. However, the accessibility of these resources in the pericellular environment greatly varies from organ to organ. This divergence in resource availability leads to variations in the potency and differentiation potential of stem cells. This study aimed to explore the distinct effects of glucose and fructose, as well as different oxygen tensions, on the growth dynamics, cytokine production, and differentiation of stem cells. We showed that replacing glucose with fructose subjected stem cells to stress, resulting in increased Hif1α expression and stability, which in turn led to a reduction in cell proliferation, and alterations in cytokine production. However, fructose failed to induce differentiation of human mesenchymal stem cells (hMSCs) as well as mouse fibroblasts into mature adipocytes compared to glucose, despite the upregulation of key markers of adipogenesis, including C/EBPβ, and PPARγ. Conversely, we showed that fructose induced undifferentiated mouse fibroblasts to release cytokines associated with senescence, including IL1α1, IL6, IL8, MCP1, and TNF1α, suggesting that these cells were undergoing lipolysis. Taken together, our results suggest that altering the culture conditions through changes in hexose levels and oxygen tension places considerable stress on stem cells. Additional research is required to further characterize the mechanisms governing stem cell response to their microenvironments. [ABSTRACT FROM AUTHOR]

Background Patients with intrahepatic cholangiocarcinoma (ICC) are prone to recurrence and poor survival. Targeted therapy related to isocitrate dehydrogenase (IDH) is an extremely important treatment. IDH1 and IDH2 mutations are generally thought to have similar effects on the tumor landscape. However, it is doubtful whether these 2 mutations have exactly the same effects on tumor cells and the tumor microenvironment. Methods All collected tumor samples were subjected to simultaneous whole-exon sequencing and proteome sequencing. Results IDH1 mutations accounted for 12.2%, and IDH2 mutations accounted for 5.5%, all missense mutations. Tumors with IDH mutations had lower proportions of KRAS and TP53 mutations. Mutated genes were obviously enriched in the kinase pathway in the tumors with IDH2 mutations. The signaling pathways were mainly enriched in the activation of cellular metabolic activities and an increase of inhibitory immune cells in the tumors with IDH mutations. Moreover, tumors had unique enrichment in DNA repair in IDH1 mutants and secretion of biological molecules in IDH2 mutants. Inhibitory immune cells might be more prominent in IDH2 mutants, and the expression of immune checkpoints PVR and HLA-DQB1 was more prominent in IDH1 mutants. IDH mutants were more related to metabolism-related and inflammation-immune response clusters, and some belonged to the DNA replication and repair cluster. Conclusions These results revealed the differential IDH1 and IDH2 mutation-related landscapes, and we have provided an important reference database to guide ICC treatment. [ABSTRACT FROM AUTHOR]

Serotonin reuptake inhibitor antidepressants such as fluoxetine are widely used to treat mood disorders. The mechanisms of action include an increase in extracellular level of serotonin, neurogenesis, and growth of vessels in the brain. We investigated whether fluoxetine could have broader peripheral regenerative properties. Following prolonged administration of fluoxetine in male mice, we showed that fluoxetine increases the number of muscle stem cells and muscle angiogenesis, associated with positive changes in skeletal muscle function. Fluoxetine also improved skeletal muscle regeneration after single and multiples injuries with an increased muscle stem cells pool and vessel density associated with reduced fibrotic lesions and inflammation. Mice devoid of peripheral serotonin treated with fluoxetine did not exhibit beneficial effects during muscle regeneration. Specifically, pharmacological, and genetic inactivation of the 5-HT1B subtype serotonin receptor also abolished the enhanced regenerative process induced by fluoxetine. We highlight here a regenerative property of serotonin on skeletal muscle. Fluoxetine is a serotonin reuptake inhibitor antidepressant. Here, the authors demonstrate the that fluoxetine can trigger muscle regeneration in male mice by acting on muscle stem cells, vascularization, and inflammation, resulting in faster muscle healing. [ABSTRACT FROM AUTHOR]