Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Advances in Rare Diseases Biomarkers

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 11608

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special issue Advances in Rare Diseases Biomarkers book cover image

Share This Special Issue

Special Issue Editor

Dr. Andrea Bernini

E-Mail Website
Guest Editor

Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
Interests: structural biology; rare diseases; metabolomics; nuclear magnetic resonance; protein dynamics; protein core & surface; transient pockets
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A rare disease is a health condition with a lower prevalence than common diseases. The World Health Organization defines a rare disease as one that strikes fewer than 65 per 100,000 people. However, their combined effect is significant: around 7000 rare diseases affect approximately 350 million people worldwide.

Biomarkers play a crucial role in diagnosing and monitoring rare diseases, which are often challenging to detect and understand due to their low prevalence and diverse clinical manifestations. Biomarkers serve as measurable indicators of biological processes or conditions in rare diseases, offering valuable insights into disease mechanisms and progression. These markers may include genetic mutations, protein levels, or other molecular signatures unique to a rare condition. The discovery and validation of such biomarkers contribute to early detection and the development of targeted therapies, allowing for more effective and personalised treatment approaches.

As technology advances, the integration of omics technologies, such as genomics, proteomics, and metabolomics, has further expanded the repertoire of potential biomarkers, fostering a deeper understanding of rare diseases and paving the way for innovative diagnostic and therapeutic strategies. Biomarkers enhance our ability to navigate diagnostic challenges and promise to improve patient care and foster breakthroughs in treatment modalities.

For the Special Issue, we continue looking for original research articles and state-of-the-art reviews on novel and established proteomic, metabolomic, or transcriptomic biomarkers that can help us better understand the underlying molecular mechanisms of rare diseases. Additionally, we are interested in biomarkers that can be used to diagnose and predict the prognosis of rare diseases and determine individual responses to therapies.

Dr. Andrea Bernini
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. 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

orphan diseases
rare diseases
inborn errors of metabolism
mitochondrial disorders
biomarker discovery

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (10 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review

17 pages, 4481 KiB

Open AccessArticle

Gastric Cancer and Intestinal Metaplasia: Differential Metabolic Landscapes and New Pathways to Diagnosis

by Seong Ji Choi, Hyuk Soon Choi, Hyunil Kim, Jae Min Lee, Seung Han Kim, Jai Hoon Yoon, Bora Keum, Hyo Jung Kim, Hoon Jai Chun and Youngja H. Park

Int. J. Mol. Sci. 2024, 25(17), 9509; https://doi.org/10.3390/ijms25179509 - 1 Sep 2024

Cited by 1 | Viewed by 1085

Abstract

Gastric cancer (GC) is the fifth most common cause of cancer-related death worldwide. Early detection is crucial for improving survival rates and treatment outcomes. However, accurate GC-specific biomarkers remain unknown. This study aimed to identify the metabolic differences between intestinal metaplasia (IM) and GC to determine the pathways involved in GC. A metabolic analysis of IM and tissue samples from 37 patients with GC was conducted using ultra-performance liquid chromatography with tandem mass spectrometry. Overall, 665 and 278 significant features were identified in the aqueous and 278 organic phases, respectively, using false discovery rate analysis, which controls the expected proportion of false positives among the significant results. sPLS-DA revealed a clear separation between IM and GC samples. Steroid hormone biosynthesis, tryptophan metabolism, purine metabolism, and arginine and proline metabolism were the most significantly altered pathways. The intensity of 11 metabolites, including N1, N2-diacetylspermine, creatine riboside, and N-formylkynurenine, showed significant elevation in more advanced GC. Based on pathway enrichment analysis and cancer stage-specific alterations, we identified six potential candidates as diagnostic biomarkers: aldosterone, N-formylkynurenine, guanosine triphosphate, arginine, S-adenosylmethioninamine, and creatine riboside. These metabolic differences between IM and GC provide valuable insights into gastric carcinogenesis. Further validation is needed to develop noninvasive diagnostic tools and targeted therapies to improve the outcomes of patients with GC. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Figure 1

22 pages, 9707 KiB

Open AccessArticle

TLR2 and TLR4 Are Expressed in Epiretinal Membranes: Possible Links with Vitreous Levels of Complement Fragments and DAMP-Related Proteins

by Lucia Dinice, Graziana Esposito, Andrea Cacciamani, Bijorn Omar Balzamino, Pamela Cosimi, Concetta Cafiero, Guido Ripandelli and Alessandra Micera

Int. J. Mol. Sci. 2024, 25(14), 7732; https://doi.org/10.3390/ijms25147732 - 15 Jul 2024

Cited by 1 | Viewed by 986

Abstract

Previous studies reported the expression of toll-like receptors (TLRs), merely TLR2 and TLR4, and complement fragments (C3a, C5b9) in vitreoretinal disorders. Other than pathogens, TLRs can recognize endogenous products of tissue remodeling as damage-associated molecular pattern (DAMPs). The aim of this study was to confirm the expression of TLR2 and TLR4 in the fibrocellular membranes and vitreal fluids (soluble TLRs) of patients suffering of epiretinal membranes (ERMs) and assess their association with disease severity, complement fragments and inflammatory profiles. Twenty (n = 20) ERMs and twelve (n = 12) vitreous samples were collected at the time of the vitrectomy. Different severity-staged ERMs were processed for: immunolocalization (IF), transcriptomic (RT-PCR) and proteomics (ELISA, IP/WB, Protein Chip Array) analysis. The investigation of targets included TLR2, TLR4, C3a, C5b9, a few selected inflammatory biomarkers (Eotaxin-2, Rantes, Vascular Endothelial Growth Factor (VEGFA), Vascular Endothelial Growth Factor receptor (VEGFR2), Interferon-γ (IFNγ), Interleukin (IL1β, IL12p40/p70)) and a restricted panel of matrix enzymes (Matrix metalloproteinases (MMPs)/Tissue Inhibitor of Metallo-Proteinases (TIMPs)). A reduced cellularity was observed as function of ERM severity. TLR2, TLR4 and myD88 transcripts/proteins were detected in membranes and decreased upon disease severity. The levels of soluble TLR2 and TLR4, as well as C3a, C5b9, Eotaxin-2, Rantes, VEGFA, VEGFR2, IFNγ, IL1β, IL12p40/p70, MMP7 and TIMP2 levels were changed in vitreal samples. Significant correlations were observed between TLRs and complement fragments and between TLRs and some inflammatory mediators. Our findings pointed at TLR2 and TLR4 over-expression at early stages of ERM formation, suggesting the participation of the local immune response in the severity of disease. These activations at the early-stage of ERM formation suggest a potential persistence of innate immune response in the early phases of fibrocellular membrane formation. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Figure 1

8 pages, 1250 KiB

Open AccessCommunication

A Plasma Pyrophosphate Cutoff Value for Diagnosing Pseudoxanthoma Elasticum

by Isabelle Rubera, Laetitia Clotaire, Audrey Laurain, Alexandre Destere, Ludovic Martin, Christophe Duranton and Georges Leftheriotis

Int. J. Mol. Sci. 2024, 25(12), 6502; https://doi.org/10.3390/ijms25126502 - 13 Jun 2024

Viewed by 817

Abstract

Pseudoxanthoma elasticum (PXE) is a rare inherited systemic disease responsible for a juvenile peripheral arterial calcification disease. The clinical diagnosis of PXE is only based on a complex multi-organ phenotypic score and/or genetical analysis. Reduced plasma inorganic pyrophosphate concentration [PPi]p has been linked to PXE. In this study, we used a novel and accurate method to measure [PPi]p in one of the largest cohorts of PXE patients, and we reported the valuable contribution of a cutoff value to PXE diagnosis. Plasma samples and clinical records from two French reference centers for PXE (PXE Consultation Center, Angers, and FAVA-MULTI South Competent Center, Nice) were assessed. Plasma PPi were measured in 153 PXE and 46 non-PXE patients. The PPi concentrations in the plasma samples were determined by a new method combining enzymatic and ion chromatography approaches. The best match between the sensitivity and specificity (Youden index) for diagnosing PXE was determined by ROC analysis. [PPi]p were lower in PXE patients (0.92 ± 0.30 µmol/L) than in non-PXE patients (1.61 ± 0.33 µmol/L, p < 0.0001), corresponding to a mean reduction of 43 ± 19% (SD). The PPi cutoff value for diagnosing PXE in all patients was 1.2 µmol/L, with a sensitivity of 83.3% and a specificity of 91.1% (AUC = 0.93), without sex differences. In patients aged <50 years (i.e., the age period for PXE diagnosis), the cutoff PPi was 1.2 µmol/L (sensitivity, specificity, and AUC of 93%, 96%, and 0.97, respectively). The [PPi]p shows high accuracy for diagnosing PXE; thus, quantifying plasma PPi represents the first blood assay for diagnosing PXE. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Figure 1

12 pages, 1677 KiB

Open AccessCommunication

Comparative Single Vesicle Analysis of Aqueous Humor Extracellular Vesicles before and after Radiation in Uveal Melanoma Eyes

by Shreya Sirivolu, Chen-Ching Peng, Paolo Neviani, Benjamin Y. Xu, Jesse L. Berry and Liya Xu

Int. J. Mol. Sci. 2024, 25(11), 6035; https://doi.org/10.3390/ijms25116035 - 30 May 2024

Viewed by 933

Abstract

Small extracellular vesicles (sEVs) have been shown to promote tumorigenesis, treatment resistance, and metastasis in multiple cancer types; however, sEVs in the aqueous humor (AH) of uveal melanoma (UM) patients have never previously been profiled. In this study, we used single particle analysis to characterize sEV subpopulations in the AH of UM patients by quantifying their size, concentration, and phenotypes based on cell surface markers, specifically the tetraspanin co-expression patterns of CD9, CD63, and CD81. sEVs were analyzed from paired pre- and post-treatment (brachytherapy, a form of radiation) AH samples collected from 19 UM patients. In post-brachytherapy samples, two subpopulations, CD63/81+ and CD9/63/81+ sEVs, were significantly increased. These trends existed even when stratified by tumor location and GEP class 1 and class 2 (albeit not significant for GEP class 2). In this initial report of single vesicle profiling of sEVs in the AH of UM patients, we demonstrated that sEVs can be detected in the AH. We further identified two subpopulations that were increased post-brachytherapy, which may suggest radiation-induced release of these particles, potentially from tumor cells. Further study of the cargo carried by these sEV subpopulations may uncover important biomarkers and insights into tumorigenesis for UM. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Figure 1

17 pages, 3608 KiB

Open AccessArticle

Exploratory Untargeted Metabolomics of Dried Blood Spot Samples from Newborns with Maple Syrup Urine Disease

by Abeer Z. Alotaibi, Reem H. AlMalki, Maha Al Mogren, Rajaa Sebaa, Mohammad Alanazi, Minnie Jacob, Ahamd Alodaib, Ahmad Alfares and Anas M. Abdel Rahman

Int. J. Mol. Sci. 2024, 25(11), 5720; https://doi.org/10.3390/ijms25115720 - 24 May 2024

Viewed by 1150

Abstract

Currently, tandem mass spectrometry-based newborn screening (NBS), which examines targeted biomarkers, is the first approach used for the early detection of maple syrup urine disease (MSUD) in newborns, followed by confirmatory genetic mutation tests. However, these diagnostic approaches have limitations, demanding the development of additional tools for the diagnosis/screening of MUSD. Recently, untargeted metabolomics has been used to explore metabolic profiling and discover the potential biomarkers/pathways of inherited metabolic diseases. Thus, we aimed to discover a distinctive metabolic profile and biomarkers/pathways for MSUD newborns using untargeted metabolomics. Herein, untargeted metabolomics was used to analyze dried blood spot (DBS) samples from 22 MSUD and 22 healthy control newborns. Our data identified 210 altered endogenous metabolites in MSUD newborns and new potential MSUD biomarkers, particularly L-alloisoleucine, methionine, and lysoPI. In addition, the most impacted pathways in MSUD newborns were the ascorbate and aldarate pathways and pentose and glucuronate interconversions, suggesting that oxidative and detoxification events may occur in early life. Our approach leads to the identification of new potential biomarkers/pathways that could be used for the early diagnosis/screening of MSUD newborns but require further validation studies. Our untargeted metabolomics findings have undoubtedly added new insights to our understanding of the pathogenicity of MSUD, which helps us select the appropriate early treatments for better health outcomes. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Figure 1

11 pages, 1536 KiB

Open AccessArticle

Serum Galectin-3 as a Non-Invasive Marker for Primary Sclerosing Cholangitis

by Ganimete Bajraktari, Tanja Elger, Muriel Huss, Johanna Loibl, Andreas Albert, Arne Kandulski, Martina Müller, Hauke Christian Tews and Christa Buechler

Int. J. Mol. Sci. 2024, 25(9), 4765; https://doi.org/10.3390/ijms25094765 - 27 Apr 2024

Viewed by 1085

Abstract

Primary sclerosing cholangitis (PSC) is a serious liver disease associated with inflammatory bowel disease (IBD). Galectin-3, an inflammatory and fibrotic molecule, has elevated circulating levels in patients with chronic liver disease and inflammatory bowel disease (IBD). This study aims to clarify whether galectin-3 can differentiate between patients with IBD, PSC, and PSC-IBD. Our study measured serum galectin-3 levels in 38 healthy controls, 55 patients with IBD, and 22 patients with PSC (11 patients had underlying IBD and 11 patients did not), alongside the urinary galectin-3 of these patients and 18 controls. Serum and urinary galectin-3 levels in IBD patients were comparable to those in controls. Among IBD patients, those with high fecal calprotectin, indicating severe disease, exhibited lower serum and elevated urinary galectin-3 levels compared to those with low calprotectin levels. Serum galectin-3 levels were inversely correlated with C-reactive protein levels. PSC patients displayed higher serum and urinary galectin-3 levels than IBD patients, with the highest serum levels observed in PSC patients with coexisting IBD. There was no correlation between serum and urinary galectin-3 levels and laboratory indicators of liver injury in both IBD and PSC patients. In conclusion, this study demonstrates that serum and urinary galectin-3 levels can distinguish IBD from PSC patients, and also reveals higher serum galectin-3 levels in PSC-IBD patients compared to those with isolated PSC. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Figure 1

Review

Jump to: Research

15 pages, 707 KiB

Open AccessReview

Biomarkers Involved in the Pathogenesis of Hemophilic Arthropathy

by Oana Viola Badulescu, Dragos-Viorel Scripcariu, Minerva Codruta Badescu, Manuela Ciocoiu, Maria Cristina Vladeanu, Carmen Elena Plesoianu, Andrei Bojan, Dan Iliescu-Halitchi, Razvan Tudor, Bogdan Huzum, Otilia Elena Frasinariu and Iris Bararu-Bojan

Int. J. Mol. Sci. 2024, 25(18), 9897; https://doi.org/10.3390/ijms25189897 - 13 Sep 2024

Viewed by 834

Abstract

Hemophilia, which is a rare disease, results from congenital deficiencies of coagulation factors VIII and IX, respectively, leading to spontaneous bleeding into joints, resulting in hemophilic arthropathy (HA). HA involves complex processes, including synovial proliferation, angiogenesis, and tissue remodeling. Despite ongoing research, factors contributing to HA progression, especially in adults with severe HA experiencing joint pain, remain unclear. Blood markers, particularly collagen-related ones, have been explored to assess joint health in hemophilia. For example, markers like CTX-I and CTX-II reflect bone and cartilage turnover, respectively. Studies indicate elevated levels of certain markers post-bleeding episodes, suggesting joint health changes. However, longitudinal studies on collagen turnover and basement membrane or endothelial cell markers in relation to joint outcomes, particularly during painful episodes, are scarce. Given the role of the CX3CL1/CX3XR1 axis in arthritis, other studies investigate its involvement in HA. The importance of different inflammatory and bone damage biomarkers should be assessed, alongside articular cartilage and synovial membrane morphology, aiming to enhance understanding of hemophilic arthropathy progression. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Figure 1

20 pages, 7218 KiB

Open AccessReview

Biomarker Landscape in RASopathies

by Noemi Ferrito, Juan Báez-Flores, Mario Rodríguez-Martín, Julián Sastre-Rodríguez, Alessio Coppola, María Isidoro-García, Pablo Prieto-Matos and Jesus Lacal

Int. J. Mol. Sci. 2024, 25(16), 8563; https://doi.org/10.3390/ijms25168563 - 6 Aug 2024

Viewed by 1274

Abstract

RASopathies are a group of related genetic disorders caused by mutations in genes within the RAS/MAPK signaling pathway. This pathway is crucial for cell division, growth, and differentiation, and its disruption can lead to a variety of developmental and health issues. RASopathies present diverse clinical features and pose significant diagnostic and therapeutic challenges. Studying the landscape of biomarkers in RASopathies has the potential to improve both clinical practices and the understanding of these disorders. This review provides an overview of recent discoveries in RASopathy molecular profiling, which extend beyond traditional gene mutation analysis. mRNAs, non-coding RNAs, protein expression patterns, and post-translational modifications characteristic of RASopathy patients within pivotal signaling pathways such as the RAS/MAPK, PI3K/AKT/mTOR, and Rho/ROCK/LIMK2/cofilin pathways are summarized. Additionally, the field of metabolomics holds potential for uncovering metabolic signatures associated with specific RASopathies, which are crucial for developing precision medicine. Beyond molecular markers, we also examine the role of histological characteristics and non-invasive physiological assessments in identifying potential biomarkers, as they provide evidence of the disease’s effects on various systems. Here, we synthesize key findings and illuminate promising avenues for future research in RASopathy biomarker discovery, underscoring rigorous validation and clinical translation. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Figure 1

20 pages, 1047 KiB

Open AccessReview

Obesity-Related Ciliopathies: Focus on Advances of Biomarkers

by Qianwen Zhang, Yiguo Huang, Shiyang Gao, Yu Ding, Hao Zhang, Guoying Chang and Xiumin Wang

Int. J. Mol. Sci. 2024, 25(15), 8484; https://doi.org/10.3390/ijms25158484 - 3 Aug 2024

Viewed by 978

Abstract

Obesity-related ciliopathies, as a group of ciliopathies including Alström Syndrome and Bardet–Biedl Syndrome, exhibit distinct genetic and phenotypic variability. The understanding of these diseases is highly significant for understanding the functions of primary cilia in the human body, particularly regarding the relationship between obesity and primary cilia. The diagnosis of these diseases primarily relies on clinical presentation and genetic testing. However, there is a significant lack of research on biomarkers to elucidate the variability in clinical manifestations, disease progression, prognosis, and treatment responses. Through an extensive literature review, the paper focuses on obesity-related ciliopathies, reviewing the advancements in the field and highlighting the potential roles of biomarkers in the clinical presentation, diagnosis, and prognosis of these diseases. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Figure 1

12 pages, 1629 KiB

Open AccessReview

The Role of MicroRNAs in Progressive Supranuclear Palsy—A Systematic Review

by Aleksandra Ćwiklińska, Grzegorz Procyk, Dariusz Koziorowski and Stanisław Szlufik

Int. J. Mol. Sci. 2024, 25(15), 8243; https://doi.org/10.3390/ijms25158243 - 28 Jul 2024

Viewed by 1019

Abstract

Progressive supranuclear palsy (PSP) is a rare, neurodegenerative movement disorder. Together with multiple system atrophy (MSA), Dementia with Lewy bodies (DLB), and corticobasal degeneration (CBD), PSP forms a group of atypical parkinsonisms. The latest diagnostic criteria, published in 2017 by the Movement Disorders Society, classify PSP diagnosis into defined, probable, and possible categories based on clinical examination. However, no single test is specific and sensitive for this disease. Microribonucleic acids (miRNAs) are promising molecules, particularly in the case of diseases that lack appropriate diagnostic and treatment tools, which supports exploring their role in PSP. We aimed to systematically review the current knowledge about the role of miRNAs in PSP. This study was registered in the Open Science Framework Registry, and the protocol is available online. Primary original studies, both clinical and preclinical, written in English and assessing miRNAs in PSP were included. Systematic reviews, meta-analyses, reviews, case reports, letters to editors, commentaries, conference abstracts, guidelines/statements, expert opinions, preprints, and book chapters were excluded. The following five databases were searched: Embase, Medline Ultimate, PubMed, Scopus, and Web of Science. Each database was last searched on 18 June 2024. Eventually, nine original studies relevant to the discussed area were included. The risk of bias was not assessed. The selected research suggests that miRNAs may be considered promising biomarkers in PSP. However, the exact involvement of miRNAs in the pathogenesis of PSP is still to be determined. Several microRNAs were found to be dysregulated in patients with PSP. This applies to both brain tissue and fluids like cerebrospinal fluid CSF or blood. Several miRNAs were found that could potentially be helpful in differentiating among PSP patients, PD patients, and healthy individuals. Although some correlations and alterations have already been found, this field requires much more research. MicroRNAs are exciting and promising small molecules, and their investigation into many diseases, including PSP, may lead to significant discoveries. Full article

(This article belongs to the Special Issue Advances in Rare Diseases Biomarkers)

► Show Figures

Journal Menu

Journal Browser

Advances in Rare Diseases Biomarkers

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (10 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI