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Mozzarelli AM, Simanshu DK, Castel P. Functional and structural insights into RAS effector proteins. Mol Cell 2024:S1097-2765(24)00534-3. [PMID: 39025071 DOI: 10.1016/j.molcel.2024.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
RAS proteins are conserved guanosine triphosphate (GTP) hydrolases (GTPases) that act as molecular binary switches and play vital roles in numerous cellular processes. Upon GTP binding, RAS GTPases adopt an active conformation and interact with specific proteins termed RAS effectors that contain a conserved ubiquitin-like domain, thereby facilitating downstream signaling. Over 50 effector proteins have been identified in the human proteome, and many have been studied as potential mediators of RAS-dependent signaling pathways. Biochemical and structural analyses have provided mechanistic insights into these effectors, and studies using model organisms have complemented our understanding of their role in physiology and disease. Yet, many critical aspects regarding the dynamics and biological function of RAS-effector complexes remain to be elucidated. In this review, we discuss the mechanisms and functions of known RAS effector proteins, provide structural perspectives on RAS-effector interactions, evaluate their significance in RAS-mediated signaling, and explore their potential as therapeutic targets.
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Affiliation(s)
- Alessandro M Mozzarelli
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter NYU Cancer Center, NYU Langone Health, New York, NY, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter NYU Cancer Center, NYU Langone Health, New York, NY, USA.
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52
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Ahmed F, Samantasinghar A, Bae MA, Choi KH. Integrated ML-Based Strategy Identifies Drug Repurposing for Idiopathic Pulmonary Fibrosis. ACS OMEGA 2024; 9:29870-29883. [PMID: 39005763 PMCID: PMC11238209 DOI: 10.1021/acsomega.4c03796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/30/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) affects an estimated global population of around 3 million individuals. IPF is a medical condition with an unknown cause characterized by the formation of scar tissue in the lungs, leading to progressive respiratory disease. Currently, there are only two FDA-approved small molecule drugs specifically for the treatment of IPF and this has created a demand for the rapid development of drugs for IPF treatment. Moreover, denovo drug development is time and cost-intensive with less than a 10% success rate. Drug repurposing currently is the most feasible option for rapidly making the drugs to market for a rare and sporadic disease. Normally, the repurposing of drugs begins with a screening of FDA-approved drugs using computational tools, which results in a low hit rate. Here, an integrated machine learning-based drug repurposing strategy is developed to significantly reduce the false positive outcomes by introducing the predock machine-learning-based predictions followed by literature and GSEA-assisted validation and drug pathway prediction. The developed strategy is deployed to 1480 FDA-approved drugs and to drugs currently in a clinical trial for IPF to screen them against "TGFB1", "TGFB2", "PDGFR-a", "SMAD-2/3", "FGF-2", and more proteins resulting in 247 total and 27 potentially repurposable drugs. The literature and GSEA validation suggested that 72 of 247 (29.14%) drugs have been tried for IPF, 13 of 247 (5.2%) drugs have already been used for lung fibrosis, and 20 of 247 (8%) drugs have been tested for other fibrotic conditions such as cystic fibrosis and renal fibrosis. Pathway prediction of the remaining 142 drugs was carried out resulting in 118 distinct pathways. Furthermore, the analysis revealed that 29 of 118 pathways were directly or indirectly involved in IPF and 11 of 29 pathways were directly involved. Moreover, 15 potential drug combinations are suggested for showing a strong synergistic effect in IPF. The drug repurposing strategy reported here will be useful for rapidly developing drugs for treating IPF and other related conditions.
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Affiliation(s)
- Faheem Ahmed
- Department
of Mechatronics Engineering, Jeju National
University, Jeju 63243, Republic
of Korea
| | - Anupama Samantasinghar
- Department
of Mechatronics Engineering, Jeju National
University, Jeju 63243, Republic
of Korea
| | - Myung Ae Bae
- Therapeutics
and Biotechnology Division, Korea Research
Institute of Chemical Technology, Daejeon 34114, Korea
| | - Kyung Hyun Choi
- Department
of Mechatronics Engineering, Jeju National
University, Jeju 63243, Republic
of Korea
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53
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Csikász-Nagy A, Fichó E, Noto S, Reguly I. Computational tools to predict context-specific protein complexes. Curr Opin Struct Biol 2024; 88:102883. [PMID: 38986166 DOI: 10.1016/j.sbi.2024.102883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/21/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024]
Abstract
Interactions between thousands of proteins define cells' protein-protein interaction (PPI) network. Some of these interactions lead to the formation of protein complexes. It is challenging to identify a protein complex in a haystack of protein-protein interactions, and it is even more difficult to predict all protein complexes of the complexome. Simulations and machine learning approaches try to crack these problems by looking at the PPI network or predicted protein structures. Clustering of PPI networks led to the first protein complex predictions, while most recently, atomistic models of protein complexes and deep-learning-based structure prediction methods have also emerged. The simulation of PPI level interactions even enables the quantitative prediction of protein complexes. These methods, the required data sources, and their potential future developments are discussed in this review.
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Affiliation(s)
- Attila Csikász-Nagy
- Cytocast Hungary Kft, Budapest, Hungary; Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary.
| | | | - Santiago Noto
- Cytocast Hungary Kft, Budapest, Hungary; Escola de Matemática Aplicada, Fundação Getúlio Vargas, Rio de Janeiro, Brazil
| | - István Reguly
- Cytocast Hungary Kft, Budapest, Hungary; Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
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54
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Huang ETC, Yang JS, Liao KYK, Tseng WCW, Lee CK, Gill M, Compas C, See S, Tsai FJ. Predicting blood-brain barrier permeability of molecules with a large language model and machine learning. Sci Rep 2024; 14:15844. [PMID: 38982309 PMCID: PMC11233737 DOI: 10.1038/s41598-024-66897-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024] Open
Abstract
Predicting the blood-brain barrier (BBB) permeability of small-molecule compounds using a novel artificial intelligence platform is necessary for drug discovery. Machine learning and a large language model on artificial intelligence (AI) tools improve the accuracy and shorten the time for new drug development. The primary goal of this research is to develop artificial intelligence (AI) computing models and novel deep learning architectures capable of predicting whether molecules can permeate the human blood-brain barrier (BBB). The in silico (computational) and in vitro (experimental) results were validated by the Natural Products Research Laboratories (NPRL) at China Medical University Hospital (CMUH). The transformer-based MegaMolBART was used as the simplified molecular input line entry system (SMILES) encoder with an XGBoost classifier as an in silico method to check if a molecule could cross through the BBB. We used Morgan or Circular fingerprints to apply the Morgan algorithm to a set of atomic invariants as a baseline encoder also with an XGBoost classifier to compare the results. BBB permeability was assessed in vitro using three-dimensional (3D) human BBB spheroids (human brain microvascular endothelial cells, brain vascular pericytes, and astrocytes). Using multiple BBB databases, the results of the final in silico transformer and XGBoost model achieved an area under the receiver operating characteristic curve of 0.88 on the held-out test dataset. Temozolomide (TMZ) and 21 randomly selected BBB permeable compounds (Pred scores = 1, indicating BBB-permeable) from the NPRL penetrated human BBB spheroid cells. No evidence suggests that ferulic acid or five BBB-impermeable compounds (Pred scores < 1.29423E-05, which designate compounds that pass through the human BBB) can pass through the spheroid cells of the BBB. Our validation of in vitro experiments indicated that the in silico prediction of small-molecule permeation in the BBB model is accurate. Transformer-based models like MegaMolBART, leveraging the SMILES representations of molecules, show great promise for applications in new drug discovery. These models have the potential to accelerate the development of novel targeted treatments for disorders of the central nervous system.
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Affiliation(s)
- Eddie T C Huang
- NVIDIA AI Technology Center, NVIDIA Corporation, Santa Clara, USA
| | - Jai-Sing Yang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Ken Y K Liao
- NVIDIA AI Technology Center, NVIDIA Corporation, Santa Clara, USA
| | - Warren C W Tseng
- NVIDIA AI Technology Center, NVIDIA Corporation, Santa Clara, USA
| | - C K Lee
- NVIDIA AI Technology Center, NVIDIA Corporation, Santa Clara, USA
| | - Michelle Gill
- NVIDIA AI Technology Center, NVIDIA Corporation, Santa Clara, USA
| | - Colin Compas
- NVIDIA AI Technology Center, NVIDIA Corporation, Santa Clara, USA
| | - Simon See
- NVIDIA AI Technology Center, NVIDIA Corporation, Santa Clara, USA
| | - Fuu-Jen Tsai
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, China Medical University Children's Hospital, No. 2, Yude Road, Taichung, 404332, Taiwan.
- China Medical University Children's Hospital, Taichung, Taiwan.
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55
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Choudhury P, Dasgupta S, Bhattacharyya P, Roychowdhury S, Chaudhury K. Understanding pulmonary hypertension: the need for an integrative metabolomics and transcriptomics approach. Mol Omics 2024; 20:366-389. [PMID: 38853716 DOI: 10.1039/d3mo00266g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Pulmonary hypertension (PH), characterised by mean pulmonary arterial pressure (mPAP) >20 mm Hg at rest, is a complex pathophysiological disorder associated with multiple clinical conditions. The high prevalence of the disease along with increased mortality and morbidity makes it a global health burden. Despite major advances in understanding the disease pathophysiology, much of the underlying complex molecular mechanism remains to be elucidated. Lack of a robust diagnostic test and specific therapeutic targets also poses major challenges. This review provides a comprehensive update on the dysregulated pathways and promising candidate markers identified in PH patients using the transcriptomics and metabolomics approach. The review also highlights the need of using an integrative multi-omics approach for obtaining insight into the disease at a molecular level. The integrative multi-omics/pan-omics approach envisaged to help in bridging the gap from genotype to phenotype is outlined. Finally, the challenges commonly encountered while conducting omics-driven studies are also discussed.
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Affiliation(s)
- Priyanka Choudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
| | - Sanjukta Dasgupta
- Department of Biotechnology, Brainware University, Barasat, West Bengal, India
| | | | | | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
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56
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Murrugarra D, Veliz-Cuba A, Dimitrova E, Kadelka C, Wheeler M, Laubenbacher R. Modular Control of Biological Networks. ARXIV 2024:arXiv:2401.12477v2. [PMID: 38344220 PMCID: PMC10854280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The concept of control is central to understanding and applications of biological network models. Some of their key structural features relate to control functions, through gene regulation, signaling, or metabolic mechanisms, and computational models need to encode these. Applications of models often focus on model-based control, such as in biomedicine or metabolic engineering. This paper presents an approach to model-based control that exploits two common features of biological networks, namely their modular structure and canalizing features of their regulatory mechanisms. The paper focuses on intracellular regulatory networks, represented by Boolean network models. A main result of this paper is that control strategies can be identified by focusing on one module at a time. This paper also presents a criterion based on canalizing features of the regulatory rules to identify modules that do not contribute to network control and can be excluded. For even moderately sized networks, finding global control inputs is computationally very challenging. The modular approach presented here leads to a highly efficient approach to solving this problem. This approach is applied to a published Boolean network model of blood cancer large granular lymphocyte (T-LGL) leukemia to identify a minimal control set that achieves a desired control objective.
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Affiliation(s)
- David Murrugarra
- Department of Mathematics, University of Kentucky, Lexington, KY 40506, USA
| | - Alan Veliz-Cuba
- Department of Mathematics, University of Dayton, Dayton, OH 45469, USA
| | - Elena Dimitrova
- Mathematics Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Claus Kadelka
- Department of Mathematics, Iowa State University, Ames, IA 50011, USA
| | - Matthew Wheeler
- Department of Medicine, University of Florida, Gainesville, FL 32610, USA
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57
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Arzamasov AA, Rodionov DA, Hibberd MC, Guruge JL, Kazanov MD, Leyn SA, Kent JE, Sejane K, Bode L, Barratt MJ, Gordon JI, Osterman AL. Integrative genomic reconstruction of carbohydrate utilization networks in bifidobacteria: global trends, local variability, and dietary adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602360. [PMID: 39005317 PMCID: PMC11245093 DOI: 10.1101/2024.07.06.602360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Bifidobacteria are among the earliest colonizers of the human gut, conferring numerous health benefits. While multiple Bifidobacterium strains are used as probiotics, accumulating evidence suggests that the individual responses to probiotic supplementation may vary, likely due to a variety of factors, including strain type(s), gut community composition, dietary habits of the consumer, and other health/lifestyle conditions. Given the saccharolytic nature of bifidobacteria, the carbohydrate composition of the diet is one of the primary factors dictating the colonization efficiency of Bifidobacterium strains. Therefore, a comprehensive understanding of bifidobacterial glycan metabolism at the strain level is necessary to rationally design probiotic or synbiotic formulations that combine bacterial strains with glycans that match their nutrient preferences. In this study, we systematically reconstructed 66 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the representation of 565 curated metabolic functional roles (catabolic enzymes, transporters, transcriptional regulators) in 2973 non-redundant cultured Bifidobacterium isolates and metagenome-assembled genomes (MAGs). Our analysis uncovered substantial heterogeneity in the predicted glycan utilization capabilities at the species and strain level and revealed the presence of a yet undescribed phenotypically distinct subspecies-level clade within the Bifidobacterium longum species. We also identified Bangladeshi isolates harboring unique gene clusters tentatively implicated in the breakdown of xyloglucan and human milk oligosaccharides. Predicted carbohydrate utilization phenotypes were experimentally characterized and validated. Our large-scale genomic analysis considerably expands the knowledge of carbohydrate metabolism in bifidobacteria and provides a foundation for rationally designing single- or multi-strain probiotic formulations of a given bifidobacterial species as well as synbiotic combinations of bifidobacterial strains matched with their preferred carbohydrate substrates.
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Affiliation(s)
- Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki L Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey, 34956
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - James E Kent
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Kristija Sejane
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
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58
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Krolick KN, Cao J, Gulla EM, Bhardwaj M, Marshall SJ, Zhou EY, Kiss AJ, Choueiry F, Zhu J, Shi H. Subregion-specific transcriptomic profiling of rat brain reveals sex-distinct gene expression impacted by adolescent stress. Neuroscience 2024; 553:19-39. [PMID: 38977070 DOI: 10.1016/j.neuroscience.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/14/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Stress during adolescence clearly impacts brain development and function. Sex differences in adolescent stress-induced or exacerbated emotional and metabolic vulnerabilities could be due to sex-distinct gene expression in hypothalamic, limbic, and prefrontal brain regions. However, adolescent stress-induced whole-genome expression changes in key subregions of these brain regions were unclear. In this study, female and male adolescent Sprague Dawley rats received one-hour restraint stress daily from postnatal day (PD) 32 to PD44. Corticosterone levels, body weights, food intake, body composition, and circulating adiposity and sex hormones were measured. On PD44, brain and blood samples were collected. Using RNA-sequencing, sex-specific differences in stress-induced differentially expressed (DE) genes were identified in subregions of the hypothalamus, limbic system, and prefrontal cortex. Canonical pathways reflected well-known sex-distinct maladies and diseases, substantiating the therapeutic potential of the DE genes found in the current study. Thus, we proposed specific sex distinct, adolescent stress-induced transcriptional changes found in the current study as examples of the molecular bases for sex differences witnessed in stress induced or exacerbated emotional and metabolic disorders. Future behavioral studies and single-cell studies are warranted to test the implications of the DE genes identified in this study in sex-distinct stress-induced susceptibilities.
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Affiliation(s)
| | - Jingyi Cao
- Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Evelyn M Gulla
- Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Meeta Bhardwaj
- Department of Biology, Miami University, Oxford, OH 45056, USA.
| | | | - Ethan Y Zhou
- Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Andor J Kiss
- Center for Bioinformatics & Functional Genomics, Miami University, Oxford, OH 45056, USA.
| | - Fouad Choueiry
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA.
| | - Jiangjiang Zhu
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
| | - Haifei Shi
- Department of Biology, Miami University, Oxford, OH 45056, USA.
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59
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Bianca C. A decade of thermostatted kinetic theory models for complex active matter living systems. Phys Life Rev 2024; 50:72-97. [PMID: 39002422 DOI: 10.1016/j.plrev.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/15/2024]
Abstract
In the last decade, the thermostatted kinetic theory has been proposed as a general paradigm for the modeling of complex systems of the active matter and, in particular, in biology. Homogeneous and inhomogeneous frameworks of the thermostatted kinetic theory have been employed for modeling phenomena that are the result of interactions among the elements, called active particles, composing the system. Functional subsystems contain heterogeneous active particles that are able to perform the same task, called activity. Active matter living systems usually operate out-of-equilibrium; accordingly, a mathematical thermostat is introduced in order to regulate the fluctuations of the activity of particles. The time evolution of the functional subsystems is obtained by introducing the conservative and the nonconservative interactions which represent activity-transition, natural birth/death, induced proliferation/destruction, and mutation of the active particles. This review paper is divided in two parts: In the first part the review deals with the mathematical frameworks of the thermostatted kinetic theory that can be found in the literature of the last decade and a unified approach is proposed; the second part of the review is devoted to the specific mathematical models derived within the thermostatted kinetic theory presented in the last decade for complex biological systems, such as wound healing diseases, the recognition process and the learning dynamics of the human immune system, the hiding-learning dynamics and the immunoediting process occurring during the cancer-immune system competition. Future research perspectives are discussed from the theoretical and application viewpoints, which suggest the important interplay among the different scholars of the applied sciences and the desire of a multidisciplinary approach or rather a theory for the modeling of every active matter system.
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Affiliation(s)
- Carlo Bianca
- EFREI Research Lab, Université Paris-Panthéon-Assas, 30/32 Avenue de la République, 94800 Villejuif, France.
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60
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Hieber C, Mustafa AHM, Neuroth S, Henninger S, Wollscheid HP, Zabkiewicz J, Lazenby M, Alvares C, Mahboobi S, Butter F, Brenner W, Bros M, Krämer OH. Inhibitors of the tyrosine kinases FMS-like tyrosine kinase-3 and WEE1 induce apoptosis and DNA damage synergistically in acute myeloid leukemia cells. Biomed Pharmacother 2024; 177:117076. [PMID: 38971011 DOI: 10.1016/j.biopha.2024.117076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/16/2024] [Accepted: 06/29/2024] [Indexed: 07/08/2024] Open
Abstract
Hyperactive FMS-like receptor tyrosine kinase-3 mutants with internal tandem duplications (FLT3-ITD) are frequent driver mutations of aggressive acute myeloid leukemia (AML). Inhibitors of FLT3 produce promising results in rationally designed cotreatment schemes. Since FLT3-ITD modulates DNA replication and DNA repair, valid anti-leukemia strategies could rely on a combined inhibition of FLT3-ITD and regulators of cell cycle progression and DNA integrity. These include the WEE1 kinase which controls cell cycle progression, nucleotide synthesis, and DNA replication origin firing. We investigated how pharmacological inhibition of FLT3 and WEE1 affected the survival and genomic integrity of AML cell lines and primary AML cells. We reveal that promising clinical grade and preclinical inhibitors of FLT3 and WEE1 synergistically trigger apoptosis in leukemic cells that express FLT3-ITD. An accumulation of single and double strand DNA damage precedes this process. Mass spectrometry-based proteomic analyses show that FLT3-ITD and WEE1 sustain the expression of the ribonucleotide reductase subunit RRM2, which provides dNTPs for DNA replication. Unlike their strong pro-apoptotic effects on leukemia cells with FLT3-ITD, inhibitors of FLT3 and WEE1 do not damage healthy human blood cells and murine hematopoietic stem cells. Thus, pharmacological inhibition of FLT3-ITD and WEE1 might become an improved, rationally designed therapeutic option.
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Affiliation(s)
- Christoph Hieber
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany; Department of Dermatology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
| | - Al-Hassan M Mustafa
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany; Department of Zoology, Faculty of Science, Aswan University, Aswan, Egypt.
| | - Sarah Neuroth
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
| | - Sven Henninger
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
| | | | - Joanna Zabkiewicz
- Department of Haematology, Cardiff Experimental Cancer Medicine Centre, Cardiff University, Wales, UK.
| | - Michelle Lazenby
- Department of Haematology, Cardiff Experimental Cancer Medicine Centre, Cardiff University, Wales, UK.
| | - Caroline Alvares
- Department of Haematology, Cardiff Experimental Cancer Medicine Centre, Cardiff University, Wales, UK.
| | - Siavosh Mahboobi
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany.
| | - Falk Butter
- Institute of Molecular Biology, Ackermannweg 4, Mainz 55128, Germany; Institute of Molecular Virology and Cell Biology (IMVZ), Friedrich Loeffler Institute, Greifswald 17493, Germany.
| | - Walburgis Brenner
- Department of Obstetrics and Gynecology, University Medical Center, Mainz 55131, Germany.
| | - Matthias Bros
- Department of Dermatology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
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61
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Ma C, Gurkan-Cavusoglu E. A comprehensive review of computational cell cycle models in guiding cancer treatment strategies. NPJ Syst Biol Appl 2024; 10:71. [PMID: 38969664 PMCID: PMC11226463 DOI: 10.1038/s41540-024-00397-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
This article reviews the current knowledge and recent advancements in computational modeling of the cell cycle. It offers a comparative analysis of various modeling paradigms, highlighting their unique strengths, limitations, and applications. Specifically, the article compares deterministic and stochastic models, single-cell versus population models, and mechanistic versus abstract models. This detailed analysis helps determine the most suitable modeling framework for various research needs. Additionally, the discussion extends to the utilization of these computational models to illuminate cell cycle dynamics, with a particular focus on cell cycle viability, crosstalk with signaling pathways, tumor microenvironment, DNA replication, and repair mechanisms, underscoring their critical roles in tumor progression and the optimization of cancer therapies. By applying these models to crucial aspects of cancer therapy planning for better outcomes, including drug efficacy quantification, drug discovery, drug resistance analysis, and dose optimization, the review highlights the significant potential of computational insights in enhancing the precision and effectiveness of cancer treatments. This emphasis on the intricate relationship between computational modeling and therapeutic strategy development underscores the pivotal role of advanced modeling techniques in navigating the complexities of cell cycle dynamics and their implications for cancer therapy.
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Affiliation(s)
- Chenhui Ma
- Department of Electrical, Computer and Systems Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Evren Gurkan-Cavusoglu
- Department of Electrical, Computer and Systems Engineering, Case Western Reserve University, Cleveland, OH, USA
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Fujikane A, Fujikane R, Hyuga S, Sechi Y, Hiyoshi T, Sakamoto A, Nishi A, Odaguchi H, Hiromatsu K, Goda Y, Ishino Y, Nabeshima S. Antiviral effect of alkaloids-free Ephedra Herb extract on respiratory syncytial virus infection. Front Pharmacol 2024; 15:1410470. [PMID: 39035985 PMCID: PMC11257991 DOI: 10.3389/fphar.2024.1410470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/17/2024] [Indexed: 07/23/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of respiratory tract infection in children. Despite decades of efforts, no effective therapies are available. We recently reported that extracts of Ephedra Herb and Cinnamon Bark interacted with the G attachment protein of RSV to inhibit infectivity. The present in vitro study aimed to investigate the antiviral effect of ephedrine alkaloids-free Ephedra Herb extract (EFE), which is characterized by free of harmful effects of ephedrine alkaloids in Ephedra Herb, on experimental RSV infection. Infection of RSV into A549 cells simultaneously with EFE resulted the significant reduction of RSV RNA, viral protein, and viral titers after the incubation of the cells. We found that RSV attachment to the cell surface was inhibited both in the presence of EFE and when RSV particles were pre-treated with EFE. We also found that EFE specifically interacted with the central conserved domain of RSV G protein by surface plasmon resonance, demonstrating that specific binding of G protein to the cellular receptor was inhibited by EFE. Another mechanism was found in which a higher concentration of EFE inhibited the viral load immediately after the viral entry into host cells, suggesting the inhibition of viral RNA replication. These results demonstrate that EFE worked against RSV infection through multiple antiviral mechanisms, a unique feature of this crude drug extract.
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Affiliation(s)
- Aya Fujikane
- Department of General Medicine, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Ryosuke Fujikane
- Department of Physiological Science and Molecular Biology, Fukuoka Dental College, Fukuoka, Japan
- Oral Medicine Research Center, Fukuoka Dental College, Fukuoka, Japan
| | - Sumiko Hyuga
- Oriental Medicine Research Center, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Yusuke Sechi
- Department of General Medicine, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Tetsuya Hiyoshi
- Department of General Medicine, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Atsuhiko Sakamoto
- Department of General Medicine, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Akinori Nishi
- TSUMURA Advanced Technology Research Laboratories, Tsumura & Co., Ibaraki, Japan
| | - Hiroshi Odaguchi
- Oriental Medicine Research Center, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Kenji Hiromatsu
- Department of Microbiology and Immunology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Yukihiro Goda
- National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Shigeki Nabeshima
- Department of General Medicine, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
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63
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Hsiao YC, Yang Y, Liu CW, Peng J, Feng J, Zhao H, Teitelbaum T, Lu K. Multiomics to Characterize the Molecular Events Underlying Impaired Glucose Tolerance in FXR-Knockout Mice. J Proteome Res 2024. [PMID: 38967328 DOI: 10.1021/acs.jproteome.3c00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The prevalence of different metabolic syndromes has grown globally, and the farnesoid X receptor (FXR), a metabolic homeostat for glucose, lipid, and bile acid metabolisms, may serve an important role in the progression of metabolic disorders. Glucose intolerance by FXR deficiency was previously reported and observed in our study, but the underlying biology remained unclear. To investigate the ambiguity, we collected the nontargeted profiles of the fecal metaproteome, serum metabolome, and liver proteome in Fxr-null (Fxr-/-) and wild-type (WT) mice with LC-HRMS. FXR deficiency showed a global impact on the different molecular levels we monitored, suggesting its serious disruption in the gut microbiota, hepatic metabolism, and circulating biomolecules. The network and enrichment analyses of the dysregulated metabolites and proteins suggested the perturbation of carbohydrate and lipid metabolism by FXR deficiency. Fxr-/- mice presented lower levels of hepatic proteins involved in glycogenesis. The impairment of glycogenesis by an FXR deficiency may leave glucose to accumulate in the circulation, which may deteriorate glucose tolerance. Lipid metabolism was dysregulated by FXR deficiency in a structural-dependent manner. Fatty acid β-oxidations were alleviated, but cholesterol metabolism was promoted by an FXR deficiency. Together, we explored the molecular events associated with glucose intolerance by impaired FXR with integrated novel multiomic data.
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Affiliation(s)
- Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Yifei Yang
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jingya Peng
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jiahao Feng
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Haoduo Zhao
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Taylor Teitelbaum
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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Elmeliegy M, Chen J, Dontabhaktuni A, Gaudy A, Kapitanov GI, Li J, Mim SR, Sharma S, Sun Q, Ait-Oudhia S. Dosing Strategies and Quantitative Clinical Pharmacology for Bispecific T-Cell Engagers Development in Oncology. Clin Pharmacol Ther 2024. [PMID: 38962850 DOI: 10.1002/cpt.3361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/09/2024] [Indexed: 07/05/2024]
Abstract
Bispecific T-cell Engagers (TCEs) are promising anti-cancer treatments that bind to both the CD3 receptors on T cells and an antigen on the surface of tumor cells, creating an immune synapse, leading to killing of malignant tumor cells. These novel therapies have unique development challenges, with specific safety risks of cytokine release syndrome. These on-target adverse events fortunately can be mitigated and deconvoluted from efficacy via innovative dosing strategies, making clinical pharmacology key in the development of these therapies. This review assesses dose selection and the role of quantitative clinical pharmacology in the development of the first eight approved TCEs. Model informed drug development (MIDD) strategies can be used at every stage to guide TCE development. Mechanistic modeling approaches allow for (1) efficacious yet safe first-in-human dose selection as compared with in vitro minimum anticipated biological effect level (MABEL) approach; (2) rapid escalation and reducing number of patients with subtherapeutic doses through model-based adaptive design; (3) virtual testing of different step-up dosing regimens that may not be feasible to be evaluated in the clinic; and (4) selection and justification of the optimal clinical step-up and full treatment doses. As the knowledge base around TCEs continues to grow, the relevance and utilization of MIDD strategies for supporting the development and dose optimization of these molecules are expected to advance, optimizing the benefit-risk profile for cancer patients.
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Affiliation(s)
- Mohamed Elmeliegy
- Oncology Research and Development, Pfizer Inc, San Diego, California, USA
| | - Joseph Chen
- Genentech Inc, South San Francisco, California, USA
| | | | | | | | - Junyi Li
- Genentech Inc, South San Francisco, California, USA
| | - Sabiha R Mim
- PharmaPro Consulting Inc, Hillsborough, New Jersey, USA
| | - Sharad Sharma
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Qin Sun
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Sihem Ait-Oudhia
- Quantitative Pharmacology and Pharmacometrics (QP2), Merck & Co., Rahway, New Jersey, USA
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Norris R, Jones J, Mancini E, Chevassut T, Simoes FA, Pepper C, Pepper A, Mitchell S. Patient-specific computational models predict prognosis in B cell lymphoma by quantifying pro-proliferative and anti-apoptotic signatures from genetic sequencing data. Blood Cancer J 2024; 14:105. [PMID: 38965209 PMCID: PMC11224250 DOI: 10.1038/s41408-024-01090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Genetic heterogeneity and co-occurring driver mutations impact clinical outcomes in blood cancers, but predicting the emergent effect of co-occurring mutations that impact multiple complex and interacting signalling networks is challenging. Here, we used mathematical models to predict the impact of co-occurring mutations on cellular signalling and cell fates in diffuse large B cell lymphoma and multiple myeloma. Simulations predicted adverse impact on clinical prognosis when combinations of mutations induced both anti-apoptotic (AA) and pro-proliferative (PP) signalling. We integrated patient-specific mutational profiles into personalised lymphoma models, and identified patients characterised by simultaneous upregulation of anti-apoptotic and pro-proliferative (AAPP) signalling in all genomic and cell-of-origin classifications (8-25% of patients). In a discovery cohort and two validation cohorts, patients with upregulation of neither, one (AA or PP), or both (AAPP) signalling states had good, intermediate and poor prognosis respectively. Combining AAPP signalling with genetic or clinical prognostic predictors reliably stratified patients into striking prognostic categories. AAPP patients in poor prognosis genetic clusters had 7.8 months median overall survival, while patients lacking both features had 90% overall survival at 120 months in a validation cohort. Personalised computational models enable identification of novel risk-stratified patient subgroups, providing a valuable tool for future risk-adapted clinical trials.
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Affiliation(s)
- Richard Norris
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - John Jones
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Erika Mancini
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Timothy Chevassut
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Fabio A Simoes
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Chris Pepper
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Andrea Pepper
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Simon Mitchell
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK.
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66
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Graham JP, Zhang Y, He L, Gonzalez-Fernandez T. CRISPR-GEM: A Novel Machine Learning Model for CRISPR Genetic Target Discovery and Evaluation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601587. [PMID: 39005295 PMCID: PMC11244939 DOI: 10.1101/2024.07.01.601587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
CRISPR gene editing strategies are shaping cell therapies through precise and tunable control over gene expression. However, achieving reliable therapeutic effects with improved safety and efficacy requires informed target gene selection. This depends on a thorough understanding of the involvement of target genes in gene regulatory networks (GRNs) that regulate cell phenotype and function. Machine learning models have been previously used for GRN reconstruction using RNA- seq data, but current techniques are limited to single cell types and focus mainly on transcription factors. This restriction overlooks many potential CRISPR target genes, such as those encoding extracellular matrix components, growth factors, and signaling molecules, thus limiting the applicability of these models for CRISPR strategies. To address these limitations, we have developed CRISPR-GEM, a multi-layer perceptron (MLP)-based synthetic GRN constructed to accurately predict the downstream effects of CRISPR gene editing. First, input and output nodes are identified as differentially expressed genes between defined experimental and target cell/tissue types respectively. Then, MLP training learns regulatory relationships in a black-box approach allowing accurate prediction of output gene expression using only input gene expression. Finally, CRISPR-mimetic perturbations are made to each input gene individually and the resulting model predictions are compared to those for the target group to score and assess each input gene as a CRISPR candidate. The top scoring genes provided by CRISPR-GEM therefore best modulate experimental group GRNs to motivate transcriptomic shifts towards a target group phenotype. This machine learning model is the first of its kind for predicting optimal CRISPR target genes and serves as a powerful tool for enhanced CRISPR strategies across a range of cell therapies.
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67
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Lagunes L, Briggs K, Martin-Holder P, Xu Z, Maurer D, Ghabra K, Deeds EJ. Modeling reveals the strength of weak interactions in stacked-ring assembly. Biophys J 2024; 123:1763-1780. [PMID: 38762753 DOI: 10.1016/j.bpj.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Cells employ many large macromolecular machines for the execution and regulation of processes that are vital for cell and organismal viability. Interestingly, cells cannot synthesize these machines as functioning units. Instead, cells synthesize the molecular parts that must then assemble into the functional complex. Many important machines, including chaperones such as GroEL and proteases such as the proteasome, comprise protein rings that are stacked on top of one another. While there is some experimental data regarding how stacked-ring complexes such as the proteasome self-assemble, a comprehensive understanding of the dynamics of stacked-ring assembly is currently lacking. Here, we developed a mathematical model of stacked-trimer assembly and performed an analysis of the assembly of the stacked homomeric trimer, which is the simplest stacked-ring architecture. We found that stacked rings are particularly susceptible to a form of kinetic trapping that we term "deadlock," in which the system gets stuck in a state where there are many large intermediates that are not the fully assembled structure but that cannot productively react. When interaction affinities are uniformly strong, deadlock severely limits assembly yield. We thus predicted that stacked rings would avoid situations where all interfaces in the structure have high affinity. Analysis of available crystal structures indicated that indeed the majority-if not all-of stacked trimers do not contain uniformly strong interactions. Finally, to better understand the origins of deadlock, we developed a formal pathway analysis and showed that, when all the binding affinities are strong, many of the possible pathways are utilized. In contrast, optimal assembly strategies utilize only a small number of pathways. Our work suggests that deadlock is a critical factor influencing the evolution of macromolecular machines and provides general principles for understanding the self-assembly efficiency of existing machines.
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Affiliation(s)
- Leonila Lagunes
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, California; Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, California
| | - Koan Briggs
- Department of Physics, University of Kansas, Lawrence, Kansas
| | - Paige Martin-Holder
- Department of Molecular Immunology, Microbiology and Genetics, UCLA, Los Angeles, California
| | - Zaikun Xu
- Center for Computational Biology, University of Kansas, Lawrence, Kansas
| | - Dustin Maurer
- Center for Computational Biology, University of Kansas, Lawrence, Kansas
| | - Karim Ghabra
- Computational and Systems Biology IDP, UCLA, Los Angeles, California
| | - Eric J Deeds
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, California; Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, California; Center for Computational Biology, University of Kansas, Lawrence, Kansas.
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Cao LM, Zhong NN, Chen Y, Li ZZ, Wang GR, Xiao Y, Liu XH, Jia J, Liu B, Bu LL. Less is more: Exploring neoadjuvant immunotherapy as a de-escalation strategy in head and neck squamous cell carcinoma treatment. Cancer Lett 2024; 598:217095. [PMID: 38964728 DOI: 10.1016/j.canlet.2024.217095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/15/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
Head and neck squamous cell carcinoma (HNSCC) constitutes a significant global cancer burden, given its high prevalence and associated mortality. Despite substantial progress in survival rates due to the enhanced multidisciplinary approach to treatment, these methods often lead to severe tissue damage, compromised function, and potential toxicity. Thus, there is an imperative need for novel, effective, and minimally damaging treatment modalities. Neoadjuvant treatment, an emerging therapeutic strategy, is designed to reduce tumor size and curtail distant metastasis prior to definitive intervention. Currently, neoadjuvant chemotherapy (NACT) has optimized the treatment approach for a subset of HNSCC patients, yet it has not produced a noticeable enhancement in overall survival (OS). In the contemporary cancer therapeutics landscape, immunotherapy is gaining traction at an accelerated pace. Notably, neoadjuvant immunotherapy (NAIT) has shown promising radiological and pathological responses, coupled with encouraging efficacy in several clinical trials. This potentially paves the way for a myriad of possibilities in treatment de-escalation of HNSCC, which warrants further exploration. This paper reviews the existing strategies and efficacies of neoadjuvant immune checkpoint inhibitors (ICIs), along with potential de-escalation strategies. Furthermore, the challenges encountered in the context of the de-escalation strategies of NAIT are explored. The aim is to inform future research directions that strive to improve the quality of life (QoL) for patients battling HNSCC.
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Affiliation(s)
- Lei-Ming Cao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Nian-Nian Zhong
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Yang Chen
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Zi-Zhan Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Guang-Rui Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Yao Xiao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Xuan-Hao Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Jun Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China; Department of Oral & Maxillofacial Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China.
| | - Bing Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China; Department of Oral & Maxillofacial Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China.
| | - Lin-Lin Bu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Somatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China; Department of Oral & Maxillofacial Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China.
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69
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Li G, Zhao Y, Ma W, Gao Y, Zhao C. Systems-level computational modeling in ischemic stroke: from cells to patients. Front Physiol 2024; 15:1394740. [PMID: 39015225 PMCID: PMC11250596 DOI: 10.3389/fphys.2024.1394740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/14/2024] [Indexed: 07/18/2024] Open
Abstract
Ischemic stroke, a significant threat to human life and health, refers to a class of conditions where brain tissue damage is induced following decreased cerebral blood flow. The incidence of ischemic stroke has been steadily increasing globally, and its disease mechanisms are highly complex and involve a multitude of biological mechanisms at various scales from genes all the way to the human body system that can affect the stroke onset, progression, treatment, and prognosis. To complement conventional experimental research methods, computational systems biology modeling can integrate and describe the pathogenic mechanisms of ischemic stroke across multiple biological scales and help identify emergent modulatory principles that drive disease progression and recovery. In addition, by running virtual experiments and trials in computers, these models can efficiently predict and evaluate outcomes of different treatment methods and thereby assist clinical decision-making. In this review, we summarize the current research and application of systems-level computational modeling in the field of ischemic stroke from the multiscale mechanism-based, physics-based and omics-based perspectives and discuss how modeling-driven research frameworks can deliver insights for future stroke research and drug development.
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Affiliation(s)
- Geli Li
- Gusu School, Nanjing Medical University, Suzhou, China
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Yanyong Zhao
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Wen Ma
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Yuan Gao
- QSPMed Technologies, Nanjing, China
| | - Chen Zhao
- School of Pharmacy, Nanjing Medical University, Nanjing, China
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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70
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Nussinov R, Yavuz BR, Demirel HC, Arici MK, Jang H, Tuncbag N. Review: Cancer and neurodevelopmental disorders: multi-scale reasoning and computational guide. Front Cell Dev Biol 2024; 12:1376639. [PMID: 39015651 PMCID: PMC11249571 DOI: 10.3389/fcell.2024.1376639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
The connection and causality between cancer and neurodevelopmental disorders have been puzzling. How can the same cellular pathways, proteins, and mutations lead to pathologies with vastly different clinical presentations? And why do individuals with neurodevelopmental disorders, such as autism and schizophrenia, face higher chances of cancer emerging throughout their lifetime? Our broad review emphasizes the multi-scale aspect of this type of reasoning. As these examples demonstrate, rather than focusing on a specific organ system or disease, we aim at the new understanding that can be gained. Within this framework, our review calls attention to computational strategies which can be powerful in discovering connections, causalities, predicting clinical outcomes, and are vital for drug discovery. Thus, rather than centering on the clinical features, we draw on the rapidly increasing data on the molecular level, including mutations, isoforms, three-dimensional structures, and expression levels of the respective disease-associated genes. Their integrated analysis, together with chromatin states, can delineate how, despite being connected, neurodevelopmental disorders and cancer differ, and how the same mutations can lead to different clinical symptoms. Here, we seek to uncover the emerging connection between cancer, including pediatric tumors, and neurodevelopmental disorders, and the tantalizing questions that this connection raises.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Bengi Ruken Yavuz
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
| | | | - M. Kaan Arici
- Graduate School of Informatics, Middle East Technical University, Ankara, Türkiye
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Nurcan Tuncbag
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Türkiye
- School of Medicine, Koc University, Istanbul, Türkiye
- Koc University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
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71
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Feng R, Li S, Zhang Y. AI-powered microscopy image analysis for parasitology: integrating human expertise. Trends Parasitol 2024; 40:633-646. [PMID: 38824067 DOI: 10.1016/j.pt.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Microscopy image analysis plays a pivotal role in parasitology research. Deep learning (DL), a subset of artificial intelligence (AI), has garnered significant attention. However, traditional DL-based methods for general purposes are data-driven, often lacking explainability due to their black-box nature and sparse instructional resources. To address these challenges, this article presents a comprehensive review of recent advancements in knowledge-integrated DL models tailored for microscopy image analysis in parasitology. The massive amounts of human expert knowledge from parasitologists can enhance the accuracy and explainability of AI-driven decisions. It is expected that the adoption of knowledge-integrated DL models will open up a wide range of applications in the field of parasitology.
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Affiliation(s)
- Ruijun Feng
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China; School of Computer Science and Engineering, University of New South Wales, Sydney, Australia
| | - Sen Li
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China.
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72
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Rawal A, Kidchob C, Ou J, Sauna ZE. Application of machine learning approaches for predicting hemophilia A severity. J Thromb Haemost 2024; 22:1909-1918. [PMID: 38718927 DOI: 10.1016/j.jtha.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/27/2024]
Abstract
BACKGROUND Hemophilia A (HA) is an X-linked congenital bleeding disorder, which leads to deficiency of clotting factor (F) VIII. It mostly affects males, and females are considered carriers. However, it is now recognized that variants of F8 in females can result in HA. Nonetheless, most females go undiagnosed and untreated for HA, and their bleeding complications are attributed to other causes. Predicting the severity of HA for female patients can provide valuable insights for treating the conditions associated with the disease, such as heavy bleeding. OBJECTIVES To predict the severity of HA based on F8 genotype using a machine learning (ML) approach. METHODS Using multiple datasets of variants in the F8 and disease severity from various repositories, we derived the sequence for the FVIII protein. Using the derived sequences, we used ML models to predict the severity of HA in female patients. RESULTS Utilizing different classification models, we highlight the validity of the datasets and our approach with predictive F1 scores of 0.88, 0.99, 0.93, 0.99, and 0.90 for all the validation sets. CONCLUSION Although with some limitations, ML-based approaches demonstrated the successful prediction of disease severity in female HA patients based on variants in the F8. This study confirms previous research findings that ML can help predict the severity of hemophilia. These results can be valuable for future studies in achieving better treatment and clinical outcomes for female patients with HA, which is an urgent unmet need.
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Affiliation(s)
- Atul Rawal
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Christopher Kidchob
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jiayi Ou
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Zuben E Sauna
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA.
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73
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McGirr T, Onar O, Jafarnejad SM. Dysregulated ribosome quality control in human diseases. FEBS J 2024. [PMID: 38949989 DOI: 10.1111/febs.17217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/31/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Precise regulation of mRNA translation is of fundamental importance for maintaining homeostasis. Conversely, dysregulated general or transcript-specific translation, as well as abnormal translation events, have been linked to a multitude of diseases. However, driven by the misconception that the transient nature of mRNAs renders their abnormalities inconsequential, the importance of mechanisms that monitor the quality and fidelity of the translation process has been largely overlooked. In recent years, there has been a dramatic shift in this paradigm, evidenced by several seminal discoveries on the role of a key mechanism in monitoring the quality of mRNA translation - namely, Ribosome Quality Control (RQC) - in the maintenance of homeostasis and the prevention of diseases. Here, we will review recent advances in the field and emphasize the biological significance of the RQC mechanism, particularly its implications in human diseases.
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Affiliation(s)
- Tom McGirr
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Okan Onar
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
- Department of Biology, Faculty of Science, Ankara University, Turkey
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74
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Valous NA, Popp F, Zörnig I, Jäger D, Charoentong P. Graph machine learning for integrated multi-omics analysis. Br J Cancer 2024; 131:205-211. [PMID: 38729996 PMCID: PMC11263675 DOI: 10.1038/s41416-024-02706-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Multi-omics experiments at bulk or single-cell resolution facilitate the discovery of hypothesis-generating biomarkers for predicting response to therapy, as well as aid in uncovering mechanistic insights into cellular and microenvironmental processes. Many methods for data integration have been developed for the identification of key elements that explain or predict disease risk or other biological outcomes. The heterogeneous graph representation of multi-omics data provides an advantage for discerning patterns suitable for predictive/exploratory analysis, thus permitting the modeling of complex relationships. Graph-based approaches-including graph neural networks-potentially offer a reliable methodological toolset that can provide a tangible alternative to scientists and clinicians that seek ideas and implementation strategies in the integrated analysis of their omics sets for biomedical research. Graph-based workflows continue to push the limits of the technological envelope, and this perspective provides a focused literature review of research articles in which graph machine learning is utilized for integrated multi-omics data analyses, with several examples that demonstrate the effectiveness of graph-based approaches.
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Affiliation(s)
- Nektarios A Valous
- Applied Tumor Immunity Clinical Cooperation Unit, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany.
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
| | - Ferdinand Popp
- Applied Tumor Immunity Clinical Cooperation Unit, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Inka Zörnig
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Dirk Jäger
- Applied Tumor Immunity Clinical Cooperation Unit, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Pornpimol Charoentong
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
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75
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Kotsuka T, Hori Y. Stability Analysis for Large-Scale Multi-Agent Molecular Communication Systems. IEEE Trans Nanobioscience 2024; 23:507-517. [PMID: 38781070 DOI: 10.1109/tnb.2024.3404592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Molecular communication (MC) is recently featured as a novel communication tool to connect individual biological nanorobots. It is expected that a large number of nanorobots can form large multi-agent MC systems through MC to accomplish complex and large-scale tasks that cannot be achieved by a single nanorobot. However, most previous models for MC systems assume a unidirectional diffusion communication channel and cannot capture the feedback between each nanorobot, which is important for multi-agent MC systems. In this paper, we introduce a system theoretic model for large-scale multi-agent MC systems using transfer functions, and then propose a method to analyze the stability for multi-agent MC systems. The proposed method decomposes the multi-agent MC system into multiple single-input and single-output (SISO) systems, which facilitates the application of simple analysis technique for SISO systems to the large-scale multi-agent MC system. Finally, we demonstrate the proposed method by analyzing the stability of a specific large-scale multi-agent MC system and clarify a parameter region to synchronize the states of nanorobots, which is important to make cooperative behaviors at a population level.
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76
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Pirak D, Sharan R. D'or: deep orienter of protein-protein interaction networks. Bioinformatics 2024; 40:btae355. [PMID: 38862241 PMCID: PMC11254290 DOI: 10.1093/bioinformatics/btae355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 04/19/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
MOTIVATION Protein-protein interactions (PPIs) provide the skeleton for signal transduction in the cell. Current PPI measurement techniques do not provide information on their directionality which is critical for elucidating signaling pathways. To date, there are hundreds of thousands of known PPIs in public databases, yet only a small fraction of them have an assigned direction. This information gap calls for computational approaches for inferring the directionality of PPIs, aka network orientation. RESULTS In this work, we propose a novel deep learning approach for PPI network orientation. Our method first generates a set of proximity scores between a protein interaction and sets of cause and effect proteins using a network propagation procedure. Each of these score sets is fed, one at a time, to a deep set encoder whose outputs are used as features for predicting the interaction's orientation. On a comprehensive dataset of oriented PPIs taken from five different sources, we achieve an area under the precision-recall curve of 0.89-0.92, outperforming previous methods. We further demonstrate the utility of the oriented network in prioritizing cancer driver genes and disease genes. AVAILABILITY AND IMPLEMENTATION D'or is implemented in Python and is publicly available at https://github.com/pirakd/DeepOrienter.
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Affiliation(s)
- Daniel Pirak
- Department of Electrical Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Roded Sharan
- Department of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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77
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Pal S, Dhar R. Living in a noisy world-origins of gene expression noise and its impact on cellular decision-making. FEBS Lett 2024; 598:1673-1691. [PMID: 38724715 DOI: 10.1002/1873-3468.14898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 07/23/2024]
Abstract
The expression level of a gene can vary between genetically identical cells under the same environmental condition-a phenomenon referred to as gene expression noise. Several studies have now elucidated a central role of transcription factors in the generation of expression noise. Transcription factors, as the key components of gene regulatory networks, drive many important cellular decisions in response to cellular and environmental signals. Therefore, a very relevant question is how expression noise impacts gene regulation and influences cellular decision-making. In this Review, we summarize the current understanding of the molecular origins of expression noise, highlighting the role of transcription factors in this process, and discuss the ways in which noise can influence cellular decision-making. As advances in single-cell technologies open new avenues for studying expression noise as well as gene regulatory circuits, a better understanding of the influence of noise on cellular decisions will have important implications for many biological processes.
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Affiliation(s)
- Sampriti Pal
- Department of Bioscience and Biotechnology, IIT Kharagpur, India
| | - Riddhiman Dhar
- Department of Bioscience and Biotechnology, IIT Kharagpur, India
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78
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Vaishnav MS, Pd D, Hegadi SS, C D, Murthy KNC, Srikanta S, Prasad R S. Accelerated microbial identification "directly" from positive blood cultures using MALDI-TOF MS: Local clinical laboratory challenges. Diagn Microbiol Infect Dis 2024; 109:116306. [PMID: 38735146 DOI: 10.1016/j.diagmicrobio.2024.116306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/14/2024]
Abstract
Rapid identification of microbial pathogens "directly" from positive blood cultures (PBCs) is critical for prompt initiation of empirical antibiotic therapy and clinical outcomes. Towards higher microbial identification rates, we modified a published initial serum separator tubes-based MALDI-TOF-MS protocol, for blood culture specimens received at a non-hospital based standalone diagnostic laboratory, Bangalore, India: (a) "Initial" protocol #1: From 28 PBCs, identification= 39% (Gram-negative= 43%: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa; Gram-positive: 36%: Enterococcus faecalis, Staphylococcus aureus, Staphylococcus haemolyticus); mis-identification= 14%; non-identification= 47%. (b) "Modified" protocol #2: Quality controls (ATCC colonies spiked in negative blood cultures) From 7 analysis, identification= 100% (Escherichia coli, Klebsiella pneumonia, Klebsiella oxytoca, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus); From 7 PBCs, identification= 57%; mis-identification= 14%; non-identification= 29%. Microbial preparations of highest quality and quantity for proteomic analysis and separate spectra matching reference databases for colonies and PBCs are needed for best clinical utility.
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Affiliation(s)
- Madhumati S Vaishnav
- Neuberg Anand Academy of Laboratory Medicine (NAALM), Bengaluru, India; Samatvam Endocrinology Diabetes Center, Jnana Sanjeevini Diabetes Hospital and Medical Center, Bengaluru, India.
| | - Deepalakshmi Pd
- Neuberg Anand Academy of Laboratory Medicine (NAALM), Bengaluru, India; Neuberg Anand Reference Laboratories (NARL), Bengaluru, India
| | - Sneha S Hegadi
- Neuberg Anand Reference Laboratories (NARL), Bengaluru, India
| | - Divya C
- Neuberg Anand Reference Laboratories (NARL), Bengaluru, India
| | | | - Sathyanarayana Srikanta
- Samatvam Endocrinology Diabetes Center, Jnana Sanjeevini Diabetes Hospital and Medical Center, Bengaluru, India
| | - Sujay Prasad R
- Neuberg Anand Academy of Laboratory Medicine (NAALM), Bengaluru, India; Neuberg Anand Reference Laboratories (NARL), Bengaluru, India
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79
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Ahmad P, Hussain A, Siqueira WL. Mass spectrometry-based proteomic approaches for salivary protein biomarkers discovery and dental caries diagnosis: A critical review. MASS SPECTROMETRY REVIEWS 2024; 43:826-856. [PMID: 36444686 DOI: 10.1002/mas.21822] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Dental caries is a multifactorial chronic disease resulting from the intricate interplay among acid-generating bacteria, fermentable carbohydrates, and several host factors such as saliva. Saliva comprises several proteins which could be utilized as biomarkers for caries prevention, diagnosis, and prognosis. Mass spectrometry-based salivary proteomics approaches, owing to their sensitivity, provide the opportunity to investigate and unveil crucial cariogenic pathogen activity and host indicators and may demonstrate clinically relevant biomarkers to improve caries diagnosis and management. The present review outlines the published literature of human clinical proteomics investigations on caries and extensively elucidates frequently reported salivary proteins as biomarkers. This review also discusses important aspects while designing an experimental proteomics workflow. The protein-protein interactions and the clinical relevance of salivary proteins as biomarkers for caries, together with uninvestigated domains of the discipline are also discussed critically.
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Affiliation(s)
- Paras Ahmad
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ahmed Hussain
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Walter L Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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80
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Li X, Ma F, Wang Y, Zhao H, Gao J. Incidence of hyperkalemia in anuric hemodialysis patients treated with sacubitril/valsartan. Hemodial Int 2024; 28:336-342. [PMID: 38558252 DOI: 10.1111/hdi.13150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION Sacubitril/valsartan is increasingly used in hemodialysis patients due to its cardioprotective benefits. However, its impact on serum potassium levels in anuric patients undergoing hemodialysis remains controversial. METHODS We conducted a retrospective data from patients undergoing hemodialysis at two dialysis centers. A total of 71 out of 332 patients receiving hemodialysis treatment were enrolled. Mean serum potassium (mean value of 6-8 determinations), peak serum potassium (maximum K value observed during follow-up observations), and other biochemical parameters were recorded at baseline and during the follow-up period. FINDINGS After 6 months of follow-up, mean serum potassium increased from 4.84 ± 0.45 mmol/L at baseline to 5.07 ± 0.46 mmol/L at 3 months and 5.04 ± 0.46 mmol/L at 6 months (p < 0.001). Notably, no significant group differences were found in peak serum potassium concentrations between baseline and 6 months after sacubitril/valsartan therapy (5.69 ± 0.56 vs. 5.75 ± 0.41, p = 0.419). Prior to starting sacubitril/valsartan treatment, none of the patients had severe hyperkalemia; however, after 3 and 6 months of sacubitril/valsartan therapy, two (2.80%) and three (4.20%) patients experienced severe hyperkalemia, respectively; however, this difference was not statistically significant. Additionally, there was a significant reduction in blood pressure; however, serum sodium, bicarbonate, and Kt/V values did not change significantly during either period. DISCUSSION Sacubitril/valsartan therapy is associated with an increase in serum potassium levels in anuric hemodialysis patients. Nevertheless, the proportion of patients with severe hyperkalemia did not increase significantly. This suggests that the use of sacubitril/valsartan in anuric patients on hemodialysis is relatively safe.
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Affiliation(s)
- Xiaofan Li
- Department of Nephrology, Peking University Shougang Hospital, Beijing, China
| | - Fei Ma
- Blood Purification Center, Chifeng Municipal Hospital, Chifeng, China
| | - Yan Wang
- Department of Internal Medicine, Beijing, China
| | - Haidan Zhao
- Department of Nephrology, Peking University Shougang Hospital, Beijing, China
| | - Jianjun Gao
- Department of Nephrology, The Chinese PLA Strategic Support Force Characteristic Medical Center, Beijing, China
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81
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Limayem A, Martin EM, Shankar S. Study on the citrus greening disease: Current challenges and novel therapies. Microb Pathog 2024; 192:106688. [PMID: 38750772 DOI: 10.1016/j.micpath.2024.106688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/06/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024]
Abstract
The unprecedented worldwide spread of the Citrus greening disorder, called Huanglongbing (HLB), has urged researchers for rapid interventions. HLB poses a considerable threat to global citriculture owing to its devastating impact on citrus species. This disease is caused by Candidatus Liberibacter species (CLs), primarily transferred through psyllid insects, such as Trioza erytreae and Diaphorina citri. It results in phloem malfunction, root decline, and altered plant source-sink relationships, leading to a deficient plant with minimal yield before it dies. Thus, many various techniques have been employed to eliminate HLB and control vector populations through the application of insecticides and antimicrobials. The latter have evidenced short-term efficiency. While nucleic acid-based analyses and symptom-based identification of the disease have been used for detection, they suffer from limitations such as false negatives, complex sample preparation, and high costs. To address these challenges, secreted protein-based biomarkers offer a promising solution for accurate, rapid, and cost-effective disease detection. This paper presents an overview of HLB symptoms in citrus plants, including leaf and fruit symptoms, as well as whole tree symptoms. The differentiation between HLB symptoms and those of nutrient deficiencies is discussed, emphasizing the importance of precise identification for effective disease management. The elusive nature of CLs and the challenges in culturing them in axenic cultures have hindered the understanding of their pathogenic mechanisms. However, genome sequencing has provided insights into CLs strains' metabolic traits and potential virulence factors. Efforts to identify potential host target genes for resistance are discussed, and a high-throughput antimicrobial testing method using Citrus hairy roots is introduced as a promising tool for rapid assessment of potential treatments. This review summarizes current challenges and novel therapies for HLB disease. It highlights the urgency of developing accurate and efficient detection methods and identifying the complex relations between CLs and their host plants. Transgenic citrus in conjunction with secreted protein-based biomarkers and innovative testing methodologies could revolutionize HLB management strategies toward achieving a sustainable citrus cultivation. It offers more reliable and practical solutions to combat this devastating disease and safeguard the global citriculture industry.
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Affiliation(s)
- Alya Limayem
- Department of Biology, College of Arts & Sciences, University of North Florida, Jacksonville, FL, USA
| | - Elizabeth M Martin
- Food Science, Department of Biological and Agricultural Engineering, University of Arkansas, AR, USA
| | - Shiv Shankar
- Research Laboratories in Science, Applied to Food, INRS-Armand-Frappier Health and Biotechnology Centre, Laval, Quebec, Canada; School of Food Science and Environmental Health, Grangegorman, Technological University Dublin, Dublin, Ireland.
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82
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Ocaña-Tienda B, Pérez-García VM. Mathematical modeling of brain metastases growth and response to therapies: A review. Math Biosci 2024; 373:109207. [PMID: 38759950 DOI: 10.1016/j.mbs.2024.109207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/04/2024] [Accepted: 05/10/2024] [Indexed: 05/19/2024]
Abstract
Brain metastases (BMs) are the most common intracranial tumor type and a significant health concern, affecting approximately 10% to 30% of all oncological patients. Although significant progress is being made, many aspects of the metastatic process to the brain and the growth of the resulting lesions are still not well understood. There is a need for an improved understanding of the growth dynamics and the response to treatment of these tumors. Mathematical models have been proven valuable for drawing inferences and making predictions in different fields of cancer research, but few mathematical works have considered BMs. This comprehensive review aims to establish a unified platform and contribute to fostering emerging efforts dedicated to enhancing our mathematical understanding of this intricate and challenging disease. We focus on the progress made in the initial stages of mathematical modeling research regarding BMs and the significant insights gained from such studies. We also explore the vital role of mathematical modeling in predicting treatment outcomes and enhancing the quality of clinical decision-making for patients facing BMs.
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Affiliation(s)
- Beatriz Ocaña-Tienda
- Mathematical Oncology Laboratory (MOLAB), University of Castilla-La Mancha, Avda. Camilo José Cela s/n, 13071, Ciudad Real, Spain.
| | - Víctor M Pérez-García
- Mathematical Oncology Laboratory (MOLAB), University of Castilla-La Mancha, Avda. Camilo José Cela s/n, 13071, Ciudad Real, Spain.
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83
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Goglia I, Węglarz-Tomczak E, Gioia C, Liu Y, Virtuoso A, Bonanomi M, Gaglio D, Salmistraro N, De Luca C, Papa M, Alberghina L, Westerhoff HV, Colangelo AM. Fusion-fission-mitophagy cycling and metabolic reprogramming coordinate nerve growth factor (NGF)-dependent neuronal differentiation. FEBS J 2024; 291:2811-2835. [PMID: 38362803 DOI: 10.1111/febs.17083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/02/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
Neuronal differentiation is regulated by nerve growth factor (NGF) and other neurotrophins. We explored the impact of NGF on mitochondrial dynamics and metabolism through time-lapse imaging, metabolomics profiling, and computer modeling studies. We show that NGF may direct differentiation by stimulating fission, thereby causing selective mitochondrial network fragmentation and mitophagy, ultimately leading to increased mitochondrial quality and respiration. Then, we reconstructed the dynamic fusion-fission-mitophagy cycling of mitochondria in a computer model, integrating these processes into a single network mechanism. Both the computational model and the simulations are able to reproduce the proposed mechanism in terms of mitochondrial dynamics, levels of reactive oxygen species (ROS), mitophagy, and mitochondrial quality, thus providing a computational tool for the interpretation of the experimental data and for future studies aiming to detail further the action of NGF on mitochondrial processes. We also show that changes in these mitochondrial processes are intertwined with a metabolic function of NGF in differentiation: NGF directs a profound metabolic rearrangement involving glycolysis, TCA cycle, and the pentose phosphate pathway, altering the redox balance. This metabolic rewiring may ensure: (a) supply of both energy and building blocks for the anabolic processes needed for morphological reorganization, as well as (b) redox homeostasis.
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Affiliation(s)
- Ilaria Goglia
- Laboratory of Neuroscience "R. Levi-Montalcini", Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Ewelina Węglarz-Tomczak
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Claudio Gioia
- Laboratory of Neuroscience "R. Levi-Montalcini", Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Yanhua Liu
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Assunta Virtuoso
- Laboratory of Morphology of Neuronal Network, Department of Public Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Marcella Bonanomi
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, Italy
| | - Daniela Gaglio
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, Italy
| | - Noemi Salmistraro
- SYSBIO Centre of Systems Biology ISBE.ITALY, University of Milano-Bicocca, Italy
| | - Ciro De Luca
- Laboratory of Morphology of Neuronal Network, Department of Public Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Michele Papa
- Laboratory of Morphology of Neuronal Network, Department of Public Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy
- SYSBIO Centre of Systems Biology ISBE.ITALY, University of Milano-Bicocca, Italy
| | - Lilia Alberghina
- SYSBIO Centre of Systems Biology ISBE.ITALY, University of Milano-Bicocca, Italy
- Infrastructure for Systems Biology Europe (ISBE), Amsterdam, The Netherlands
| | - Hans V Westerhoff
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
- Infrastructure for Systems Biology Europe (ISBE), Amsterdam, The Netherlands
- Molecular Cell Physiology, VU University Amsterdam, The Netherlands
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, UK
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, South Africa
| | - Anna Maria Colangelo
- Laboratory of Neuroscience "R. Levi-Montalcini", Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
- SYSBIO Centre of Systems Biology ISBE.ITALY, University of Milano-Bicocca, Italy
- Infrastructure for Systems Biology Europe (ISBE), Amsterdam, The Netherlands
- NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, Italy
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84
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Lee CT, Bell M, Bonilla-Quintana M, Rangamani P. Biophysical Modeling of Synaptic Plasticity. Annu Rev Biophys 2024; 53:397-426. [PMID: 38382115 DOI: 10.1146/annurev-biophys-072123-124954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Dendritic spines are small, bulbous compartments that function as postsynaptic sites and undergo intense biochemical and biophysical activity. The role of the myriad signaling pathways that are implicated in synaptic plasticity is well studied. A recent abundance of quantitative experimental data has made the events associated with synaptic plasticity amenable to quantitative biophysical modeling. Spines are also fascinating biophysical computational units because spine geometry, signal transduction, and mechanics work in a complex feedback loop to tune synaptic plasticity. In this sense, ideas from modeling cell motility can inspire us to develop multiscale approaches for predictive modeling of synaptic plasticity. In this article, we review the key steps in postsynaptic plasticity with a specific focus on the impact of spine geometry on signaling, cytoskeleton rearrangement, and membrane mechanics. We summarize the main experimental observations and highlight how theory and computation can aid our understanding of these complex processes.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Miriam Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Mayte Bonilla-Quintana
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
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85
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Banerjee U, Borbora SM, Guha M, Yadav V, Sanjay V, Singh A, Balaji KN, Chandra N. Inhibition of leukotriene-B4 signalling-mediated host response to tuberculosis is a potential mode of adjunctive host-directed therapy. Immunology 2024; 172:392-407. [PMID: 38504502 DOI: 10.1111/imm.13781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
Treatment of tuberculosis (TB) is faced with several challenges including the long treatment duration, drug toxicity and tissue pathology. Host-directed therapy provides promising avenues to find compounds for adjunctively assisting antimycobacterials in the TB treatment regimen, by promoting pathogen eradication or limiting tissue destruction. Eicosanoids are a class of lipid molecules that are potent mediators of inflammation and have been implicated in aspects of the host response against TB. Here, we have explored the blood transcriptome of pulmonary TB patients to understand the activity of leukotriene B4, a pro-inflammatory eicosanoid. Our study shows a significant upregulation in the leukotriene B4 signalling pathway in active TB patients, which is reversed with TB treatment. We have further utilized our in-house network analysis algorithm, ResponseNet, to identify potential downstream signal effectors of leukotriene B4 in TB patients including STAT1/2 and NADPH oxidase at a systemic as well as local level, followed by experimental validation of the same. Finally, we show the potential of inhibiting leukotriene B4 signalling as a mode of adjunctive host-directed therapy against TB. This study provides a new mode of TB treatment along with mechanistic insights which can be further explored in pre-clinical trials.
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Affiliation(s)
- Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Salik Miskat Borbora
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Madhura Guha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Vikas Yadav
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - V Sanjay
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | | | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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86
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Kong S, Zhu M, Roeder AHK. Self-organization underlies developmental robustness in plants. Cells Dev 2024:203936. [PMID: 38960068 DOI: 10.1016/j.cdev.2024.203936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
Development is a self-organized process that builds on cells and their interactions. Cells are heterogeneous in gene expression, growth, and division; yet how development is robust despite such heterogeneity is a fascinating question. Here, we review recent progress on this topic, highlighting how developmental robustness is achieved through self-organization. We will first discuss sources of heterogeneity, including stochastic gene expression, heterogeneity in growth rate and direction, and heterogeneity in division rate and precision. We then discuss cellular mechanisms that buffer against such noise, including Paf1C- and miRNA-mediated denoising, spatiotemporal growth averaging and compensation, mechanisms to improve cell division precision, and coordination of growth rate and developmental timing between different parts of an organ. We also discuss cases where such heterogeneity is not buffered but utilized for development. Finally, we highlight potential directions for future studies of noise and developmental robustness.
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Affiliation(s)
- Shuyao Kong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Mingyuan Zhu
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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87
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Frenkel M, Raman S. Discovering mechanisms of human genetic variation and controlling cell states at scale. Trends Genet 2024; 40:587-600. [PMID: 38658256 DOI: 10.1016/j.tig.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/26/2024]
Abstract
Population-scale sequencing efforts have catalogued substantial genetic variation in humans such that variant discovery dramatically outpaces interpretation. We discuss how single-cell sequencing is poised to reveal genetic mechanisms at a rate that may soon approach that of variant discovery. The functional genomics toolkit is sufficiently modular to systematically profile almost any type of variation within increasingly diverse contexts and with molecularly comprehensive and unbiased readouts. As a result, we can construct deep phenotypic atlases of variant effects that span the entire regulatory cascade. The same conceptual approach to interpreting genetic variation should be applied to engineering therapeutic cell states. In this way, variant mechanism discovery and cell state engineering will become reciprocating and iterative processes towards genomic medicine.
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Affiliation(s)
- Max Frenkel
- Cellular and Molecular Biology Graduate Program, University of Wisconsin, Madison, WI, USA; Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA; Department of Bacteriology, University of Wisconsin, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, USA.
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88
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López-Valverde L, Vázquez-Mosquera ME, Colón-Mejeras C, Bravo SB, Barbosa-Gouveia S, Álvarez JV, Sánchez-Martínez R, López-Mendoza M, López-Rodríguez M, Villacorta-Argüelles E, Goicoechea-Diezhandino MA, Guerrero-Márquez FJ, Ortolano S, Leao-Teles E, Hermida-Ameijeiras Á, Couce ML. Characterization of the plasma proteomic profile of Fabry disease: Potential sex- and clinical phenotype-specific biomarkers. Transl Res 2024; 269:47-63. [PMID: 38395389 DOI: 10.1016/j.trsl.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Fabry disease (FD) is a X-linked rare lysosomal storage disorder caused by deficient α-galactosidase A (α-GalA) activity. Early diagnosis and the prediction of disease course are complicated by the clinical heterogeneity of FD, as well as by the frequently inconclusive biochemical and genetic test results that do not correlate with clinical course. We sought to identify potential biomarkers of FD to better understand the underlying pathophysiology and clinical phenotypes. We compared the plasma proteomes of 50 FD patients and 50 matched healthy controls using DDA and SWATH-MS. The >30 proteins that were differentially expressed between the 2 groups included proteins implicated in processes such as inflammation, heme and haemoglobin metabolism, oxidative stress, coagulation, complement cascade, glucose and lipid metabolism, and glycocalyx formation. Stratification by sex revealed that certain proteins were differentially expressed in a sex-dependent manner. Apolipoprotein A-IV was upregulated in FD patients with complications, especially those with chronic kidney disease, and apolipoprotein C-III and fetuin-A were identified as possible markers of FD with left ventricular hypertrophy. All these proteins had a greater capacity to identify the presence of complications in FD patients than lyso-GB3, with apolipoprotein A-IV standing out as being more sensitive and effective in differentiating the presence and absence of chronic kidney disease in FD patients than renal markers such as creatinine, glomerular filtration rate and microalbuminuria. Identification of these potential biomarkers can help further our understanding of the pathophysiological processes that underlie the heterogeneous clinical manifestations associated with FD.
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Affiliation(s)
- Laura López-Valverde
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases. RICORS-SAMID, CIBERER. University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain; Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain
| | - María E Vázquez-Mosquera
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases. RICORS-SAMID, CIBERER. University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain; Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain
| | - Cristóbal Colón-Mejeras
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases. RICORS-SAMID, CIBERER. University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain; Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain
| | - Susana B Bravo
- Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain; Proteomic Platform, University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain
| | - Sofía Barbosa-Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases. RICORS-SAMID, CIBERER. University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain; Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain
| | - J Víctor Álvarez
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases. RICORS-SAMID, CIBERER. University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain; Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain
| | - Rosario Sánchez-Martínez
- Internal Medicine Department, Alicante General University Hospital-Alicante Institute of Health and Biomedical Research (ISABIAL), Pintor Baeza 12, Alicante 03010, Spain
| | - Manuel López-Mendoza
- Department of Nephrology, Hospital Universitario Virgen del Rocío, Manuel Siurot s/n, Sevilla 41013, Spain
| | - Mónica López-Rodríguez
- Internal Medicine Department, Hospital Universitario Ramón y Cajal, IRYCIS, Colmenar Viejo, Madrid 28034, Spain; Faculty of Medicine and Health Sciences, Universidad de Alcalá (UAH), Av. de Madrid, Alcalá de Henares 28871, Spain
| | - Eduardo Villacorta-Argüelles
- Department of Cardiology, Complejo Asistencial Universitario de Salamanca, P°. de San Vicente 58, Salamanca 37007, Spain
| | | | - Francisco J Guerrero-Márquez
- Department of Cardiology, Internal Medicine Service, Hospital de la Serranía, San Pedro, Ronda, Málaga 29400, Spain
| | - Saida Ortolano
- Rare Diseases and Pediatric Medicine Research Group, Galicia Sur Health Research Institute-SERGAS-UVIGO, Clara Campoamor 341, Vigo 36213, Spain
| | - Elisa Leao-Teles
- Centro de Referência de Doenças Hereditárias do Metabolismo, Centro Hospitalar Universitário de São João, Prof. Hernâni Monteiro, Porto 4200-319, Portugal
| | - Álvaro Hermida-Ameijeiras
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases. RICORS-SAMID, CIBERER. University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain; Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain.
| | - María L Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases. RICORS-SAMID, CIBERER. University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain; Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Choupana s/n, Santiago de Compostela, A Coruña 15706, Spain.
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89
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Xiong Z, Cao J, Wang K, Yang Y, Hu Y, Nie J, Zeng Q, Hu Y, Zhu L, Li X, Wu H. Characterization and functional analysis of chicken CDK protein. Poult Sci 2024; 103:103833. [PMID: 38810563 PMCID: PMC11166876 DOI: 10.1016/j.psj.2024.103833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
The family of cell cycle-dependent kinases (CDKs) serves as catalytic subunits within protein kinase complexes, playing a crucial role in cell cycle progression. While the function of CDK proteins in regulating mammalian innate immune responses and virus replication is well-documented, their role in chickens remains unclear. To address this, we cloned several chicken CDKs, specifically CDK6 through CDK10. We observed that CDK6 is widely expressed across various chicken tissues, with localization in the cytoplasm, nucleus, or both in DF-1 cells. In addition, we also found that multiple chicken CDKs negatively regulate IFN-β signaling induced by chicken MAVS or chicken STING by targeting different steps. Moreover, during infection with infectious bursal disease virus (IBDV), various chicken CDKs, except CDK10, were recruited and co-localized with viral protein VP1. Interestingly, overexpression of CDK6 in chickens significantly enhanced IBDV replication. Conversely, knocking down CDK6 led to a marked increase in IFN-β production, triggered by chMDA5. Furthermore, targeting endogenous CDK6 with RNA interference substantially reduced IBDV replication. These findings collectively suggest that chicken CDKs, particularly CDK6, act as suppressors of IFN-β production and play a facilitative role in IBDV replication.
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Affiliation(s)
- Zhixuan Xiong
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jingjing Cao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, 266237, China
| | - Ke Wang
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yuling Yang
- College of Forestry, Jiangxi Agricultural University, East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration, Camphor Engineering Research Center of NFGA, Jiangxi Province, Nanchang 330045, China
| | - Ying Hu
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiangjiang Nie
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qinghua Zeng
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yu Hu
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lina Zhu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Advanced Medical Research Institute, Shandong University, Qingdao, Shandong, 266237, China
| | - Xiangzhi Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Advanced Medical Research Institute, Shandong University, Qingdao, Shandong, 266237, China
| | - Huansheng Wu
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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90
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Bülow RD, Lan YC, Amann K, Boor P. [Artificial intelligence in kidney transplant pathology]. PATHOLOGIE (HEIDELBERG, GERMANY) 2024; 45:277-283. [PMID: 38598097 DOI: 10.1007/s00292-024-01324-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Artificial intelligence (AI) systems have showed promising results in digital pathology, including digital nephropathology and specifically also kidney transplant pathology. AIM Summarize the current state of research and limitations in the field of AI in kidney transplant pathology diagnostics and provide a future outlook. MATERIALS AND METHODS Literature search in PubMed and Web of Science using the search terms "deep learning", "transplant", and "kidney". Based on these results and studies cited in the identified literature, a selection was made of studies that have a histopathological focus and use AI to improve kidney transplant diagnostics. RESULTS AND CONCLUSION Many studies have already made important contributions, particularly to the automation of the quantification of some histopathological lesions in nephropathology. This likely can be extended to automatically quantify all relevant lesions for a kidney transplant, such as Banff lesions. Important limitations and challenges exist in the collection of representative data sets and the updates of Banff classification, making large-scale studies challenging. The already positive study results make future AI support in kidney transplant pathology appear likely.
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Affiliation(s)
- Roman David Bülow
- Institut für Pathologie, Sektion Nephropathologie, Universitätsklinikum RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Deutschland
| | - Yu-Chia Lan
- Institut für Pathologie, Sektion Nephropathologie, Universitätsklinikum RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Deutschland
| | - Kerstin Amann
- Abteilung Nephropathologie, Institut für Pathologie, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Deutschland
| | - Peter Boor
- Institut für Pathologie, Sektion Nephropathologie, Universitätsklinikum RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Deutschland.
- Medizinische Klinik II, Universitätsklinikum RWTH Aachen, Aachen, Deutschland.
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91
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Moeckel C, Mouratidis I, Chantzi N, Uzun Y, Georgakopoulos-Soares I. Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights. Bioessays 2024; 46:e2300210. [PMID: 38715516 DOI: 10.1002/bies.202300210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Understanding the influence of cis-regulatory elements on gene regulation poses numerous challenges given complexities stemming from variations in transcription factor (TF) binding, chromatin accessibility, structural constraints, and cell-type differences. This review discusses the role of gene regulatory networks in enhancing understanding of transcriptional regulation and covers construction methods ranging from expression-based approaches to supervised machine learning. Additionally, key experimental methods, including MPRAs and CRISPR-Cas9-based screening, which have significantly contributed to understanding TF binding preferences and cis-regulatory element functions, are explored. Lastly, the potential of machine learning and artificial intelligence to unravel cis-regulatory logic is analyzed. These computational advances have far-reaching implications for precision medicine, therapeutic target discovery, and the study of genetic variations in health and disease.
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Affiliation(s)
- Camille Moeckel
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ioannis Mouratidis
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Nikol Chantzi
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Yasin Uzun
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ilias Georgakopoulos-Soares
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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92
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Desai TA, Hedman ÅK, Dimitriou M, Koprulu M, Figiel S, Yin W, Johansson M, Watts EL, Atkins JR, Sokolov AV, Schiöth HB, Gunter MJ, Tsilidis KK, Martin RM, Pietzner M, Langenberg C, Mills IG, Lamb AD, Mälarstig A, Key TJ, Travis RC, Smith-Byrne K. Identifying proteomic risk factors for overall, aggressive, and early onset prostate cancer using Mendelian Randomisation and tumour spatial transcriptomics. EBioMedicine 2024; 105:105168. [PMID: 38878676 PMCID: PMC11233900 DOI: 10.1016/j.ebiom.2024.105168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
BACKGROUND Understanding the role of circulating proteins in prostate cancer risk can reveal key biological pathways and identify novel targets for cancer prevention. METHODS We investigated the association of 2002 genetically predicted circulating protein levels with risk of prostate cancer overall, and of aggressive and early onset disease, using cis-pQTL Mendelian randomisation (MR) and colocalisation. Findings for proteins with support from both MR, after correction for multiple-testing, and colocalisation were replicated using two independent cancer GWAS, one of European and one of African ancestry. Proteins with evidence of prostate-specific tissue expression were additionally investigated using spatial transcriptomic data in prostate tumour tissue to assess their role in tumour aggressiveness. Finally, we mapped risk proteins to drug and ongoing clinical trials targets. FINDINGS We identified 20 proteins genetically linked to prostate cancer risk (14 for overall [8 specific], 7 for aggressive [3 specific], and 8 for early onset disease [2 specific]), of which the majority replicated where data were available. Among these were proteins associated with aggressive disease, such as PPA2 [Odds Ratio (OR) per 1 SD increment = 2.13, 95% CI: 1.54-2.93], PYY [OR = 1.87, 95% CI: 1.43-2.44] and PRSS3 [OR = 0.80, 95% CI: 0.73-0.89], and those associated with early onset disease, including EHPB1 [OR = 2.89, 95% CI: 1.99-4.21], POGLUT3 [OR = 0.76, 95% CI: 0.67-0.86] and TPM3 [OR = 0.47, 95% CI: 0.34-0.64]. We confirmed an inverse association of MSMB with prostate cancer overall [OR = 0.81, 95% CI: 0.80-0.82], and also found an inverse association with both aggressive [OR = 0.84, 95% CI: 0.82-0.86] and early onset disease [OR = 0.71, 95% CI: 0.68-0.74]. Using spatial transcriptomics data, we identified MSMB as the genome-wide top-most predictive gene to distinguish benign regions from high grade cancer regions that comparatively had five-fold lower MSMB expression. Additionally, ten proteins that were associated with prostate cancer risk also mapped to existing therapeutic interventions. INTERPRETATION Our findings emphasise the importance of proteomics for improving our understanding of prostate cancer aetiology and of opportunities for novel therapeutic interventions. Additionally, we demonstrate the added benefit of in-depth functional analyses to triangulate the role of risk proteins in the clinical aggressiveness of prostate tumours. Using these integrated methods, we identify a subset of risk proteins associated with aggressive and early onset disease as priorities for investigation for the future prevention and treatment of prostate cancer. FUNDING This work was supported by Cancer Research UK (grant no. C8221/A29017).
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Affiliation(s)
- Trishna A Desai
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom.
| | - Åsa K Hedman
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marios Dimitriou
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mine Koprulu
- MRC Epidemiology Unit, University of Cambridge, United Kingdom
| | - Sandy Figiel
- University of Oxford, Nuffield Department of Surgical Sciences, Oxford, United Kingdom
| | - Wencheng Yin
- University of Oxford, Nuffield Department of Surgical Sciences, Oxford, United Kingdom
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Eleanor L Watts
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Joshua R Atkins
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom
| | - Aleksandr V Sokolov
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience Uppsala University, 75124, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience Uppsala University, 75124, Uppsala, Sweden
| | - Marc J Gunter
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, United Kingdom
| | - Konstantinos K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, United Kingdom; Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Richard M Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; NIHR Bristol Biomedical Research Centre, Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, United Kingdom
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge, United Kingdom; Computational Medicine, Berlin Institute of HealthHealth (BIH) at Charité - Univeritätsmedizin- Universitätsmedizin Berlin, Berlin, Germany; Precision Healthcare University Research Institute, Queen Mary University of London, London, United Kingdom
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, United Kingdom; Computational Medicine, Berlin Institute of HealthHealth (BIH) at Charité - Univeritätsmedizin- Universitätsmedizin Berlin, Berlin, Germany; Precision Healthcare University Research Institute, Queen Mary University of London, London, United Kingdom
| | - Ian G Mills
- University of Oxford, Nuffield Department of Surgical Sciences, Oxford, United Kingdom
| | - Alastair D Lamb
- University of Oxford, Nuffield Department of Surgical Sciences, Oxford, United Kingdom
| | - Anders Mälarstig
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Tim J Key
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom
| | - Ruth C Travis
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom
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93
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Sun J, Zhu W, Luan M, Xing Y, Feng Z, Zhu J, Ma X, Wang Y, Jia Y. Positive GLI1/INHBA feedback loop drives tumor progression in gastric cancer. Cancer Sci 2024; 115:2301-2317. [PMID: 38676428 PMCID: PMC11247559 DOI: 10.1111/cas.16193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
GLI1, a key transcription factor of the Hedgehog (Hh) signaling pathway, plays an important role in the development of cancer. However, the function and mechanisms by which GLI1 regulates gene transcription are not fully understood in gastric cancer (GC). Here, we found that GLI1 induced the proliferation and metastasis of GC cells, accompanied by transcriptional upregulation of INHBA. This increased INHBA expression exerted a promoting activity on Smads signaling and then transcriptionally activated GLI1 expression. Notably, our results demonstrate that disrupting the interaction between GLI1 and INHBA could inhibit GC tumorigenesis in vivo. More intriguingly, we confirmed the N6-methyladenosine (m6A) activation mechanism of the Helicobacter pylori/FTO/YTHDF2/GLI1 pathway in GC cells. In conclusion, our study confirmed that the GLI1/INHBA positive feedback loop influences GC progression and revealed the mechanism by which H. pylori upregulates GLI1 expression through m6A modification. This positive GLI1/INHBA feedback loop suggests a novel noncanonical mechanism of GLI1 activity in GC and provides potential therapeutic targets for GC treatment.
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Affiliation(s)
- Jingguo Sun
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Wenshuai Zhu
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Muhua Luan
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China
| | - Yuanxin Xing
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhaotian Feng
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jingyu Zhu
- Department of Gastroenterology, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiaoli Ma
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yunshan Wang
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yanfei Jia
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, China
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
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94
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Li Y, Wang Q, Zheng X, Xu B, Hu W, Zhang J, Kong X, Zhou Y, Huang T, Zhou Y. ScHGSC-IGDC: Identifying genes with differential correlations of high-grade serous ovarian cancer based on single-cell RNA sequencing analysis. Heliyon 2024; 10:e32909. [PMID: 38975079 PMCID: PMC11226911 DOI: 10.1016/j.heliyon.2024.e32909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/29/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
Due to the high heterogeneity of ovarian cancer (OC), it occupies the main cause of cancer-related death among women. As the most aggressive and frequent subtype of OC, high-grade serous cancer (HGSC) represents around 70 % of all patients. With the booming progress of single-cell RNA sequencing (scRNA-seq), unique and subtle changes among different cell states have been identified including novel risk genes and pathways. Here, our present study aims to identify differentially correlated core genes between normal and tumor status through HGSC scRNA-seq data analysis. R package high-dimension Weighted Gene Co-expression Network Analysis (hdWGCNA) was implemented for building gene interaction networks based on HGSC scRNA-seq data. DiffCorr was integrated for identifying differentially correlated genes between tumor and their adjacent normal counterparts. Software Cytoscape was implemented for constructing and visualizing biological networks. Real-time qPCR (RT-qPCR) was utilized to confirm expression pattern of new genes. We introduced ScHGSC-IGDC (Identifying Genes with Differential Correlations of HGSC based on scRNA-seq analysis), an in silico framework for identifying core genes in the development of HGSC. We detected thirty-four modules in the network. Scores of new genes with opposite correlations with others such as NDUFS5, TMSB4X, SERPINE2 and ITPR2 were identified. Further survival and literature validation emphasized their great values in the HGSC management. Meanwhile, RT-qPCR verified expression pattern of NDUFS5, TMSB4X, SERPINE2 and ITPR2 in human OC cell lines and tissues. Our research offered novel perspectives on the gene modulatory mechanisms from single cell resolution, guiding network based algorithms in cancer etiology field.
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Affiliation(s)
- Yuanqi Li
- Tumor Biological Diagnosis and Treatment Center, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, China
- Institute of Cell Therapy, Soochow University, Changzhou, 213003, China
| | - Qi Wang
- Tumor Biological Diagnosis and Treatment Center, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, China
- Institute of Cell Therapy, Soochow University, Changzhou, 213003, China
| | - Xiao Zheng
- Tumor Biological Diagnosis and Treatment Center, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, China
- Institute of Cell Therapy, Soochow University, Changzhou, 213003, China
| | - Bin Xu
- Tumor Biological Diagnosis and Treatment Center, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, China
- Institute of Cell Therapy, Soochow University, Changzhou, 213003, China
| | - Wenwei Hu
- Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, China
- Institute of Cell Therapy, Soochow University, Changzhou, 213003, China
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
| | - Jinping Zhang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Xiangyin Kong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yi Zhou
- Tumor Biological Diagnosis and Treatment Center, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, China
- Institute of Cell Therapy, Soochow University, Changzhou, 213003, China
| | - Tao Huang
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - You Zhou
- Tumor Biological Diagnosis and Treatment Center, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou, 213003, China
- Institute of Cell Therapy, Soochow University, Changzhou, 213003, China
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95
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Kim JW, Manickam R, Sinha P, Xuan W, Huang J, Awad K, Brotto M, Tipparaju SM. P7C3 ameliorates barium chloride-induced skeletal muscle injury activating transcriptomic and epigenetic modulation of myogenic regulatory factors. J Cell Physiol 2024. [PMID: 38946152 DOI: 10.1002/jcp.31346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 07/02/2024]
Abstract
Skeletal muscle injury affects the quality of life in many pathologies, including volumetric muscle loss, contusion injury, and aging. We hypothesized that the nicotinamide phosphoribosyltransferase (Nampt) activator P7C3 improves muscle repair following injury. In the present study, we tested the effect of P7C3 (1-anilino-3-(3,6-dibromocarbazol-9-yl) propan-2-ol) on chemically induced muscle injury. Muscle injury was induced by injecting 50 µL 1.2% barium chloride (BaCl2) into the tibialis anterior (TA) muscle in C57Bl/6J wild-type male mice. Mice were then treated with either 10 mg/kg body weight of P7C3 or Vehicle intraperitoneally for 7 days and assessed for histological, biochemical, and molecular changes. In the present study, we show that the acute BaCl2-induced TA muscle injury was robust and the P7C3-treated mice displayed a significant increase in the total number of myonuclei and blood vessels, and decreased serum CK activity compared with vehicle-treated mice. The specificity of P7C3 was evaluated using Nampt+/- mice, which did not display any significant difference in muscle repair capacity among treated groups. RNA-sequencing analysis of the injured TA muscles displayed 368 and 212 genes to be exclusively expressed in P7C3 and Veh-treated mice, respectively. There was an increase in the expression of genes involved in cellular processes, inflammatory response, angiogenesis, and muscle development in P7C3 versus Veh-treated mice. Conversely, there is a decrease in muscle structure and function, myeloid cell differentiation, glutathione, and oxidation-reduction, drug metabolism, and circadian rhythm signaling pathways. Chromatin immunoprecipitation-quantitative polymerase chain reaction (qPCR) and reverse transcription-qPCR analyses identified increased Pax7, Myf5, MyoD, and Myogenin expression in P7C3-treated mice. Increased histone lysine (H3K) methylation and acetylation were observed in P7C3-treated mice, with significant upregulation in inflammatory markers. Moreover, P7C3 treatment significantly increased the myotube fusion index in the BaCl2-injured human skeletal muscle in vitro. P7C3 also inhibited the lipopolysaccharide-induced inflammatory response and mitochondrial membrane potential of RAW 264.7 macrophage cells. Overall, we demonstrate that P7C3 activates muscle stem cells and enhances muscle injury repair with increased angiogenesis.
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Affiliation(s)
- Joung W Kim
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Ravikumar Manickam
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Puja Sinha
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Wanling Xuan
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Jian Huang
- Bone-Muscle Research Center, College of Nursing & Health Innovation, University of Texas at Arlington, Arlington, Texas, USA
| | - Kamal Awad
- Bone-Muscle Research Center, College of Nursing & Health Innovation, University of Texas at Arlington, Arlington, Texas, USA
| | - Marco Brotto
- Bone-Muscle Research Center, College of Nursing & Health Innovation, University of Texas at Arlington, Arlington, Texas, USA
| | - Srinivas M Tipparaju
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
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96
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Zhang Z, Zabaikina I, Nieto C, Vahdat Z, Bokes P, Singh A. Stochastic Gene Expression in Proliferating Cells: Differing Noise Intensity in Single-Cell and Population Perspectives. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601263. [PMID: 38979195 PMCID: PMC11230457 DOI: 10.1101/2024.06.28.601263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Random fluctuations (noise) in gene expression can be studied from two complementary perspectives: following expression in a single cell over time or comparing expression between cells in a proliferating population at a given time. Here, we systematically investigated scenarios where both perspectives lead to different levels of noise in a given gene product. We first consider a stable protein, whose concentration is diluted by cellular growth, and the protein inhibits growth at high concentrations, establishing a positive feedback loop. For a stochastic model with molecular bursting of gene products, we analytically predict and contrast the steady-state distributions of protein concentration in both frameworks. Although positive feedback amplifies the noise in expression, this amplification is much higher in the population framework compared to following a single cell over time. We also study other processes that lead to different noise levels even in the absence of such dilution-based feedback. When considering randomness in the partitioning of molecules between daughters during mitosis, we find that in the single-cell perspective, the noise in protein concentration is independent of noise in the cell cycle duration. In contrast, partitioning noise is amplified in the population perspective by increasing randomness in cell-cycle time. Overall, our results show that the commonly used single-cell framework that does not account for proliferating cells can, in some cases, underestimate the noise in gene product levels. These results have important implications for studying the inter-cellular variation of different stress-related expression programs across cell types that are known to inhibit cellular growth.
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Affiliation(s)
- Zhanhao Zhang
- Department of Electrical and Computer Engineering, University of Delaware. Newark, DE 19716, USA
| | - Iryna Zabaikina
- Department of Applied Mathematics and Statistics, Comenius University, Bratislava 84248, Slovakia
| | - César Nieto
- Department of Electrical and Computer Engineering, University of Delaware. Newark, DE 19716, USA
| | - Zahra Vahdat
- Department of Electrical and Computer Engineering, University of Delaware. Newark, DE 19716, USA
| | - Pavol Bokes
- Department of Applied Mathematics and Statistics, Comenius University, Bratislava 84248, Slovakia
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware. Newark, DE 19716, USA
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97
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Haikonen J, Szrinivasan R, Ojanen S, Rhee JK, Ryazantseva M, Sulku J, Zumaraite G, Lauri SE. GluK1 kainate receptors are necessary for functional maturation of parvalbumin interneurons regulating amygdala circuit function. Mol Psychiatry 2024:10.1038/s41380-024-02641-2. [PMID: 38942774 DOI: 10.1038/s41380-024-02641-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Parvalbumin expressing interneurons (PV INs) are key players in the local inhibitory circuits and their developmental maturation coincides with the onset of adult-type network dynamics in the brain. Glutamatergic signaling regulates emergence of the unique PV IN phenotype, yet the receptor mechanisms involved are not fully understood. Here we show that GluK1 subunit containing kainate receptors (KARs) are necessary for development and maintenance of the neurochemical and functional properties of PV INs in the lateral and basal amygdala (BLA). Ablation of GluK1 expression specifically from PV INs resulted in low parvalbumin expression and loss of characteristic high firing rate throughout development. In addition, we observed reduced spontaneous excitatory synaptic activity at adult GluK1 lacking PV INs. Intriguingly, inactivation of GluK1 expression in adult PV INs was sufficient to abolish their high firing rate and to reduce PV expression levels, suggesting a role for GluK1 in dynamic regulation of PV IN maturation state. The PV IN dysfunction in the absence of GluK1 perturbed the balance between evoked excitatory vs. inhibitory synaptic inputs and long-term potentiation (LTP) in LA principal neurons, and resulted in aberrant development of the resting-state functional connectivity between mPFC and BLA. Behaviorally, the absence of GluK1 from PV INs associated with hyperactivity and increased fear of novelty. These results indicate a critical role for GluK1 KARs in regulation of PV IN function across development and suggest GluK1 as a potential therapeutic target for pathologies involving PV IN malfunction.
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Affiliation(s)
- Joni Haikonen
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Rakenduvadhana Szrinivasan
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Simo Ojanen
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Jun Kyu Rhee
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Maria Ryazantseva
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Janne Sulku
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Gabija Zumaraite
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Sari E Lauri
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland.
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98
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Dorešić D, Grein S, Hasenauer J. Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data. Bioinformatics 2024; 40:i558-i566. [PMID: 38940161 PMCID: PMC11211815 DOI: 10.1093/bioinformatics/btae210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Quantitative dynamical models facilitate the understanding of biological processes and the prediction of their dynamics. The parameters of these models are commonly estimated from experimental data. Yet, experimental data generated from different techniques do not provide direct information about the state of the system but a nonlinear (monotonic) transformation of it. For such semi-quantitative data, when this transformation is unknown, it is not apparent how the model simulations and the experimental data can be compared. RESULTS We propose a versatile spline-based approach for the integration of a broad spectrum of semi-quantitative data into parameter estimation. We derive analytical formulas for the gradients of the hierarchical objective function and show that this substantially increases the estimation efficiency. Subsequently, we demonstrate that the method allows for the reliable discovery of unknown measurement transformations. Furthermore, we show that this approach can significantly improve the parameter inference based on semi-quantitative data in comparison to available methods. AVAILABILITY AND IMPLEMENTATION Modelers can easily apply our method by using our implementation in the open-source Python Parameter EStimation TOolbox (pyPESTO) available at https://github.com/ICB-DCM/pyPESTO.
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Affiliation(s)
- Domagoj Dorešić
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Institute of Computational Biology, Helmholtz Zentrum München – German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stephan Grein
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Jan Hasenauer
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Institute of Computational Biology, Helmholtz Zentrum München – German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Center for Mathematics, Technische Universität München, 85748 Garching, Germany
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99
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Rukhlenko OS, Imoto H, Tambde A, McGillycuddy A, Junk P, Tuliakova A, Kolch W, Kholodenko BN. Cell State Transition Models Stratify Breast Cancer Cell Phenotypes and Reveal New Therapeutic Targets. Cancers (Basel) 2024; 16:2354. [PMID: 39001416 PMCID: PMC11240448 DOI: 10.3390/cancers16132354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/17/2024] [Accepted: 06/23/2024] [Indexed: 07/16/2024] Open
Abstract
Understanding signaling patterns of transformation and controlling cell phenotypes is a challenge of current biology. Here we applied a cell State Transition Assessment and Regulation (cSTAR) approach to a perturbation dataset of single cell phosphoproteomic patterns of multiple breast cancer (BC) and normal breast tissue-derived cell lines. Following a separation of luminal, basal, and normal cell states, we identified signaling nodes within core control networks, delineated causal connections, and determined the primary drivers underlying oncogenic transformation and transitions across distinct BC subtypes. Whereas cell lines within the same BC subtype have different mutational and expression profiles, the architecture of the core network was similar for all luminal BC cells, and mTOR was a main oncogenic driver. In contrast, core networks of basal BC were heterogeneous and segregated into roughly four major subclasses with distinct oncogenic and BC subtype drivers. Likewise, normal breast tissue cells were separated into two different subclasses. Based on the data and quantified network topologies, we derived mechanistic cSTAR models that serve as digital cell twins and allow the deliberate control of cell movements within a Waddington landscape across different cell states. These cSTAR models suggested strategies of normalizing phosphorylation networks of BC cell lines using small molecule inhibitors.
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Affiliation(s)
- Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Hiroaki Imoto
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Ayush Tambde
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- Stratford College, D06 T9V3 Dublin, Ireland
| | - Amy McGillycuddy
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biological, Health and Sports Sciences, Technological University, D07 H6K8 Dublin, Ireland
| | - Philipp Junk
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Anna Tuliakova
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Boris N Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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100
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Li Y, Frederick RA, George D, Cogan SF, Pancrazio JJ, Bleris L, Hernandez-Reynoso AG. NeurostimML: a machine learning model for predicting neurostimulation-induced tissue damage. J Neural Eng 2024; 21:036054. [PMID: 38885676 DOI: 10.1088/1741-2552/ad593e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 06/17/2024] [Indexed: 06/20/2024]
Abstract
Objective. The safe delivery of electrical current to neural tissue depends on many factors, yet previous methods for predicting tissue damage rely on only a few stimulation parameters. Here, we report the development of a machine learning approach that could lead to a more reliable method for predicting electrical stimulation-induced tissue damage by incorporating additional stimulation parameters.Approach. A literature search was conducted to build an initial database of tissue response information after electrical stimulation, categorized as either damaging or non-damaging. Subsequently, we used ordinal encoding and random forest for feature selection, and investigated four machine learning models for classification: Logistic Regression, K-nearest Neighbor, Random Forest, and Multilayer Perceptron. Finally, we compared the results of these models against the accuracy of the Shannon equation.Main Results. We compiled a database with 387 unique stimulation parameter combinations collected from 58 independent studies conducted over a period of 47 years, with 195 (51%) categorized as non-damaging and 190 (49%) categorized as damaging. The features selected for building our model with a Random Forest algorithm were: waveform shape, geometric surface area, pulse width, frequency, pulse amplitude, charge per phase, charge density, current density, duty cycle, daily stimulation duration, daily number of pulses delivered, and daily accumulated charge. The Shannon equation yielded an accuracy of 63.9% using akvalue of 1.79. In contrast, the Random Forest algorithm was able to robustly predict whether a set of stimulation parameters was classified as damaging or non-damaging with an accuracy of 88.3%.Significance. This novel Random Forest model can facilitate more informed decision making in the selection of neuromodulation parameters for both research studies and clinical practice. This study represents the first approach to use machine learning in the prediction of stimulation-induced neural tissue damage, and lays the groundwork for neurostimulation driven by machine learning models.
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Affiliation(s)
- Yi Li
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, United States of America
- Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, United States of America
| | - Rebecca A Frederick
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, United States of America
| | - Daniel George
- Department of Computer Science, The University of Texas at Dallas, Richardson, TX, United States of America
| | - Stuart F Cogan
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, United States of America
| | - Joseph J Pancrazio
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, United States of America
| | - Leonidas Bleris
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, United States of America
- Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, United States of America
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, United States of America
| | - Ana G Hernandez-Reynoso
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, United States of America
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