bluuebunny/crossref_metadata_2025 huggingface dataset:
Pharmacokinetics and pharmacodynamics of high-dose isoniazid for the treatment of rifampicin- or multidrug-resistant tuberculosis in Indonesia
Authors: Yunivita Vycke , Gafar Fajri , Santoso Prayudi , Chaidir Lidya , Soeroto Arto Y , Meirina Triana N , Te Brake Lindsey , Menzies Dick , Aarnoutse Rob E , Ruslami Rovina
Published: March 2024

Background

Pharmacokinetic data on high-dose isoniazid for the treatment of rifampicin-/multidrug-resistant tuberculosis (RR/MDR-TB) are limited. We aimed to describe the pharmacokinetics of high-dose isoniazid, estimate exposure target attainment, identify predictors of exposures, and explore exposure–response relationships in RR/MDR-TB patients.

Methods

We performed an observational pharmacokinetic study, with exploratory pharmacokinetic/pharmacodynamic analyses, in Indonesian adults aged 18–65 years treated for pulmonary RR/MDR-TB with standardized regimens containing high-dose isoniazid (10–15 mg/kg/day) for 9–11 months. Intensive pharmacokinetic sampling was performed after ≥2 weeks of treatment. Total plasma drug exposure (AUC0–24) and peak concentration (Cmax) were assessed using non-compartmental analyses. AUC0–24/MIC ratio of 85 and Cmax/MIC ratio of 17.5 were used as exposure targets. Multivariable linear and logistic regression analyses were used to identify predictors of drug exposures and responses, respectively.

Results

We consecutively enrolled 40 patients (median age 37.5 years). The geometric mean isoniazid AUC0–24 and Cmax were 35.4 h·mg/L and 8.5 mg/L, respectively. Lower AUC0–24 and Cmax values were associated (P < 0.05) with non-slow acetylator phenotype, and lower Cmax values were associated with male sex. Of the 26 patients with MIC data, less than 25% achieved the proposed targets for isoniazid AUC0–24/MIC (n = 6/26) and Cmax/MIC (n = 5/26). Lower isoniazid AUC0–24 values were associated with delayed sputum culture conversion (>2 months of treatment) [adjusted OR 0.18 (95% CI 0.04–0.89)].

Conclusions

Isoniazid exposures below targets were observed in most patients, and certain risk groups for low isoniazid exposures may require dose adjustment. The effect of low isoniazid exposures on delayed culture conversion deserves attention.
Analysis of over 250 novel synthetic opioids and xylazine by LC–MS-MS in blood and urine
Authors: Diekhans Katie , Yu Jihau , Farley Megan , Rodda Luke N
Published: March 2024

Novel Synthetic Opioids (NSO) are frequently found in postmortem (PM) and human performance (HP) forensic toxicology casework, resulting in impairment and fatal overdoses. Developing a broad NSO method benefits public health, as it can be used to identify trends in potent opioid use to develop risk management programs. This project aimed to design a comprehensive, rapid and routine method for the selective analysis of over 250 novel synthetic opioids in blood and urine. This method rapidly extracted 150 µL of blood or urine via protein precipitation followed by size-exclusion filtration, evaporation and reconstitution. Separation and data acquisition were achieved on a 12 min LC–MS-MS method using an F5 column. Data processing was expedited with a custom built-in query created in-house that automated processing and enhanced quality assurance. Validation according to ASB/ANSI Standard 036 was performed and applicability of the method was assessed using proficiency test and authentic casework samples. Assessed in blood and urine qualitatively were 261 unique analytes including fentanyl analogs (fentalogs), nitazenes and other miscellaneous synthetic opioids. As 59 isomeric target analytes were placed into groups due to co-elution, there were 202 distinct acquired targets or target - groups. To demonstrate applicability, 27 proficiency test blood samples received over an approximate 4-year period were analyzed with 126 expected results assessed comprising 25 unique target analytes. Additionally, 617 fatal accidental overdoses within San Francisco in 2022 were retroactively analyzed by this method with almost 10% of cases containing a new NSO substance(s). Such trends and NSO substances were previously unknown in this community.
Identification of clobromazolam in Australian emergency department intoxications using data-independent high-resolution mass spectrometry and the HighResNPS.com database
Authors: Castle Jared W , Syrjanen Rebekka , Di Rago Matthew , Schumann Jennifer L , Greene Shaun L , Glowacki Linda L , Gerostamoulos Dimitri
Published: March 2024

The proliferation of novel psychoactive substances (NPSs) continues to challenge toxicology laboratories. In particular, the United Nations Office on Drugs and Crime considers designer benzodiazepines to be a current primary threat among all NPSs. Herein, we report detection of a new emerging designer benzodiazepine, clobromazolam, using high-resolution mass spectrometry and untargeted data acquisition in combination with a “suspect screening” method built from the crowd-sourced HighResNPS.com database. Our laboratory first detected clobromazolam in emergency department presenting intoxications included within the Emerging Drugs Network of Australia—Victoria project in the state of Victoria, Australia, from April 2022 to March 2023. Clobromazolam was the most frequent designer benzodiazepine detected in this cohort (100/993 cases, 10%). No patients reported intentional administration of clobromazolam, although over half reported exposure to alprazolam, which was detected in only 7% of cases. Polydrug use was prevalent (98%), with phenazepam (45%), methylamphetamine (71%) and other benzodiazepines (60%) most frequently co-detected. This is the first case series published in the literature concerning clobromazolam in clinical patients. The identification of clobromazolam in patients presenting to emergency departments in Victoria demonstrates how high-resolution mass spectrometry coupled with the HighResNPS.com database can be a valuable tool to assist toxicology laboratories in keeping abreast of emerging psychoactive drug use.
Evaluation of a novel triple-action adulticide containing a pyrethroid, macrocyclic lactone, and fatty acid against pyrethroid-resistant Aedes aegypti and Culex quinquefasciatus (Diptera: Culicidae)
Authors: Lucas Keira J , Heinig Rebecca , Lake Leanne , Williams Katie , Parker-Crockett Casey , Bales Rachel , McDuffie Decyo
Published: March 2024

Insecticide resistance in mosquito populations has long been recognized as a significant global public health challenge, motivating the development of new control chemistries. ReMoa Tri is a novel triple-action space spray that employs a different mode of action than traditional adult mosquito control formulations. It combines 3 components: fenpropathrin, a mixed-type I/II pyrethroid; abamectin, a macrocyclic lactone; and C8910, a patented fatty acid chain. As an ultra-low volume adulticide, ReMoa Tri has the potential to target mosquito species that are resistant to pyrethroid and organophosphate-based control materials. To determine whether ReMoa Tri effectively targets resistant mosquito species in Florida’s Collier County, United States, we conducted ground-based field cage trials using field-caught pyrethroid-resistant Culex quinquefasciatus (Say) and Aedes aegypti (L.), of which the latter also displayed developing resistance to organophosphates. Trials were also conducted against the same mosquito populations with Merus 3.0, a pyrethrin-based adulticide used by the Collier Mosquito Control District. ReMoa Tri was effective against Collier’s pyrethroid-resistant Cx. quinquefasciatus, resulting in more than 95% mortality in semifield cage trials by 24 h postapplication. Similarly, ReMoa Tri applications against Collier’s pyrethroid-resistant Ae. aegypti resulted in 72%–89% mortality at 24 h postapplication and 74%–97% mortality at 48 h postapplication. This study represents the first field data on this novel space spray, and its findings shed light on the performance of ReMoa Tri against local mosquito populations that have developed resistance to currently available adulticides.
All That Is Solid Bursts into Flame: Capitalism and Fire in the Nineteenth-Century United States
Authors: Immerwahr Daniel
Published: March 2024

Industrial capitalism arrived in Europe as great urban fires were already retreating. The United States, however, was generously timbered and far more reliant on wooden construction. As a result, its infernos continued, and even increased, well into its age of capital. They especially struck places of intense commodification: hastily built settler towns, slave cities, financial centres and sites of mineral extraction. Noting the connection between fire and capitalism, a class of upwardly mobile strivers came to appreciate fires for their ability to disrupt social hierarchies, reset property relations and nurture economic dynamism. Oddly, many who had suffered fires even interpreted them as ‘blessings in disguise’. This pyrophilia was not universal, however, and the richest men of the Gilded Age strenuously opposed it, seeking instead to fireproof the environment. The clash between pyrophobes and pyrophiles was between economic incumbents and economic insurgents, and it touched on many areas of late nineteenth-century culture. Familiar Gilded Age artefacts such as Chicago’s White City and L. Frank Baum’s The Wonderful Wizard of Oz can be productively understood in terms of this widespread fight over the value of fire, and thus the shape of capitalism.
Rheumatoid arthritis and risk of osteoarticular infection and death following Staphylococcus aureus bacteraemia: a nationwide cohort study
Authors: Dieperink Sabine S , Nørgaard Mette , Mehnert Frank , Oestergaard Louise B , Benfield Thomas , Torp-Pedersen Christian , Petersen Andreas , Glintborg Bente , Hetland Merete L
Published: March 2024

Objectives

Osteoarticular infection (OAI) is a feared complication of Staphylococcus aureus bacteraemia (SAB) and is associated with poor outcomes. We aimed to explore the risk of OAI and death following SAB in patients with and without rheumatoid arthritis (RA) and to identify risk factors for OAI in patients with RA.

Methods

Danish nationwide cohort study of all patients with microbiologically verified first-time SAB between 2006–18. We identified RA, SAB, comorbidities, and RA-related characteristics (e.g. orthopaedic implants and antirheumatic treatment) in national registries including the rheumatology registry DANBIO. We estimated the cumulative incidence of OAI and death and adjusted hazard ratios (HRs, multivariate Cox regression).

Results

We identified 18 274 patients with SAB (n = 367 with RA). The 90-day cumulative incidence of OAI was 23.1% (95% CI 18.8; 27.6) for patients with RA and 12.5% (12.1; 13.0) for patients without RA (non-RA) [HR 1.93 (1.54; 2.41)]. For RA patients with orthopaedic implants cumulative incidence was 29.4% (22.9; 36.2) [HR 1.75 (1.08; 2.85)], and for current users of tumor necrosis factor inhibitors (TNFi) it was 41.9% (27.0; 56.1) [HR 2.27 (1.29; 3.98) compared with non-users]. All-cause 90-day mortality following SAB was similar in RA [35.4% (30.6; 40.3)] and non-RA [33.9% (33.2; 34.5), HR 1.04 (0.87; 1.24)].

Conclusion

Following SAB, almost one in four patients with RA contracted OAI corresponding to a doubled risk compared with non-RA. In RA, orthopaedic implants and current TNFi use were associated with approximately doubled OAI risk. One in three died within 90 days in both RA and non-RA. These findings encourage vigilance in RA patients with SAB to avoid treatment delay of OAI.
The Rejuvenation and Functional Restoration of Aged Adipose Stem Cells by DUXAP10 Knockdown via the Regulation of the miR-214-3p/RASSF5 Axis
Authors: Ren Sen , Li Chengcheng , Xiong Hewei , Wu Qian , Wu Xiaohui , Xiong Zhongwei , Dong Lixing , Shu Bing , Wei Wei , Ma Chao , Li Xiang , Chen Jincao
Published: March 2024

Adipose stem cell (ASC)-based therapies provide an encouraging option for tissue repair and regeneration. However, the function of these cells declines with aging, which limits their clinical transformation. Recent studies have outlined the involvement of long non-coding RNAs in stem cell aging. Here, we reanalyzed our published RNA sequencing (RNA-seq) data profiling differences between ASCs from young and old donors and identified a lncRNA named double homeobox A pseudogene 10 (DUXAP10) as significantly accumulated in aged ASCs. Knocking down DUXAP10 promoted stem cell proliferation and migration and halted cell senescence and the secretion of proinflammatory cytokines. In addition, DUXAP10 was located in the cytoplasm and functioned as a decoy for miR-214-3p. miR-214-3p was downregulated in aged ASCs, and its overexpression rejuvenated aged ASCs and reversed the harm caused by DUXAP10. Furthermore, Ras Association Domain Family Member 5 (RASSF5) was the target of miR-214-3p and was upregulated in aged ASCs. Overexpressing DUXAP10 and inhibiting miR-214-3p both enhanced RASSF5 content in ASCs, while DUXAP10 knockdown promoted the therapeutic ability of aged ASCs for skin wound healing. Overall, this study offers new insights into the mechanism of age-related ASC dysfunction and names DUXAP10 and miR-214-3p as potential targets for energizing aged stem cells.
Multidisciplinary Approach for the Management of Metastatic Poorly Differentiated Neuroendocrine Carcinoma of the Pancreas
Authors: Nakasone Elizabeth S. , Bustillos Hannah C. , Gui Xianyong , Konnick Eric Q. , Sham Jonathan G. , Cohen Stacey A.
Published: March 2024

Poorly differentiated pancreatic neuroendocrine carcinomas (pNECs) are rare, highly aggressive neoplasms. Frequently metastatic at diagnosis, prognosis is poor with median overall survival estimated to be less than 1 year. Although multidisciplinary management, including systemic medications and locoregional therapies aimed at reducing and preventing symptoms caused by mass effect, is the mainstay of treatment for patients with metastatic well-differentiated pancreatic neuroendocrine tumors, rapid progression, organ dysfunction, and poor performance status often preclude initiation of even single-modality palliative chemotherapy for patients with metastatic pNEC, limiting the use of and recommendation for multidisciplinary management.

We describe the case of a 51-year-old male patient diagnosed with pNEC metastatic to liver and lymph nodes presenting with impending cholestatic liver failure for whom we were able to successfully initiate and dose-escalate cytotoxic chemotherapy with excellent radiographic response. After multidisciplinary review of his case, the patient underwent pancreaticoduodenectomy and hepatic wedge biopsies, with pathology demonstrating a pathologic complete response to chemotherapy in both the pancreas and liver. Surveillance scans at 2 years from initial diagnosis and 1 year from surgery remain without evidence of locoregional or distant recurrence, highlighting the importance and utility of multidisciplinary management in select cases.
Precision Enhancement of CAR-NK Cells through Non-Viral Engineering and Highly Multiplexed Base Editing
Authors: Wang Minjing , Krueger Joshua B. , Gilkey Alexandria K. , Stelljes Erin M. , Kluesner Mitchell G. , Pomeroy Emily J. , Skeate Joseph G. , Slipek Nicholas J. , Lahr Walker S. , Vázquez Patricia N. Claudio , Zhao Yueting , Eaton Ella J. , Laoharawee Kanut , Webber Beau R. , Moriarity Branden S.
Published: March 2024

Natural killer (NK) cells’ unique ability to kill transformed cells expressing stress ligands or lacking major histocompatibility complexes (MHC) has prompted their development for immunotherapy. However, NK cells have demonstrated only moderate responses against cancer in clinical trials and likely require advanced genome engineering to reach their full potential as a cancer therapeutic. Multiplex genome editing with CRISPR/Cas9 base editors (BE) has been used to enhance T cell function and has already entered clinical trials but has not been reported in human NK cells. Here, we report the first application of BE in primary NK cells to achieve both loss-of-function and gain-of-function mutations. We observed highly efficient single and multiplex base editing, resulting in significantly enhanced NK cell function. Next, we combined multiplex BE with non-viralTcBustertransposon-based integration to generate IL-15 armored CD19 CAR-NK cells with significantly improved functionality in a highly suppressive model of Burkitt’s lymphoma bothin vitroandin vivo. The use of concomitant non-viral transposon engineering with multiplex base editing thus represents a highly versatile and efficient platform to generate CAR-NK products for cell-based immunotherapy and affords the flexibility to tailor multiple gene edits to maximize the effectiveness of the therapy for the cancer type being treated.
Spectroscopic assessment of flavor-related chemical compounds in fresh tea shoots using deep learning
Authors: Denaro Lino Garda , Lin Shu-Yen , Huang Cho-ying
Published: March 2024

This study employs a deep-learning method, Y-Net, to estimate 10 tea flavor-related chemical compounds (TFCC), including gallic acid, caffeine and eight catechin isomers, using fresh tea shoot reflectance and transmittance. The unique aspect of Y-Net lies in its utilization of dual inputs, reflectance and transmittance, which are seamlessly integrated within the Y-Net architecture. This architecture harnesses the power of a convolutional neural network-based residual network to fuse tea shoot spectra effectively. This strategic combination enhances the capacity of the model to discern intricate patterns in the optical characteristics of fresh tea shoots, providing a comprehensive framework for TFCC estimation. In this study, we destructively sampled tea shoots from tea farms in Alishan (Ali-Mountain) in Central Taiwan within the elevation range of 879–1552 m a.s.l. Tea shoot reflectance and transmittance data (n = 2032) within the optical region (400–2500 nm) were measured using a portable spectroradiometer and pre-processed using an algorithm; corresponding TFCC were qualified using the high-performance liquid chromatography analysis. To enhance the robustness and performance of Y-Net, we employed data augmentation techniques for model training. We compared the performances of Y-Net and seven other commonly utilized statistical, machine-/deep-learning models (partial least squared regression, Gaussian process, cubist, random forests and three feedforward neural networks) using root-mean-square error (RMSE). Furthermore, we assessed the prediction accuracies of Y-Net and Y-Net using spectra within the visible and near-infrared (VNIR) regions (for higher energy throughput and low-cost instruments) and reflectance only (for airborne and spaceborne remote sensing applications). The results showed that overall Y-Net (mean RMSE ± standard deviation [SD] = 2.51 ± 2.20 mg g−1) outperformed the other statistical, machine- and deep-learning models (≥ 2.59 ± 2.64 mg g−1), demonstrating its superiority in predicting TFCC. In addition, this original Y-Net also yielded slightly lower mean RMSE (± SD) compared with VNIR (2.76 ± 2.41 mg g−1) and reflectance-only (2.68 ± 2.74 mg g−1) Y-Nets using validation data. This study highlights the feasibility of using spectroscopy and Y-Net to assess minor biochemical components in fresh tea shoots and sheds light on the potential of the proposed approach for effective regional monitoring of tea shoot quality.
Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex
Authors: Goswami Pratik , Banks Charles A.S. , Thornton Janet , Bengs Bethany , Sardiu Mihaela E. , Florens Laurence , Washburn Michael P.
Published: March 2024

Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC complexes, and the function of most of these members remains poorly understood. SAP25, a previously identified Sin3A associated protein of 25 kDa, has been proposed to participate in regulating gene expression programs involved in the immune response but the exact mechanism of this regulation is unclear. SAP25 is not expressed in HEK293 cells, which hence serve as a natural knockout system to decipher the molecular functions uniquely carried out by this Sin3/HDAC subunit. Using molecular, proteomic, protein engineering, and interaction network approaches, we show that SAP25 interacts with distinct enzymatic and regulatory protein complexes in addition to Sin3/HDAC. While the O-GlcNAc transferase (OGT) and the TET1 /TET2/TET3 methylcytosine dioxygenases have been previously linked to Sin3/HDAC, in HEK293 cells, these interactions were only observed in the affinity purification in which an exogenously expressed SAP25 was the bait. Additional proteins uniquely recovered from the Halo-SAP25 pull-downs included the SCF E3 ubiquitin ligase complex SKP1/FBXO3/CUL1 and the ubiquitin carboxyl-terminal hydrolase 11 (USP11), which have not been previously associated with Sin3/HDAC. Finally, we use mutational analysis to demonstrate that distinct regions of SAP25 participate in its interaction with USP11, OGT/TETs, and SCF(FBXO3).) These results suggest that SAP25 may function as an adaptor protein to coordinate the assembly of different enzymatic complexes to control Sin3/HDAC-mediated gene expression.
Machine Learning Assisted Spectral Fingerprinting for Immune Cell Phenotyping
Authors: Nadeem Aceer , Lyons Sarah , Kindopp Aidan , Jamieson Amanda , Roxbury Daniel
Published: March 2024

Spectral fingerprinting has emerged as a powerful tool, adept at identifying chemical compounds and deciphering complex interactions within cells and engineered nanomaterials. Using near-infrared (NIR) fluorescence spectral fingerprinting coupled with machine learning techniques, we uncover complex interactions between DNA-functionalized single-walled carbon nanotubes (DNA-SWCNTs) and live macrophage cells, enablingin situphenotype discrimination. Through the use of Raman microscopy, we showcase statistically higher DNA-SWCNT uptake and a significantly lower defect ratio in M1 macrophages as compared to M2 and naïve phenotypes. NIR fluorescence data also indicate that distinctive intra-endosomal environments of these cell types give rise to significant differences in many optical features such as emission peak intensities, center wavelengths, and peak intensity ratios. Such features serve as distinctive markers for identifying different macrophage phenotypes. We further use a support vector machine (SVM) model trained on SWCNT fluorescence data to identify M1 and M2 macrophages, achieving an impressive accuracy of > 95%. Finally, we observe that the stability of DNA-SWCNT complexes, influenced by DNA sequence length, is a crucial consideration for applications such as cell phenotyping or mapping intra-endosomal microenvironments using AI techniques. Our findings suggest that shorter DNA-sequences like GT6give rise to more improved model accuracy (> 87%) due to increased active interactions of SWCNTs with biomolecules in the endosomal microenvironment. Implications of this research extend to the development of nanomaterial-based platforms for cellular identification, holding promise for potential applications in real time monitoring ofin vivocellular differentiation.

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Identification of Druggable Binding Sites and Small Molecules as Modulators of TMC1
Authors: De-la-Torre Pedro , Martínez-García Claudia , Gratias Paul , Mun Matthew , Santana Paula , Akyuz Nurunisa , González Wendy , Indzhykulian Artur A. , Ramírez David
Published: March 2024

Our ability to hear and maintain balance relies on the proper functioning of inner ear sensory hair cells, which translate mechanical stimuli into electrical signals via mechano-electrical transducer (MET) channels, composed of TMC1/2 proteins. However, the therapeutic use of ototoxic drugs, such as aminoglycosides and cisplatin, which can enter hair cells through MET channels, often leads to profound auditory and vestibular dysfunction. Despite extensive research on otoprotective compounds targeting MET channels, our understanding of how small-molecule modulators interact with these channels remains limited, hampering the discovery of novel drugs. Here, we propose a structure-based screening approach, integrating 3D-pharmacophore modeling, molecular dynamics simulations of the TMC1+CIB2+TMIE complex, and experimental validation. Our pipeline successfully identified several novel compounds and FDA-approved drugs that reduced dye uptake in cultured cochlear explants, indicating MET-modulation activity. Simulations, molecular docking and free-energy estimations allowed us to identify three potential drug-binding sites within the channel pore, phospholipids, key amino acids involved in modulator interactions, and TMIE as a flexible component of the MET complex. We also identified shared ligand-binding features between TMC and structurally related TMEM16 proteins, providing novel insights into their distinct inhibition. Our pipeline offers a broad application for discovering modulators for mechanosensitive ion channels.
CoupleVAE: coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data
Authors: Wu Yahao , Liu Jing , Liu Songyan , Xiao Yanni , Zhang Shuqin , Li Limin
Published: March 2024

With the rapid advances in single-cell sequencing technology, it is now feasible to conduct in-depth genetic analysis in individual cells. Study on the dynamics of single cells in response to perturbations is of great significance for understanding the functions and behaviours of living organisms. However, the acquisition of post-perturbation cellular states via biological experiments is frequently cost-prohibitive. Predicting the single-cell perturbation responses poses a critical challenge in the field of computational biology. In this work, we propose a novel deep learning method called coupled variational autoencoders (CoupleVAE), devised to predict the post-perturbation single-cell RNA-Seq data. CoupleVAE is composed of two coupled VAEs connected by a coupler, initially extracting latent features for both controlled and perturbed cells via two encoders, subsequently engaging in mutual translation within the latent space through two nonlinear mappings via a coupler, and ultimately generating controlled and perturbed data by two separate decoders to process the encoded and translated features. CoupleVAE facilitates a more intricate state transformation of single cells within the latent space. Experiments in three real datasets on infection, stimulation and cross-species prediction show that CoupleVAE surpasses the existing comparative models in effectively predicting single-cell RNA-seq data for perturbed cells, achieving superior accuracy.
Conformational switch of a peptide provides a novel strategy to design peptide loaded porous organic polymer for Pyroptosis pathway mediated cancer therapy
Authors: Mishra Snehasis , Sannigrahi Achinta , Ruidas Santu , Chatterjee Sujan , Roy Kamalesh , Misra Deblina , Maity Barun Kumar , Paul Rabindranath , Das Saha Krishna , Bhaumik Asim , Chattopadhyay Krishnananda
Published: March 2024

While peptide-based drug development is now extensively explored, this strategy does have limitations, which come from their rapid excretion from the body (or shorter half-life in the body), and vulnerability to protease-mediated degradation. To overcome these limitations, here we introduce a novel strategy for the development of a peptide-based anticancer agent using the conformation switch property of a chameleon sequence stretch, which we derived from a mycobacterium secretory protein, MPT63. Then, we loaded this peptide in a new porous organic polymer (PG-DFC-POP) synthesized using phloroglucinol and acresolderivative via condensation reaction for delivering the peptide selectively to the cancer cells. Employing an ensemble and single molecule approaches, we demonstrate that this peptide undergoes a disordered to alpha-helical conformational transition, which is triggered by a low pH environment inside cancer cells. This adopted alpha-helical conformation results in the formation of proteolysis-resistant oligomers, which show efficient membrane pore-forming activity selectively for negatively charged phospholipid which is accumulated in cancer cell membrane. Ourin vitroandin vivoexperimental results demonstrate that the peptide-loaded nanomaterial PG-DFC-POP-PEP 1 exhibits significant cytotoxicity in cancer cells, leading to cell death through the Pyroptosis pathway that is confirmed by monitoring numerous associated events starting from lysosome membrane damage to GSDMD-induced cell membrane demolition. We believe that this novel conformational switch-based drug design strategy has great potential in endogenous environment-responsive cancer therapy and the development of future drug candidates to mitigate cancers.
Shear Stress Promotes Remodeling of Platelet Glycosylation via Upregulation of Platelet Glycosidase Activity: The Ulterior Cause of MCS-Related Thrombocytopenia?
Authors: Roka-Moiia Yana , Lewis Sabrina , Cleveland Estevan , Italiano Joseph E. , Slepian Marvin J.
Published: March 2024

Objective

Mechanical circulatory support (MCS) is a mainstay of therapy for advanced and end-stage heart failure. Accompanied by systemic anticoagulation, contemporary MCS has become less thrombogenic, with bleeding complications emerging as a major cause of readmission and 1-year mortality of device-supported patients. Shear-mediated platelet dysfunction (SMPD) and thrombocytopenia of undefined etiology are primary drivers of MCS-related bleeding. Recently, it has been demonstrated that deprivation of platelet surface glycosylation is associated with the decline of hemostatic function, microvesiculation, and premature apoptosis. We tested the hypothesis that shear stress induces remodeling of platelet surface glycosylation via upregulation of glycosidase activity, thus facilitating platelet count decline and intense microvesiculation.

Approach and Results

Human gel-filtered platelets were exposed to continuous shear stressin vitro. Platelets and platelet-derived microparticles were quantified via flow cytometry using size standard fluorescent nanobeads. Platelet surface glycosylation was evaluated using lectin staining and multicolor flow cytometry; lectin blotting was utilized to verify glycosylation of individual glycoproteins. Platelet neuraminidase, galactosidase, hexosaminidase, and mannosidase activities were quantified using 4-methylumbelliferone-based fluorogenic substrates. We demonstrated that shear stress promotes selective remodeling of platelet glycosylation via downregulation of 2,6-sialylation, terminal galactose, and mannose, while 2,3-sialylation remained largely unchanged. Shear-mediated deglycosylation is partially attenuated by neuraminidase inhibitors DANA and zanamivir, strongly suggesting involvement of platelet neuraminidase in observed phenomena. Platelets exhibited high basal hexosaminidase and mannosidase activities; basal activities of platelet neuraminidase and galactosidase were rather low and were significantly upregulated by shear stress. Shear stress of increased magnitude and duration potentiated an incremental decline of platelet count and immense microvesiculation, both being further exacerbated by neuraminidase.

Conclusions

Our data indicate that shear stress accumulation, consistent with supraphysiologic conditions of device-supported circulation, promotes remodeling of platelet glycosylation via selective upregulation of platelet glycosidase activity. Shear-mediated platelet deglycosylation is associated with platelet count drop and increased microvesiculation, thus offering a direct link between deglycosylation and thrombocytopenia observed in device-supported patients.

GRAPHICAL ABSTRACT
Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules
Authors: Ashkarran Ali Akbar , Gharibi Hassan , Sadeghi Seyed Amirhossein , Modaresi Seyed Majed , Wang Qianyi , Lin Teng-Jui , Yerima Ghafar , Tamadon Ali , Sayadi Maryam , Jafari Maryam , Lin Zijin , Ritz Danilo , Kakhniashvili David , Guha Avirup , Mofrad Mohammad R.K. , Sun Liangliang , Landry Markita P. , Saei Amir Ata , Mahmoudi Morteza
Published: March 2024

The protein corona, a dynamic biomolecular layer that forms on nanoparticle (NP) surfaces upon exposure to biological fluids is emerging as a valuable diagnostic tool for improving plasma proteome coverage analyzed by liquid chromatography-mass spectrometry (LC-MS/MS). Here, we show that spiking small molecules, including metabolites, lipids, vitamins, and nutrients (namely, glucose, triglyceride, diglycerol, phosphatidylcholine, phosphatidylethanolamine, L-α-phosphatidylinositol, inosine 5′-monophosphate, and B complex), into plasma can induce diverse protein corona patterns on otherwise identical NPs, significantly enhancing the depth of plasma proteome profiling. The protein coronas on polystyrene NPs when exposed to plasma treated with an array of small molecules (n=10) allowed for detection of 1793 proteins marking an 8.25-fold increase in the number of quantified proteins compared to plasma alone (218 proteins) and a 2.63-fold increase relative to the untreated protein corona (681 proteins). Furthermore, we discovered that adding 1000 µg/ml phosphatidylcholine could singularly enable the detection of 897 proteins. At this specific concentration, phosphatidylcholine selectively depleted the four most abundant plasma proteins, including albumin, thus reducing the dynamic range of plasma proteome and enabling the detection of proteins with lower abundance. By employing an optimized data-independent acquisition (DIA) approach, the inclusion of phosphatidylcholine led to the detection of 1436 proteins in a single plasma sample. Our molecular dynamic results revealed that phosphatidylcholine interacts with albumin via hydrophobic interactions, h-bonds, and water-bridges. Addition of phosphatidylcholine also enabled the detection of 337 additional proteoforms compared to untreated protein corona using a top-down proteomics approach. These significant achievements are made utilizing only a single NP type and one small molecule to analyze a single plasma sample, setting a new standard in plasma proteome profiling. Given the critical role of plasma proteomics in biomarker discovery and disease monitoring, we anticipate widespread adoption of this methodology for identification and clinical translation of proteomic biomarkers into FDA approved diagnostics.
Engineering an in vitro retinothalamic nerve model
Authors: Amos Giulia , Ihle Stephan J , Clément Blandine F , Duru Jens , Girardin Sophie , Maurer Benedikt , Delipinar Tuğçe , Vörös János , Ruff Tobias
Published: March 2024

Understanding the retinogeniculate pathwayin vitrocan offer insights into its development and potential for future therapeutic applications. This study presents a Polydimethylsiloxane-based two-chamber system with axon guidance channels, designed to replicate unidirectional retinogeniculate signal transmissionin vitro. The system enables the formation of up to 20 identical functional retinothalamic networks on a single transparent microelectrode array. Using embryonic rat retinas, we developed a model where retinal spheroids innervate thalamic targets through up to 6 mm long microfluidic channels. We found that network integrity depends on channel length, with 0.5-2 mm channels maintaining over 90 % morphological and 40 % functional integrity. A reduced network integrity was recorded in longer channels. The results indicate a notable reduction in forward spike propagation in channels longer than 4 mm. Additionally, spike conduction fidelity decreased with increasing channel length. Yet, stimulation-induced thalamic target activity remained unaffected by channel length. Finally, we assessed the impact of stimulation frequency and channel length on the sustainability of the thalamic target spheroid response. The study found that a sustained thalamic calcium response could be elicited with stimulation frequencies up to 31 Hz, with higher frequencies leading to transient responses. In conclusion, this study shows how channel length affects retina to brain network formation and signal transmissionin vitro.
Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation
Authors: Engelbrecht Eric , Rodriguez Oscar L. , Watson Corey T.
Published: March 2024

The expressed antibody repertoire is a critical determinant of immune-related phenotypes. Antibody-encoding transcripts are distinct from other expressed genes because they are transcribed from somatically rearranged gene segments. Human antibodies are composed of two identical heavy and light chain polypeptides derived from genes in the immunoglobulin heavy chain (IGH) locus and one of two light chain loci. The combinatorial diversity that results from antibody gene rearrangement and the pairing of different heavy and light chains contributes to the immense diversity of the baseline antibody repertoire. During rearrangement, antibody gene selection is mediated by factors that influence chromatin architecture, promoter/enhancer activity, and V(D)J recombination. Interindividual variation in the composition of the antibody repertoire associates with germline variation in IGH, implicating polymorphism in antibody gene regulation. Determining how IGH variants directly mediate gene regulation will require integration of these variants with other functional genomic datasets. Here, we argue that standard approaches using short reads have limited utility for characterizing regulatory regions in IGH at haplotype-resolution. Using simulated and ChIP-seq reads, we define features of IGH that limit use of short reads and a single reference genome, namely 1) the highly duplicated nature of DNA sequence in IGH and 2) structural polymorphisms that are frequent in the population. We demonstrate that personalized diploid references enhance performance of short-read data for characterizing mappable portions of the locus, while also showing that long-read profiling tools will ultimately be needed to fully resolve functional impacts of IGH germline variation on expressed antibody repertoires.
Antigenicity assessment of SARS-CoV-2 saltation variant BA.2.87.1
Authors: Yang Sijie , Yu Yuanling , Jian Fanchong , Yisimayi Ayijiang , Song Weiliang , Liu Jingyi , Wang Peng , Xu Yanli , Wang Jing , Niu Xiao , Yu Lingling , Wang Yao , Shao Fei , Jin Ronghua , Wang Youchun , Cao Yunlong
Published: March 2024

The recent emergence of a SARS-CoV-2 saltation variant, BA.2.87.1, which features 65 spike mutations relative to BA.2, has attracted worldwide attention. In this study, we elucidate the antigenic characteristics and immune evasion capability of BA.2.87.1. Our findings reveal that BA.2.87.1 is more susceptible to XBB-induced humoral immunity compared to JN.1. Notably, BA.2.87.1 lacks critical escaping mutations in the receptor binding domain (RBD) thus allowing various classes of neutralizing antibodies (NAbs) that were escaped by XBB or BA.2.86 subvariants to neutralize BA.2.87.1, although the deletions in the N-terminal domain (NTD), specifically 15-23del and 136-146del, compensate for the resistance to humoral immunity. Interestingly, several neutralizing antibody drugs have been found to restore their efficacy against BA.2.87.1, including SA58, REGN-10933 and COV2-2196. Hence, our results suggest that BA.2.87.1 may not become widespread until it acquires multiple RBD mutations to achieve sufficient immune evasion comparable to that of JN.1.
Rapid Degradation of the Human ACE2 Receptor Upon Binding and Internalization of SARS-Cov-2-Spike-RBD Protein
Authors: Feinstein Paul
Published: March 2024

It is widely accepted that the SARS-CoV-2 betacoronavirus infects humans through binding the human Angiotensin Receptor 2 (ACE2) that lines the nasal cavity and lungs, followed by import into a cell utilizing the Transmembrane Protease, Serine 2 (TMPRSS2) cofactor. ACE2 binding is mediated by an approximately 200-residue portion of the SARS-CoV-2 extracellular spike protein, the receptor binding domain (RBD). Robust interactions are shown using a novel cell-based assay between an RBD membrane tethered-GFP fusion protein and the membrane bound ACE2-Cherry fusion protein. Several observations were not predicted including, quick and sustained interactions leading to internalization of RBD fusion protein into the ACE2 cells and rapid downregulation of the ACE2-Cherry fluorescence. Targeted mutation in the RBD disulfide Loop 4 led to a loss of internalization for several variants tested. However, a secreted RBD did not cause ACE2 downregulation of ACE2-Cherry fluorescence. Thus, the membrane associated form of RBD found on the viral coat may have long-term system wide consequences on ACE2 expressing cells.
JAK-STAT pathway activation compromises nephrocyte function in aDrosophilahigh-fat diet model of chronic kidney disease
Authors: Zhao Yunpo , Duan Jianli , van de Leemput Joyce , Han Zhe
Published: March 2024

Chronic kidney disease is a major healthy issue and is gaining prevalence. Using aDrosophilamodel for chronic kidney disease we show that a high-fat diet (HFD) disrupts the slit diaphragm filtration structure in nephrocytes, the fly functional equivalent of mammalian podocytes. The structural disruption resulted in reduced filtration function in the affected nephrocytes. We demonstrate that a HFD activates the JAK-STAT pathway in nephrocytes, which has previously been linked to diabetic kidney disease. JAK-STAT activation was initiated by increased expression and release of the adipokine, Upd2, from the fat body. This leptin-like hormone is a known ligand of JAK-STAT. Both genetic and pharmacological inhibition of JAK-STAT restored nephrocyte HFD-associated dysfunction. Altogether, our study reveals the importance of the JAK-STAT signaling pathway in the adipose tissue−nephrocyte axis and its contribution to HFD-associated nephropathy. These findings open new avenues for intervention in treating diabetic nephropathy and chronic kidney disease.

HIGHLIGHTS

High-fat diet (HFD) disrupt nephrocyte slit diaphragm structure and filtration

HFD releases fat body adipokine, Upd2, which activates JAK-STAT in nephrocytes

Genetic/pharmacological inhibition of JAK-STAT reverses HFD nephrocyte dysfunction

JAK-STAT signaling mediates adipose-nephrocyte axis in HFD-associated nephropathy

IMPACT STATEMENT

Using aDrosophilamodel for chronic kidney disease, Zhao et al. show that a high-fat diet induces excretion of a leptin-like JAK-STAT ligand from the fat body. Thus, driving the adipose-nephrocyte (podocyte equivalent) axis through activated JAK-STAT signaling. These findings link obesity to kidney disease, implicating new avenues for therapeutics.
Midbrain Dopaminergic Neuron Development is Regulated by Two Molecularly Distinct Subtypes of Radial Glia Cells
Authors: Ásgrímsdóttir Emilía Sif , Bassini Luca Fusar , di Val Cervo Pia Rivetti , Gyllborg Daniel , Pastor Clàudia Puigsasllosas , Lee Kawai , Grigsby Christopher , Islam Saiful , Lönneberg Peter , Villaescusa Carlos , Saltó Carmen , Linnarsson Sten , La Manno Gioele , Toledo Enrique M. , Arenas Ernest
Published: March 2024

Understanding midbrain dopaminergic (mDA) neuron development is key to advancing cell replacement therapies for Parkinson’s disease (PD). Recent single-cell RNA-sequencing (scRNA-seq) studies have identified different subtypes of transient radial glia (Rgl) cell types in the developing mouse and human ventral midbrain. However, their individual functions and their impact on mDA neuron development are unclear. Here we analyze the transcriptome of endogenous mouse and human ventral midbrain Rgl and assess the function of key midbrain floor plate Rgl factors in human stem cells during mDA neuron differentiation. We find that Rgl1 is defined by a neurogenic network centered onArntl, and that this transcription factor regulates human mDA neurogenesis. Conversely, the transcriptome of Rgl3 is dominated by signaling and extracellular matrix molecules that control different aspects of human mDA neuron development. Thus, our results suggest a function of Rgl1 as a mDA progenitor, and of Rgl3 as a signaling mDA niche cell. Moreover, using human stem cells we demonstrate that new knowledge of cell-type specific intrinsic and extrinsic developmental factors can readily be applied to improve the generation of cells with therapeutic interest, such as human mDA neurons for PD.
Ratiometric control of two microbial populations via a dual chamber bioreactor
Authors: Brancato Sara Maria , Salzano Davide , Fiore Davide , Russo Giovanni , di Bernardo Mario
Published: March 2024

Maintaining stable coexistence in microbial consortia, particularly when one species grows faster than another (i.e. the species are non-complementary), poses significant challenges. We introduce a novel control architecture that employs two bioreactors. In this system, the slower-growing species is cultivated separately before being introduced into the main mixing chamber. We analyze the open-loop dynamics of this setup and propose a switching feedback mechanism that controls the dilution rates to ensure robust regulation of population density and composition within the microbial consortium. Validatedin silicousing parameters from real experiments, our approach demonstrates effective and robust maintenance of microbial balance across various strains without requiring genetic modifications.
Diffusion kurtosis MRI tracks gray matter myelin content in the primate cerebral cortex
Authors: Reveley Colin , Ye Frank Q , Leopold David A
Published: March 2024

Diffusion magnetic resonance imaging (dMRI) has been widely employed to model the trajectory of myelinated fiber bundles in white matter. Increasingly, dMRI is also used to assess local tissue properties throughout the brain. In the cerebral cortex, myelin content is a critical indicator of the maturation, regional variation, and disease related degeneration of gray matter tissue. Gray matter myelination can be measured and mapped using several non-diffusion MRI strategies; however, first order diffusion statistics such as fractional anisotropy (FA) show only weak spatial correlation with cortical myelin content. Here we show that a simple higher order diffusion parameter, the mean diffusion kurtosis (MK), is strongly correlated with the laminar and regional variation of myelin in the primate cerebral cortex. We carried out ultra-high resolution, multi-shelled dMRI in ex vivo marmoset monkey brains and compared dMRI parameters from a number of higher order models (diffusion kurtosis, NODDI and MAP MRI) to the distribution of myelin obtained using histological staining, and via Magnetization Transfer Ratio MRI (MTR), a non-diffusion MRI method. In contrast to FA, MK closely matched the myelin content assessed by histology and by MTR in the same sample. The parameter maps from MAP-MRI and NODDI also showed good correspondence with cortical myelin content. The results demonstrate that dMRI can be used to assess the variation of local myelin content in the primate cortical cortex, which may be of great value for assessing tissue integrity and tracking disease in living human patients.