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Biomedicines
Special Issues
Improvements in Methods for Biomedical Research in Oncology and Immunology
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Improvements in Methods for Biomedical Research in Oncology and Immunology

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular and Translational Medicine".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 4360

Special Issue Editors

Dr. Fatima Macedo

E-Mail Website
Guest Editor
1. Cell Activation and Gene Expression Group, Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
2. Department of Medical Sciences, University of Aveiro (UA), 3810-193 Aveiro, Portugal
Interests: lysosome; immunology; NKT; fabry disease
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Luisa Alejandra Helguero

E-Mail Website
Guest Editor
Departamento de Ciências Médicas, IBiMed, Universidade de Aveiro, Aveiro, Portugal
Interests: hormone-receptor positive breast cancer; endocrine therapy; unfolded protein response; proteomics and gene expression
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Laboratory methodology in biomedical research is key for the reproducibility of the results as well as its overall quality and application. The increased availability of novel technologies and the development of new methods and multicentric studies highlight the growing need to establish new and optimized research methodologies and practices. This Special Issue aims to contribute to the best practices in laboratory biomedical research by providing an overview on improvements in laboratorial methodology in oncology and immunology research as well as their applications. Potential topics include, but are not limited to, best practices in biomedical sample collection, storage and transportation for biomedical research, cell isolation and subpopulation enrichment, laboratory immunology, laboratory research in oncology, organoids and explant cultures, pre-analytical variables, and public omics data analysis.

Dr. Fatima Macedo
Prof. Dr. Luisa Alejandra Helguero
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. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • immunology
  • oncology
  • research methods

Published Papers (3 papers)

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10 pages, 990 KiB  
Article
Detection of PTCH1 Copy-Number Variants in Mosaic Basal Cell Nevus Syndrome
by Guido M. J. M. Roemen, Tom E. J. Theunissen, Ward W. J. Hoezen, Anja R. M. Steyls, Aimee D. C. Paulussen, Klara Mosterd, Elisa Rahikkala, Axel zur Hausen, Ernst Jan M. Speel and Michel van Geel
Biomedicines 2024, 12(2), 330; https://doi.org/10.3390/biomedicines12020330 - 31 Jan 2024
Viewed by 563
Abstract
Basal cell nevus syndrome (BCNS) is an inherited disorder characterized mainly by the development of basal cell carcinomas (BCCs) at an early age. BCNS is caused by heterozygous small-nucleotide variants (SNVs) and copy-number variants (CNVs) in the Patched1 (PTCH1) gene. Genetic [...] Read more.
Basal cell nevus syndrome (BCNS) is an inherited disorder characterized mainly by the development of basal cell carcinomas (BCCs) at an early age. BCNS is caused by heterozygous small-nucleotide variants (SNVs) and copy-number variants (CNVs) in the Patched1 (PTCH1) gene. Genetic diagnosis may be complicated in mosaic BCNS patients, as accurate SNV and CNV analysis requires high-sensitivity methods due to possible low variant allele frequencies. We compared test outcomes for PTCH1 CNV detection using multiplex ligation-probe amplification (MLPA) and digital droplet PCR (ddPCR) with samples from a BCNS patient heterozygous for a PTCH1 CNV duplication and the patient’s father, suspected to have a mosaic form of BCNS. ddPCR detected a significantly increased PTCH1 copy-number ratio in the index patient’s blood, and the father’s blood and tissues, indicating that the father was postzygotic mosaic and the index patient inherited the CNV from him. MLPA only detected the PTCH1 duplication in the index patient’s blood and in hair and saliva from the mosaic father. Our data indicate that ddPCR more accurately detects CNVs, even in low-grade mosaic BCNS patients, which may be missed by MLPA. In general, quantitative ddPCR can be of added value in the genetic diagnosis of mosaic BCNS patients and in estimating the recurrence risk for offspring. Full article
(This article belongs to the Special Issue Improvements in Methods for Biomedical Research in Oncology and Immunology)
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21 pages, 1733 KiB  
Article
A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets
by Alice Nevone, Francesca Lattarulo, Monica Russo, Giada Panno, Paolo Milani, Marco Basset, Maria Antonietta Avanzini, Giampaolo Merlini, Giovanni Palladini and Mario Nuvolone
Biomedicines 2023, 11(4), 1079; https://doi.org/10.3390/biomedicines11041079 - 03 Apr 2023
Cited by 2 | Viewed by 1820
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we [...] Read more.
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed “housekeeping” genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available. Full article
(This article belongs to the Special Issue Improvements in Methods for Biomedical Research in Oncology and Immunology)
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9 pages, 1955 KiB  
Brief Report
Buffy Coat Processing Impacts on Monocytes’ Capacity to Present Lipid Antigens
by Inês Mondragão-Rodrigues and M. Fátima Macedo
Biomedicines 2023, 11(3), 833; https://doi.org/10.3390/biomedicines11030833 - 09 Mar 2023
Viewed by 1615
Abstract
Buffy Coats, generated from a blood donor’s whole blood bag unit, are commonly used in biomedical research as a source of leukocytes due to the high number of cells that can be recovered from each Buffy Coat. Buffy Coats are leukocyte-enriched residual units [...] Read more.
Buffy Coats, generated from a blood donor’s whole blood bag unit, are commonly used in biomedical research as a source of leukocytes due to the high number of cells that can be recovered from each Buffy Coat. Buffy Coats are leukocyte-enriched residual units obtained by centrifugation of whole blood. At the blood bank, blood can be processed using two different protocols according to the time interval between blood collection and processing. When blood collection and processing occur on the same day, it gives rise to Fresh Blood Buffy Coats. Alternatively, if blood processing only happens on the day after blood collection, Overnight Blood Buffy Coats are created. In this study, we aimed to address whether these two different Buffy Coat-processing protocols could differently impact monocyte function as antigen-presenting cells. For this purpose, we analyzed in the same experiment monocytes isolated from Fresh Blood and from Overnight Blood Buffy Coats. We assessed lipid antigen presentation by CD1d to invariant Natural Killer T (iNKT) cells. CD1d is a non-polymorphic MHC class I-like protein, which facilitates the study of antigen presentation among allogeneic samples. The results show that monocytes from Fresh Blood Buffy Coats have a better capacity to present antigens by CD1d, and consequently to activate iNKT cells, when compared to monocytes from Overnight Blood Buffy Coats. The differences observed were not explained by disparities in monocyte viability, CD1d expression, or basal activation state (monocyte expression of CD40 and CD80). Buffy Coats are a valid source of blood cells available daily. Hence, the type of protocol for Buffy Coat processing should be carefully considered in day-to-day research, since it may lead to different outcomes. Full article
(This article belongs to the Special Issue Improvements in Methods for Biomedical Research in Oncology and Immunology)
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