J Biomed Mater Res B Appl Biomater. 2023 Mar 2. doi: 10.1002/jbm.b.35241. Online ahead of print.

ABSTRACT

In vitro cytotoxicity evaluation of linear copolymer (LC) containing choline ionic liquid units and its conjugates with an antibacterial drug in anionic form, that is, p-aminosalicylate (LC_PAS), clavulanate (LC_CLV), or piperacillin (LC_PIP) was carried out. These systems were tested against normal: human bronchial epithelial cells (BEAS-2B), and cancers: adenocarcinoma human alveolar basal epithelial cells (A549), and human non-small cell lung carcinoma cell line (H1299). Cells viability, after linear copolymer LC and their conjugates addition for 72 h, was measured at concentration range of 3.125-100 μg/mL. The MTT test allowed the designation of IC50 index, which was higher for BEAS-2B, and significantly lower in the case of cancer cell lines. The cytometric analyzes, that is, Annexin-V FITC apoptosis assay and cell cycle analysis as well as gene expression measurements for interleukins IL6 and IL8 were carried out, and showed pro-inflammatory activity of tested compounds toward cancer cells, while it was not observed against normal cell line.

PMID:36863708 | DOI:10.1002/jbm.b.35241

Transl Res. 2023 Feb 28:S1931-5244(23)00038-5. doi: 10.1016/j.trsl.2023.02.006. Online ahead of print.

ABSTRACT

Fabry disease (FD) is an X-linked lysosomal rare disease due to a deficiency of α-galactosidase A activity. The accumulation of glycosphingolipids mainly affects the kidney, heart, and central nervous system, considerably reducing life expectancy. Although the accumulation of undegraded substrate is considered the primary cause of FD, it is established that secondary dysfunctions at the cellular, tissue, and organ levels ultimately give rise to the clinical phenotype. To parse this biological complexity, a large-scale deep plasma targeted proteomic profiling has been performed. We analyzed the plasma protein profiles of FD deeply phenotyped patients (n = 55) compared to controls (n = 30) using next-generation plasma proteomics including 1463 proteins. Systems biology and machine learning approaches have been used. The analysis enabled the identification of proteomic profiles that unambiguously separated FD patients from controls (615 differentially expressed proteins, 476 upregulated, and 139 downregulated) and 365 proteins are newly reported. We observed functional remodeling of several processes, such as cytokine-mediated pathways, extracellular matrix, and vacuolar/lysosomal proteome. Using network strategies, we probed patient-specific tissue metabolic remodeling and described a robust predictive consensus protein signature including 17 proteins CD200, SPINT1, CD34, FGFR2, GRN, ERBB4, AXL, ADAM15, PTPRM, IL13RA1, NBL1, NOTCH1, VASN, ROR1, AMBP, CCN3, and HAVCR2. Our findings highlight the pro-inflammatory cytokines' involvement in FD pathogenesis along with extracellular matrix remodeling. The study shows a tissue-wide metabolic remodeling connection to plasma proteomics in FD. These results will facilitate further studies to understand the molecular mechanisms in FD to pave the way for better diagnostics and therapeutics.

PMID:36863609 | DOI:10.1016/j.trsl.2023.02.006

Stem Cell Res. 2023 Feb 26;68:103056. doi: 10.1016/j.scr.2023.103056. Online ahead of print.

ABSTRACT

Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an abnormal length of CAG repeats in the gene HTT, leading to an elongated poly-glutamine (poly-Q) sequence in huntingtin (HTT). We used non-integrative Sendai virus to reprogram fibroblasts from a patient with juvenile onset HD to induced pluripotent stem cells (iPSCs). Reprogrammed iPSCs expressed pluripotency-associated markers, exhibited a normal karyotype, and following directed differentiation generated cell types belonging to the three germ layers. PCR analysis and sequencing confirmed the HD patient-derived iPSC line had one normal HTT allele and one with elongated CAG repeats, equivalent to ≥180Q.

PMID:36863131 | DOI:10.1016/j.scr.2023.103056

PLoS One. 2023 Mar 2;18(3):e0277572. doi: 10.1371/journal.pone.0277572. eCollection 2023.

ABSTRACT

In this work, we introduce a novel deep learning architecture, MUCRAN (Multi-Confound Regression Adversarial Network), to train a deep learning model on clinical brain MRI while regressing demographic and technical confounding factors. We trained MUCRAN using 17,076 clinical T1 Axial brain MRIs collected from Massachusetts General Hospital before 2019 and demonstrated that MUCRAN could successfully regress major confounding factors in the vast clinical dataset. We also applied a method for quantifying uncertainty across an ensemble of these models to automatically exclude out-of-distribution data in AD detection. By combining MUCRAN and the uncertainty quantification method, we showed consistent and significant increases in the AD detection accuracy for newly collected MGH data (post-2019; 84.6% with MUCRAN vs. 72.5% without MUCRAN) and for data from other hospitals (90.3% from Brigham and Women's Hospital and 81.0% from other hospitals). MUCRAN offers a generalizable approach for deep-learning-based disease detection in heterogenous clinical data.

PMID:36862751 | DOI:10.1371/journal.pone.0277572

Cell Rep. 2023 Feb 28;42(3):112173. doi: 10.1016/j.celrep.2023.112173. Online ahead of print.

ABSTRACT

The specification of synaptic properties is fundamental for the function of neuronal circuits. "Terminal selector" transcription factors coordinate terminal gene batteries that specify cell-type-specific properties. Moreover, pan-neuronal splicing regulators have been implicated in directing neuronal differentiation. However, the cellular logic of how splicing regulators instruct specific synaptic properties remains poorly understood. Here, we combine genome-wide mapping of mRNA targets and cell-type-specific loss-of-function studies to uncover the contribution of the RNA-binding protein SLM2 to hippocampal synapse specification. Focusing on pyramidal cells and somatostatin (SST)-positive GABAergic interneurons, we find that SLM2 preferentially binds and regulates alternative splicing of transcripts encoding synaptic proteins. In the absence of SLM2, neuronal populations exhibit normal intrinsic properties, but there are non-cell-autonomous synaptic phenotypes and associated defects in a hippocampus-dependent memory task. Thus, alternative splicing provides a critical layer of gene regulation that instructs specification of neuronal connectivity in a trans-synaptic manner.

PMID:36862556 | DOI:10.1016/j.celrep.2023.112173

New Phytol. 2023 Apr;238(1):8-10. doi: 10.1111/nph.18804.

NO ABSTRACT

PMID:36862529 | DOI:10.1111/nph.18804

J Comput Biol. 2023 Mar 1. doi: 10.1089/cmb.2022.0376. Online ahead of print.

ABSTRACT

A major challenge in molecular systems biology is to understand how proteins work to transmit external signals to changes in gene expression. Computationally reconstructing these signaling pathways from protein interaction networks can help understand what is missing from existing pathway databases. We formulate a new pathway reconstruction problem, one that iteratively grows directed acyclic graphs (DAGs) from a set of starting proteins in a protein interaction network. We present an algorithm that provably returns the optimal DAGs for two different cost functions and evaluate the pathway reconstructions when applied to six diverse signaling pathways from the NetPath database. The optimal DAGs outperform an existing k-shortest paths method for pathway reconstruction, and the new reconstructions are enriched for different biological processes. Growing DAGs is a promising step toward reconstructing pathways that provably optimize a specific cost function.

PMID:36862510 | DOI:10.1089/cmb.2022.0376

Ergonomics. 2023 Mar 2:1-16. doi: 10.1080/00140139.2023.2186322. Online ahead of print.

ABSTRACT

Process control room operators (PCRO) perform a range of complex cognitive safety-critical tasks. The aim of this exploratory sequential mixed methods study was to develop an occupation specific tool to measure the task load of PCRO using NASA Task Load Index (TLX) methodology. Participants were 30 human factors experts and 146 PCRO at two refinery complexes in Iran. Dimensions were developed via a cognitive task analysis, a research review, and three expert panel. Six dimensions were identified: perceptual demand, performance, mental demand, time pressure, effort and stress. Data from 120 PCRO confirmed that the developed PCRO-TLX has acceptable psychometric properties, and a comparison with the NASA-TLX confirmed that perceptual, not physical, demand was relevant for measuring workload in PCRO. There was a positive convergence of scores of the Subjective Workload Assessment Technique and the PCRO-TLX. This reliable tool (α = 0.83) is recommended for risk assessing the task load of PCRO.

PMID:36861453 | DOI:10.1080/00140139.2023.2186322

Front Genet. 2023 Feb 13;14:1062052. doi: 10.3389/fgene.2023.1062052. eCollection 2023.

ABSTRACT

Recent studies have revealed that neural functions are involved in possibly every aspect of a cancer development, serving as bridges connecting microenvironmental stressors, activities of intracellular subsystems, and cell survival. Elucidation of the functional roles played by the neural system could provide the missing links in developing a systems-level understanding of cancer biology. However, the existing information is highly fragmented and scattered across the literature and internet databases, making it difficult for cancer researchers to use. We have conducted computational analyses of transcriptomic data of cancer tissues in TCGA and tissues of healthy organs in GTEx, aiming to demonstrate how the functional roles by the neural genes could be derived and what non-neural functions they are associated with, across different stages of 26 cancer types. Several novel discoveries are made, including i) the expressions of certain neural genes can predict the prognosis of a cancer patient; ii) cancer metastasis tends to involve specific neural functions; iii) cancers of low survival rates involve more neural interactions than those with high survival rates; iv) more malignant cancers involve more complex neural functions; and v) neural functions are probably induced to alleviate stresses and help the associated cancer cells to survive. A database, called NGC, is developed for organizing such derived neural functions and associations, along with gene expressions and functional annotations collected from public databases, aiming to provide an integrated and publicly available information resource to enable cancer researchers to take full advantage of the relevant information in their research, facilitated by tools provided by NGC.

PMID:36861131 | PMC:PMC9968960 | DOI:10.3389/fgene.2023.1062052

Front Immunol. 2023 Feb 10;14:1114368. doi: 10.3389/fimmu.2023.1114368. eCollection 2023.

ABSTRACT

The critical balance between intended and adverse effects in allogeneic hematopoietic stem cell transplantation (alloHSCT) depends on the fate of individual donor T-cells. To this end, we tracked αβT-cell clonotypes during stem cell mobilization treatment with granulocyte-colony stimulating factor (G-CSF) in healthy donors and for six months during immune reconstitution after transfer to transplant recipients. More than 250 αβT-cell clonotypes were tracked from donor to recipient. These clonotypes consisted almost exclusively of CD8+ effector memory T cells (CD8TEM), which exhibited a different transcriptional signature with enhanced effector and cytotoxic functions compared to other CD8TEM. Importantly, these distinct and persisting clonotypes could already be delineated in the donor. We confirmed these phenotypes on the protein level and their potential for selection from the graft. Thus, we identified a transcriptional signature associated with persistence and expansion of donor T-cell clonotypes after alloHSCT that may be exploited for personalized graft manipulation strategies in future studies.

PMID:36860867 | PMC:PMC9969884 | DOI:10.3389/fimmu.2023.1114368

Metab Eng Commun. 2023 Feb 16;16:e00220. doi: 10.1016/j.mec.2023.e00220. eCollection 2023 Jun.

ABSTRACT

Methyl methacrylate (MMA) is an important petrochemical with many applications. However, its manufacture has a large environmental footprint. Combined biological and chemical synthesis (semisynthesis) may be a promising alternative to reduce both cost and environmental impact, but strains that can produce the MMA precursor (citramalate) at low pH are required. A non-conventional yeast, Issatchenkia orientalis, may prove ideal, as it can survive extremely low pH. Here, we demonstrate the engineering of I. orientalis for citramalate production. Using sequence similarity network analysis and subsequent DNA synthesis, we selected a more active citramalate synthase gene (cimA) variant for expression in I. orientalis. We then adapted a piggyBac transposon system for I. orientalis that allowed us to simultaneously explore the effects of different cimA gene copy numbers and integration locations. A batch fermentation showed the genome-integrated-cimA strains produced 2.0 g/L citramalate in 48 h and a yield of up to 7% mol citramalate/mol consumed glucose. These results demonstrate the potential of I. orientalis as a chassis for citramalate production.

PMID:36860699 | PMC:PMC9969067 | DOI:10.1016/j.mec.2023.e00220

Neuro Oncol. 2023 Mar 1:noad014. doi: 10.1093/neuonc/noad014. Online ahead of print.

NO ABSTRACT

PMID:36860191 | DOI:10.1093/neuonc/noad014

J Hazard Mater. 2023 Apr 15;448:130997. doi: 10.1016/j.jhazmat.2023.130997. Epub 2023 Feb 12.

ABSTRACT

Microplastics are one of the major pollutants in aquatic environments. Among their components, Bisphenol A (BPA) is one of the most abundant and dangerous, leading to endocrine disorders deriving even in different types of cancer in mammals. However, despite this evidence, the xenobiotic effects of BPA over plantae and microalgae still need to be better understood at the molecular level. To fill this gap, we characterized the physiological and proteomic response of Chlamydomonas reinhardtii during long-term BPA exposure by analyzing physiological and biochemical parameters combined with proteomics. BPA imbalanced iron and redox homeostasis, disrupting cell function and triggering ferroptosis. Intriguingly, this microalgae defense against this pollutant is recovering at both molecular and physiological levels while starch accumulation at 72 h of BPA exposure. In this work, we addressed the molecular mechanisms involved in BPA exposure, demonstrating for the first time the induction of ferroptosis in a eukaryotic alga and how ROS detoxification mechanisms and other specific proteomic rearrangements reverted this situation. These results are of great significance not only for understanding the BPA toxicology or exploring the molecular mechanisms of ferroptosis in microalgae but also for defining novel target genes for microplastic bioremediation efficient strain development.

PMID:36860062 | DOI:10.1016/j.jhazmat.2023.130997

Commun Biol. 2023 Mar 1;6(1):230. doi: 10.1038/s42003-023-04617-4.

ABSTRACT

A thermophilic, chemolithoautotrophic, and aerobic microbial consortium (termed carbonitroflex) growing in a nutrient-poor medium and an atmosphere containing N2, O2, CO2, and CO is investigated as a model to expand our understanding of extreme biological systems. Here we show that the consortium is dominated by Carbonactinospora thermoautotrophica (strain StC), followed by Sphaerobacter thermophilus, Chelatococcus spp., and Geobacillus spp. Metagenomic analysis of the consortium reveals a mutual relationship among bacteria, with C. thermoautotrophica StC exhibiting carboxydotrophy and carbon-dioxide storage capacity. C. thermoautotrophica StC, Chelatococcus spp., and S. thermophilus harbor genes encoding CO dehydrogenase and formate oxidase. No pure cultures were obtained under the original growth conditions, indicating that a tightly regulated interactive metabolism might be required for group survival and growth in this extreme oligotrophic system. The breadwinner hypothesis is proposed to explain the metabolic flux model and highlight the vital role of C. thermoautotrophica StC (the sole keystone species and primary carbon producer) in the survival of all consortium members. Our data may contribute to the investigation of complex interactions in extreme environments, exemplifying the interconnections and dependency within microbial communities.

PMID:36859706 | DOI:10.1038/s42003-023-04617-4

Mol Biotechnol. 2023 Mar 1. doi: 10.1007/s12033-023-00699-x. Online ahead of print.

ABSTRACT

Glioblastoma (GBM) is a malignant cancer that is fatal even after standard therapy and the effects of current available therapeutics are not promising due its complex and evolving epigenetic and genetic profile. The mysteries that lead to GBM intratumoral heterogeneity and subtype transitions are not entirely clear. Systems medicine is an approach to view the patient in a whole picture integrating systems biology and synthetic biology along with computational techniques. Since the GBM oncogenesis involves genetic mutations, various therapies including gene therapeutics based on CRISPR-Cas technique, MicroRNAs, and implanted synthetic cells endowed with synthetic circuits against GBM with neural stem cells and mesenchymal stem cells acting as potential vehicles carrying therapeutics via the intranasal route, avoiding the risks of invasive methods in order to reach the GBM cells in the brain are discussed and proposed in this review. Systems medicine approach is a rather novel strategy, and since the GBM of a patient is complex and unique, thus to devise an individualized treatment strategy to tailor personalized multimodal treatments for the individual patient taking into account the phenotype of the GBM, the unique body health profile of the patient and individual responses according to the systems medicine concept might show potential to achieve optimum effects.

PMID:36859639 | DOI:10.1007/s12033-023-00699-x

Nature. 2023 Mar 1. doi: 10.1038/s41586-023-05750-0. Online ahead of print.

ABSTRACT

Gram-negative bacteria surround their cytoplasmic membrane with a peptidoglycan (PG) cell wall and an outer membrane (OM) with an outer leaflet composed of lipopolysaccharide (LPS)1. This complex envelope presents a formidable barrier to drug entry and is a major determinant of the intrinsic antibiotic resistance of these organisms2. The biogenesis pathways that build the surface are also targets of many of our most effective antibacterial therapies3. Understanding the molecular mechanisms underlying the assembly of the Gram-negative envelope therefore promises to aid the development of new treatments effective against the growing problem of drug-resistant infections. Although the individual pathways for PG and OM synthesis and assembly are well characterized, almost nothing is known about how the biogenesis of these essential surface layers is coordinated. Here we report the discovery of a regulatory interaction between the committed enzymes for the PG and LPS synthesis pathways in the Gram-negative pathogen Pseudomonas aeruginosa. We show that the PG synthesis enzyme MurA interacts directly and specifically with the LPS synthesis enzyme LpxC. Moreover, MurA was shown to stimulate LpxC activity in cells and in a purified system. Our results support a model in which the assembly of the PG and OM layers in many proteobacterial species is coordinated by linking the activities of the committed enzymes in their respective synthesis pathways.

PMID:36859542 | DOI:10.1038/s41586-023-05750-0

Breast Cancer Res. 2023 Mar 1;25(1):23. doi: 10.1186/s13058-023-01621-8.

ABSTRACT

Stratifying breast cancer into specific molecular or histologic subtypes aids in therapeutic decision-making and predicting outcomes; however, these subtypes may not be as distinct as previously thought. Patients with luminal-like, estrogen receptor (ER)-expressing tumors have better prognosis than patients with more aggressive, triple-negative or basal-like tumors. There is, however, a subset of luminal-like tumors that express lower levels of ER, which exhibit more basal-like features. We have found that breast tumors expressing lower levels of ER, traditionally considered to be luminal-like, represent a distinct subset of breast cancer characterized by the emergence of basal-like features. Lineage tracing of low-ER tumors in the MMTV-PyMT mouse mammary tumor model revealed that basal marker-expressing cells arose from normal luminal epithelial cells, suggesting that luminal-to-basal plasticity is responsible for the evolution and emergence of basal-like characteristics. This plasticity allows tumor cells to gain a new lumino-basal phenotype, thus leading to intratumoral lumino-basal heterogeneity. Single-cell RNA sequencing revealed SOX10 as a potential driver for this plasticity, which is known among breast tumors to be almost exclusively expressed in triple-negative breast cancer (TNBC) and was also found to be highly expressed in low-ER tumors. These findings suggest that basal-like tumors may result from the evolutionary progression of luminal tumors with low ER expression.

PMID:36859337 | DOI:10.1186/s13058-023-01621-8

J Cyst Fibros. 2023 Feb 27:S1569-1993(23)00056-5. doi: 10.1016/j.jcf.2023.02.005. Online ahead of print.

ABSTRACT

BACKGROUND: Extracellular vesicles (EVs) are emerging as biomarkers of disease with diagnostic potential in CF. With the advent of highly effective modulator therapy, sputum production is less common and there is a need to identify novel markers of CF disease progression, exacerbation and response to therapies in accessible fluids such as serum.

METHODS: We used size exclusion chromatography (SEC) to isolate and characterise EVs from the blood of PWCF of different ages and compared to ultracentrifugation (UC). We used nanoparticle tracking analysis to measure the number of EVs present in serum obtained from children and adults with CF. Mass spectrometry based proteomics was used to characterise protein expression changes between the groups.

RESULTS: EVs were successfully isolated in SEC fractions from 250 µl serum from PWCF in greater numbers (p <0.01) than density ultracentrifugation. There was not a significant difference in EV numbers between young children with CF and controls. However, there was significantly more EVs in adults compared to children (<6yrs) (p < 0.05). EVs from PWCF before and after Kaftrio treatment were also analysed. Significant protein expression changes were observed within all 3 group. The largest changes detected were between children and adults with CF (57 proteins had a 1.5 fold change in expression with 19 significant changes p < 0.05) and PWCF taking Kaftrio (24 significant changes in EV protein expression was observed 12 months post treatment).

CONCLUSION: In this pilot study, we performed an initial characterisation of EVs in serum from PWCF demonstrating the potential of serum EVs for further diagnostic investigation.

PMID:36858853 | DOI:10.1016/j.jcf.2023.02.005

J Ethnopharmacol. 2023 Feb 27:116306. doi: 10.1016/j.jep.2023.116306. Online ahead of print.

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: Network pharmacology is a new discipline based on systems biology theory, biological system network analysis, and multi-target drug molecule design specific signal node selection. The mechanism of action of TCM formula has the characteristics of multiple targets and levels. The mechanism is similar to the integrity, systematization and comprehensiveness of network pharmacology, so network pharmacology is suitable for the study of the pharmacological mechanism of Chinese medicine compounds.

AIM OF THE STUDY: The paper summarizes the present application status and existing problems of network pharmacology in the field of Chinese medicine formula, and formulates the research ideas, up-to-date key technology and application method and strategy of network pharmacology. Its purpose is to provide guidance and reference for using network pharmacology to reveal the modern scientific connotation of Chinese medicine.

MATERIALS AND METHODS: Literatures in this review were searched in PubMed, China National Knowledge Infrastructure (CNKI), Web of Science, ScienceDirect and Google Scholar using the keywords "traditional Chinese medicine", "Chinese herb medicine" and "network pharmacology". The literature cited in this review dates from 2002 to 2022.

RESULTS: Using network pharmacology methods to predict the basis and mechanism of pharmacodynamic substances of traditional Chinese medicines has become a trend.

CONCLUSION: Network pharmacology is a promising approach to reveal the pharmacology mechanism of Chinese medicine formula.

PMID:36858276 | DOI:10.1016/j.jep.2023.116306

J Infect. 2023 Feb 27:S0163-4453(23)00118-4. doi: 10.1016/j.jinf.2023.02.033. Online ahead of print.

NO ABSTRACT

PMID:36858179 | DOI:10.1016/j.jinf.2023.02.033