Protocol for observing lipid droplet dynamics in chicken cone cells.

Chicken cone cells are an excellent model for studying the regulation of lipid droplet dynamics. Here, we present a protocol for studying cone cell lipid droplets from in vivo and ex vitro cultured retinas of chicken embryos. We describe steps for dissecting chicken retinas, electroporating retinas, culturing retinas ex vivo and in vitro, and staining lipid droplets with neutral lipid dye. This protocol is also applicable to investigating other organelles in retinas. For complete details on the use and execution of this protocol, please refer to Pan et al.1.

Global prevalence of Borrelia burgdorferi and Anaplasma phagocytophilum coinfection in Ixodes tick populations: protocol for a systematic review and meta-analysis.

INTRODUCTION: Ixodes ticks are pivotal in transmitting diseases like Lyme disease and human granulocytic anaplasmosis, caused by Borrelia burgdorferi and Anaplasma phagocytophilum, respectively. These pathogens not only affect humans through single or multiple tick bites but also pose risks to animal hosts, leading to potential coinfections. Despite regional studies indicating significant prevalence, their global coinfection data remain sparse. This study aims to bridge this gap through a systematic review and meta-analysis of B. burgdorferi and A. phagocytophilum coinfections in Ixodes ticks worldwide. Addressing data limitations and study variability, it seeks to provide a nuanced understanding of coinfection patterns, their epidemiological implications and inform targeted prevention strategies. METHODS AND ANALYSIS: Following Preferred Reporting Items for Systematic Review and Meta-analysis Protocols 2015 guidelines and PROSPERO registration, this study will undertake a thorough database search without constraints on language or publication date, using standardised screening and data extraction protocols. The quality and bias of studies will be evaluated using Joanna Briggs Institute tools. In the statistical analysis phase, conducted in R, we will initially determine the use of fixed or random-effects models based on the assessment of data heterogeneity. This choice will guide the framework for subsequent analyses. Within the selected model's framework, we will perform subgroup analyses and meta-regression to investigate the effects of various factors, ensuring that each step is tailored to the initial model selection to maintain analytical consistency. ETHICS AND DISSEMINATION: As this study does not involve clinical research or data collection from subjects, ethical approval is not required. We will uphold ethical standards in synthesising and reporting data. Study outcomes will be published in peer-reviewed journals, communicating findings to the scientific community and contributing to the understanding of Ixodes tickborne diseases. PROSPERO REGISTRATION NUMBER: CRD42023449735.

Natural background levels, source apportionment and health risks of potentially toxic elements in groundwater of highly urbanized area.

Identifying the natural background levels (NBLs), threshold values (TVs), sources and health risks of potentially toxic elements in groundwater is crucial for ensuring the water security of residents in highly urbanized areas. In this study, 96 groundwater samples were collected in urban area of Sichuan Basin, SW China. The concentrations of potentially toxic elements (Li, Fe, Cu, Zn, Al, Pb, B, Ba and Ni) were analyzed for investigating the NBLs, TVs, sources and health risks. The potentially toxic elements followed the concentration order of Fe > Ba > B > Al > Zn > Li > Cu > Ni > Pb. The NBLs and TVs indicated the contamination of potentially toxic elements mainly occurred in the northern and central parts of the study area. The Positive Matrix Factorization (PMF) model identified elevated concentrations of Fe, Al, Li, and B were found to determine groundwater quality. The primary sources of Fe, Al, Pb, and Ni were attributed to the dissolution of oxidation products, with Fe additionally affected by anthropogenic reduction environments. Li and B were determined to be originated from the weathering of tourmaline. High levels of Ni and Cu concentrations were derived from electronic waste leakage, while excessive Ba and Zn were linked to factory emissions and tire wear. The reasonable maximum exposure (RME) of hazard index (HI) was higher than safety standard and reveal the potential health risks in the southwestern study area. Sensitivity analysis demonstrated the Li concentrations possessed the highest weight contributing to health risk. This study provides a valuable information for source-specific risk assessments of potentially toxic elements in groundwater associated with urban areas.

Groundwater suitability assessment for irrigation and drinking purposes by integrating spatial analysis, machine learning, water quality index, and health risk model.

An in-depth understanding of nitrate-contaminated surface water and groundwater quality and associated risks is important for groundwater management. Hydrochemical characteristics and driving forces of groundwater quality and non-carcinogenic risks of nitrate were revealed by the integrated approaches of self-organizing map analysis, spatial visualization by geography information system, entropy and irrigation water quality indices, and human health risk model. Groundwater samples were categorized into two clusters by SOM analysis. Cluster I including three samples were Ca-SO4 type and cluster II of remaining 136 samples were Ca-HCO3 type. Hydrochemical compositions of two cluster samples were dominated by water-rock interaction: (1) calcite and gypsum dissolution for cluster I samples and (2) calcite dissolution, silicate weathering, and positive cation exchange for cluster II samples. Nitrate contamination occurred in both cluster I and II samples, primarily induced by agricultural nitrogen fertilizer. The EWQI results showed that 90.97% in total groundwater samples were suitable for drinking purpose, while the IWQI results demonstrated that 65.03% in total groundwater samples were appropriate for irrigation purpose. The HHR model and Monte Carlo simulation indicated that the non-carcinogenic nitrated risk was highest in children. Exposure frequency was the most sensitive factor (86.33% in total) influencing the total non-carcinogenic risk, indicated by sensitivity analysis. Compared with the two clusters of groundwater, surface water has a shorter circulation cycle and lower ion concentrations resulting in better water quality. This study can provide scientific basis for groundwater quality evaluation in other parts of the world.

An open auscultation dataset for machine learning-based respiratory diagnosis studies.

Machine learning enabled auscultating diagnosis can provide promising solutions especially for prescreening purposes. The bottleneck for its potential success is that high-quality datasets for training are still scarce. An open auscultation dataset that consists of samples and annotations from patients and healthy individuals is established in this work for the respiratory diagnosis studies with machine learning, which is of both scientific importance and practical potential. A machine learning approach is examined to showcase the use of this new dataset for lung sound classifications with different diseases. The open dataset is available to the public online.

Postoperative leukocyte counts as a surrogate for surgical stress response in matched robot- and video-assisted thoracoscopic surgery cohorts of patients: A preliminary report.

The objective is to preliminary evaluated postoperative leukocyte counts as a surrogate for the surgical stress response in NSCLC patients who underwent RATS or VATS for further prospective analyses with proper assessment of surgical stress response and tissue trauma. We retrospectively analyzed patients with stageI-IIIA NSCLC who underwent RATS or VATS at a hospital between 8 May 2020 and 31 December 2021. Analysis of leukocytes (including neutrophils and lymphocytes) and albumin on postoperative days (PODs) 1 and 3 in patients with NSCLC treated with RATS or VATS after propensity score matching (PSM). In total, 1824 patients (565 RATS and 1259 VATS) were investigated. The two MIS groups differed significantly with regard to operative time (p < 0.001), chronic lung disease (p < 0.001), the type of pulmonary resection (p < 0.001), the excision site of lobectomy (p = 0.004), and histology of the tumor (p = 0.028). After PSM, leukocyte and neutrophil levels in the RATS group were lower than those in the VATS group on PODs 1 and 3, with those on POD 3 (p < 0.001) being particularly notable. While lymphocyte levels in the RATS group were significantly lower than those in the VATS group only at POD 1 (p = 0.016). There was no difference in albumin levels between the RATS and VATS groups on PODs 1 and 3. The surgical stress response and tissue trauma was less severe in NSCLC patients who underwent RATS than in those who underwent VATS, especially reflected in the neutrophils of leukocytes.

Structure-based discovery of a new series of nucleoside-derived ring-opening PRMT5 inhibitors.

The ubiquitous methyltransferases employing SAM as the methyl donor have emerged as potential targets in many disease treatments, especially in anticancer. Therefore, developing SAM-competitive inhibitors of methyltransferases is of great interest to the drug research. To explore this direction, herein, we rationally designed a series of nucleoside derivatives as potent PRMT5 inhibitors with novel scaffold. The representative compounds A2 and A8 exhibited highly potent PRMT5 inhibition activity as well as good selectivity over other PRMTs and PKMTs. Further cellular experiments revealed that compounds A2 and A8 potently reduced the level of sDMA and inhibited the proliferation of Z-138 and MOLM-13 cell lines by inducing apoptosis. Moreover, compounds A8 which had favorable pharmacokinetic properties exhibited potent antitumor efficacy without the loss of body weight in a subcutaneous MOLM-13 xenograft model. In summary, our efforts provided a series of novel nucleoside analogs as potent PRMT5 inhibitors and may also offer a new strategy to develop SAM analogs as other methyltransferases' inhibitors.

Discovery of Novel PROTAC Degraders of p300/CBP as Potential Therapeutics for Hepatocellular Carcinoma.

Adenoviral E1A binding protein 300 kDa (p300) and its closely related paralog CREB binding protein (CBP) are promising therapeutic targets for human cancer. Here, we report the first discovery of novel potent small-molecule PROTAC degraders of p300/CBP against hepatocellular carcinoma (HCC), one of the most common solid tumors. Based upon the clinical p300/CBP bromodomain inhibitor CCS1477, a conformational restriction strategy was used to optimize the linker to generate a series of PROTACs, culminating in the identification of QC-182. This compound effectively induces p300/CBP degradation in the SK-HEP-1 HCC cells in a dose-, time-, and ubiquitin-proteasome system-dependent manner. QC-182 significantly downregulates p300/CBP-associated transcriptome in HCC cells, leading to more potent cell growth inhibition compared to the parental inhibitors and the reported degrader dCBP-1. Notably, QC-182 potently depletes p300/CBP proteins in mouse SK-HEP-1 xenograft tumor tissue. QC-182 is a promising lead compound toward the development of p300/CBP-targeted HCC therapy.

Type 2 cytokine signaling in macrophages protects from cellular senescence and organismal aging.

Accumulation of senescent cells in organs and tissues is a hallmark of aging and known to contribute to age-related diseases. Although aging-associated immune dysfunction, or immunosenescence, is known to contribute to this process, the underlying mechanism remains elusive. Here, we report that type 2 cytokine signaling deficiency accelerated aging and, conversely, that the interleukin-4 (IL-4)-STAT6 pathway protected macrophages from senescence. Mechanistically, activated STAT6 promoted the expression of genes involved in DNA repair both via homologous recombination and Fanconi anemia pathways. Conversely, STAT6 deficiency induced release of nuclear DNA into the cytoplasm to promote tissue inflammation and organismal aging. Importantly, we demonstrate that IL-4 treatment prevented macrophage senescence and improved the health span of aged mice to an extent comparable to senolytic treatment, with further additive effects when combined. Together, our findings support that type 2 cytokine signaling protects macrophages from immunosenescence and thus hold therapeutic potential for improving healthy aging.

Stay in touch with the endoplasmic reticulum.

The endoplasmic reticulum (ER), which is composed of a continuous network of tubules and sheets, forms the most widely distributed membrane system in eukaryotic cells. As a result, it engages a variety of organelles by establishing membrane contact sites (MCSs). These contacts regulate organelle positioning and remodeling, including fusion and fission, facilitate precise lipid exchange, and couple vital signaling events. Here, we systematically review recent advances and converging themes on ER-involved organellar contact. The molecular basis, cellular influence, and potential physiological functions for ER/nuclear envelope contacts with mitochondria, Golgi, endosomes, lysosomes, lipid droplets, autophagosomes, and plasma membrane are summarized.

Discovery of a PROTAC degrader for METTL3-METTL14 complex.

N6-methyladenosine (m6A) methylation is the most abundant type of RNA modification that is mainly catalyzed by the METTL3-METTL14 methyltransferase complex. This complex has been linked to multiple cancers and is considered a promising therapeutic target for acute myeloid leukemia (AML). However, only a few METTL3 inhibitors targeting the catalytic activity were developed recently. Here, we present the discovery of WD6305 as the potent and selective proteolysis-targeting chimera (PROTAC) degrader of METTL3-METTL14 complex. WD6305 suppresses m6A modification and the proliferation of AML cells, and promotes apoptosis much more effectively than its parent inhibitor. WD6305 also affects a variety of signaling pathways related to the development and proliferation of AML. Collectively, our study reveals PROTAC degradation of METTL3-METTL14 complex as a potential anti-leukemic strategy and provides desirable chemical tool for further understanding METTL3-METTL14 protein functions.

Electrochemical Oxidation of Furfural on NiMoP/NF: Boosting Current Density with Enhanced Adsorption of Oxygenates.

Substituting the low-value oxygen evolution reaction (OER) with thermodynamically more favored organic oxidation such as furfural oxidation reaction (FOR) is regarded as a perspective approach to decrease energy cost of hydrogen evolution from water splitting. However, the kinetic of FOR can be even more sluggish than OER under large current density. In this work, a strategy is proposed to accelerate FOR by enhancing the adsorption of oxygenates on active sites. Over the prepared NiMoP/NF anode, only 1.46 V versus RHE is required in furfural solution to achieve 500 mA cm-2 , significantly better than the OER activity over commercial RuO2 /NF under the same current density (1.57 V vs RHE).

Impaired dNKAP function drives genome instability and tumorigenic growth in Drosophila epithelia.

Mutations or dysregulated expression of NF-kappaB activating protein (NKAP) family genes have been found in human cancers. How NKAP family gene mutations promote tumor initiation and progression remains to be determined. Here, we characterized dNKAP, the Drosophila homolog of NKAP, and showed that impaired dNKAP function causes genome instability and tumorigenic growth in a Drosophila epithelial tumor model. dNKAP-knockdown wing imaginal discs exhibit tumorigenic characteristics, including tissue overgrowth, cell invasive behavior, abnormal cell polarity, and cell adhesion defects. dNKAP knockdown causes both R-loop accumulation and DNA damage, indicating the disruption of genome integrity. Further analysis showed that dNKAP knockdown induces c-Jun N-terminal kinase (JNK)-dependent apoptosis and causes changes in cell proliferation in distinct cell populations. Activation of the Notch and JAK/STAT signaling pathways contributes to the tumorigenic growth of dNKAP-knockdown tissues. Furthermore, JNK signaling is essential for dNKAP depletion-mediated cell invasion. Transcriptome analysis of dNKAP-knockdown tissues confirmed the misregulation of signaling pathways involved in promoting tumorigenesis and revealed abnormal regulation of metabolic pathways. dNKAP knockdown and oncogenic Ras, Notch, or Yki mutations show synergies in driving tumorigenesis, further supporting the tumor-suppressive role of dNKAP. In summary, this study demonstrates that dNKAP plays a tumor-suppressive role by preventing genome instability in Drosophila epithelia and thus provides novel insights into the roles of human NKAP family genes in tumor initiation and progression.

Tri©DB: an integrated platform of knowledgebase and reporting system for cancer precision medicine.

BACKGROUND: With the development of cancer precision medicine, a huge amount of high-dimensional cancer information has rapidly accumulated regarding gene alterations, diseases, therapeutic interventions and various annotations. The information is highly fragmented across multiple different sources, making it highly challenging to effectively utilize and exchange the information. Therefore, it is essential to create a resource platform containing well-aggregated, carefully mined, and easily accessible data for effective knowledge sharing. METHODS: In this study, we have developed "Consensus Cancer Core" (Tri©DB), a new integrative cancer precision medicine knowledgebase and reporting system by mining and harmonizing multifaceted cancer data sources, and presenting them in a centralized platform with enhanced functionalities for accessibility, annotation and analysis. RESULTS: The knowledgebase provides the currently most comprehensive information on cancer precision medicine covering more than 40 annotation entities, many of which are novel and have never been explored previously. Tri©DB offers several unique features: (i) harmonizing the cancer-related information from more than 30 data sources into one integrative platform for easy access; (ii) utilizing a variety of data analysis and graphical tools for enhanced user interaction with the high-dimensional data; (iii) containing a newly developed reporting system for automated annotation and therapy matching for external patient genomic data. Benchmark test indicated that Tri©DB is able to annotate 46% more treatments than two officially recognized resources, oncoKB and MCG. Tri©DB was further shown to have achieved 94.9% concordance with administered treatments in a real clinical trial. CONCLUSIONS: The novel features and rich functionalities of the new platform will facilitate full access to cancer precision medicine data in one single platform and accommodate the needs of a broad range of researchers not only in translational medicine, but also in basic biomedical research. We believe that it will help to promote knowledge sharing in cancer precision medicine. Tri©DB is freely available at www.biomeddb.org , and is hosted on a cutting-edge technology architecture supporting all major browsers and mobile handsets.

Transcriptional repression of beige fat innervation via a YAP/TAZ-S100B axis.

Sympathetic innervation is essential for the development of functional beige fat that maintains body temperature and metabolic homeostasis, yet the molecular mechanisms controlling this innervation remain largely unknown. Here, we show that adipocyte YAP/TAZ inhibit sympathetic innervation of beige fat by transcriptional repression of neurotropic factor S100B. Adipocyte-specific loss of Yap/Taz induces S100b expression to stimulate sympathetic innervation and biogenesis of functional beige fat both in subcutaneous white adipose tissue (WAT) and browning-resistant visceral WAT. Mechanistically, YAP/TAZ compete with C/EBPß for binding to the zinc finger-2 domain of PRDM16 to suppress S100b transcription, which is released by adrenergic-stimulated YAP/TAZ phosphorylation and inactivation. Importantly, Yap/Taz loss in adipocytes or AAV-S100B overexpression in visceral WAT restricts both age-associated and diet-induced obesity, and improves metabolic homeostasis by enhancing energy expenditure of mice. Together, our data reveal that YAP/TAZ act as a brake on the beige fat innervation by blocking PRDM16-C/EBPß-mediated S100b expression.

Metabolic plasticity sustains the robustness of Caenorhabditis elegans embryogenesis.

Embryogenesis is highly dependent on maternally loaded materials, particularly those used for energy production. Different environmental conditions and genetic backgrounds shape embryogenesis. The robustness of embryogenesis in response to extrinsic and intrinsic changes remains incompletely understood. By analyzing the levels of two major nutrients, glycogen and neutral lipids, we discovered stage-dependent usage of these two nutrients along with mitochondrial morphology changes during Caenorhabditis elegans embryogenesis. ATGL, the rate-limiting lipase in cellular lipolysis, is expressed and required in the hypodermis to regulate mitochondrial function and support embryogenesis. The embryonic lethality of atgl-1 mutants can be suppressed by reducing sinh-1/age-1-akt signaling, likely through modulating glucose metabolism to maintain sustainable glucose consumption. The embryonic lethality of atgl-1(xd314) is also affected by parental nutrition. Parental glucose and oleic acid supplements promote glycogen storage in atgl-1(xd314) embryos to compensate for the impaired lipolysis. The rescue by parental vitamin B12 supplement is likely through enhancing mitochondrial function in atgl-1 mutants. These findings reveal that metabolic plasticity contributes to the robustness of C. elegans embryogenesis.

Centrins control chicken cone cell lipid droplet dynamics through lipid-droplet-localized SPDL1.

As evolutionarily conserved organelles, lipid droplets (LDs) carry out numerous functions and have various subcellular localizations in different cell types and species. In avian cone cells, there is a single apically localized LD. We demonstrated that CIDEA (cell death inducing DFFA like effector a) and microtubules promote the formation of the single LD in chicken cone cells. Centrins, which are well-known centriole proteins, target to the cone cell LD via their C-terminal calcium-binding domains. Centrins localize on cone cell LDs with the help of SPDL1-L (spindle apparatus coiled-coil protein 1-L), a previously uncharacterized isoform of the kinetochore-associated dynein adaptor SPDL1. The loss of CETN3 or overexpression of a truncated CETN1 abrogates the apical localization of the cone cell LD. Simulation analysis showed that multiple LDs or a single mispositioned LD reduces the light sensitivity. Collectively, our findings identify a role of centrins in the regulation of cone cell LD localization, which is important for the light sensitivity of cone cells.

Antibody-drug conjugates: the paradigm shifts in the targeted cancer therapy.

Cancer is one of the deadliest diseases, causing million of deaths each year globally. Conventional anti-cancer therapies are non-targeted and have systemic toxicities limiting their versatile applications in many cancers. So, there is an unmet need for more specific therapeutic options that will be effective as well as free from toxicities. Antibody-drug conjugates (ADCs) are suitable alternatives with the right potential and improved therapeutic index for cancer therapy. The ADCs are highly precise new class of biopharmaceutical products that covalently linked a monoclonal antibody (mAb) (binds explicitly to a tumor-associated surface antigen) with a customized cytotoxic drug (kills cancer cells) and tied via a chemical linker (releases the drug). Due to its precise design, it brings about the target cell killing sparing the normal counterpart and free from the toxicities of conventional chemotherapy. It has never been so easy to develop potential ADCs for successful therapeutic usage. With relentless efforts, it took almost a century for scientists to advance the formula and design ADCs for its current clinical applications. Until now, several ADCs have passed successfully through preclinical and clinical trials and because of proven efficacy, a few are approved by the FDA to treat various cancer types. Even though ADCs posed some shortcomings like adverse effects and resistance at various stages of development, with continuous efforts most of these limitations are addressed and overcome to improve their efficacy. In this review, the basics of ADCs, physical and chemical properties, the evolution of design, limitations, and future potentials are discussed.

Performance of DAPT Score and ESC Criteria for Predicting Clinical Outcomes in Chinese Patients with Acute Coronary Syndrome.

Purpose: The values of European Society of Cardiology (ESC) criteria and dual antiplatelet therapy (DAPT) score in the stratification of ischemic risk were assessed in this study. Methods: A total of 489 patients with acute coronary syndrome who received DAPT at discharge between June 2020 and August 2020 were enrolled. The primary endpoint was the occurrence of major adverse cardiovascular events (MACE), which included recurrent ACS or unplanned revascularization, all-cause death, or ischemic stroke during a 27-month follow-up period. Results: Patients with ESC-defined high-risk showed a significantly higher risk of MACE (HR 2.75, 95% CI 1.78-4.25), all-cause death (HR 2.49, 95% CI 1.14-5.43), and recurrent ACS or unplanned revascularization (HR 2.80, 95% CI 1.57-4.99) than those with ESC-defined low/medium-risk during follow-up. The results of landmark analysis showed that patients in the high-risk group had a significantly higher risk of MACE (HR 2.80,95 CI% 1.57-4.97), recurrent ACS or unplanned revascularization (HR 3.19,95 CI% 1.47-6.93) within one year, and a higher risk of MACE (HR 2.69,95 CI% 1.38-5.23) after one year. There was no significant difference in the incidence of MACE between patients with a DAPT score ≥2 and a DAPT score <2. The C-indices of ESC criteria and DAPT score for prediction of MACE were 0.63 (95% CI 0.57-0.70) and 0.54 (95% CI 0.48-0.61), respectively. The predictive value of ESC criteria for MACE was better than the DAPT score according to the DeLong test (z-statistic=2.30, P=0.020). Conclusion: Patients with ESC-defined high-risk had a higher risk of MACE compared to those with ESC-defined low/medium-risk. The discriminant ability of the ESC criteria was better than the DAPT score for MACE. The ESC criteria demonstrated moderate discriminatory capacity of MACE in ACS patients treated with DAPT.

Molecular subtyping and immune score system by a novel pyroptosis-based gene signature precisely predict immune infiltrating, survival and response to immune-checkpoint blockade in breast cancer.

Breast cancer is one of the most prevalent and lethal types of cancer affecting women globally. Pyroptosis is a recently elucidated form of inflammatory cell death mediated by the gasdermin family and is considered to be associated with the tumor immune microenvironment. However, the impact of pyroptosis on breast cancer patients remains unclear. In this study, we identified 31 Pyroptosis-Related-Genes (PRGs) and investigated their association with patient survival using data from the TCGA database. We then established a gene signature comprising 6 PRGs that were significantly correlated with prognosis, and used these genes to classify breast cancer into 2 molecular subtypes. We investigated the characteristics of these two subtypes and found that our molecular subtyping accurately separated the samples into two groups with distinct immune infiltration and prognosis. Patients with higher expression of these genes had significantly greater immune infiltrating, T cell signaling, and better prognosis. Moreover, we developed an immune score system based on these 6 genes that accurately predicted the immune infiltrating of patients and their response to immune-checkpoint blockade, which was difficult to achieve with previous models. Additionally, through single-cell analyses, we found that patients with higher immune scores had stronger cytotoxic immune cells. In summary, our study identified a novel gene set and developed an immune scoring system based on this gene set that can precisely predict the immune microenvironment and responses to immunotherapy of breast cancer (BRCA) patients, which could be useful in clinical trials.