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Engagement of sialylated glycans with Siglec receptors on suppressive myeloid cells inhibits anticancer immunity via CCL2

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Cellular & Molecular Immunology 2024年第5期21卷 495-509页

作者： Ronja Wieboldt Michael Sandholzer Emanuele Carlini Chia-wei Lin Anastasiya Börsch Andreas Zingg Didier Lardinois Petra Herzig Leyla Don Alfred Zippelius Heinz Läubli Natalia Rodrigues Mantuano Laboratory for Cancer Immunotherapy Department of BiomedicineUniversity Hospital and University of BaselBaselSwitzerland. Functional Genomics Center Zurich ETH ZurichZurichSwitzerland. Bioinformatics Core Facility Department of BiomedicineUniversity of Basel and Swiss Institute of BioinformaticsBaselSwitzerland. Department of Thoracic Surgery University Hospital BaselBaselSwitzerland. Laboratory of Cancer Immunology Department of BiomedicineUniversity Hospital and University of BaselBaselSwitzerland. Division of Oncology University Hospital BaselBaselSwitzerland.

The overexpression of sialic acids on glycans,called hypersialylation,is a common alteration found in cancer *** glycans can enhance immune evasion by interacting with sialic acid-binding immunoglobulin-like lectin(Siglec)receptors on tumorinfiltrating immune ***,we investigated the effect of sialylated glycans and their interaction with Siglec receptors on myeloid-derived suppressor cells(MDSCs).We found that MDSCs derived from the blood of lung cancer patients and tumor-bearing mice strongly express inhibitory Siglec receptors and are highly *** murine cancer models of emergency myelopoiesis,Siglec-E knockout in myeloid cells resulted in prolonged survival and increased tumor infiltration of activated T *** suppressive myeloid cells by blocking Siglec receptors or desialylation strongly reduced their suppressive *** further identified CCL2 as a mediator involved in T-cell suppression upon interaction between sialoglycans and Siglec receptors on *** results demonstrated that sialylated glycans inhibit anticancer immunity by modulating CCL2 expression.

关键词： sialoglycans Sialic acid-binding immunoglobulin-like lectin tumor microenvironment myeloid derived suppressor cells

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Design and in vitro evaluation of novel tetrazole derivatives of dianisidine as anticancer agents targeting Bcl-2 apoptosis regulator

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Scientific Reports 2025年第1期15卷 1-16页

作者： Wioletta Olejarz Karol Sadowski Piotr Roszkowski Anna Bielenica Marta Struga Daniel Szulczyk Maciej Wiśniewski Department of Biochemistry and Pharmacogenomics Faculty of Pharmacy Medical University of Warsaw 02-097 Warsaw Poland Centre for Preclinical Research Medical University of Warsaw 02-097 Warsaw Poland Faculty of Chemistry University of Warsaw Pasteura 1 02-093 Warszawa Poland Department of Biochemistry Medical University of Warsaw 02-097 Warsaw Poland Laboratory of Bioinformatics and Computational Genomics Faculty of Mathematics and Information Science Warsaw University of Technology Warsaw Poland Laboratory of Functional and Structural Genomics Centre of New Technologies University of Warsaw Warsaw Poland

This study examines the synthesis and biological evaluation of novel tetrazole derivatives of 3,3′-dimethoxybenzidine as potential anticancer agents, focusing on their cytotoxic, apoptotic, and anti-inflammatory properties. Ten derivatives were synthesized using thioureas as precursors, characterized through spectroscopic methods, and assessed for their in silico toxicological profiles using the ADMET-AI and ProTox 3.0 platforms. In vitro cytotoxic activity was evaluated against four human cancer cell lines (HTB-140, A549, HeLa, SW620) and one normal cell line (HaCaT) using MTT and LDH assays. Mechanistic studies included apoptosis assessment via flow cytometry and interleukin-6 (IL-6) analysis using ELISA. The synthesized tetrazole derivatives demonstrated significant anticancer potential, exhibiting selective cytotoxicity against cancer cell lines, robust induction of apoptosis, and a notable reduction in IL-6 levels. Their favorable toxicity profiles, as observed in both in silico and in vitro evaluations, support their potential as promising candidates for further development. The tested compounds showed strong inhibitory activity against the apoptosis regulator Bcl-2, with binding affinities comparable to those of native ligands. Western blot analysis revealed a dramatic loss of Bcl-2 protein expression in selected cancer cells during exposure to compound5. Additionally, this research highlights the innovative use of hazardous substrates in drug discovery, aligning with the principles of green chemistry. Future efforts should focus on optimizing the most active derivatives and conducting in vivo studies to confirm their therapeutic potential and safety.

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Revelation of potential antiviral activity of Azadirachta indica against Zika virus protease: An integrated molecular docking and dynamic simulation approach

Computational and Structural Biotechnology Reports

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Computational and Structural Biotechnology Reports 2025年 2卷

作者： Md. Habib Ullah Masum Rehana Parvin Syed Mohammad Lokman Zarin Tasnim Md. Mazharul Alam Jannatul Ferdous Department of Genomics and Bioinformatics Faculty of Biotechnology and Genetic Engineering Chattogram Veterinary and Animal Sciences University Khulshi 4225 Bangladesh Department of Pathology and Parasitology Faculty of Veterinary Medicine Chattogram Veterinary and Animal Sciences University Khulshi 4225 Bangladesh Asian University for Women (AUW) Chattogram 4000 Bangladesh Department of Industrial Biotechnology Faculty of Biotechnology and Genetic Engineering Chattogram Veterinary and Animal Sciences University Khulshi 4225 Bangladesh Functional Genomics and Proteomics Laboratory (FGPL) Department of Genetic Engineering and Biotechnology Faculty of Biological Sciences University of Chittagong Chattogram 4331 Bangladesh Department of Obstetrics and Gynecology Chittagong Medical College Hospital Chattogram 4203 Bangladesh

The Zika virus (ZIKV) is an RNA virus that mostly affects humans and primates and is transmitted via Aedes mosquitoes . The emergence of ZIKV has intensified global health concerns, emphasizing the urgent need for effective antiviral therapies. As a vital enzyme in the replication of ZIKV, the NS2B-NS3 protease offers a promising therapeutic target. This study leverages computer-aided drug design to identify bioactive compounds capable of inhibiting the ZIKV NS2B-NS3 protease, thereby disrupting viral replication. Bioactive compounds from Azadirachta indica were screened through virtual approaches, resulting in six with exceptional docking scores (<-5.5 kcal/mol). Analyses of the physicochemical properties validated the drug-like traits of the IMPHY014854 and IMPHY014908, conveying suitable hydrogen bonding profiles and moderate solubility (Log S: −2.22 to −3.60). Evaluations of pharmacokinetics suggested significant gastrointestinal absorption while exposing no permeability across the blood-brain barrier, thereby reducing interactions with the central nervous system. Toxicity evaluations revealed limited toxic effects, while several bioactive compounds exhibited particular toxicological issues. Molecular dynamics simulations further revealed the stability and interaction dynamics of ZIKV protease-ligand complexes, where the IMPHY014854 and IMPHY014908 exhibited significant residue flexibility, compactness, and solvent accessibility profiles over a 100 ns simulation. Principal component analysis revealed conformational distinctions, while Gibbs's free energy analysis demonstrated greater stability for the ZIKV protease-IMPHY014908 complex. This integrative computational strategy highlights the potential of phytochemicals as the ZIKV protease inhibitors and provides a foundation for developing effective antiviral drugs. Further, in vivo studies must be implemented to validate these findings and advance therapeutic prospects against ZIKV.

关键词： Mosquito-borne Phytodynamics Biocomputational Neem plant Protease inhibitor Antiviral drug

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Comparison of self-similarity measures for multi-modal non-rigid registration of 3D-PLI brain images

Comparison of self-similarity measures for multi-modal non-r...

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Workshop on Bildverarbeitung fur die Medizin, 2018

作者： Ali, Sharib Lin, Dehui Axer, Markus Rohr, Karl Department of Bioinformatics and Functional Genomics Biomedical Computer Vision Group BIOQUANT IPMB DKFZ University of Heidelberg Heidelberg Germany Institute of Neuroscience and Medicine 1 Research Centre Jülich Jülich Germany

ISBN: (纸本)9783662580950

We introduce self-similarity measures in a spline-based nonrigid registration method. We applied our method to register multimodal 3D polarized light imaging and blockface image data of human and rat brain sections. Quantitative evaluations demonstrate that using self-similarity measures increases the accuracy and robustness compared to a traditional mutual information measure. © Springer-Verlag GmbH Deutschland 2018.

关键词： Brain mapping

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Analyzing the regulation of metabolic pathways in human breast cancer

Analyzing the regulation of metabolic pathways in human brea...

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LWA 2009 - Workshop-Woche: Lernen-Wissen-Adaptivitat - Learning, Knowledge and Adaptivity

作者： Surmann, Eva Maria Schramm, Gunnar Wiesberg, Stefan Oswald, Marcus Reinelt, Gerhard Eils, Roland König, Rainer Department of Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology and Bioquant University of Heidelberg INF 267 69120 Heidelberg Germany Interdisciplinary Center for Scientific Computing University of Heidelberg 69120 Heidelberg Germany Theoretical Bioinformatics German Cancer Research Center 69121 Heidelberg Germany

Tumor therapy mainly attacks the metabolism to interfere their anabolism and signaling of proliferative second messengers. However, the metabolic demands of different cancers are very heterogenous and depend on their origin of tissue, age, gender and other clinical parameters. We wanted to find out tumor specific regulation for the metabolism of breast cancer. For this, we mapped gene expression data from microarrays onto the corresponding enzymes and their metabolic reaction network. We used Haar Wavelet transforms on optimally arranged grid representations of metabolic pathways as a pattern recognition method to detect orchestrated regulation of neighboring enzymes in the network. Significant combined expression pattern were used to select metabolic pathways showing shifted regulation of the aggressive tumors. Besides up-regulation for energy production and nucleotide anabolism, we found an interesting cellular switch in the interplay of biosynthesis of steroids and bile acids. The biosynthesis of steroids was up-regulated for estrogen synthesis which is needed in breast cancer for proliferative signaling. In turn, the decomposition of steroid precursors was blocked by down-regulation of the bile acid pathway. In conclusion, we applied an intelligent pattern recognition method on networks and elucidated substantial regulation of human breast cancer pointing to specific treatment.

关键词： Tumors

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The enigma of introns: Intronic miRNA-directed mechanisms and alternative splicing diversify alternative oxidase potential in Vitis vinifera

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International journal of biological macromolecules 2025年 144300页

作者： Shahid Aziz Thais Andrade Germano Antonio Edson Rocha Oliveira José Ednésio da Cruz Freire Matheus Finger Ramos de Oliveira Karine Leitão Lima Thiers Birgit Arnholdt-Schmitt Jose Helio Costa Functional Genomics and Bioinformatics Department of Biochemistry and Molecular Biology Federal University of Ceara Fortaleza Ceara Brazil Non-Institutional Competence Focus (NICFocus) 'Functional Cell Reprogramming and Organism Plasticity' (FunCROP) coordinated from Foros de Vale de Figueira Alentejo Portugal. Electronic address: shahidaziz.cl@***. Non-Institutional Competence Focus (NICFocus) 'Functional Cell Reprogramming and Organism Plasticity' (FunCROP) coordinated from Foros de Vale de Figueira Alentejo Portugal. Nucleus of Experimental Biology University of Fortaleza Fortaleza Ceará Brazil. Biochemistry and Gene Expression Laboratory Superior Institute of Biomedical Sciences State University of Ceará Fortaleza Ceará Brazil. Functional Genomics and Bioinformatics Department of Biochemistry and Molecular Biology Federal University of Ceara Fortaleza Ceara Brazil. Non-Institutional Competence Focus (NICFocus) 'Functional Cell Reprogramming and Organism Plasticity' (FunCROP) coordinated from Foros de Vale de Figueira Alentejo Portugal. Electronic address: biarnaflora@***. Non-Institutional Competence Focus (NICFocus) 'Functional Cell Reprogramming and Organism Plasticity' (FunCROP) coordinated from Foros de Vale de Figueira Alentejo Portugal INCTAgriS - National Institute of Science and Technology in Sustainable Agriculture in the Tropical Semi-Arid Region Brazil. Electronic address: helio.costa@ufc.br.

Alternative oxidase (AOX) transcript levels were associated with efficiently balanced respiration and validated to assist selection on multiple-resilience. Consistently, AOX has also been identified as a target for weakening the survival capabilities of parasites and microorganisms responsible for severe human diseases. Despite the unique features of AOX in Vitis vinifera, particularly intense constitutive expression of AOX2 in the presence of unusually large introns that challenge the dogma of gene expression in eukaryotes, V. vinifera has been overlooked in AOX research. This study uncovered two distinct alternative splicing variants of the AOX: AOX1a-Alternative variant attributed to unusual retention of the intron-4 in the 3´UTR, and AOX2-alternative variant, which is intron-1-dependent, involving the skipping of exon-1. The AOX2-alternative variant differed in that cystine-I changed to serine, which is linked to different metabolite stimulation. However, molecular docking suggested that AOX2 and the variant proteins exhibit the same catalytic activities and binding affinities for ubiquinol. The unique large introns in AOX2 exhibited 16 miRNAs, including the master regulator of development and stress responses, mir-398. Among these, nine were conserved and validated in other plant species, whereas seven were considered potential novel miRNA candidates. Transcriptome analyses revealed down- and up-regulation of AOX1a-Alternative during shrivelling and water deficiency, and up-regulation of AOX2-Alternative with increasing temperatures. Consistent with previous studies, AOX1a and AOX1d were linked to biotic and abiotic stress, whereas AOX2 showed constitutive or developmental regulation. This study encourages hypothesis-driven advanced research on early mechanisms and functionality of newly discovered alternative splicing events and intronic miRNAs. Given functional marker-assisted breeding, it strengthened the requirement to consider overall AOX transcript levels

关键词： Alternative splicing Intron retention Large intron Transcription factors Ubiquinol miRNA

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Automated analysis of siRNA screens of virus infected cells based on immunofluorescence microscopy

Automated analysis of siRNA screens of virus infected cells ...

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Workshops Bildverarbeitung fur die Medizin: Algorithmen - Systeme - Anwendungen, BVM 2008 - Workshop on Image Processing for Medicine: Algorithms - Systems - Applications, BVM 2008

作者： Matula, Petr Kumar, Anil Wörz, Ilka Harder, Nathalie Erfle, Holger Bartenschlager, Ralf Eils, Roland Rohr, Karl BIOQUANT IPMB University of Heidelberg Germany Dept. Bioinformatics and Functional Genomics Biomedical Computer Vision Group DKFZ Heidelberg Germany Department of Molecular Virology University of Heidelberg Germany BIOQUANT University of Heidelberg Germany

ISBN: (纸本)9783540786399

We present an image analysis approach as part of a high-throughput microscopy screening system based on cell arrays for the identification of genes involved in Hepatitis C and Dengue virus replication. Our approach comprises: cell nucleus segmentation, quantification of virus replication level in cells, localization of regions with transfected cells, cell classification by infection status, and quality assessment of an experiment. The approach is fully automatic and has been successfully applied to a large number of cell array images from screening experiments. The experimental results show a good agreement with the expected behavior of positive as well as negative controls and encourage the application to screens from further high-throughput experiments.

关键词： Cytology

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Development of homozygous tetraploid potato and whole genome doubling-induced the enrichment of H3K27ac and potentially enhanced resistance to cold-induced sweetening in tubers

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Horticulture Research 2023年第3期10卷 271-283页

作者： Hongwei Guo Min Zhou Guoyan Zhang Li He Caihong Yan Min Wan Jianjun Hu Wei He Deying Zeng Bo Zhu Zixian Zeng Department of Biological Science College of Life SciencesSichuan Normal UniversityChengdu 610101SichuanChina Plant Functional Genomics and Bioinformatics Research Center Sichuan Normal UniversityChengdu 610101SichuanChina Crop Research Institute Sichuan Academy of Agricultural SciencesChengdu 610066China Horticulture Institute Sichuan Academy of Agricultural SciencesChengdu 610066China

Polyploid plants typically display advantages on some agronomically important traits over their diploid *** studies have shown genetic,transcriptomic,and epigenetic dynamics upon polyploidization in multiple plant ***,few studies have unveiled those alternations imposed only by ploidy level,without any interference from *** potato is highly ***,in this study,we developed two homozygous autotetraploid lines and one homozygous diploid line in parallel from a homozygous diploid *** confirmed their ploidy levels using chloroplast counting and ***-FISH and genome re-sequencing validated that these potato lines are nearly *** investigated variations in phenotypes,transcription,and histone modifications between two *** autotetraploid lines produced larger but fewer tubers than the diploid ***,each autotetraploid line displayed ploidy-related differential expression for various *** also discovered a genomewide enrichment of H3K27ac in genic regions upon whole-genome doubling(WGD).However,such enrichment was not associated with the differential gene expression between two *** tetraploid lines may exhibit better resistance to cold-induced sweetening(CIS)than the diploid line in tubers,potentially regulated through the expression of CIS-related key genes,which seems to be associated with the levels of H3K4me3 in cold-stored *** findings will help to understand the impacts of autotetraploidization on dynamics of phenotypes,transcription,and histone modifications,as well as on CIS-related genes in response to cold storage.

关键词： homozygous doubling resistance

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High-precision localization and quantification of 3D tubular structures

High-precision localization and quantification of 3D tubular...

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IEEE International Symposium on Biomedical Imaging

作者： K. Rohr S. Worz Department Bioinformatics and Functional Genomics Biomedical Computer Vision Group University of Heidelberg Heidelberg Germany

We derive analytic lower bounds for estimating the position and width of 3D tubular structures. Based on a continuous image model comprising blur and noise introduced by an imaging system we analyze three different intensity models of 3D tubular structures with increasing complexity. The derived formulas indicate that quantification of 3D tubular structures can be performed with very high precision under certain assumptions. The theoretical results are substantiated by experimental investigations based on discretized and quantized 3D image data

关键词： Biomedical imaging Image analysis Uncertainty bioinformatics Data visualization Blood vessels Performance analysis Parameter estimation genomics Computer vision

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Scale-invariant biomarker discovery in urine and plasma metabolite fingerprints

arXiv

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arXiv 2017年

作者： Zacharias, Helena U. Rehberg, Thorsten Mehrl, Sebastian Richtmann, Daniel Wettig, Tilo Oefner, Peter J. Spang, Rainer Gronwald, Wolfram Altenbuchinger, Michael Institute of Functional Genomics University of Regensburg Regensburg Germany Statistical Bioinformatics Institute of Functional Genomics University of Regensburg Regensburg Germany Department of Physics University of Regensburg Regensburg Germany

Motivation: Metabolomics data is typically scaled to a common reference like a constant volume of body fluid, a constant creatinine level, or a constant area under the spectrum. Such normalization of the data, however, may affect the selection of biomarkers and the biological interpretation of results in unforeseen ways. Results: First, we study how the outcome of hypothesis tests for differential metabolite concentration is affected by the choice of scale. Furthermore, we observe this interdependence also for different classification approaches. Second, to overcome this problem and establish a scale-invariant biomarker discovery algorithm, we extend linear zero-sum regression to the logistic regression framework and show in two applications to 1H NMRbased metabolomics data how this approach overcomes the scaling problem. Copyright © 2017, The Authors. All rights reserved.

关键词： Biomarkers

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