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Sevenich L, Heiland DH. [Tumor-host cell interaction in the microenvironment: new target points for treatment?]. Nervenarzt 2024; 95:104-110. [PMID: 38180512 DOI: 10.1007/s00115-023-01604-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Primary brain tumors and metastases in the central nervous system (CNS) are characterized by their unique microenvironment, which interacts with neuronal structures and influences structural and adaptive immunity. OBJECTIVE How significant are various tumor-host interactions from a prognostic and therapeutic perspective? MATERIAL AND METHOD A literature search was carried out for relevant articles on the topic: microenvironment glioblastoma or metastasis through PubMed and Medline. RESULTS Modern high-throughput methods, such as spatial and single-cell resolution molecular characterization of tumors and their microenvironment enable a detailed mapping of changes and adaptation of individual cells within the microenvironment of tumors; however, treatment approaches based on altered tumor-host cell interactions, such as immune modeling, cell-based treatment methods or checkpoint inhibition have so far not shown any significant advantages for survival. CONCLUSION A deeper understanding of the complex immune landscape and the microenvironment of metastases of the CNS and intracerebral tumors is essential to optimize future treatment strategies.
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Affiliation(s)
- Lisa Sevenich
- Institut für Tumorbiologie und experimentelle Therapie, Georg-Speyer-Haus, Frankfurt am Main, Deutschland
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Deutschland
- Partner Site Frankfurt/Mainz, Deutsches Konsortium für Translationale Krebsforschung, Frankfurt am Main, Deutschland
| | - Dieter Henrik Heiland
- Klinik für Neurochirurgie, Medical Center, Universität Freiburg, Freiburg, Deutschland.
- Microenvironment and Immunology Research Laboratory, Department of Neurosurgery, Medical Center Universität Freiburg, Breisacher Str. 64, 79106, Freiburg, Deutschland.
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, USA.
- Partner Site Freiburg, Deutsches Konsortium für Translationale Krebsforschung, Freiburg, Deutschland.
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Alfatah M, Zhang Y, Naaz A, Cheng TYN, Eisenhaber F. PICLS with human cells is the first high throughput screening method for identifying novel compounds that extend lifespan. Biol Direct 2024; 19:8. [PMID: 38254217 PMCID: PMC10804585 DOI: 10.1186/s13062-024-00455-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
Gerontology research on anti-aging interventions with drugs could be an answer to age-related diseases, aiming at closing the gap between lifespan and healthspan. Here, we present two methods for assaying chronological lifespan in human cells: (1) a version of the classical outgrowth assay with quantitative assessment of surviving cells and (2) a version of the PICLS method (propidium iodide fluorescent-based measurement of cell death). Both methods are fast, simple to conduct, cost-effective, produce quantitative data for further analysis and can be used with diverse human cell lines. Whereas the first method is ideal for validation and testing the post-intervention reproductive potential of surviving cells, the second method has true high-throughput screening potential. The new technologies were validated with known anti-aging compounds (2,5-anhydro-D-mannitol and rapamycin). Using the high-throughput screening method, we screened a library of 162 chemical entities and identified three compounds that extend the longevity of human cells.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore.
| | - Yizhong Zhang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
| | - Arshia Naaz
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore, 138672, Republic of Singapore
| | - Trishia Yi Ning Cheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, 637551, Republic of Singapore
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Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Curr Opin Struct Biol 2023; 80:102593. [PMID: 37099901 DOI: 10.1016/j.sbi.2023.102593] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/28/2023]
Abstract
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein-protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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Osborne B, Bakula D, Ben Ezra M, Dresen C, Hartmann E, Kristensen SM, Mkrtchyan GV, Nielsen MH, Petr MA, Scheibye-Knudsen M. New methodologies in ageing research. Ageing Res Rev 2020; 62:101094. [PMID: 32512174 DOI: 10.1016/j.arr.2020.101094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/14/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023]
Abstract
Ageing is arguably the most complex phenotype that occurs in humans. To understand and treat ageing as well as associated diseases, highly specialised technologies are emerging that reveal critical insight into the underlying mechanisms and provide new hope for previously untreated diseases. Herein, we describe the latest developments in cutting edge technologies applied across the field of ageing research. We cover emerging model organisms, high-throughput methodologies and machine-driven approaches. In all, this review will give you a glimpse of what will be pushing the field onwards and upwards.
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Affiliation(s)
- Brenna Osborne
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Daniela Bakula
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Michael Ben Ezra
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Dresen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Esben Hartmann
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Stella M Kristensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Garik V Mkrtchyan
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Malte H Nielsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Michael A Petr
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
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Abstract
Aptamers are small, functional nucleic acids that bind a variety of targets, often with high specificity and affinity. Genomic aptamers constitute the ligand-binding domains of riboswitches, whereas synthetic aptamers find applications as diagnostic and therapeutic tools, and as ligand-binding domains of regulatory RNAs in synthetic biology. Discovery and characterization of aptamers has been limited by a lack of high-throughput approaches that uncover the target-binding domains and the biochemical properties of individual sequences. With the advent of high-throughput sequencing, large-scale analysis of in vitro selected populations of aptamers (and catalytic nucleic acids, such as ribozymes and DNAzmes) became possible. In recent years the development of new experimental approaches and software tools has led to significant streamlining of the selection-pool analysis. This article provides an overview of post-selection data analysis and describes high-throughput methods that facilitate rapid discovery and biochemical characterization of aptamers.
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Affiliation(s)
- Kyle H Cole
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Andrej Lupták
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States; Department of Pharmaceutical Sciences, University of California, Irvine, CA, United States; Department of Chemistry, University of California, Irvine, CA, United States.
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Abstract
The discovery of pervasive transcription in eukaryotic genomes provided one of many surprising (and perhaps most surprising) findings of the genomic era and led to the uncovering of a large number of previously unstudied transcriptional events. This pervasive transcription leads to the production of large numbers of noncoding RNAs (ncRNAs) and thus opened the window to study these diverse, abundant transcripts of unclear relevance and unknown function. Since that discovery, recent advances in high-throughput sequencing technologies have identified a large collection of ncRNAs, from microRNAs to long noncoding RNAs (lncRNAs). Subsequent discoveries have shown that many lncRNAs play important roles in various eukaryotic processes; these discoveries have profoundly altered our understanding of the regulation of eukaryotic gene expression. Although the identification of ncRNAs has become a standard experimental approach, the functional characterization of these diverse ncRNAs remains a major challenge. In this chapter, we highlight recent progress in the methods to identify lncRNAs and the techniques to study the molecular function of these lncRNAs and the application of these techniques to the study of plant lncRNAs.
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Affiliation(s)
- Hsiao-Lin V Wang
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
- Present address: Department of Biology, Emory University, Atlanta, GA, USA
| | - Julia A Chekanova
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China.
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Karvelis T, Gasiunas G, Siksnys V. Methods for decoding Cas9 protospacer adjacent motif (PAM) sequences: A brief overview. Methods 2017; 121-122:3-8. [PMID: 28344037 DOI: 10.1016/j.ymeth.2017.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/09/2017] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Recently the Cas9, an RNA guided DNA endonuclease, emerged as a powerful tool for targeted genome manipulations. Cas9 protein can be reprogrammed to cleave, bind or nick any DNA target by simply changing crRNA sequence, however a short nucleotide sequence, termed PAM, is required to initiate crRNA hybridization to the DNA target. PAM sequence is recognized by Cas9 protein and must be determined experimentally for each Cas9 variant. Exploration of Cas9 orthologs could offer a diversity of PAM sequences and novel biochemical properties that may be beneficial for genome editing applications. Here we briefly review and compare Cas9 PAM identification assays that can be adopted for other PAM-dependent CRISPR-Cas systems.
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Affiliation(s)
- Tautvydas Karvelis
- Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedrius Gasiunas
- Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
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Abstract
Keratoconus (KTCN) is a degenerative disorder of the eye characterized by the conical shape and thinning of the cornea. The abnormal structure of KTCN-affected cornea results in loss of visual acuity. While many studies examine how environmental factors influence disease development, finding the genetic triggers has been a major emphasis of KTCN research. This paper focuses on genomic strategies that were implemented for finding candidate genes, including linkage and association studies, and presents different approaches of mutation screening. The advantages and limitations of particular tools are discussed based on literature and personal experience. Since etiology underlying KTCN is complex, numerous findings indicating heterogeneity of genetic factors involved KTCN etiology are presented.
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Affiliation(s)
- Justyna A Karolak
- Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Swiecickiego 4, Poznan, 60-781, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, Poznan, 60-479, Poland
| | - Marzena Gajecka
- Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Swiecickiego 4, Poznan, 60-781, Poland. .,Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, Poznan, 60-479, Poland.
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Furman D, Davis MM. New approaches to understanding the immune response to vaccination and infection. Vaccine 2015; 33:5271-81. [PMID: 26232539 DOI: 10.1016/j.vaccine.2015.06.117] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/26/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
Abstract
The immune system is a network of specialized cell types and tissues that communicates via cytokines and direct contact, to orchestrate specific types of defensive responses. Until recently, we could only study immune responses in a piecemeal, highly focused fashion, on major components like antibodies to the pathogen. But recent advances in technology and in our understanding of the many components of the system, innate and adaptive, have made possible a broader approach, where both the multiple responding cells and cytokines in the blood are measured. This systems immunology approach to a vaccine response or an infection gives us a more holistic picture of the different parts of the immune system that are mobilized and should allow us a much better understanding of the pathways and mechanisms of such responses, as well as to predict vaccine efficacy in different populations well in advance of efficacy studies. Here we summarize the different technologies and methods and discuss how they can inform us about the differences between diseases and vaccines, and how they can greatly accelerate vaccine development.
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Affiliation(s)
- David Furman
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, United States; Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, United States; Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA, United States.
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