1
|
Liu X, Wang H, Gao J. scIALM: A method for sparse scRNA-seq expression matrix imputation using the Inexact Augmented Lagrange Multiplier with low error. Comput Struct Biotechnol J 2024; 23:549-558. [PMID: 38274995 PMCID: PMC10809077 DOI: 10.1016/j.csbj.2023.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a high-throughput sequencing technology that quantifies gene expression profiles of specific cell populations at the single-cell level, providing a foundation for studying cellular heterogeneity and patient pathological characteristics. It is effective for developmental, fertility, and disease studies. However, the cell-gene expression matrix of single-cell sequencing data is often sparse and contains numerous zero values. Some of the zero values derive from noise, where dropout noise has a large impact on downstream analysis. In this paper, we propose a method named scIALM for imputation recovery of sparse single-cell RNA data expression matrices, which employs the Inexact Augmented Lagrange Multiplier method to use sparse but clean (accurate) data to recover unknown entries in the matrix. We perform experimental analysis on four datasets, calling the expression matrix after Quality Control (QC) as the original matrix, and comparing the performance of scIALM with six other methods using mean squared error (MSE), mean absolute error (MAE), Pearson correlation coefficient (PCC), and cosine similarity (CS). Our results demonstrate that scIALM accurately recovers the original data of the matrix with an error of 10e-4, and the mean value of the four metrics reaches 4.5072 (MSE), 0.765 (MAE), 0.8701 (PCC), 0.8896 (CS). In addition, at 10%-50% random masking noise, scIALM is the least sensitive to the masking ratio. For downstream analysis, this study uses adjusted rand index (ARI) and normalized mutual information (NMI) to evaluate the clustering effect, and the results are improved on three datasets containing real cluster labels.
Collapse
Affiliation(s)
- Xiaohong Liu
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Han Wang
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jingyang Gao
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| |
Collapse
|
2
|
King MR, Ruff KM, Pappu RV. Emergent microenvironments of nucleoli. Nucleus 2024; 15:2319957. [PMID: 38443761 PMCID: PMC10936679 DOI: 10.1080/19491034.2024.2319957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.
Collapse
Affiliation(s)
- Matthew R. King
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| |
Collapse
|
3
|
Škulj S, Kožić M, Barišić A, Vega A, Biarnés X, Piantanida I, Barisic I, Bertoša B. Comparison of two peroxidases with high potential for biotechnology applications - HRP vs. APEX2. Comput Struct Biotechnol J 2024; 23:742-751. [PMID: 38298178 PMCID: PMC10828542 DOI: 10.1016/j.csbj.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/01/2024] [Accepted: 01/01/2024] [Indexed: 02/02/2024] Open
Abstract
Peroxidases are essential elements in many biotechnological applications. An especially interesting concept involves split enzymes, where the enzyme is separated into two smaller and inactive proteins that can dimerize into a fully active enzyme. Such split forms were developed for the horseradish peroxidase (HRP) and ascorbate peroxidase (APX) already. Both peroxidases have a high potential for biotechnology applications. In the present study, we performed biophysical comparisons of these two peroxidases and their split analogues. The active site availability is similar for all four structures. The split enzymes are comparable in stability with their native analogues, meaning that they can be used for further biotechnology applications. Also, the tertiary structures of the two peroxidases are similar. However, differences that might help in choosing one system over another for biotechnology applications were noticed. The main difference between the two systems is glycosylation which is not present in the case of APX/sAPEX2, while it has a high impact on the HRP/sHRP stability. Further differences are calcium ions and cysteine bridges that are present only in the case of HRP/sHRP. Finally, computational results identified sAPEX2 as the systems with the smallest structural variations during molecular dynamics simulations showing its dominant stability comparing to other simulated proteins. Taken all together, the sAPEX2 system has a high potential for biotechnological applications due to the lack of glycans and cysteines, as well as due to high stability.
Collapse
Affiliation(s)
- Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Matej Kožić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Aitor Vega
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10 000 Zagreb, Croatia
| | - Ivan Barisic
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
- Eko Refugium, Crno Vrelo 2, Slunj 47240, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| |
Collapse
|
4
|
Franceus J, Steynen M, Allaert Y, Bredael K, D'hooghe M, Desmet T. High-yield synthesis of 2-O-α-D-glucosyl-D-glycerate by a bifunctional glycoside phosphorylase. Appl Microbiol Biotechnol 2024; 108:55. [PMID: 38175244 DOI: 10.1007/s00253-023-12970-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/02/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Osmolytes are produced by various microorganisms as a defense mechanism to protect cells and macromolecules from damage caused by external stresses in harsh environments. Due to their useful stabilizing properties, these molecules are applied as active ingredients in a wide range of cosmetics and healthcare products. The metabolic pathways and biocatalytic syntheses of glycosidic osmolytes such as 2-O-α-D-glucosyl-D-glycerate often involve the action of a glycoside phosphorylase. Here, we report the discovery of a glucosylglycerate phosphorylase from carbohydrate-active enzyme family GH13 that is also active on sucrose, which contrasts the strict specificity of known glucosylglycerate phosphorylases that can only use α-D-glucose 1-phosphate as glycosyl donor in transglycosylation reactions. The novel enzyme can be distinguished from other phosphorylases from the same family by the presence of an atypical conserved sequence motif at specificity-determining positions in the active site. The promiscuity of the sucrose-active glucosylglycerate phosphorylase can be exploited for the high-yielding and rapid synthesis of 2-O-α-D-glucosyl-D-glycerate from sucrose and D-glycerate. KEY POINTS: • A Xylanimonas protaetiae glycoside phosphorylase can use both d-glycerate and fructose as glucosyl acceptor with high catalytic efficiency • Biocatalytic synthesis of the osmolyte 2-O-α-d-glucosyl-d-glycerate • Positions in the active site of GH13 phosphorylases act as convenient specificity fingerprints.
Collapse
Affiliation(s)
- Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Manon Steynen
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Yentl Allaert
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Kato Bredael
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Matthias D'hooghe
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
| |
Collapse
|
5
|
Fu Z, Jiang S, Sun Y, Zheng S, Zong L, Li P. Cut&tag: a powerful epigenetic tool for chromatin profiling. Epigenetics 2024; 19:2293411. [PMID: 38105608 PMCID: PMC10730171 DOI: 10.1080/15592294.2023.2293411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. Chromatin immunoprecipitation is the most popular and powerful approach for mapping chromatin, and other enzyme-tethering techniques have recently become available for living cells. Among these, Cleavage Under Targets and Tagmentation (CUT&Tag) is a relatively novel chromatin profiling method that has rapidly gained popularity in the field of epigenetics since 2019. It has also been widely adapted to map chromatin modifications and TFs in different species, illustrating the association of these chromatin epitopes with various physiological and pathological processes. Scalable single-cell CUT&Tag can be combined with distinct platforms to distinguish cellular identity, epigenetic features and even spatial chromatin profiling. In addition, CUT&Tag has been developed as a strategy for joint profiling of the epigenome, transcriptome or proteome on the same sample. In this review, we will mainly consolidate the applications of CUT&Tag and its derivatives on different platforms, give a detailed explanation of the pros and cons of this technique as well as the potential development trends and applications in the future.
Collapse
Affiliation(s)
- Zhijun Fu
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Sanjie Jiang
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Yiwen Sun
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Shanqiao Zheng
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Liang Zong
- BGI Tech Solutions Co, Ltd. BGI-Wuhan, Wuhan, China
| | - Peipei Li
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| |
Collapse
|
6
|
Sun J, Li J, He Y, Kang W, Ye X. Identification and validation of protein biomarkers for predicting gastrointestinal stromal tumor recurrence. Comput Struct Biotechnol J 2024; 23:1065-1075. [PMID: 38455069 PMCID: PMC10918489 DOI: 10.1016/j.csbj.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
We conducted a proteomic analysis using mass spectrometry to identify and validate protein biomarkers for accurately predicting recurrence risk in gastrointestinal stromal tumors (GIST) patients, focusing on differentially expressed proteins in metastatic versus primary GIST tissues. We selected five biomarkers-GPX4, RBM4, TPM3, PFKFB2, and PGAM5-and validated their expressions in primary tumors of recurrent and non-recurrent GIST patients via immunohistochemistry. Our analysis of the association between these biomarkers with recurrence-free survival (RFS) and overall survival (OS), along with their interrelationships, revealed that immunohistochemistry confirmed significantly higher expressions of these biomarkers in primary GIST tissues of recurrent patients. Kaplan-Meier survival analysis showed that high expressions of GPX4, RBM4, TPM3, PFKFB2, and PGAM5 correlated with lower RFS, and GPX4 and RBM4 with lower OS. All biomarker pairs showed positive associations, with high expressions correlating with increased recurrence rates, and GPX4 and RBM4 with higher mortality rates. In conclusion, the biomarkers GPX4, RBM4, TPM3, PFKFB2, and PGAM5 are clinically relevant for predicting GIST recurrence, with their high expressions in primary tumors linked to poorer RFS and OS. They serve as potential prognostic indicators, enabling early treatment and improved outcomes. The observed interrelationships among these biomarkers further validate their accuracy in predicting GIST recurrence.
Collapse
Affiliation(s)
| | | | - Yixuan He
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weiming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Ye
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
7
|
Drozdova P, Gurkov A, Saranchina A, Vlasevskaya A, Zolotovskaya E, Indosova E, Timofeyev M, Borvinskaya E. Transcriptional response of Saccharomyces cerevisiae to lactic acid enantiomers. Appl Microbiol Biotechnol 2024; 108:121. [PMID: 38229303 DOI: 10.1007/s00253-023-12863-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/16/2023] [Accepted: 10/24/2023] [Indexed: 01/18/2024]
Abstract
The model yeast, Saccharomyces cerevisiae, is a popular object for both fundamental and applied research, including the development of biosensors and industrial production of pharmaceutical compounds. However, despite multiple studies exploring S. cerevisiae transcriptional response to various substances, this response is unknown for some substances produced in yeast, such as D-lactic acid (DLA). Here, we explore the transcriptional response of the BY4742 strain to a wide range of DLA concentrations (from 0.05 to 45 mM), and compare it to the response to 45 mM L-lactic acid (LLA). We recorded a response to 5 and 45 mM DLA (125 and 113 differentially expressed genes (DEGs), respectively; > 50% shared) and a less pronounced response to 45 mM LLA (63 DEGs; > 30% shared with at least one DLA treatment). Our data did not reveal natural yeast promoters quantitatively sensing DLA but provide the first description of the transcriptome-wide response to DLA and enrich our understanding of the LLA response. Some DLA-activated genes were indeed related to lactate metabolism, as well as iron uptake and cell wall structure. Additional analyses showed that at least some of these genes were activated only by acidic form of DLA but not its salt, revealing the role of pH. The list of LLA-responsive genes was similar to those published previously and also included iron uptake and cell wall genes, as well as genes responding to other weak acids. These data might be instrumental for optimization of lactate production in yeast and yeast co-cultivation with lactic acid bacteria. KEY POINTS: • We present the first dataset on yeast transcriptional response to DLA. • Differential gene expression was correlated with yeast growth inhibition. • The transcriptome response to DLA was richer in comparison to LLA.
Collapse
Affiliation(s)
- Polina Drozdova
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation.
- Baikal Research Centre, Rabochaya Str. 5V, Irkutsk, 664011, Russian Federation.
| | - Anton Gurkov
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
- Baikal Research Centre, Rabochaya Str. 5V, Irkutsk, 664011, Russian Federation
| | | | | | - Elena Zolotovskaya
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
| | - Elizaveta Indosova
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
| | - Maxim Timofeyev
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
| | | |
Collapse
|
8
|
Matarredona L, Zafrilla B, Rubio-Portillo E, Bonete MJ, Esclapez J. Deepening the knowledge of universal stress proteins in Haloferax mediterranei. Appl Microbiol Biotechnol 2024; 108:124. [PMID: 38229402 DOI: 10.1007/s00253-023-12899-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 01/18/2024]
Abstract
Haloarchaea, like many other microorganisms, have developed defense mechanisms such as universal stress proteins (USPs) to cope with environmental stresses affecting microbial growth. Despite the wide distribution of these proteins in Archaea, their biochemical characteristics still need to be discovered, and there needs to be more knowledge about them focusing on halophilic Archaea. Therefore, elucidating the role of USPs would provide valuable information to improve future biotechnological applications. Accordingly, transcriptional expression of the 37 annotated USPs in the Haloferax mediterranei genome has been examined under different stress conditions. From a global perspective, finding a clear tendency between particular USPs and specific stress conditions was not possible. Contrary, data analysis indicates that there is a recruitment mechanism of proteins with a similar sequence able to modulate the H. mediterranei growth, accelerating or slowing it, depending on their number. In fact, only three of these USPs were expressed in all the tested conditions, pointing to the cell needing a set of USPs to cope with stress conditions. After analysis of the RNA-Seq data, three differentially expressed USPs were selected and homologously overexpressed. According to the growth data, the overexpression of USPs induces a gain of tolerance in response to stress, as a rule. Therefore, this is the only work that studies all the USPs in an archaeon. It represents a significant first base to continue advancing, not only in this important family of stress proteins but also in the field of biotechnology and, at an industrial level, to improve applications such as designing microorganisms resistant to stress situations. KEY POINTS: • Expression of Haloferax mediterranei USPs has been analyzed in stress conditions. • RNA-seq analysis reveals that most of the USPs in H. mediterranei are downregulated. • Homologous overexpression of USPs results in more stress-tolerant strains.
Collapse
Affiliation(s)
- Laura Matarredona
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - Basilio Zafrilla
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| |
Collapse
|
9
|
Yanagibashi S, Bamba T, Kirisako T, Kondo A, Hasunuma T. The potency of mitochondria enlargement for mitochondria-mediated terpenoid production in yeast. Appl Microbiol Biotechnol 2024; 108:110. [PMID: 38229297 DOI: 10.1007/s00253-023-12922-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 01/18/2024]
Abstract
Terpenoids are widely used in the food, beverage, cosmetics, and pharmaceutical industries. Microorganisms have been extensively studied for terpenoid production. In yeast, the introduction of the mevalonate (MVA) pathway in organelles in addition to the augmentation of its own MVA pathway have been challenging. Introduction of the MVA pathway into mitochondria is considered a promising approach for terpenoid production because acetyl-CoA, the starting molecule of the MVA pathway, is abundant in mitochondria. However, mitochondria comprise only a small percentage of the entire cell. Therefore, we hypothesized that increasing the total mitochondrial volume per cell would increase terpenoid production. First, we ascertained that the amounts of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the final molecules of the MVA pathway, were 15-fold higher of the strain expressing the MVA pathway in mitochondria than in the wild-type yeast strain. Second, we found that different deletion mutants induced different mitochondrial volumes by measuring the mitochondrial volume in various deletion mutants affecting mitochondrial morphology; for example,Δmdm32 increased mitochondrial volume, and Δfzo1 decreased it. Finally, the effects of mitochondrial volume on amounts of IPP/DMAPP and terpenoids (squalene or β-carotene) were investigated using mutants harboring large or small mitochondria expressing the MVA pathway in mitochondria. Amounts of IPP/DMAPP and terpenoids (squalene or β-carotene) increased when the mitochondrial volume expanded. Introducing the MVA pathway into mitochondria for terpenoid production in yeast may become more attractive by enlarging the mitochondrial volume. KEY POINTS: • IPP/DMAPP content increased in the strain expressing the MVA pathway in mitochondria • IPP/DMAPP and terpenoid contents are positively correlated with mitochondrial volume • Enlarging the mitochondria may improve mitochondria-mediated terpenoid production.
Collapse
Affiliation(s)
- So Yanagibashi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1-12-12 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Takahiro Bamba
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 6578501, Japan
| | - Takayoshi Kirisako
- Kirin Central Research Institute, Kirin Holdings Company, Ltd., 26-1-12-12 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 6578501, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 6578501, Japan.
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa, 230-0045, Japan.
| |
Collapse
|
10
|
Cyriac R, Lee K. Glutaminase inhibition as potential cancer therapeutics: current status and future applications. J Enzyme Inhib Med Chem 2024; 39:2290911. [PMID: 38078371 DOI: 10.1080/14756366.2023.2290911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Alterations in normal metabolic processes are defining features of cancer. Glutamine, an abundant amino acid in the human blood, plays a critical role in regulating several biosynthetic and bioenergetic pathways that support tumour growth. Glutaminolysis is a metabolic pathway that converts glutamine into various metabolites involved in the tricarboxylic acid (TCA) cycle and generates antioxidants that are vital for tumour cell survival. As glutaminase catalyses the initial step of this metabolic pathway, it is of great significance in cancer metabolism and tumour progression. Inhibition of glutaminase and targeting of glutaminolysis have emerged as promising strategies for cancer therapy. This review explores the role of glutaminases in cancer metabolism and discusses various glutaminase inhibitors developed as potential therapies for tumour regression.
Collapse
Affiliation(s)
- Rajath Cyriac
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Medicinal Chemistry & Pharmacology, Korea National University of Science and Technology, Daejeon, South Korea
| | - Kwangho Lee
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Medicinal Chemistry & Pharmacology, Korea National University of Science and Technology, Daejeon, South Korea
| |
Collapse
|
11
|
Telek A, Molnár Z, Takács K, Varga B, Grolmusz V, Tasnádi G, Vértessy BG. Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining. Appl Microbiol Biotechnol 2024; 108:101. [PMID: 38229296 DOI: 10.1007/s00253-023-12871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 01/18/2024]
Abstract
Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap. KEY POINTS: • Six new opine dehydrogenases have been discovered from a hot spring metagenome • The newly identified enzymes display a unique substrate scope • Substrate specificity is governed by two correlated active-site residues.
Collapse
Grants
- K119493 National Research, Development and Innovation Office
- K135231 National Research, Development and Innovation Office
- VEKOP-2.3.2-16-2017-00013 National Research, Development and Innovation Office
- NKP-2018-1.2.1-NKP-2018-00005 National Research, Development and Innovation Office
- TKP2021-EGA-02 National Research, Development and Innovation Office
- ÚNKP-22-4-II-BME-158 National Research, Development and Innovation Office
- RRF-2.3.1-21-2022-000 15 National Research, Development and Innovation Office
- C1580174 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- ELTE TKP 2021-NKTA-62 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- 2022-1.2.2-TÉT-IPARI-UZ-2022-00003 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
Collapse
Affiliation(s)
- András Telek
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary
| | - Zsófia Molnár
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Kristóf Takács
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Bálint Varga
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Gábor Tasnádi
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary.
| | - Beáta G Vértessy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary.
| |
Collapse
|
12
|
Fare CM, Rothstein JD. Nuclear pore dysfunction and disease: a complex opportunity. Nucleus 2024; 15:2314297. [PMID: 38383349 PMCID: PMC10883112 DOI: 10.1080/19491034.2024.2314297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
The separation of genetic material from bulk cytoplasm has enabled the evolution of increasingly complex organisms, allowing for the development of sophisticated forms of life. However, this complexity has created new categories of dysfunction, including those related to the movement of material between cellular compartments. In eukaryotic cells, nucleocytoplasmic trafficking is a fundamental biological process, and cumulative disruptions to nuclear integrity and nucleocytoplasmic transport are detrimental to cell survival. This is particularly true in post-mitotic neurons, where nuclear pore injury and errors to nucleocytoplasmic trafficking are strongly associated with neurodegenerative disease. In this review, we summarize the current understanding of nuclear pore biology in physiological and pathological contexts and discuss potential therapeutic approaches for addressing nuclear pore injury and dysfunctional nucleocytoplasmic transport.
Collapse
Affiliation(s)
- Charlotte M Fare
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey D Rothstein
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
| |
Collapse
|
13
|
Wang Z, Chen H, Sun L, Wang X, Xu Y, Tian S, Liu X. Uncovering the potential of APOD as a biomarker in gastric cancer: A retrospective and multi-center study. Comput Struct Biotechnol J 2024; 23:1051-1064. [PMID: 38455068 PMCID: PMC10918487 DOI: 10.1016/j.csbj.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
Gastric cancer (GC) poses a significant health challenge worldwide, necessitating the identification of predictive biomarkers to improve prognosis. Dysregulated lipid metabolism is a well-recognized hallmark of tumorigenesis, prompting investigation into apolipoproteins (APOs). In this study, we focused on apolipoprotein D (APOD) following comprehensive analyses of APOs in pan-cancer. Utilizing data from the TCGA-STAD and GSE62254 cohorts, we elucidated associations between APOD expression and multiple facets of GC, including prognosis, tumor microenvironment (TME), cancer biomarkers, mutations, and immunotherapy response, and identified potential anti-GC drugs. Single-cell analyses and immunohistochemical staining confirmed APOD expression in fibroblasts within the GC microenvironment. Additionally, we independently validated the prognostic significance of APOD in the ZN-GC cohort. Our comprehensive analyses revealed that high APOD expression in GC patients was notably associated with unfavorable clinical outcomes, reduced microsatellite instability and tumor mutation burden, alterations in the TME, and diminished response to immunotherapy. These findings provide valuable insights into the potential prognostic and therapeutic implications of APOD in GC.
Collapse
Affiliation(s)
- Zisong Wang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Hongshan Chen
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Le Sun
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xuanyu Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Yihang Xu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Sufang Tian
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xiaoping Liu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| |
Collapse
|
14
|
Korhonen PK, Wang T, Young ND, Byrne JJ, Campos TL, Chang BC, Taki AC, Gasser RB. Analysis of Haemonchus embryos at single cell resolution identifies two eukaryotic elongation factors as intervention target candidates. Comput Struct Biotechnol J 2024; 23:1026-1035. [PMID: 38435301 PMCID: PMC10907403 DOI: 10.1016/j.csbj.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024] Open
Abstract
Advances in single cell technologies are allowing investigations of a wide range of biological processes and pathways in animals, such as the multicellular model organism Caenorhabditis elegans - a free-living nematode. However, there has been limited application of such technology to related parasitic nematodes which cause major diseases of humans and animals worldwide. With no vaccines against the vast majority of parasitic nematodes and treatment failures due to drug resistance or inefficacy, new intervention targets are urgently needed, preferably informed by a deep understanding of these nematodes' cellular and molecular biology - which is presently lacking for most worms. Here, we created the first single cell atlas for an early developmental stage of Haemonchus contortus - a highly pathogenic, C. elegans-related parasitic nematode. We obtained and curated RNA sequence (snRNA-seq) data from single nuclei from embryonating eggs of H. contortus (150,000 droplets), and selected high-quality transcriptomic data for > 14,000 single nuclei for analysis, and identified 19 distinct clusters of cells. Guided by comparative analyses with C. elegans, we were able to reproducibly assign seven cell clusters to body wall muscle, hypodermis, neuronal, intestinal or seam cells, and identified eight genes that were transcribed in all cell clusters/types, three of which were inferred to be essential in H. contortus. Two of these genes (i.e. Hc-eef-1A and Hc-eef1G), coding for eukaryotic elongation factors (called Hc-eEF1A and Hc-eEF1G), were also demonstrated to be transcribed and expressed in all key developmental stages of H. contortus. Together with these findings, sequence- and structure-based comparative analyses indicated the potential of Hc-eEF1A and/or Hc-eEF1G as intervention targets within the protein biosynthesis machinery of H. contortus. Future work will focus on single cell studies of all key developmental stages and tissues of H. contortus, and on evaluating the suitability of the two elongation factor proteins as drug targets in H. contortus and related nematodes, with a view to finding new nematocidal drug candidates.
Collapse
Affiliation(s)
- Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tulio L. Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C.H. Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
15
|
Türkyılmaz O, Darcan C. Resistance mechanism of Escherichia coli strains with different ampicillin resistance levels. Appl Microbiol Biotechnol 2024; 108:5. [PMID: 38165477 DOI: 10.1007/s00253-023-12929-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 01/03/2024]
Abstract
Antibiotic resistance is an important problem that threatens medical treatment. Differences in the resistance levels of microorganisms cause great difficulties in understanding the mechanisms of antibiotic resistance. Therefore, the molecular reasons underlying the differences in the level of antibiotic resistance need to be clarified. For this purpose, genomic and transcriptomic analyses were performed on three Escherichia coli strains with varying degrees of adaptive resistance to ampicillin. Whole-genome sequencing of strains with different levels of resistance detected five mutations in strains with 10-fold resistance and two additional mutations in strains with 95-fold resistance. Overall, three of the seven mutations occurred as a single base change, while the other four occurred as insertions or deletions. While it was thought that 10-fold resistance was achieved by the effect of mutations in the ftsI, marAR, and rpoC genes, it was found that 95-fold resistance was achieved by the synergistic effect of five mutations and the ampC mutation. In addition, when the general transcriptomic profiles were examined, it was found that similar transcriptomic responses were elicited in strains with different levels of resistance. This study will improve our view of resistance mechanisms in bacteria with different levels of resistance and provide the basis for our understanding of the molecular mechanism of antibiotic resistance in ampicillin-resistant E. coli strains. KEY POINTS: •The mutation of the ampC promoter may act synergistically with other mutations and lead to higher resistance. •Similar transcriptomic responses to ampicillin are induced in strains with different levels of resistance. •Low antibiotic concentrations are the steps that allow rapid achievement of high antibiotic resistance.
Collapse
Affiliation(s)
- Osman Türkyılmaz
- Biotechnology Application & Research Centre, Bilecik Seyh Edebali University, Bilecik, Turkey.
| | - Cihan Darcan
- Department of Molecular Biology and Genetics, Bilecik Seyh Edebali University, Bilecik, Turkey
| |
Collapse
|
16
|
Barchi A, Massimino L, Mandarino FV, Vespa E, Sinagra E, Almolla O, Passaretti S, Fasulo E, Parigi TL, Cagliani S, Spanò S, Ungaro F, Danese S. Microbiota profiling in esophageal diseases: Novel insights into molecular staining and clinical outcomes. Comput Struct Biotechnol J 2024; 23:626-637. [PMID: 38274997 PMCID: PMC10808859 DOI: 10.1016/j.csbj.2023.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024] Open
Abstract
Gut microbiota is recognized nowadays as one of the key players in the development of several gastro-intestinal diseases. The first studies focused mainly on healthy subjects with staining of main bacterial species via culture-based techniques. Subsequently, lots of studies tried to focus on principal esophageal disease enlarged the knowledge on esophageal microbial environment and its role in pathogenesis. Gastro Esophageal Reflux Disease (GERD), the most widespread esophageal condition, seems related to a certain degree of mucosal inflammation, via interleukin (IL) 8 potentially enhanced by bacterial components, lipopolysaccharide (LPS) above all. Gram- bacteria, producing LPS), such as Campylobacter genus, have been found associated with GERD. Barrett esophagus (BE) seems characterized by a Gram- and microaerophils-shaped microbiota. Esophageal cancer (EC) development leads to an overturn in the esophageal environment with the shift from an oral-like microbiome to a prevalently low-abundant and low-diverse Gram--shaped microbiome. Although underinvestigated, also changes in the esophageal microbiome are associated with rare chronic inflammatory or neuropathic disease pathogenesis. The paucity of knowledge about the microbiota-driven mechanisms in esophageal disease pathogenesis is mainly due to the scarce sensitivity of sequencing technology and culture methods applied so far to study commensals in the esophagus. However, the recent advances in molecular techniques, especially with the advent of non-culture-based genomic sequencing tools and the implementation of multi-omics approaches, have revolutionized the microbiome field, with promises of implementing the current knowledge, discovering more mechanisms underneath, and giving insights into the development of novel therapies aimed to re-establish the microbial equilibrium for ameliorating esophageal diseases..
Collapse
Affiliation(s)
- Alberto Barchi
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Luca Massimino
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Edoardo Vespa
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Emanuele Sinagra
- Gastroenterology & Endoscopy Unit, Fondazione Istituto G. Giglio, Cefalù, Italy
| | - Omar Almolla
- Università Vita-Salute San Raffaele, Faculty of Medicine, Milan, Italy
| | - Sandro Passaretti
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ernesto Fasulo
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Tommaso Lorenzo Parigi
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Faculty of Medicine, Milan, Italy
| | - Stefania Cagliani
- Università Vita-Salute San Raffaele, Faculty of Medicine, Milan, Italy
| | - Salvatore Spanò
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Federica Ungaro
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Silvio Danese
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Faculty of Medicine, Milan, Italy
| |
Collapse
|
17
|
Esteban-Medina M, de la Oliva Roque VM, Herráiz-Gil S, Peña-Chilet M, Dopazo J, Loucera C. drexml: A command line tool and Python package for drug repurposing. Comput Struct Biotechnol J 2024; 23:1129-1143. [PMID: 38510973 PMCID: PMC10950807 DOI: 10.1016/j.csbj.2024.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
We introduce drexml, a command line tool and Python package for rational data-driven drug repurposing. The package employs machine learning and mechanistic signal transduction modeling to identify drug targets capable of regulating a particular disease. In addition, it employs explainability tools to contextualize potential drug targets within the functional landscape of the disease. The methodology is validated in Fanconi Anemia and Familial Melanoma, two distinct rare diseases where there is a pressing need for solutions. In the Fanconi Anemia case, the model successfully predicts previously validated repurposed drugs, while in the Familial Melanoma case, it identifies a promising set of drugs for further investigation.
Collapse
Affiliation(s)
- Marina Esteban-Medina
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Víctor Manuel de la Oliva Roque
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Sara Herráiz-Gil
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U714, Madrid, Spain
- Departamento de Bioingeniería, Universidad Carlos III de Madrid (UC3M), Madrid, Spain
- Regenerative Medicine and Tissue Engineering Group, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - María Peña-Chilet
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Platform of Big Data, AI and Biostatistics, Health Research Institute La Fe (IISLAFE), Valencia, Spain
| | - Joaquín Dopazo
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
- FPS/ELIXIR-es, Hospital Virgen del Rocío, Seville, Spain
| | - Carlos Loucera
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
| |
Collapse
|
18
|
Hou D, Liu R, Hao S, Dou Y, Chen G, Liu L, Li T, Cao Y, Huang H, Duan C. Notoginsenoside R1 improves intestinal microvascular functioning in sepsis by targeting Drp1-mediated mitochondrial quality imbalance. Pharm Biol 2024; 62:250-260. [PMID: 38389274 PMCID: PMC10896147 DOI: 10.1080/13880209.2024.2318349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
CONTEXT Sepsis can result in critical organ failure, and notoginsenoside R1 (NGR1) offers mitochondrial protection. OBJECTIVE To determine whether NGR1 improves organ function and prognosis after sepsis by protecting mitochondrial quality. MATERIALS AND METHODS A sepsis model was established in C57BL/6 mice using cecum ligation puncture (CLP) and an in vitro model with lipopolysaccharide (LPS, 10 µg/mL)-stimulated primary intestinal microvascular endothelial cells (IMVECs) and then determine NGR1's safe dosage. Groups for each model were: in vivo-a control group, a CLP-induced sepsis group, and a CLP + NGR1 treatment group (30 mg/kg/d for 3 d); in vitro-a control group, a LPS-induced sepsis group, and a LPS + NGR1 treatment group (4 μM for 30 min). NGR1's effects on survival, intestinal function, mitochondrial quality, and mitochondrial dynamic-related protein (Drp1) were evaluated. RESULTS Sepsis resulted in approximately 60% mortality within 7 days post-CLP, with significant reductions in intestinal microvascular perfusion and increases in vascular leakage. Severe mitochondrial quality imbalance was observed in IMVECs. NGR1 (IC50 is 854.1 μM at 30 min) targeted Drp1, inhibiting mitochondrial translocation, preventing mitochondrial fragmentation and restoring IMVEC morphology and function, thus protecting against intestinal barrier dysfunction, vascular permeability, microcirculatory flow, and improving sepsis prognosis. DISCUSSION AND CONCLUSIONS Drp1-mediated mitochondrial quality imbalance is a potential therapeutic target for sepsis. Small molecule natural drugs like NGR1 targeting Drp1 may offer new directions for organ protection following sepsis. Future research should focus on clinical trials to evaluate NGR1's efficacy across various patient populations, potentially leading to novel treatments for sepsis.
Collapse
Affiliation(s)
- Dongyao Hou
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Ruixue Liu
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Shuai Hao
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, P.R. China
| | - Yong Dou
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Guizhen Chen
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Liangming Liu
- Department of Shock and Transfusion, State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Tao Li
- Department of Shock and Transfusion, State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Yunxing Cao
- Department of Intensive Care Unit, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - He Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Chenyang Duan
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| |
Collapse
|
19
|
Marmion M, Macori G, Barroug S, Soro AB, Bourke P, Tiwari BK, Whyte P, Scannell AGM. Added insult to injury? The response of meat-associated pathogens to proposed antimicrobial interventions. Appl Microbiol Biotechnol 2024; 108:87. [PMID: 38189954 PMCID: PMC10774175 DOI: 10.1007/s00253-023-12849-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 01/09/2024]
Abstract
Modern requirements for 'green label' meat products have led to the design of novel antimicrobial innovations which prioritise quality, safety and longevity. Plasma-functionalised water (PFW), ultraviolet light and natural antimicrobial compositions have been investigated and optimised for control of foodborne pathogens like Campylobacter jejuni and Salmonella enterica serovar Typhimurium. However, given the adaptive mechanisms present in bacteria under external stresses, it is imperative to understand the effect that sublethal treatment may have on the bacterial transcriptome. In this study, Salmonella Typhimurium and C. jejuni were treated with sublethal doses of ultraviolet light, a citrus juice/essential oil marinade, and 'spark' or 'glow' cold plasma generation system-produced PFW. Immediately after treatment, cells were lysed and RNA was extracted and purified. mRNA was converted to cDNA by reverse transcription-PCR and sequenced by an Illumina MiSeq® system. Sequences were filtered and analysed using the Tuxedo workflow. Sublethal treatment of Campylobacter jejuni and Salmonella Typhimurium led to increased immediate cellular and metabolic activity, as well as diversification in protein and metabolic functioning. There was further expression of pathogenesis and virulence-associated traits associated with spark PFW and marinade treatment of Salmonella Typhimurium. However, similar concerns were not raised with glow PFW or UV-treated samples. This study provides science-based evidence of the efficacy of multi-hurdle antimicrobial system using green-label marinades and PFW or UV to inactivate pathogens without upregulating virulence traits in surviving cells. This study will inform policymakers and food industry stakeholders and reinforces the need to incorporate in-line novel technologies to ensure consumer safety. KEY POINTS: • Salmonella and C. jejuni showed increased cell activity in immediate response to stress. • Virulence genes showed increased expression when treated with natural antimicrobials and sPFW. • Reduced immediate transcriptomic response to gPFW and UV treatment indicates lower risk.
Collapse
Affiliation(s)
- Maitiú Marmion
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland.
- UCD Centre for Food Safety, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland.
| | - Guerrino Macori
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
- UCD Centre for Food Safety, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
| | - Soukaina Barroug
- UCD School of Biosystems and Engineering, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
| | - Arturo B Soro
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
- Department of Food Chemistry and Technology, Teagasc Food Research Centre, Ashtown, Dublin 15, D15 KN3K, Ireland
| | - Paula Bourke
- UCD School of Biosystems and Engineering, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
| | - Brijesh K Tiwari
- Department of Food Chemistry and Technology, Teagasc Food Research Centre, Ashtown, Dublin 15, D15 KN3K, Ireland
| | - Paul Whyte
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
| | - Amalia G M Scannell
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
- UCD Centre for Food Safety, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
- UCD Institute of Food and Health, University College Dublin, Belfield, Dublin 4, D04V4W8, Ireland
| |
Collapse
|
20
|
Fernández-Edreira D, Liñares-Blanco J, V.-del-Río P, Fernandez-Lozano C. VIBES: A consensus subtyping of the vaginal microbiota reveals novel classification criteria. Comput Struct Biotechnol J 2024; 23:148-156. [PMID: 38144944 PMCID: PMC10749217 DOI: 10.1016/j.csbj.2023.11.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023] Open
Abstract
This study aimed to develop a robust classification scheme for stratifying patients based on vaginal microbiome. By employing consensus clustering analysis, we identified four distinct clusters using a cohort that includes individuals diagnosed with Bacterial Vaginosis (BV) as well as control participants, each characterized by unique patterns of microbiome species abundances. Notably, the consistent distribution of these clusters was observed across multiple external cohorts, such as SRA022855, SRA051298, PRJNA208535, PRJNA797778, and PRJNA302078 obtained from public repositories, demonstrating the generalizability of our findings. We further trained an elastic net model to predict these clusters, and its performance was evaluated in various external cohorts. Moreover, we developed VIBES, a user-friendly R package that encapsulates the model for convenient implementation and enables easy predictions on new data. Remarkably, we explored the applicability of this new classification scheme in providing valuable insights into disease progression, treatment response, and potential clinical outcomes in BV patients. Specifically, we demonstrated that the combined output of VIBES and VALENCIA scores could effectively predict the response to metronidazole antibiotic treatment in BV patients. Therefore, this study's outcomes contribute to our understanding of BV heterogeneity and lay the groundwork for personalized approaches to BV management and treatment selection.
Collapse
Affiliation(s)
- Diego Fernández-Edreira
- Department of Computer Science and Information Technologies, Faculty of Computer Science, CITIC-Research Center of Information and Communication Technologies, Universidade da Coruña, A Coruña, Spain
| | | | - Patricia V.-del-Río
- Servicio de Ginecología, Hospital Universitario Lucus Augusti (HULA). Servizo Galego de Saúde (SERGAS), Spain
| | - Carlos Fernandez-Lozano
- Department of Computer Science and Information Technologies, Faculty of Computer Science, CITIC-Research Center of Information and Communication Technologies, Universidade da Coruña, A Coruña, Spain
| |
Collapse
|
21
|
Musilova J, Vafek Z, Puniya BL, Zimmer R, Helikar T, Sedlar K. Augusta: From RNA-Seq to gene regulatory networks and Boolean models. Comput Struct Biotechnol J 2024; 23:783-790. [PMID: 38312198 PMCID: PMC10837063 DOI: 10.1016/j.csbj.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of a GRN inferred from expression data is further refined by predicting transcription factor binding motifs in promoters of regulated genes and by incorporating verified interactions obtained from databases. Moreover, a refined GRN is transformed into a draft BN by searching in the curated model database and setting logical rules to incoming edges of target genes, which can be further manually edited as the model is provided in the SBML file format. The approach is applicable even if information about the organism under study is not available in the databases, which is typically the case for non-model organisms including most microbes. Augusta can be operated from the command line and, thus, is easy to use for automated prediction of models for various genomes. The Augusta package is freely available at github.com/JanaMus/Augusta. Documentation and tutorials are available at augusta.readthedocs.io.
Collapse
Affiliation(s)
- Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno 61600, Czech Republic
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Zdenek Vafek
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
- Institute of Forensic Engineering, Brno University of Technology, Brno 61200, Czech Republic
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Ralf Zimmer
- Department of Informatics, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Tomas Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno 61600, Czech Republic
- Department of Informatics, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| |
Collapse
|
22
|
Abstract
Single-cell RNA sequencing (scRNA-seq) is a relatively new technology that has stimulated enormous interest in statistics, data science, and computational biology due to the high dimensionality, complexity, and large scale associated with scRNA-seq data. Nonnegative matrix factorization (NMF) offers a unique approach due to its meta-gene interpretation of resulting low-dimensional components. However, NMF approaches suffer from the lack of multiscale analysis. This work introduces two persistent Laplacian regularized NMF methods, namely, topological NMF (TNMF) and robust topological NMF (rTNMF). By employing a total of 12 datasets, we demonstrate that the proposed TNMF and rTNMF significantly outperform all other NMF-based methods. We have also utilized TNMF and rTNMF for the visualization of popular Uniform Manifold Approximation and Projection (UMAP) and t -distributed stochastic neighbor embedding (t -SNE).
Collapse
Affiliation(s)
- Yuta Hozumi
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
23
|
Aldas-Vargas A, Kers JG, Smidt H, Rijnaarts HHM, Sutton NB. Bioaugmentation has temporary effect on anaerobic pesticide biodegradation in simulated groundwater systems. Biodegradation 2024; 35:281-297. [PMID: 37439919 PMCID: PMC10951022 DOI: 10.1007/s10532-023-10039-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/30/2023] [Indexed: 07/14/2023]
Abstract
Groundwater is the most important source for drinking water in The Netherlands. Groundwater quality is threatened by the presence of pesticides, and biodegradation is a natural process that can contribute to pesticide removal. Groundwater conditions are oligotrophic and thus biodegradation can be limited by the presence and development of microbial communities capable of biodegrading pesticides. For that reason, bioremediation technologies such as bioaugmentation (BA) can help to enhance pesticide biodegradation. We studied the effect of BA using enriched mixed inocula in two column bioreactors that simulate groundwater systems at naturally occurring redox conditions (iron and sulfate-reducing conditions). Columns were operated for around 800 days, and two BA inoculations (BA1 and BA2) were conducted in each column. Inocula were enriched from different wastewater treatment plants (WWTPs) under different redox-conditions. We observed a temporary effect of BA1, reaching 100% removal efficiency of the pesticide 2,4-D after 100 days in both columns. In the iron-reducing column, 2,4-D removal was in general higher than under sulfate-reducing conditions demonstrating the influence of redox conditions on overall biodegradation. We observed a temporary shift in microbial communities after BA1 that is relatable to the increase in 2,4-D removal efficiency. After BA2 under sulfate-reducing conditions, 2,4-D removal efficiency decreased, but no change in the column microbial communities was observed. The present study demonstrates that BA with a mixed inoculum can be a valuable technique for improving biodegradation in anoxic groundwater systems at different redox-conditions.
Collapse
Affiliation(s)
- Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Jannigje G Kers
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Huub H M Rijnaarts
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands.
| |
Collapse
|
24
|
Saad MG, Beyenal H, Dong WJ. Dual roles of the conditional extracellular vesicles derived from Pseudomonas aeruginosa biofilms: Promoting and inhibiting bacterial biofilm growth. Biofilm 2024; 7:100183. [PMID: 38380422 PMCID: PMC10876606 DOI: 10.1016/j.bioflm.2024.100183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/19/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Antibiotic-resistant biofilm infections have emerged as public health concerns because of their enhanced tolerance to high-dose antibiotic treatments. The biofilm life cycle involves multiple developmental stages, which are tightly regulated by active cell-cell communication via specific extracellular signal messengers such as extracellular vesicles. This study was aimed at exploring the roles of extracellular vesicles secreted by Pseudomonas aeruginosa at different developmental stages in controlling biofilm growth. Our results show that extracellular vesicles secreted by P. aeruginosa biofilms during their exponential growth phase (G-EVs) enhance biofilm growth. In contrast, extracellular vesicles secreted by P. aeruginosa biofilms during their death/survival phase (D-EVs) can effectively inhibit/eliminate P. aeruginosa PAO1 biofilms up to 4.8-log10 CFU/cm2. The inhibition effectiveness of D-EVs against P. aeruginosa biofilms grown for 96 h improved further in the presence of 10-50 μM Fe3+ ions. Proteomic analysis suggests the inhibition involves an iron-dependent ferroptosis mechanism. This study is the first to report the functional role of bacterial extracellular vesicles in bacterial growth, which depends on the developmental stage of the parent bacteria. The finding of D-EV-activated ferroptosis-based bacterial death may have significant implications for preventing antibiotic resistance in biofilms.
Collapse
Affiliation(s)
- Marwa Gamal Saad
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99164, USA
| | - Haluk Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99164, USA
| | - Wen-Ji Dong
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99164, USA
| |
Collapse
|
25
|
Qiu Y, Liu W, Wu M, Bao H, Sun X, Dou Q, Jia H, Liu W, Shen Y. Construction of an alternative NADPH regeneration pathway improves ethanol production in Saccharomyces cerevisiae with xylose metabolic pathway. Synth Syst Biotechnol 2024; 9:269-276. [PMID: 38469586 PMCID: PMC10926300 DOI: 10.1016/j.synbio.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Full conversion of glucose and xylose from lignocellulosic hydrolysates is required for obtaining a high ethanol yield. However, glucose and xylose share flux in the pentose phosphate pathway (PPP) and glycolysis pathway (EMP), with glucose having a competitive advantage in the shared metabolic pathways. In this work, we knocked down ZWF1 to preclude glucose from entering the PPP. This reduced the [NADPH] level and disturbed growth on both glucose or xylose, confirming that the oxidative PPP, which begins with Zwf1p and ultimately leads to CO2 production, is the primary source of NADPH in both glucose and xylose. Upon glucose depletion, gluconeogenesis is necessary to generate glucose-6-phosphate, the substrate of Zwf1p. We re-established the NADPH regeneration pathway by replacing the endogenous NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene TDH3 with heterogenous NADP + -GAPDH genes GDH, gapB, and GDP1. Among the resulting strains, the strain BZP1 (zwf1Δ, tdh3::GDP1) exhibited a similar xylose consumption rate before glucose depletion, but a 1.6-fold increased xylose consumption rate following glucose depletion compared to the original strain BSGX001, and the ethanol yield for total consumed sugars of BZP1 was 13.5% higher than BSGX001. This suggested that using the EMP instead of PPP to generate NADPH reduces the wasteful metabolic cycle and excess CO2 release from oxidative PPP. Furthermore, we used a copper-repressing promoter to modulate the expression of ZWF1 and optimize the timing of turning off the ZWF1, therefore, to determine the competitive equilibrium between glucose-xylose co-metabolism. This strategy allowed fast growth in the early stage of fermentation and low waste in the following stages of fermentation.
Collapse
Affiliation(s)
- Yali Qiu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Wei Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Meiling Wu
- Advanced Medical Research Institute, Shandong University, Jinan, 250012, China
| | - Haodong Bao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xinhua Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Qin Dou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Hongying Jia
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| |
Collapse
|
26
|
Burger PA. Integrating One Health into Systems Science. One Health 2024; 18:100701. [PMID: 38468609 PMCID: PMC10926283 DOI: 10.1016/j.onehlt.2024.100701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
One Health Systems Science. The three subsystems of One Health (ecosystem, human and animal health) are integrated in the Systems Science concept, where objects or adaptive agents (circles) interact with a dynamic environment, and Systems Thinking can lead it intervations (Systems Design) generating a change in One Health outcomes. Real-time genomic data retrieved from the three subsystems porvide information fo Systems Thinking and Systems Design.Unlabelled Image.
Collapse
Affiliation(s)
- Pamela A. Burger
- University of Veterinary Medicine Vienna, Research Institute of Wildlife Ecology, Savoyenstrasse 1, 1160 Vienna, Austria
| |
Collapse
|
27
|
Buchan JR. Stress granule and P-body clearance: Seeking coherence in acts of disappearance. Semin Cell Dev Biol 2024; 159-160:10-26. [PMID: 38278052 PMCID: PMC10939798 DOI: 10.1016/j.semcdb.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/28/2024]
Abstract
Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into how cells regulate biomolecular condensate formation and function, and identify therapeutic strategies in disease states where aberrant persistence of stress granules in particular is implicated. Here, I review and compare the contributions of chaperones, the cytoskeleton, post-translational modifications, RNA helicases, granulophagy and the proteasome to stress granule and P-body clearance. Additionally, I highlight the potentially vital role of RNA regulation, cellular energy, and changes in the interaction networks of stress granules and P-bodies as means of eliciting clearance. Finally, I discuss evidence for interplay of distinct clearance mechanisms, suggest future experimental directions, and suggest a simple working model of stress granule clearance.
Collapse
Affiliation(s)
- J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85716, United States.
| |
Collapse
|
28
|
Nowrouzi B, Torres-Montero P, Kerkhoven EJ, Martínez JL, Rios-Solis L. Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production. Metab Eng Commun 2024; 18:e00229. [PMID: 38098801 PMCID: PMC10716015 DOI: 10.1016/j.mec.2023.e00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Saccharomyces cerevisiae has been conveniently used to produce Taxol® anticancer drug early precursors. However, the harmful impact of oxidative stress by the first cytochrome P450-reductase enzymes (CYP725A4-POR) of Taxol® pathway has hampered sufficient progress in yeast. Here, we evolved an oxidative stress-resistant yeast strain with three-fold higher titre of their substrate, taxadiene. The performance of the evolved and parent strains were then evaluated in galactose-limited chemostats before and under the oxidative stress by an oxidising agent. The interaction of evolution and oxidative stress was comprehensively evaluated through transcriptomics and metabolite profiles integration in yeast enzyme-constrained genome scale model. Overall, the evolved strain showed improved respiration, reduced overflow metabolites production and oxidative stress re-induction tolerance. The cross-protection mechanism also potentially contributed to better heme, flavin and NADPH availability, essential for CYP725A4 and POR optimal activity in yeast. The results imply that the evolved strain is a robust cell factory for future efforts towards Taxol© production.
Collapse
Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Pablo Torres-Montero
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Eduard J. Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - José L. Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| |
Collapse
|
29
|
González-Hernández Y, Perré P. Building blocks needed for mechanistic modeling of bioprocesses: A critical review based on protein production by CHO cells. Metab Eng Commun 2024; 18:e00232. [PMID: 38501051 PMCID: PMC10945193 DOI: 10.1016/j.mec.2024.e00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/12/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
This paper reviews the key building blocks needed to develop a mechanistic model for use as an operational production tool. The Chinese Hamster Ovary (CHO) cell, one of the most widely used hosts for antibody production in the pharmaceutical industry, is considered as a case study. CHO cell metabolism is characterized by two main phases, exponential growth followed by a stationary phase with strong protein production. This process presents an appropriate degree of complexity to outline the modeling strategy. The paper is organized into four main steps: (1) CHO systems and data collection; (2) metabolic analysis; (3) formulation of the mathematical model; and finally, (4) numerical solution, calibration, and validation. The overall approach can build a predictive model of target variables. According to the literature, one of the main current modeling challenges lies in understanding and predicting the spontaneous metabolic shift. Possible candidates for the trigger of the metabolic shift include the concentration of lactate and carbon dioxide. In our opinion, ammonium, which is also an inhibiting product, should be further investigated. Finally, the expected progress in the emerging field of hybrid modeling, which combines the best of mechanistic modeling and machine learning, is presented as a fascinating breakthrough. Note that the modeling strategy discussed here is a general framework that can be applied to any bioprocess.
Collapse
Affiliation(s)
- Yusmel González-Hernández
- Université Paris-Saclay, CentraleSupélec, Laboratoire de Génie des Procédés et Matériaux, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), 3 Rue des Rouges Terres, 51110, Pomacle, France
| | - Patrick Perré
- Université Paris-Saclay, CentraleSupélec, Laboratoire de Génie des Procédés et Matériaux, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), 3 Rue des Rouges Terres, 51110, Pomacle, France
| |
Collapse
|
30
|
Maree M, Ushijima Y, Fernandes PB, Higashide M, Morikawa K. SCC mec transformation requires living donor cells in mixed biofilms. Biofilm 2024; 7:100184. [PMID: 38440091 PMCID: PMC10909703 DOI: 10.1016/j.bioflm.2024.100184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen that has emerged through the horizontal acquisition of the staphylococcal cassette chromosome mec (SCCmec). Previously, we showed that SCCmec from heat-killed donors can be transferred via natural transformation in biofilms at frequencies of 10-8-10-7. Here, we show an improved transformation assay of SCCmec with frequencies up to 10-2 using co-cultured biofilms with living donor cells. The Ccr-attB system played an important role in SCCmec transfer, and the deletion of ccrAB recombinase genes reduced the frequency ∼30-fold. SCCmec could be transferred from either MRSA or methicillin-resistant coagulase-negative staphylococci to some methicillin-sensitive S. aureus recipients. In addition, the transformation of other plasmid or chromosomal genes is enhanced by using living donor cells. This study emphasizes the role of natural transformation as an evolutionary ability of S. aureus and in MRSA emergence.
Collapse
Affiliation(s)
- Mais Maree
- Institute of Medicine, University of Tsukuba, Japan
| | | | | | - Masato Higashide
- Kotobiken Medical Laboratories, Inc., Kamiyokoba, Tsukuba, Japan
| | | |
Collapse
|
31
|
Wan W, Wu W, Amier Y, Li X, Yang J, Huang Y, Xun Y, Yu X. Engineered microorganisms: A new direction in kidney stone prevention and treatment. Synth Syst Biotechnol 2024; 9:294-303. [PMID: 38510204 PMCID: PMC10950756 DOI: 10.1016/j.synbio.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Numerous studies have shown that intestinal and urinary tract flora are closely related to the formation of kidney stones. The removal of probiotics represented by lactic acid bacteria and the colonization of pathogenic bacteria can directly or indirectly promote the occurrence of kidney stones. However, currently existing natural probiotics have limitations. Synthetic biology is an emerging discipline in which cells or living organisms are genetically designed and modified to have biological functions that meet human needs, or even create new biological systems, and has now become a research hotspot in various fields. Using synthetic biology approaches of microbial engineering and biological redesign to enable probiotic bacteria to acquire new phenotypes or heterologous protein expression capabilities is an important part of synthetic biology research. Synthetic biology modification of microorganisms in the gut and urinary tract can effectively inhibit the development of kidney stones by a range of means, including direct degradation of metabolites that promote stone production or indirect regulation of flora homeostasis. This article reviews the research status of engineered microorganisms in the prevention and treatment of kidney stones, to provide a new and effective idea for the prevention and treatment of kidney stones.
Collapse
Affiliation(s)
- Wenlong Wan
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Weisong Wu
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yirixiatijiang Amier
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xianmiao Li
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Junyi Yang
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yisheng Huang
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yang Xun
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiao Yu
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| |
Collapse
|
32
|
Jiang C, Zhao G, Wang H, Zheng W, Zhang R, Wang L, Zheng Z. Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto. Gene 2024; 907:148264. [PMID: 38346457 DOI: 10.1016/j.gene.2024.148264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
This research combined Whole-Genome sequencing, intraspecific comparative genomics and transposon mutagenesis to investigate the menaquinone-7 (MK-7) synthesis potential in Bacillus subtilis natto. First, Whole-Genome sequencing showed that Bacillus subtilis natto BN-P15-11-1 contains one single circular chromosome in size of 3,982,436 bp with a GC content of 43.85 %, harboring 4,053 predicted coding genes. Next, the comparative genomics analysis among strain BN-P15-11-1 with model Bacillus subtilis 168 and four typical Bacillus subtilis natto strains proves that the closer evolutionary relationship Bacillus subtilis natto BN-P15-11-1 and Bacillus subtilis 168 both exhibit strong biosynthetic potential. To further dig for MK-7 biosynthesis latent capacity of BN-P15-11-1, we constructed a mutant library using transposons and a high throughput screening method using microplates. We obtained a YqgQ deficient high MK-7 yield strain F4 with a yield 3.02 times that of the parent strain. Experiments also showed that the high yield mutants had defects in different transcription and translation regulatory factor genes, indicating that regulatory factor defects may affect the biosynthesis and accumulation of MK-7 by altering the overall metabolic level. The findings of this study will provide more novel insights on the precise identification and rational utilization of the Bacillus subtilis subspecies for biosynthesis latent capacity.
Collapse
Affiliation(s)
- Chunxu Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Genhai Zhao
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Han Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Wenqian Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Rui Zhang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Li Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Zhiming Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| |
Collapse
|
33
|
Alosaimi ME, Alotaibi BS, Abduljabbar MH, Alnemari RM, Almalki AH, Serag A. Therapeutic implications of dapagliflozin on the metabolomics profile of diabetic rats: A GC-MS investigation coupled with multivariate analysis. J Pharm Biomed Anal 2024; 242:116018. [PMID: 38341926 DOI: 10.1016/j.jpba.2024.116018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Diabetes mellitus is a complex metabolic disorder with systemic implications, necessitating the search for reliable biomarkers and therapeutic strategies. This study investigates the metabolomics profile alterations in diabetic rats, with a focus on the therapeutic effects of Dapagliflozin, a drug known to inhibit renal glucose reabsorption, using Gas Chromatography-Mass Spectrometry analysis. METHODS A GC-MS based metabolomics approach combined with multivariate and univariate statistical analyses was utilized to study serum samples from a diabetic model of Wistar rats, treated with dapagliflozin. Metabolomics pathways analysis was also performed to identify the altered metabolic pathways associated with the disease and the intervention. RESULTS Dapagliflozin treatment in diabetic rats resulted in normalized levels of metabolites associated with insulin resistance, notably branched-chain and aromatic amino acids. Improvements in glycine metabolism were observed, suggesting a modulatory role of the drug. Additionally, reduced palmitic acid levels indicated an alleviation of lipotoxic effects. The metabolic changes indicate a restorative effect of dapagliflozin on diabetes-induced metabolic perturbations. CONCLUSIONS The comprehensive metabolomics analysis demonstrated the potential of GC-MS in revealing significant metabolic pathway alterations due to dapagliflozin treatment in diabetic model rats. The therapy induced normalization of key metabolic disturbances, providing insights that could advance personalized diabetes mellitus management and therapeutic monitoring, highlighting the utility of metabolomics in understanding drug mechanisms and effects.
Collapse
Affiliation(s)
- Manal E Alosaimi
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Badriyah S Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Maram H Abduljabbar
- Department of Pharmacology and Toxicology, College of Pharmacy, Taif University, P.O. Box 11099, 21944 Taif, Saudi Arabia
| | - Reem M Alnemari
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, 21944 Taif, Saudi Arabia; Addiction and Neuroscience Research Unit, Health Science Campus, Taif University, P.O. Box 11099, 21944 Taif, Saudi Arabia
| | - Ahmed Serag
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, 11751 Nasr City, Cairo, Egypt.
| |
Collapse
|
34
|
Kovacheva E, Gevezova M, Maes M, Sarafian V. The mast cells - Cytokines axis in Autism Spectrum Disorder. Neuropharmacology 2024; 249:109890. [PMID: 38431049 DOI: 10.1016/j.neuropharm.2024.109890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/19/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disturbance, diagnosed in early childhood. It is associated with varying degrees of dysfunctional communication and social skills, repetitive and stereotypic behaviors. Regardless of the constant increase in the number of diagnosed patients, there are still no established treatment schemes in global practice. Many children with ASD have allergic symptoms, often in the absence of mast cell (MC) positive tests. Activation of MCs may release molecules related to inflammation and neurotoxicity, which contribute to the pathogenesis of ASD. The aim of the present paper is to enrich the current knowledge regarding the relationship between MCs and ASD by providing PPI network analysis-based data that reveal key molecules and immune pathways associated with MCs in the pathogenesis of autism. Network and enrichment analyzes were performed using receptor information and secreted molecules from activated MCs identified in ASD patients. Our analyses revealed cytokines and key marker molecules for MCs degranulation, molecular pathways of key mediators released during cell degranulation, as well as various receptors. Understanding the relationship between ASD and the activation of MCs, as well as the involved molecules and interactions, is important for elucidating the pathogenesis of ASD and developing effective future treatments for autistic patients by discovering new therapeutic target molecules.
Collapse
Affiliation(s)
- Eleonora Kovacheva
- Department of Medical Biology, Medical University-Plovdiv, Plovdiv, Bulgaria; Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Maria Gevezova
- Department of Medical Biology, Medical University-Plovdiv, Plovdiv, Bulgaria; Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Michael Maes
- Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria; Sichuan Provincial Center for Mental Health, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China; Key Laboratory of Psychosomatic Medicine, Chinese Academy of Medical Sciences, Chengdu, 610072, China; Department of Psychiatry, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand; Cognitive Fitness and Technology Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Department of Psychiatry, Medical University-Plovdiv, Plovdiv, Bulgaria; Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, South Korea
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, Plovdiv, Bulgaria; Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria.
| |
Collapse
|
35
|
Wong CH, Wingett SW, Qian C, Hunter MR, Taliaferro JM, Ross-Thriepland D, Bullock SL. Genome-scale requirements for dynein-based transport revealed by a high-content arrayed CRISPR screen. J Cell Biol 2024; 223:e202306048. [PMID: 38448164 PMCID: PMC10916854 DOI: 10.1083/jcb.202306048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 01/10/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
The microtubule motor dynein plays a key role in cellular organization. However, little is known about how dynein's biosynthesis, assembly, and functional diversity are orchestrated. To address this issue, we have conducted an arrayed CRISPR loss-of-function screen in human cells using the distribution of dynein-tethered peroxisomes and early endosomes as readouts. From a genome-wide gRNA library, 195 validated hits were recovered and parsed into those impacting multiple dynein cargoes and those whose effects are restricted to a subset of cargoes. Clustering of high-dimensional phenotypic fingerprints revealed co-functional proteins involved in many cellular processes, including several candidate novel regulators of core dynein functions. Further analysis of one of these factors, the RNA-binding protein SUGP1, indicates that it promotes cargo trafficking by sustaining functional expression of the dynein activator LIS1. Our data represent a rich source of new hypotheses for investigating microtubule-based transport, as well as several other aspects of cellular organization captured by our high-content imaging.
Collapse
Affiliation(s)
- Chun Hao Wong
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Centre for Genomic Research, Discovery Sciences, AstraZeneca , Cambridge, UK
| | - Steven W Wingett
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Chen Qian
- Quantitative Biology, Discovery Sciences, AstraZeneca , Cambridge, UK
| | - Morag Rose Hunter
- Centre for Genomic Research, Discovery Sciences, AstraZeneca , Cambridge, UK
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Simon L Bullock
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| |
Collapse
|
36
|
Brenner D, Sieverding K, Srinidhi J, Zellner S, Secker C, Yilmaz R, Dyckow J, Amr S, Ponomarenko A, Tunaboylu E, Douahem Y, Schlag JS, Rodríguez Martínez L, Kislinger G, Niemann C, Nalbach K, Ruf WP, Uhl J, Hollenbeck J, Schirmer L, Catanese A, Lobsiger CS, Danzer KM, Yilmazer-Hanke D, Münch C, Koch P, Freischmidt A, Fetting M, Behrends C, Parlato R, Weishaupt JH. A TBK1 variant causes autophagolysosomal and motoneuron pathology without neuroinflammation in mice. J Exp Med 2024; 221:e20221190. [PMID: 38517332 PMCID: PMC10959724 DOI: 10.1084/jem.20221190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 05/05/2023] [Accepted: 02/16/2024] [Indexed: 03/23/2024] Open
Abstract
Heterozygous mutations in the TBK1 gene can cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The majority of TBK1-ALS/FTD patients carry deleterious loss-of-expression mutations, and it is still unclear which TBK1 function leads to neurodegeneration. We investigated the impact of the pathogenic TBK1 missense variant p.E696K, which does not abolish protein expression, but leads to a selective loss of TBK1 binding to the autophagy adaptor protein and TBK1 substrate optineurin. Using organelle-specific proteomics, we found that in a knock-in mouse model and human iPSC-derived motor neurons, the p.E696K mutation causes presymptomatic onset of autophagolysosomal dysfunction in neurons precipitating the accumulation of damaged lysosomes. This is followed by a progressive, age-dependent motor neuron disease. Contrary to the phenotype of mice with full Tbk1 knock-out, RIPK/TNF-α-dependent hepatic, neuronal necroptosis, and overt autoinflammation were not detected. Our in vivo results indicate autophagolysosomal dysfunction as a trigger for neurodegeneration and a promising therapeutic target in TBK1-ALS/FTD.
Collapse
Affiliation(s)
- David Brenner
- Division of Neurodegeneration, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | - Jahnavi Srinidhi
- Division of Neurodegeneration, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | - Susanne Zellner
- Medical Faculty, Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-University München, Munich, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Rüstem Yilmaz
- Division of Neurodegeneration, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | - Julia Dyckow
- Division of Neuroimmunology, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | - Shady Amr
- Faculty of Medicine, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany
| | - Anna Ponomarenko
- Department of Neurology, University of Ulm, Ulm, Germany
- Institute of Anatomy and Cell Biology, Ulm University School of Medicine, Ulm, Germany
| | - Esra Tunaboylu
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Yasmin Douahem
- Division of Neurodegeneration, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | - Joana S. Schlag
- Division of Neurodegeneration, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | - Lucía Rodríguez Martínez
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Georg Kislinger
- Electron Microscopy Hub, German Center for Neurodegenerative Diseases, Munich, Germany
| | - Cornelia Niemann
- Electron Microscopy Hub, German Center for Neurodegenerative Diseases, Munich, Germany
| | - Karsten Nalbach
- Medical Faculty, Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-University München, Munich, Germany
| | | | - Jonathan Uhl
- Division of Neurodegeneration, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | - Johanna Hollenbeck
- Division of Neurodegeneration, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | - Lucas Schirmer
- Division of Neuroimmunology, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | - Alberto Catanese
- Institute of Anatomy and Cell Biology, Ulm University School of Medicine, Ulm, Germany
| | - Christian S. Lobsiger
- Institut du Cerveau—Paris Brain Institute—Institut du Cerveau et de la Moelle épinière, Inserm, Centre National de la Recherche Scientifique, Assistance Publique–Hôpitaux de Paris, Hôpital de la Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - Karin M. Danzer
- Department of Neurology, University of Ulm, Ulm, Germany
- German Center for Neurodegenerative Diseases, Ulm, Germany
| | - Deniz Yilmazer-Hanke
- Department of Neurology, Clinical Neuroanatomy Unit, University of Ulm, Ulm, Germany
| | - Christian Münch
- Institute of Anatomy and Cell Biology, Ulm University School of Medicine, Ulm, Germany
| | - Philipp Koch
- University of Heidelberg/Medical Faculty Mannheim, Central Institute of Mental Health, Mannheim, Germany
- Hector Institute for Translational Brain Research, Mannheim, Germany
- German Cancer Research Center, Heidelberg, Germany
| | | | - Martina Fetting
- Medical Faculty, Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-University München, Munich, Germany
- Electron Microscopy Hub, German Center for Neurodegenerative Diseases, Munich, Germany
| | - Christian Behrends
- Medical Faculty, Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-University München, Munich, Germany
| | - Rosanna Parlato
- Division of Neurodegeneration, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | - Jochen H. Weishaupt
- Division of Neurodegeneration, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| |
Collapse
|
37
|
Di Meo D, Kundu T, Ravindran P, Shah B, Püschel AW. Pip5k1γ regulates axon formation by limiting Rap1 activity. Life Sci Alliance 2024; 7:e202302383. [PMID: 38438249 PMCID: PMC10912816 DOI: 10.26508/lsa.202302383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
During their differentiation, neurons establish a highly polarized morphology by forming axons and dendrites. Cortical and hippocampal neurons initially extend several short neurites that all have the potential to become an axon. One of these neurites is then selected as the axon by a combination of positive and negative feedback signals that promote axon formation and prevent the remaining neurites from developing into axons. Here, we show that Pip5k1γ is required for the formation of a single axon as a negative feedback signal that regulates C3G and Rap1 through the generation of phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2). Impairing the function of Pip5k1γ results in a hyper-activation of the Fyn/C3G/Rap1 pathway, which induces the formation of supernumerary axons. Application of a hyper-osmotic shock to modulate membrane tension has a similar effect, increasing Rap1 activity and inducing the formation of supernumerary axons. In both cases, the induction of supernumerary axons can be reverted by expressing constitutively active Pip5k. Our results show that PI(4,5)P2-dependent membrane properties limit the activity of C3G and Rap1 to ensure the extension of a single axon.
Collapse
Affiliation(s)
- Danila Di Meo
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
- https://ror.org/00pd74e08 Cells-in-Motion Interfaculty Center, University of Münster, Münster, Germany
| | - Trisha Kundu
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
- https://ror.org/00pd74e08 Cells-in-Motion Interfaculty Center, University of Münster, Münster, Germany
| | - Priyadarshini Ravindran
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
| | - Bhavin Shah
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
| | - Andreas W Püschel
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
- https://ror.org/00pd74e08 Cells-in-Motion Interfaculty Center, University of Münster, Münster, Germany
| |
Collapse
|
38
|
Wei L, Dankwa S, Vijayan K, Smith JD, Kaushansky A. Interrogating endothelial barrier regulation by temporally resolved kinase network generation. Life Sci Alliance 2024; 7:e202302522. [PMID: 38467420 PMCID: PMC10927359 DOI: 10.26508/lsa.202302522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Kinases are key players in endothelial barrier regulation, yet their temporal function and regulatory phosphosignaling networks are incompletely understood. We developed a novel methodology, Temporally REsolved KInase Network Generation (TREKING), which combines a 28-kinase inhibitor screen with machine learning and network reconstruction to build time-resolved, functional phosphosignaling networks. We demonstrated the utility of TREKING for identifying pathways mediating barrier integrity after activation by thrombin with or without TNF preconditioning in brain endothelial cells. TREKING predicted over 100 kinases involved in barrier regulation and discerned complex condition-specific pathways. For instance, the MAPK-activated protein kinase 2 (MAPKAPK2/MK2) had early barrier-weakening activity in both inflammatory conditions but late barrier-strengthening activity exclusively with thrombin alone. Using temporal Western blotting, we confirmed that MAPKAPK2/MK2 was differentially phosphorylated under the two inflammatory conditions. We further showed with lentivirus-mediated knockdown of MAPK14/p38α and drug targeting the MAPK14/p38α-MAPKAPK2/MK2 complex that a MAP3K20/ZAK-MAPK14/p38α axis controlled the late activation of MAPKAPK2/MK2 in the thrombin-alone condition. Beyond the MAPKAPK2/MK2 switch, TREKING predicts extensive interconnected networks that control endothelial barrier dynamics.
Collapse
Affiliation(s)
- Ling Wei
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Selasi Dankwa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kamalakannan Vijayan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Joseph D Smith
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| |
Collapse
|
39
|
Grewal T, Nguyen MKL, Buechler C. Cholesterol and COVID-19-therapeutic opportunities at the host/virus interface during cell entry. Life Sci Alliance 2024; 7:e202302453. [PMID: 38388172 PMCID: PMC10883773 DOI: 10.26508/lsa.202302453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
The rapid development of vaccines to combat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has been critical to reduce the severity of COVID-19. However, the continuous emergence of new SARS-CoV-2 subtypes highlights the need to develop additional approaches that oppose viral infections. Targeting host factors that support virus entry, replication, and propagation provide opportunities to lower SARS-CoV-2 infection rates and improve COVID-19 outcome. This includes cellular cholesterol, which is critical for viral spike proteins to capture the host machinery for SARS-CoV-2 cell entry. Once endocytosed, exit of SARS-CoV-2 from the late endosomal/lysosomal compartment occurs in a cholesterol-sensitive manner. In addition, effective release of new viral particles also requires cholesterol. Hence, cholesterol-lowering statins, proprotein convertase subtilisin/kexin type 9 antibodies, and ezetimibe have revealed potential to protect against COVID-19. In addition, pharmacological inhibition of cholesterol exiting late endosomes/lysosomes identified drug candidates, including antifungals, to block SARS-CoV-2 infection. This review describes the multiple roles of cholesterol at the cell surface and endolysosomes for SARS-CoV-2 entry and the potential of drugs targeting cholesterol homeostasis to reduce SARS-CoV-2 infectivity and COVID-19 disease severity.
Collapse
Affiliation(s)
- Thomas Grewal
- https://ror.org/0384j8v12 School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Mai Khanh Linh Nguyen
- https://ror.org/0384j8v12 School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Christa Buechler
- https://ror.org/01226dv09 Department of Internal Medicine I, Regensburg University Hospital, Regensburg, Germany
| |
Collapse
|
40
|
Kurgan N, Kjærgaard Larsen J, Deshmukh AS. Harnessing the power of proteomics in precision diabetes medicine. Diabetologia 2024; 67:783-797. [PMID: 38345659 DOI: 10.1007/s00125-024-06097-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 03/21/2024]
Abstract
Precision diabetes medicine (PDM) aims to reduce errors in prevention programmes, diagnosis thresholds, prognosis prediction and treatment strategies. However, its advancement and implementation are difficult due to the heterogeneity of complex molecular processes and environmental exposures that influence an individual's disease trajectory. To address this challenge, it is imperative to develop robust screening methods for all areas of PDM. Innovative proteomic technologies, alongside genomics, have proven effective in precision cancer medicine and are showing promise in diabetes research for potential translation. This narrative review highlights how proteomics is well-positioned to help improve PDM. Specifically, a critical assessment of widely adopted affinity-based proteomic technologies in large-scale clinical studies and evidence of the benefits and feasibility of using MS-based plasma proteomics is presented. We also present a case for the use of proteomics to identify predictive protein panels for type 2 diabetes subtyping and the development of clinical prediction models for prevention, diagnosis, prognosis and treatment strategies. Lastly, we discuss the importance of plasma and tissue proteomics and its integration with genomics (proteogenomics) for identifying unique type 2 diabetes intra- and inter-subtype aetiology. We conclude with a call for action formed on advancing proteomics technologies, benchmarking their performance and standardisation across sites, with an emphasis on data sharing and the inclusion of diverse ancestries in large cohort studies. These efforts should foster collaboration with key stakeholders and align with ongoing academic programmes such as the Precision Medicine in Diabetes Initiative consortium.
Collapse
Affiliation(s)
- Nigel Kurgan
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Kjærgaard Larsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
41
|
Tinkov AA, Korobeinikova TV, Morozova GD, Aschner M, Mak DV, Santamaria A, Rocha JBT, Sotnikova TI, Tazina SI, Skalny AV. Association between serum trace element, mineral, and amino acid levels with non-alcoholic fatty liver disease (NAFLD) in adult women. J Trace Elem Med Biol 2024; 83:127397. [PMID: 38290269 DOI: 10.1016/j.jtemb.2024.127397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/29/2023] [Accepted: 01/13/2024] [Indexed: 02/01/2024]
Abstract
The objective of the present study is assessment of serum trace element and amino acid levels in non-alcoholic fatty liver disease (NAFLD) patients with subsequent evaluation of its independent associations with markers of liver injury and metabolic risk. MATERIALS AND METHODS 140 women aged 20-90 years old with diagnosed NAFLD and 140 healthy women with a respective age range were enrolled in the current study. Analysis of serum and hair levels of trace elements and minerals was performed with inductively-coupled plasma mass-spectrometry (ICP-MS). Serum amino acid concentrations were evaluated by high-pressure liquid chromatography (HPLC) with UV-detection. In addition, routine biochemical parameters including liver damage markers, alanine aminotransferase (ALT) and gamma-glutamyltransferase (GGT), were assessed spectrophotometrically. RESULTS The findings demonstrated that patients with NAFLD were characterized by higher ALT, GGT, lactate dehydrogenase (LDH) and cholinesterase (CE) activity, as well as increased levels of total cholesterol, low-density lipoprotein cholesterol, triglycerides, and uric acid. NAFLD patients were characterized by reduced serum and hair Co, Se, and Zn levels, as well as hair Cu content and serum Mn concentrations in comparison to controls. Circulating Ala, Cit, Glu, Gly, Ile, Leu, Phe, and Tyr levels in NAFLD patients exceeded those in the control group. Multiple linear regression demonstrated that serum and hair trace element levels were significantly associated with circulating amino acid levels after adjustment for age, BMI, and metabolic parameters including liver damage markers. CONCLUSION It is proposed that altered trace element handling may contribute to NAFLD pathogenesis through modulation of amino acid metabolism.
Collapse
Affiliation(s)
- Alexey A Tinkov
- Center of Bioelementology and Human Ecology, and World-Class Research Center "Digital Biodesign and Personalized Healthcare", and Department of Therapy of the Institute of Postgraduate Education, IM Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia; Laboratory of Ecobiomonitoring and Quality Control, Yaroslavl State University, 150003 Yaroslavl, Russia; Department of Medical Elementology, Peoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia.
| | - Tatiana V Korobeinikova
- Center of Bioelementology and Human Ecology, and World-Class Research Center "Digital Biodesign and Personalized Healthcare", and Department of Therapy of the Institute of Postgraduate Education, IM Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia; Department of Medical Elementology, Peoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Galina D Morozova
- Center of Bioelementology and Human Ecology, and World-Class Research Center "Digital Biodesign and Personalized Healthcare", and Department of Therapy of the Institute of Postgraduate Education, IM Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 10461 Bronx, NY, USA
| | - Daria V Mak
- Center of Bioelementology and Human Ecology, and World-Class Research Center "Digital Biodesign and Personalized Healthcare", and Department of Therapy of the Institute of Postgraduate Education, IM Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Abel Santamaria
- Faculty of Sciencies, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Joao B T Rocha
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria 97105-900 RS, Brazil
| | - Tatiana I Sotnikova
- Center of Bioelementology and Human Ecology, and World-Class Research Center "Digital Biodesign and Personalized Healthcare", and Department of Therapy of the Institute of Postgraduate Education, IM Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia; City Clinical Hospital n. a. S.P. Botkin of the Moscow City Health Department, 125284 Moscow, Russia
| | - Serafima Ia Tazina
- Center of Bioelementology and Human Ecology, and World-Class Research Center "Digital Biodesign and Personalized Healthcare", and Department of Therapy of the Institute of Postgraduate Education, IM Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia; City Clinical Hospital n. a. S.P. Botkin of the Moscow City Health Department, 125284 Moscow, Russia
| | - Anatoly V Skalny
- Center of Bioelementology and Human Ecology, and World-Class Research Center "Digital Biodesign and Personalized Healthcare", and Department of Therapy of the Institute of Postgraduate Education, IM Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia; Laboratory of Ecobiomonitoring and Quality Control, Yaroslavl State University, 150003 Yaroslavl, Russia; Department of Medical Elementology, Peoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| |
Collapse
|
42
|
Gopalan AB, van Uden L, Sprenger RR, Fernandez-Novel Marx N, Bogetofte H, Neveu PA, Meyer M, Noh KM, Diz-Muñoz A, Ejsing CS. Lipotype acquisition during neural development is not recapitulated in stem cell-derived neurons. Life Sci Alliance 2024; 7:e202402622. [PMID: 38418090 PMCID: PMC10902711 DOI: 10.26508/lsa.202402622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
During development, different tissues acquire distinct lipotypes that are coupled to tissue function and homeostasis. In the brain, where complex membrane trafficking systems are required for neural function, specific glycerophospholipids, sphingolipids, and cholesterol are highly abundant, and defective lipid metabolism is associated with abnormal neural development and neurodegenerative disease. Notably, the production of specific lipotypes requires appropriate programming of the underlying lipid metabolic machinery during development, but when and how this occurs is unclear. To address this, we used high-resolution MSALL lipidomics to generate an extensive time-resolved resource of mouse brain development covering early embryonic and postnatal stages. This revealed a distinct bifurcation in the establishment of the neural lipotype, whereby the canonical lipid biomarkers 22:6-glycerophospholipids and 18:0-sphingolipids begin to be produced in utero, whereas cholesterol attains its characteristic high levels after birth. Using the resource as a reference, we next examined to which extent this can be recapitulated by commonly used protocols for in vitro neuronal differentiation of stem cells. Here, we found that the programming of the lipid metabolic machinery is incomplete and that stem cell-derived cells can only partially acquire a neural lipotype when the cell culture media is supplemented with brain-specific lipid precursors. Altogether, our work provides an extensive lipidomic resource for early mouse brain development and highlights a potential caveat when using stem cell-derived neuronal progenitors for mechanistic studies of lipid biochemistry, membrane biology and biophysics, which nonetheless can be mitigated by further optimizing in vitro differentiation protocols.
Collapse
Affiliation(s)
- Anusha B Gopalan
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Candidate for Joint PhD Degree Between EMBL and Heidelberg University, Heidelberg, Germany
| | - Lisa van Uden
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Richard R Sprenger
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | | | - Helle Bogetofte
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Pierre A Neveu
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Neurology, Odense University Hospital, Odense, Denmark
- BRIDGE, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Kyung-Min Noh
- https://ror.org/03mstc592 Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alba Diz-Muñoz
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christer S Ejsing
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
43
|
Kuttikrishnan S, Prabhu KS, Khan AQ, Uddin S. Signaling networks guiding erythropoiesis. Curr Opin Hematol 2024; 31:89-95. [PMID: 38335037 DOI: 10.1097/moh.0000000000000808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
PURPOSE OF REVIEW Cytokine-mediated signaling pathways, including JAK/STAT, PI3K/AKT, and Ras/MAPK pathways, play an important role in the process of erythropoiesis. These pathways are involved in the survival, proliferation, and differentiation function of erythropoiesis. RECENT FINDINGS The JAK/STAT pathway controls erythroid progenitor differentiation, proliferation, and survival. The PI3K/AKT signaling cascade facilitates erythroid progenitor survival, proliferation, and final differentiation. During erythroid maturation, MAPK, triggered by EPO, suppresses myeloid genes, while PI3K is essential for differentiation. Pro-inflammatory cytokines activate signaling pathways that can alter erythropoiesis like EPOR-triggered signaling, including survival, differentiation, and proliferation. SUMMARY A comprehensive understanding of signaling networks is crucial for the formulation of treatment approaches for hematologic disorders. Further investigation is required to fully understand the mechanisms and interactions of these signaling pathways in erythropoiesis.
Collapse
Affiliation(s)
| | | | | | - Shahab Uddin
- Translational Research Institute
- Dermatology Institute, Academic Health System, Hamad Medical Corporation
- Laboratory of Animal Center, Qatar University, Doha, Qatar
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, India
| |
Collapse
|
44
|
Ramirez Flores RO, Schäfer PSL, Küchenhoff L, Saez-Rodriguez J. Complementing Cell Taxonomies with a Multicellular Analysis of Tissues. Physiology (Bethesda) 2024; 39:0. [PMID: 38319138 DOI: 10.1152/physiol.00001.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting of cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of single-cell dynamics upon shared external queues and spatial organizations. However, little is known about the relationship between single-cell heterogeneity and the emergence and maintenance of robust multicellular processes in developed tissues and its role in (patho)physiology. Here, we present emerging computational modeling strategies that use increasingly available large-scale cross-condition single-cell and spatial datasets to study multicellular organization in tissues and complement cell taxonomies. This perspective should enable us to better understand how cells within tissues collectively process information and adapt synchronized responses in disease contexts and to bridge the gap between structural changes and functions in tissues.
Collapse
Affiliation(s)
- Ricardo Omar Ramirez Flores
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Sven Lars Schäfer
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Leonie Küchenhoff
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
45
|
Pilva P, Bülow R, Boor P. Deep learning applications for kidney histology analysis. Curr Opin Nephrol Hypertens 2024; 33:291-297. [PMID: 38411024 DOI: 10.1097/mnh.0000000000000973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
PURPOSE OF REVIEW Nephropathology is increasingly incorporating computational methods to enhance research and diagnostic accuracy. The widespread adoption of digital pathology, coupled with advancements in deep learning, will likely transform our pathology practices. Here, we discuss basic concepts of deep learning, recent applications in nephropathology, current challenges in implementation and future perspectives. RECENT FINDINGS Deep learning models have been developed and tested in various areas of nephropathology, for example, predicting kidney disease progression or diagnosing diseases based on imaging and clinical data. Despite their promising potential, challenges remain that hinder a wider adoption, for example, the lack of prospective evidence and testing in real-world scenarios. SUMMARY Deep learning offers great opportunities to improve quantitative and qualitative kidney histology analysis for research and clinical nephropathology diagnostics. Although exciting approaches already exist, the potential of deep learning in nephropathology is only at its beginning and we can expect much more to come.
Collapse
Affiliation(s)
| | | | - Peter Boor
- Institute of Pathology
- Department of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
| |
Collapse
|
46
|
Montserrat-Gomez M, Gogl G, Carrasco K, Betzi S, Durbesson F, Cousido-Siah A, Kostmann C, Essig DJ, Strømgaard K, Østergaard S, Morelli X, Trave G, Vincentelli R, Bailly E, Borg JP. PDZome-wide and structural characterization of the PDZ-binding motif of VANGL2. Biochim Biophys Acta Proteins Proteom 2024; 1872:140989. [PMID: 38142947 DOI: 10.1016/j.bbapap.2023.140989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
VANGL2 is a core component of the non-canonical Wnt/Planar Cell Polarity signaling pathway that uses its highly conserved carboxy-terminal type 1 PDZ-binding motif (PBM) to bind a variety of PDZ proteins. In this study, we characterize and quantitatively assess the largest VANGL2 PDZome-binding profile documented so far, using orthogonal methods. The results of our holdup approach support VANGL2 interactions with a large panel of both long-recognized and unprecedented PDZ domains. Truncation and point mutation analyses of the VANGL2 PBM establish that, beyond the strict requirement of the P-0 / V521 and P-2 / T519 amino acids, upstream residues, including E518, Q516 and R514 at, respectively, P-3, P-5 and P-7 further contribute to the robustness of VANGL2 interactions with two distinct PDZ domains, SNX27 and SCRIBBLE-PDZ3. In agreement with these data, incremental amino-terminal deletions of the VANGL2 PBM causes its overall affinity to progressively decline. Moreover, the holdup data establish that the PDZome binding repertoire of VANGL2 starts to diverge significantly with the truncation of E518. A structural analysis of the SYNJ2BP-PDZ/VANGL2 interaction with truncated PBMs identifies a major conformational change in the binding direction of the PBM peptide after the P-2 position. Finally, we report that the PDZome binding profile of VANGL2 is dramatically rearranged upon phosphorylation of S517, T519 and S520. Our crystallographic approach illustrates how SYNJ2BP accommodates a S520-phosphorylated PBM peptide through the ideal positioning of two basic residues, K48 and R86. Altogether our data provides a comprehensive view of the VANGL2 PDZ network and how this network specifically responds to the post-translation modification of distinct PBM residues. These findings should prove useful in guiding future functional and molecular studies of the key PCP component VANGL2.
Collapse
Affiliation(s)
- Marta Montserrat-Gomez
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France
| | - Gergo Gogl
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Kendall Carrasco
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Stephane Betzi
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Fabien Durbesson
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France
| | - Alexandra Cousido-Siah
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Camille Kostmann
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Dominic J Essig
- Center for Biopharmaceuticals, Jagtvej 162, 2100 Copenhagen, Denmark; Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | | | - Søren Østergaard
- Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | - Xavier Morelli
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Gilles Trave
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Renaud Vincentelli
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France.
| | - Eric Bailly
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France.
| | - Jean-Paul Borg
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France; Institut Universitaire de France (IUF), France.
| |
Collapse
|
47
|
Muñoz-Juan A, Assié A, Esteve-Codina A, Gut M, Benseny-Cases N, Samuel BS, Dalfó E, Laromaine A. Caenorhabditis elegans endorse bacterial nanocellulose fibers as functional dietary Fiber reducing lipid markers. Carbohydr Polym 2024; 331:121815. [PMID: 38388067 DOI: 10.1016/j.carbpol.2024.121815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/24/2024]
Abstract
Bacterial nanocellulose (BNC) is a promising dietary fiber with potential as a functional food additive. We evaluated BNC fibers (BNCf) in the Caenorhabditis elegans model to obtain insight into the BNCf's biointeraction with its gastrointestinal tract while reducing the variables of higher complex animals. BNCf were uptaken and excreted by worms without crossing the intestinal barrier, confirming its biosafety regarding survival rate, reproduction, and aging for concentrations up to 34 μg/ml BNCf. However, a slight decrease in the worms' length was detected. A possible nutrient shortage or stress produced by BNCf was discarded by measuring stress and chemotactic response pathways. Besides, we detected a lipid-lowering effect of BNCf in N2 C. elegans in normal and high-caloric diets. Oxidative damage was computed in N2 worms and Rac1/ced-10 mutants. The GTPase Rac1 is involved in neurological diseases, where its dysregulation enhances ROS production and neuronal damage. BNCf reduced the lipid oxidative markers produced by ROS species in this worm strain. Finally, we detected that BNCf activated the genetic expression of the immunological response and lipid catabolic process. These results strengthen the use of BNCf as a functional dietary fiber and encourage the potential treatment of neurological disease by modulating diet.
Collapse
Affiliation(s)
- Amanda Muñoz-Juan
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra 08193, Spain
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Anna Esteve-Codina
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Núria Benseny-Cases
- Universitat Autònoma de Barcelona, Biophysics Unit, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Avinguda de Can Domènech, 08193 Cerdanyola del Vallès, Spain
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Esther Dalfó
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500 Vic, Spain; Institute for Research and Innovation in Life Sciences and Health in Central Catalonia (IRIS-CC), Can Baumann, 08500, Vic, Spain; Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Laromaine
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra 08193, Spain.
| |
Collapse
|
48
|
Abley K, Goswami R, Locke JCW. Bet-hedging and variability in plant development: seed germination and beyond. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230048. [PMID: 38432313 PMCID: PMC10909506 DOI: 10.1098/rstb.2023.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/28/2023] [Indexed: 03/05/2024] Open
Abstract
When future conditions are unpredictable, bet-hedging strategies can be advantageous. This can involve isogenic individuals producing different phenotypes, under the same environmental conditions. Ecological studies provide evidence that variability in seed germination time has been selected for as a bet-hedging strategy. We demonstrate how variability in germination time found in Arabidopsis could function as a bet-hedging strategy in the face of unpredictable lethal stresses. Despite a body of knowledge on how the degree of seed dormancy versus germination is controlled, relatively little is known about how differences between isogenic seeds in a batch are generated. We review proposed mechanisms for generating variability in germination time and the current limitations and new possibilities for testing the model predictions. We then look beyond germination to the role of variability in seedling and adult plant growth and review new technologies for quantification of noisy gene expression dynamics. We discuss evidence for phenotypic variability in plant traits beyond germination being under genetic control and propose that variability in stress response gene expression could function as a bet-hedging strategy. We discuss open questions about how noisy gene expression could lead to between-plant heterogeneity in gene expression and phenotypes. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
Collapse
Affiliation(s)
- Katie Abley
- The Sainsbury Laboratory, University of Cambridge, Cambridge, Cambridgeshire CB2 1LR, UK
| | - Rituparna Goswami
- The Sainsbury Laboratory, University of Cambridge, Cambridge, Cambridgeshire CB2 1LR, UK
| | - James C. W. Locke
- The Sainsbury Laboratory, University of Cambridge, Cambridge, Cambridgeshire CB2 1LR, UK
| |
Collapse
|
49
|
Jenkins D, Chubb JR, Galea G. Stochastic processes in development and disease. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230043. [PMID: 38432319 PMCID: PMC10909502 DOI: 10.1098/rstb.2023.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024] Open
Affiliation(s)
- Dagan Jenkins
- Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Jonathan R. Chubb
- UCL Laboratory of Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Gabriel Galea
- Developmental Biology and Cancer Programme, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| |
Collapse
|
50
|
Maizels RJ. A dynamical perspective: moving towards mechanism in single-cell transcriptomics. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230049. [PMID: 38432314 PMCID: PMC10909508 DOI: 10.1098/rstb.2023.0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/31/2023] [Indexed: 03/05/2024] Open
Abstract
As the field of single-cell transcriptomics matures, research is shifting focus from phenomenological descriptions of cellular phenotypes to a mechanistic understanding of the gene regulation underneath. This perspective considers the value of capturing dynamical information at single-cell resolution for gaining mechanistic insight; reviews the available technologies for recording and inferring temporal information in single cells; and explores whether better dynamical resolution is sufficient to adequately capture the causal relationships driving complex biological systems. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
Collapse
Affiliation(s)
- Rory J. Maizels
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- University College London, London WC1E 6BT, UK
| |
Collapse
|