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A special issue of Journal of Personalized Medicine (ISSN 2075-4426). This special issue belongs to the section "Omics/Informatics".

Deadline for manuscript submissions: closed (5 August 2021) | Viewed by 41918

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Special Issue Editor

Dr. Roberto Díaz Peña

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Guest Editor

Fundación Publica Galega de Medicina Xenómica, SERGAS, Grupo de Medicina Xenomica-USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
Interests: autoimmunity; rheumatology; genetics; genomics; bioinformatics; oncology; liquid biopsy

Special Issue Information

Dear Colleagues,

The ultimate aim of genomic studies in autoimmunity, and in any human disease, is to understand their pathogenesis in order to identify novel therapeutic approaches. The implementation of -omics techniques will bring considerable progress to our knowledge of disease etiology and manifestations and have a determinant impact on the discovery of new biomarkers suitable for clinical practice.

Genomics is the key component in biomedical research toward personalized medicine. This Special Issue of the Journal of Personalized Medicine aims to highlight the current state of the utilization or implementation of genomic technologies in autoimmunity. Mainly, we call for papers that are focused on the field of genomics in autoimmune diseases, and their potential to be useful for the diagnosis and treatment of these conditions. We encourage the submission of reviews and original articles which describe a personalized medicine approach to the diagnosis, classification, and treatment approach to autoimmune diseases.

Dr. Roberto Díaz Peña
Guest Editor

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. Journal of Personalized Medicine 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

Personalized medicine
Genomics
Autoimmune diseases
Polygenic risk scores
Inflammation
Biomarkers
Proteomics
Epigenetics
Transcriptomics
Pharmacogenomics

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review

3 pages, 192 KiB

Open AccessEditorial

Personalized Medicine in Autoimmune Diseases

by Roberto Díaz-Peña

J. Pers. Med. 2021, 11(11), 1181; https://doi.org/10.3390/jpm11111181 - 11 Nov 2021

Cited by 3 | Viewed by 1591

Abstract

Autoimmune diseases are multifactorial disorders caused by both genetic and environmental factors and without a known cure [...] Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

Research

Jump to: Editorial, Review

20 pages, 2790 KiB

Open AccessArticle

Acquisition of New Migratory Properties by Highly Differentiated CD4+CD28^null T Lymphocytes in Rheumatoid Arthritis Disease

by Beatriz Rioseras, Marco Antonio Moro-García, Alejandra García-Torre, Eva Bueno-García, Rocio López-Martínez, Maria Iglesias-Escudero, Roberto Diaz-Peña, Patricia Castro-Santos, Miguel Arias-Guillén and Rebeca Alonso-Arias

J. Pers. Med. 2021, 11(7), 594; https://doi.org/10.3390/jpm11070594 - 24 Jun 2021

Cited by 4 | Viewed by 2255

Abstract

Expanded CD4+CD28^null T lymphocytes are found in the tissues and peripheral blood of patients with many autoimmune diseases, such as rheumatoid arthritis (RA). These highly differentiated cells present potent inflammatory activity and capability to induce tissue destruction, which has been suggested to predispose to the development of more aggressive disease. In fact, preferential migration to inflammatory sites has been proposed to be a contributing factor in the progression of autoimmune and cardiovascular diseases frequently found in these patients. The functional activity of CD4+CD28^null T lymphocytes is largely dependent on interleukin 15 (IL-15), and this cytokine may also act as a selective attractor of these cells to local inflammatory infiltrates in damaged tissues. We have analysed, in RA patients, the migratory properties and transcriptional motility profile of CD4+CD28^null T lymphocytes compared to their counterparts CD28+ T lymphocytes and the enhancing role of IL-15. Identification of the pathways involved in this process will allow us to design strategies directed to block effector functions that CD4+CD28^null T lymphocytes have in the target tissue, which may represent therapeutic approaches in this immune disorder. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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17 pages, 1478 KiB

Open AccessFeature PaperArticle

New Evidence of Potential Benefits of Dexamethasone and Added on Therapy of Fludrocortisone on Clinical Outcomes of Corticosteroid in Sepsis Patients: A Systematic Review and Meta-Analysis

by Ji-young Son, Sooyoung Shin and Yeo Jin Choi

J. Pers. Med. 2021, 11(6), 544; https://doi.org/10.3390/jpm11060544 - 11 Jun 2021

Cited by 5 | Viewed by 2831

Abstract

The aim of this study is to investigate clinical outcomes of corticosteroid treatment in patients with sepsis or septic shock. An electronic keyword searches of PubMed, EMBASE, and Google Scholar were conducted per PRISMA guidelines. The pooled analyses on the corticosteroid impact on mortality, adverse events, and clinical outcomes were performed. Subgroup analyses on the clinical outcomes in relation to corticosteroid dose, duration, and agents were performed. Pooled analyses of 21 randomized control trials revealed substantially reduced mortality (RR 0.93, 95% CI 0.88–0.99, p = 0.02) and length of stay in intensive care unit (SMD −1.66, 95% CI −1.91–−1.40, p < 0.00001) without increased risks of adverse events (RR 1.04, 95% CI 0.96–1.12, p = 0.38). No significant improvements of other clinical outcomes were observed. Subgroup analyses demonstrated substantially reduced mortality with short-term (≤7 days) low-dose (<400 mg/day) corticosteroid treatment (RR 0.91, 95% CI 0.87–0.95, p < 0.0001). Moreover, dexamethasone (RR 0.40, 95% CI 0.20–0.81, p = 0.01) and combined hydrocortisone and fludrocortisone treatment (RR 0.89, 95% CI 0.84–0.94, p < 0.00001) provided substantial reduction of mortality whereas hydrocortisone alone did not reduce the mortality risk in sepsis patients. Thus, further controlled studies on the clinical outcomes of potential corticosteroid options on sepsis-related clinical outcomes are warranted. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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13 pages, 590 KiB

Open AccessFeature PaperArticle

Genetic Factors of Predisposition and Clinical Characteristics of Rheumatoid Arthritis in Russian Patients

by Ekaterina A. Vetchinkina, Dmitry S. Mikhaylenko, Ekaterina B. Kuznetsova, Tatiana A. Deryagina, Ekaterina A. Alekseeva, Irina V. Bure, Andrey A. Zamyatnin, Jr. and Marina V. Nemtsova

J. Pers. Med. 2021, 11(6), 469; https://doi.org/10.3390/jpm11060469 - 25 May 2021

Cited by 9 | Viewed by 3058

Abstract

Rheumatoid arthritis (RA) is a multifactorial disease caused by a genetic predisposition and environmental factors. Predisposing alleles of various genes have a relatively small influence on the disease risk when they appear separately, but in combination, they predispose an individual to RA development. We genotyped 125 patients with RA including 60 SNPs and sequenced coding part of six genes by next-generation sequencing (NGS) technology on a target panel (IAD177464_185). According to our data, the alleles HLA-DRB1*04, HLA-DRB1*01, HLA-B*27, PTPN22 (rs2476601), TNF (rs1800629), TPMT (rs2842934), and IL4 (rs2243250), and genotypes HLA-DRB1*04:04, HLA-DRB1*01:16, PTPN22 (rs2476601), TPMT (rs2842934), were significantly associated with the RA development. Associations with clinical criteria (DAS28-CRP, HAQ-DI, and CDAI) and biochemical factors were investigated. We have shown that the PADI4 genotypes (rs11203367, rs2240340, rs11203366, and rs874881) are significantly associated with the baseline levels of DAS28-CRP, HAQ-DI, and CDAI; genotypes IL23R (rs7530511) and TNFRSF1A (rs748004, rs2228144) with the level of anti citrullinated peptide antibodies (ACPA); the genotypes DHODH (rs3213422) and MTHFR (rs180113) with the concentration of C-reactive protein (CRP); and the genotypes IL2RA (rs2104286), IRAK3 (rs11541076), and IL4R (rs1801275) with the level of rheumatoid factor (RF). Application of targeted NGS panel contributes to expanded genotyping to identify risk groups among the RA patients. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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15 pages, 797 KiB

Open AccessArticle

Analysis of miRNA Expression in Patients with Rheumatoid Arthritis during Olokizumab Treatment

by Irina V. Bure, Dmitry S. Mikhaylenko, Ekaterina B. Kuznetsova, Ekaterina A. Alekseeva, Kristina I. Bondareva, Alexey I. Kalinkin, Alexander N. Lukashev, Vadim V. Tarasov, Andrey A. Zamyatnin, Jr. and Marina V. Nemtsova

J. Pers. Med. 2020, 10(4), 205; https://doi.org/10.3390/jpm10040205 - 31 Oct 2020

Cited by 7 | Viewed by 2808

Abstract

Rheumatoid arthritis (RA) is the most common autoimmune disease worldwide. Epigenetic alternations of microRNAs (miRNAs) can contribute to its pathogenesis and progression. As the first line therapy with DMARDs is not always successful, other drugs and therapeutic targets should be applied. This study aims to measure the expression level of plasma miRNAs in RA patients treated with olokizumab and to evaluate their potential as prognostic biomarkers. The expression of 9 miRNAs was quantified in 103 RA patients before treatment and at weeks 12 and 24 of olokizumab therapy by reverse transcription-polymerase chain reaction (RT-PCR) assay and analyzed in groups of responders and non-responders. Almost all miRNAs changed their expression during therapy. The ROC curve analysis of the most prominent of them together with consequent univariate and multivariate regression analysis revealed statistically significant associations with the olokizumab therapy efficiency scores for miR-26b, miR-29, miR-451, and miR-522. Therefore, these miRNAs might be a potential therapeutic response biomarker. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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14 pages, 1357 KiB

Open AccessArticle

Amerindian Ancestry Influences Genetic Susceptibility to Chronic Obstructive Pulmonary Disease

by Roberto Díaz-Peña, Felix Boekstegers, Rafael S. Silva, Sergio Jaime, H. Dean Hosgood III, Marc Miravitlles, Àlvar Agustí, Justo Lorenzo Bermejo and Jordi Olloquequi

J. Pers. Med. 2020, 10(3), 93; https://doi.org/10.3390/jpm10030093 - 18 Aug 2020

Cited by 8 | Viewed by 3724

Abstract

The contribution of genetic ancestry on chronic obstructive pulmonary disease (COPD) predisposition remains unclear. To explore this relationship, we analyzed the associations between 754,159 single nucleotide polymorphisms (SNPs) and risk of COPD (n = 214 cases, 193 healthy controls) in Talca, Chile, considering the genetic ancestry and established risk factors. The proportion of Mapuche ancestry (PMA) was based on a panel of 45 Mapuche reference individuals. Five PRDM15 SNPs and two PPP1R12B SNPs were associate with COPD risk (p = 0.05 to 5 × 10⁻⁴) in those individuals with lower PMA. Based on linkage disequilibrium and sliding window analyses, an adjacent PRDM15 SNPs were associated with COPD risk in the lower PMA group (p = 10⁻³ to 3.77 × 10⁻⁸). Our study is the first to report an association between PPP1R12B and COPD risk, as well as effect modification between ethnicity and PRDM15 SNPs in determining COPD risk. Our results are biologically plausible given that PPP1R12B and PRDM15 are involved in immune dysfunction and autoimmunity, providing mechanistic evidence for COPD pathogenesis and highlighting the importance to conduct more genome wide association studies (GWAS) in admixed populations with Amerindian descent. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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Review

Jump to: Editorial, Research

24 pages, 2747 KiB

Open AccessReview

Selective Targeting of Epigenetic Readers and Histone Deacetylases in Autoimmune and Inflammatory Diseases: Recent Advances and Future Perspectives

by Mohammed Ghiboub, Ahmed M. I. Elfiky, Menno P. J. de Winther, Nicola R. Harker, David F. Tough and Wouter J. de Jonge

J. Pers. Med. 2021, 11(5), 336; https://doi.org/10.3390/jpm11050336 - 23 Apr 2021

Cited by 15 | Viewed by 4381

Abstract

Histone deacetylases (HDACs) and bromodomain-containing proteins (BCPs) play a key role in chromatin remodeling. Based on their ability to regulate inducible gene expression in the context of inflammation and cancer, HDACs and BCPs have been the focus of drug discovery efforts, and numerous small-molecule inhibitors have been developed. However, dose-limiting toxicities of the first generation of inhibitors, which typically target multiple HDACs or BCPs, have limited translation to the clinic. Over the last decade, an increasing effort has been dedicated to designing class-, isoform-, or domain-specific HDAC or BCP inhibitors, as well as developing strategies for cell-specific targeted drug delivery. Selective inhibition of the epigenetic modulators is helping to elucidate the functions of individual epigenetic proteins and has the potential to yield better and safer therapeutic strategies. In accordance with this idea, several in vitro and in vivo studies have reported the ability of more selective HDAC/BCP inhibitors to recapitulate the beneficial effects of pan-inhibitors with less unwanted adverse events. In this review, we summarize the most recent advances with these strategies, discussing advantages and limitations of these approaches as well as some therapeutic perspectives, focusing on autoimmune and inflammatory diseases. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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14 pages, 1080 KiB

Open AccessReview

Circulating Free DNA and Its Emerging Role in Autoimmune Diseases

by Patricia Mondelo-Macía, Patricia Castro-Santos, Adrián Castillo-García, Laura Muinelo-Romay and Roberto Diaz-Peña

J. Pers. Med. 2021, 11(2), 151; https://doi.org/10.3390/jpm11020151 - 20 Feb 2021

Cited by 38 | Viewed by 4983

Abstract

Liquid biopsies can be used to analyse tissue-derived information, including cell-free DNA (cfDNA), circulating rare cells, and circulating extracellular vesicles in the blood or other bodily fluids, representing a new way to guide therapeutic decisions in cancer. Among the new challenges of liquid biopsy, we found clinical application in nontumour pathologies, including autoimmune diseases. Since the discovery of the presence of high levels of cfDNA in patients with systemic lupus erythaematosus (SLE) in the 1960s, cfDNA research in autoimmune diseases has mainly focused on the overall quantification of cfDNA and its association with disease activity. However, with technological advancements and the increasing understanding of the role of DNA sensing receptors in inflammation and autoimmunity, interest in cfDNA and autoimmune diseases has not expanded until recently. In this review, we provide an overview of the basic biology of cfDNA in the context of autoimmune diseases as a biomarker of disease activity, progression, and prediction of the treatment response. We discuss and integrate available information about these important aspects. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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19 pages, 1297 KiB

Open AccessReview

Skin Immunomodulation during Regeneration: Emerging New Targets

by Loubna Mazini, Luc Rochette, Yousra Hamdan and Gabriel Malka

J. Pers. Med. 2021, 11(2), 85; https://doi.org/10.3390/jpm11020085 - 30 Jan 2021

Cited by 29 | Viewed by 5636

Abstract

Adipose-Derived Stem Cells (ADSC) are present within the hypodermis and are also expected to play a pivotal role in wound healing, immunomodulation, and rejuvenation activities. They orchestrate, through their exosome, the mechanisms associated to cell differentiation, proliferation, and cell migration by upregulating genes implicated in different functions including skin barrier, immunomodulation, cell proliferation, and epidermal regeneration. ADSCs directly interact with their microenvironment and specifically the immune cells, including macrophages and T and B cells, resulting in differential inflammatory and anti-inflammatory mechanisms impacting, in return, ADSCs microenvironment and thus skin function. These useful features of ADSCs are involved in tissue repair, where the required cell proliferation, angiogenesis, and anti-inflammatory responses should occur rapidly in damaged sites. Different pathways involved have been reported such as Growth Differentiation Factor-11 (GDF11), Tumor Growth Factor (TGF)-β, Metalloproteinase (MMP), microRNA, and inflammatory cytokines that might serve as specific biomarkers of their immunomodulating capacity. In this review, we try to highlight ADSCs’ network and explore the potential indicators of their immunomodulatory effect in skin regeneration and aging. Assessment of these biomarkers might be useful and should be considered when designing new clinical therapies using ADSCs or their specific exosomes focusing on their immunomodulation activity. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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17 pages, 1859 KiB

Open AccessReview

Latin American Genes: The Great Forgotten in Rheumatoid Arthritis

by Roberto Díaz-Peña, Luis A. Quiñones, Patricia Castro-Santos, Josefina Durán and Alejandro Lucia

J. Pers. Med. 2020, 10(4), 196; https://doi.org/10.3390/jpm10040196 - 26 Oct 2020

Cited by 3 | Viewed by 3025

Abstract

The successful implementation of personalized medicine will rely on the integration of information obtained at the level of populations with the specific biological, genetic, and clinical characteristics of an individual. However, because genome-wide association studies tend to focus on populations of European descent, there is a wide gap to bridge between Caucasian and non-Caucasian populations before personalized medicine can be fully implemented, and rheumatoid arthritis (RA) is not an exception. In this review, we discuss advances in our understanding of genetic determinants of RA risk among global populations, with a focus on the Latin American population. Geographically restricted genetic diversity may have important implications for health and disease that will remain unknown until genetic association studies have been extended to include Latin American and other currently under-represented ancestries. The next few years will witness many breakthroughs in personalized medicine, including applications for common diseases and risk stratification instruments for targeted prevention/intervention strategies. Not all of these applications may be extrapolated from the Caucasian experience to Latin American or other under-represented populations. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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19 pages, 1678 KiB

Open AccessReview

The Genetics of Spondyloarthritis

by Roberto Díaz-Peña, Patricia Castro-Santos, Josefina Durán, Catalina Santiago and Alejandro Lucia

J. Pers. Med. 2020, 10(4), 151; https://doi.org/10.3390/jpm10040151 - 2 Oct 2020

Cited by 22 | Viewed by 5992

Abstract

The term spondyloarthritis (SpA) encompasses a group of chronic inflammatory diseases with common features in terms of clinical presentation and genetic predisposition. SpA is characterized by inflammation of the spine and peripheral joints, and is also be associated with extra-articular inflammatory manifestations such as psoriasis, uveitis, or inflammatory bowel disease (IBD). The etiology of SpA is not completely understood, but it is known to have a strong genetic component dominated by the human leukocyte antigen (HLA)-B27. In the last few years, our understanding of genetic susceptibility to SpA, particularly ankylosing spondylitis (AS), has greatly improved thanks to the findings derived from powered genome-wide association studies (GWAS) based on single nucleotide polymorphism (SNP) arrays. These studies have identified many candidate genes, therefore providing new potential directions in the exploration of disease mechanisms, especially with regard to the key role of the immune system in the pathogenesis of SpA. SpA is a complex disease where genetic variability, environmental factors, and random events interact to trigger pathological pathways. The aim of this review is to summarize current findings on the genetics of SpA, some of which might help to study new treatment approaches. Full article

(This article belongs to the Special Issue Personalized Medicine in Autoimmune Diseases)

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