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Immunoanalytical and Bioinformatics Methods in Immunology Research
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Immunoanalytical and Bioinformatics Methods in Immunology Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 14827

Special Issue Editors

Prof. Dr. Almira Ramanaviciene

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Guest Editor
1. NanoTechnas—Center of Nanotechnology and Materials Science, Institute of Chemistry, Vilniaus Universitetas, LT-01513 Vilnius, Lithuania
2. Department of Immunology, State Research Institute Centre for Innovative Medicine, LT-08410 Vilnius, Lithuania
Interests: immunosensors and biosensors for bioanalytical and biomedical application; electrochemical, optical and piezoelectric signal transducers; nanoparticles and nanostructured surfaces; synthesis and application of conducting polymers; immobilization of biomolecules; site-directed antibody immobilization
Special Issues, Collections and Topics in MDPI journals
Dr. Anton Popov

E-Mail Website
Guest Editor
1. NanoTechnas—Center of Nanotechnology and Materials Science, Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, LT-03225 Vilnius, Lithuania
2. Department of Immunology and Bioelectrochemistry, State Research Institute Centre for Innovative Medicine, LT-08406 Vilnius, Lithuania
Interests: immunosensors; biosensors; the use of nanomaterials for the fabrication of sensors; conducting polymers
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A globally strong focus on disease control and prevention requires sensitive, selective, and rapid immunoanalytical methods, while for the control of dynamic biomolecules in organisms and the prediction of biomolecules’ interactions bioinformatics methods have high potential. Immunosensors and other immunoanalytical techniques registering a specific interaction between an antigen and a specific antibody immobilized on a corresponding transducer surface have high potential in the biomedical and bioanalytical fields. The sensitivity of immunoanalytical methods can be improved by using various nanomaterials to modify the sensing surface or enhance the analytical signal. Additionally, the proper orientation of biomolecules has a high impact on the sensitivity of immunosensors and immunoassays.

This Special Issue aims to provide a multidisciplinary approach for research by applying advanced technologies for the ultrasensitive and selective detection and control of relevant biomarkers. Original research papers, communications, and review articles are welcome.

Prof. Dr. Almira Ramanaviciene
Dr. Anton Popov
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • immunoassay
  • immunosensors
  • nanoparticles
  • mathematical calculations and modeling
  • biomarkers

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Published Papers (7 papers)

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Editorial

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3 pages, 170 KiB  
Editorial
Special Issue “Immunoanalytical and Bioinformatics Methods in Immunology Research”
by Anton Popov and Almira Ramanaviciene
Int. J. Mol. Sci. 2024, 25(2), 979; https://doi.org/10.3390/ijms25020979 - 12 Jan 2024
Viewed by 749
Abstract
To effectively control and prevent diseases on a global scale, it is essential to employ precise, sensitive, selective, and rapid immunoanalytical methods [...] Full article
(This article belongs to the Special Issue Immunoanalytical and Bioinformatics Methods in Immunology Research)

Research

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22 pages, 14482 KiB  
Article
Key Disease-Related Genes and Immune Cell Infiltration Landscape in Inflammatory Bowel Disease: A Bioinformatics Investigation
by Kawthar S. Alghamdi, Rahaf H. Kassar, Wesam F. Farrash, Ahmad A. Obaid, Shakir Idris, Alaa Siddig, Afnan M. Shakoori, Sallwa M. Alshehre, Faisal Minshawi and Abdulrahman Mujalli
Int. J. Mol. Sci. 2024, 25(17), 9751; https://doi.org/10.3390/ijms25179751 - 9 Sep 2024
Viewed by 1435
Abstract
Inflammatory Bowel Diseases (IBD), which encompass ulcerative colitis (UC) and Crohn’s disease (CD), are characterized by chronic inflammation and tissue damage of the gastrointestinal tract. This study aimed to uncover novel disease-gene signatures, dysregulated pathways, and the immune cell infiltration landscape of inflamed [...] Read more.
Inflammatory Bowel Diseases (IBD), which encompass ulcerative colitis (UC) and Crohn’s disease (CD), are characterized by chronic inflammation and tissue damage of the gastrointestinal tract. This study aimed to uncover novel disease-gene signatures, dysregulated pathways, and the immune cell infiltration landscape of inflamed tissues. Eight publicly available transcriptomic datasets, including inflamed and non-inflamed tissues from CD and UC patients were analyzed. Common differentially expressed genes (DEGs) were identified through meta-analysis, revealing 180 DEGs. DEGs were implicated in leukocyte transendothelial migration, PI3K-Akt, chemokine, NOD-like receptors, TNF signaling pathways, and pathways in cancer. Protein–protein interaction network and cluster analysis identified 14 central IBD players, which were validated using eight external datasets. Disease module construction using the NeDRex platform identified nine out of 14 disease-associated genes (CYBB, RAC2, GNAI2, ITGA4, CYBA, NCF4, CPT1A, NCF2, and PCK1). Immune infiltration profile assessment revealed a significantly higher degree of infiltration of neutrophils, activated dendritic cells, plasma cells, mast cells (resting/activated), B cells (memory/naïve), regulatory T cells, and M0 and M1 macrophages in inflamed IBD tissue. Collectively, this study identified the immune infiltration profile and nine disease-associated genes as potential modulators of IBD pathogenesis, offering insights into disease molecular mechanisms, and highlighting potential disease modulators and immune cell dynamics. Full article
(This article belongs to the Special Issue Immunoanalytical and Bioinformatics Methods in Immunology Research)
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15 pages, 2153 KiB  
Article
Revealing the SARS-CoV-2 Spike Protein and Specific Antibody Immune Complex Formation Mechanism for Precise Evaluation of Antibody Affinity
by Ieva Plikusiene, Vincentas Maciulis, Vilius Vertelis, Silvija Juciute, Saulius Balevicius, Arunas Ramanavicius, Julian Talbot and Almira Ramanaviciene
Int. J. Mol. Sci. 2023, 24(17), 13220; https://doi.org/10.3390/ijms241713220 - 25 Aug 2023
Cited by 5 | Viewed by 1481
Abstract
The profound understanding and detailed evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (SCoV2-S) protein and specific antibody interaction mechanism is of high importance in the development of immunosensors for COVID-19. In the present work, we studied a model system of [...] Read more.
The profound understanding and detailed evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (SCoV2-S) protein and specific antibody interaction mechanism is of high importance in the development of immunosensors for COVID-19. In the present work, we studied a model system of immobilized SCoV2-S protein and specific monoclonal antibodies by molecular dynamics of immune complex formation in real time. We simultaneously applied spectroscopic ellipsometry and quartz crystal microbalance with dissipation to reveal the features and steps of the immune complex formation. We showed direct experimental evidence based on acoustic and optical measurements that the immune complex between covalently immobilized SCoV2-S and specific monoclonal antibodies is formed in two stages. Based on these findings it was demonstrated that applying a two-step binding mathematical model for kinetics analysis leads to a more precise determination of interaction rate constants than that determined by the 1:1 Langmuir binding model. Our investigation showed that the equilibrium dissociation constants (KD) determined by a two-step binding model and the 1:1 Langmuir model could differ significantly. The reported findings can facilitate a deeper understanding of antigen–antibody immune complex formation steps and can open a new way for the evaluation of antibody affinity towards corresponding antigens. Full article
(This article belongs to the Special Issue Immunoanalytical and Bioinformatics Methods in Immunology Research)
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9 pages, 3771 KiB  
Article
Strong Coupling between Surface Plasmon Resonance and Exciton of Labeled Protein–Dye Complex for Immunosensing Applications
by Povilas Jurkšaitis, Ernesta Bužavaitė-Vertelienė and Zigmas Balevičius
Int. J. Mol. Sci. 2023, 24(3), 2029; https://doi.org/10.3390/ijms24032029 - 19 Jan 2023
Cited by 1 | Viewed by 1603
Abstract
In this study, we present an analysis of the optical response of strong coupling between SPR and labeled proteins. We demonstrate a sensing methodology that allows to evaluate the protein mass adsorbed to the gold’s surface from the Rabi gap, which is a [...] Read more.
In this study, we present an analysis of the optical response of strong coupling between SPR and labeled proteins. We demonstrate a sensing methodology that allows to evaluate the protein mass adsorbed to the gold’s surface from the Rabi gap, which is a direct consequence of the strong light–matter interaction between surface plasmon polariton and dye exciton of labeled protein. The total internal reflection ellipsometry optical configuration was used for simulation of the optical response for adsorption of HSA-Alexa633 dye-labeled protein to a thin gold layer onto the glass prism. It was shown that Rabi oscillations had parabolic dependence on the number of labeled proteins attached to the sensor surface; however, for photonic–plasmonic systems in real experimental conditions, the range of the Rabi energy is rather narrow, thus it can be linearly approximated. This approach based on the strong coupling effect paves the alternative way for detection and monitoring of the interaction of the proteins on the transducer surface through the change of coupling strengths between plasmonic resonance and the protein–dye complex. Full article
(This article belongs to the Special Issue Immunoanalytical and Bioinformatics Methods in Immunology Research)
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18 pages, 2844 KiB  
Article
Identification of Novel Hub Genes Associated with Psoriasis Using Integrated Bioinformatics Analysis
by Qi Yue, Zhaoxiang Li, Qi Zhang, Quanxin Jin, Xinyuan Zhang and Guihua Jin
Int. J. Mol. Sci. 2022, 23(23), 15286; https://doi.org/10.3390/ijms232315286 - 4 Dec 2022
Cited by 11 | Viewed by 2726
Abstract
Psoriasis is a chronic, prolonged, and recurrent inflammatory skin disease and the current therapeutics can only alleviate the symptoms rather than cure it completely. Therefore, we aimed to identify the molecular signatures and specific biomarkers of psoriasis to provide novel clues for psoriasis [...] Read more.
Psoriasis is a chronic, prolonged, and recurrent inflammatory skin disease and the current therapeutics can only alleviate the symptoms rather than cure it completely. Therefore, we aimed to identify the molecular signatures and specific biomarkers of psoriasis to provide novel clues for psoriasis and targeted therapy. In the present study, the Gene Expression Omnibus (GEO) database was used to retrieve three microarray datasets (GSE166388, GSE50790 and GSE42632) and to explore the differentially expressed genes (DEGs) in psoriasis using the Affy package in R software. The gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment were utilized to determine the common DEGs and their capabilities. The STRING database was used to develop DEG-encoded proteins and a protein–protein interaction network (PPI) and the Cytohubba plugin to classify hub genes. Using the NetworkAnalyst platform, we detected transcription factors (TFs), microRNAs and drug candidates interacting with hub genes. In addition, the expression levels of hub genes in HaCaT cells were detected by western blot. We screened the up- and downregulated DEGs from the transcriptome microarrays of corresponding psoriasis patients. Functional enrichment of DEGs in psoriasis was mainly associated with positive regulation of leukocyte cell–cell adhesion and T cell activation, cytokine binding, cytokine activity and the Wnt signaling pathway. Through further data processing, we obtained 57 intersecting genes in the three datasets and probed them in STRING to determine the interaction of their expressed proteins and we obtained the critical 10 hub genes in the Cytohubba plugin, including TOP2A, CDKN3, MCM10, PBK, HMMR, CEP55, ASPM, KIAA0101, ESC02, and IL-1β. Using these hub genes as targets, we obtained 35 TFs and 213 miRNAs that may regulate these genes and 33 potential therapeutic agents for psoriasis. Furthermore, the expression levels of TOP2A, MCM10, PBK, ASPM, KIAA0101 and IL-1β were observably increased in HaCaT cells. In conclusion, we identified potential biomarkers, risk factors and drugs for psoriasis. Full article
(This article belongs to the Special Issue Immunoanalytical and Bioinformatics Methods in Immunology Research)
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14 pages, 1733 KiB  
Article
Experimental Evaluation of Quantum Dots and Antibodies Conjugation by Surface Plasmon Resonance Spectroscopy
by Anton Popov, Viktorija Lisyte, Asta Kausaite-Minkstimiene, Eiva Bernotiene and Almira Ramanaviciene
Int. J. Mol. Sci. 2022, 23(20), 12626; https://doi.org/10.3390/ijms232012626 - 20 Oct 2022
Cited by 7 | Viewed by 2452
Abstract
The application of antibody-functionalized quantum dots (QDs) in different areas has been widely described in the literature. However, a standard routine method for obtaining information on the conjugation efficiency of QDs with antibodies in terms of the interaction of the functionalized QDs with [...] Read more.
The application of antibody-functionalized quantum dots (QDs) in different areas has been widely described in the literature. However, a standard routine method for obtaining information on the conjugation efficiency of QDs with antibodies in terms of the interaction of the functionalized QDs with a specific antigen is still lacking. Herein, surface plasmon resonance (SPR) spectroscopy is proposed for this purpose. Gold-coated SPR sensor disks were modified with a self-assembled monolayer of 11-mercaptoundecanoic acid, and carbodiimide cross-linker chemistry was used to covalently immobilize the CD44 biomarker on the premodified surface (Au/CD44). Meanwhile, QDs functionalized with amine-derivatized polyethylene glycol (PEG) (QDs-NH2) were chosen for conjugation with antibodies because of their low non-specific adsorption on the Au/CD44 surface. Prior to conjugation, the surface binding capacity (Bmax) and equilibrium dissociation constant (KD) of the specific antibodies against CD44 (anti-CD44) were found to be 263.32 ± 2.44 m° and 1.00 × 10−7 ± 2.29 × 10−9 M, respectively. QDs-NH2 and anti-CD44 were conjugated at their initial molar ratios of 1:3, 1:5, 1:10 and 1:12. SPR measurements showed that the conjugates (QDs-anti-CD44) prepared using 1:10 and 1:12 molar ratios interacted comparably with immobilized CD44 biomarkers. The equilibrium angles in the case of 10- and 12-fold concentrations of anti-CD44 were calculated to be 60.43 ± 4.51 and 61.36 ± 4.40 m°, respectively. This could be explained by the QDs-NH2 and anti-CD44 having a similar surface loading (about four molecules per QDs-NH2) and similar hydrodynamic diameters, which were 46.63 ± 3.86 and 42.42 ± 0.80 nm for the 1:10 and 1:12 ratios, respectively. An initial QDs-NH2: anti-CD44 molar ratio of 1:10 was chosen as being optimal. SPR spectroscopy proved to be the right choice for QDs-anti-CD44 conjugation optimization, and can be used for the evaluation of conjugation efficiency for other nanostructures with various bio-recognition molecules. Full article
(This article belongs to the Special Issue Immunoanalytical and Bioinformatics Methods in Immunology Research)
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Review

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33 pages, 4072 KiB  
Review
Immunoassays: Analytical and Clinical Performance, Challenges, and Perspectives of SERS Detection in Comparison with Fluorescent Spectroscopic Detection
by Xeniya Terzapulo, Aiym Kassenova and Rostislav Bukasov
Int. J. Mol. Sci. 2024, 25(4), 2080; https://doi.org/10.3390/ijms25042080 - 8 Feb 2024
Cited by 7 | Viewed by 3145
Abstract
Immunoassays (IAs) with fluorescence-based detection are already well-established commercialized biosensing methods, such as enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay (LFIA). Immunoassays with surface-enhanced Raman spectroscopy (SERS) detection have received significant attention from the research community for at least two decades, but [...] Read more.
Immunoassays (IAs) with fluorescence-based detection are already well-established commercialized biosensing methods, such as enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay (LFIA). Immunoassays with surface-enhanced Raman spectroscopy (SERS) detection have received significant attention from the research community for at least two decades, but so far they still lack a wide clinical commercial application. This review, unlike any other review that we have seen, performs a three-dimensional performance comparison of SERS IAs vs. fluorescence IAs. First, we compared the limit of detection (LOD) as a key performance parameter for 30 fluorescence and 30 SERS-based immunoassays reported in the literature. We also compared the clinical performances of a smaller number of available reports for SERS vs. fluorescence immunoassays (FIAs). We found that the median and geometric average LODs are about 1.5–2 orders of magnitude lower for SERS-based immunoassays in comparison to fluorescence-based immunoassays. For instance, the median LOD for SERS IA is 4.3 × 10−13 M, whereas for FIA, it is 1.5 × 10−11 M. However, there is no significant difference in average relative standard deviation (RSD)—both are about 5–6%. The analysis of sensitivity, selectivity, and accuracy reported for a limited number of the published clinical studies with SERS IA and FIA demonstrates an advantage of SERS IA over FIA, at least in terms of the median value for all three of those parameters. We discussed common and specific challenges to the performances of both SERS IA and FIA, while proposing some solutions to mitigate those challenges for both techniques. These challenges include non-specific protein binding, non-specific interactions in the immunoassays, sometimes insufficient reproducibility, relatively long assay times, photobleaching, etc. Overall, this review may be useful for a large number of researchers who would like to use immunoassays, but particularly for those who would like to make improvements and move forward in both SERS-based IAs and fluorescence-based IAs. Full article
(This article belongs to the Special Issue Immunoanalytical and Bioinformatics Methods in Immunology Research)
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