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New Breakthroughs in Molecular Diagnostic Tools for Human Diseases
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New Breakthroughs in Molecular Diagnostic Tools for Human Diseases

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: 20 July 2025 | Viewed by 7060

Special Issue Editors

Prof. Dr. Vittorio Fineschi

E-Mail Website
Guest Editor
Department of Anatomical, Histological, Forensic and Orthopaedic Sciences, Sapienza University of Rome, Viale Regina Elena 336, 00161 Rome, Italy
Interests: forensic pathology; sudden cardiac death; molecular mechanisms; traumatic brain injury & oxidative stress; immunohistochemistry; drugs of abuse; oxidative stress; maternal mortality; miRNA; forensic pathologies
Special Issues, Collections and Topics in MDPI journals
Dr. Aniello Maiese

E-Mail Website
Guest Editor
Department of Surgical Pathology, Medical, Molecular and Critical Area, Institute of Legal Medicine, University of Pisa, 56126 Pisa, Italy
Interests: forensic pathology; autopsy; histology; immunohistochemistry; miRNAs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Major technological advances have made diagnostics much more accurate, particularly in light of genetic and proteomic developments. Despite laboratory development, the clinical autopsies and diagnoses of the cause of death remain a multidisciplinary approach requiring the use of technology and scientific knowledge with irreplaceable human input. Currently, the decisive genetic causality in many cardiovascular, neoplastic, and metabolic diseases is known. Naturally occurring cardiac deaths share complex features such as incomplete penetrance and molecularly variable expressivity; moreover, upon macro/microscopic evaluation, they are not easy to diagnose as they sometimes present nonspecific pictures. Multiple abnormalities in genes related to both potassium and cardiac sodium channels are involved in many cases of sudden cardiac death. Proteomic studies are therefore likely to provide new insights into the cellular mechanisms involved in organ dysfunction and may also provide new diagnostics for many diseases and for sudden cardiac death. The proteomic investigations of diseases have identified candidate proteins altered with pathologic states, therefore complementing the traditional biochemical observations of the past. Advanced laboratory techniques can be utilized to develop molecular diagnostic tools that calibrate technology selections against diagnostic hypotheses, and specific ancillary methods to support and confirm diagnosis can be utilized. With this in mind, this Special Issue aims to promote a debate on the contribution of genetic, epigenetic, and technological methods through the sharing of the current development status of molecular diagnostic tools. We encourage the establishment of Hospital Mortality Review Committees for a systematic proactive approach to the continuous improvement of the safety of care and the quality of care. The outlined survey includes methodologies extended to further centers with the aim of placing greater weight on the results obtained by ensuring their influence in health policy planning. In this Special Issue on “New Breakthroughs in Molecular Diagnostic Tools for Human Diseases”, we invite front-line researchers, pathologists, and investigators to submit original research and review articles regarding topics that include, but are not limited to, the following:

  • molecular pathology;
  • molecular diagnostics;
  • genetics;
  • epigenetics;
  • proteomics;
  • immunohistochemistry;
  • thrombo-embolic disease;
  • sudden cardiac death;
  • the molecular pathology of traumatic injuries;
  • hypoxic–ischemic brain damage;
  • the experimental models of injury and diseases;
  • the targeted therapy of injuries and diseases;
  • drug abuse;
  • histological diagnosis;
  • the epigenetics of organs injuries;
  • miRNA and the prognosis of diseases;
  • novel approaches and proofs of principle in therapy.

Prof. Dr. Vittorio Fineschi
Dr. Aniello Maiese
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

  • molecular pathology
  • molecular diagnostics
  • genetics
  • epigenetics
  • proteomics
  • immunohistochemistry
  • thrombo-embolic disease
  • sudden cardiac death
  • molecular pathology of traumatic injuries
  • hypoxic–ischemic brain damage
  • experimental models of injury and diseases
  • targeted therapy of injuries and diseases
  • drug abuse
  • histological diagnosis
  • epigenetics of organs injuries
  • miRNA and prognosis of diseases
  • novel approaches and proofs of principle in therapy

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Published Papers (5 papers)

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Research

11 pages, 2086 KiB  
Communication
Evaluation of Apoptotic Caspase-3 Immunopositivity in Human Model of Asphyxial Death
by Fabio Del Duca, Michele Treglia, Raffaele La Russa, Stefania De Simone, Luigi Cipolloni, Aniello Maiese and Paola Frati
Int. J. Mol. Sci. 2025, 26(7), 3317; https://doi.org/10.3390/ijms26073317 - 2 Apr 2025
Viewed by 311
Abstract
The pathological mechanisms underlying the ligature mark in hanging involve the skin layers and an ischemic mechanism. The apoptotic process develops whenever ischemic mechanisms affect the dermal and epidermal layers. Effector caspase-3 appears to play a crucial role in both acute and chronic [...] Read more.
The pathological mechanisms underlying the ligature mark in hanging involve the skin layers and an ischemic mechanism. The apoptotic process develops whenever ischemic mechanisms affect the dermal and epidermal layers. Effector caspase-3 appears to play a crucial role in both acute and chronic pressure-induced skin ischemia. The aim of this study is to identify the role of caspase-3 as a marker of supravitality in the diagnosis of premortem hanging. Skin samples from ligature marks in hanging cases were collected to investigate this apoptotic process. The caspase-3 levels in compressed skin were significantly higher compared to those found in healthy skin (p < 0.005). The apoptotic process in ischemic epidermal cells begins with stable mechanical stress, as seen in the hanging model. Caspase-3 expression seems to vary from minutes after the initial stress input. Caspase-3 activation is an ATP-dependent process and can only occur if the victim was alive before the pressure was applied. Caspase-3 is a reliable marker of supravitality in ligature marks in premortem hanging cases. Full article
(This article belongs to the Special Issue New Breakthroughs in Molecular Diagnostic Tools for Human Diseases)
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10 pages, 819 KiB  
Article
Quantitative Analysis of Pseudogene-Associated Errors During Germline Variant Calling
by Artem Podvalnyi, Arina Kopernik, Mariia Sayganova, Mary Woroncow, Gauhar Zobkova, Anna Smirnova, Anton Esibov, Andrey Deviatkin, Pavel Volchkov and Eugene Albert
Int. J. Mol. Sci. 2025, 26(1), 363; https://doi.org/10.3390/ijms26010363 - 3 Jan 2025
Viewed by 1141
Abstract
A pseudogene is a non-functional copy of a protein-coding gene. Processed pseudogenes, which are created by the reverse transcription of mRNA and subsequent integration of the resulting cDNA into the genome, being a major pseudogene class, represent a significant challenge in genome analysis [...] Read more.
A pseudogene is a non-functional copy of a protein-coding gene. Processed pseudogenes, which are created by the reverse transcription of mRNA and subsequent integration of the resulting cDNA into the genome, being a major pseudogene class, represent a significant challenge in genome analysis due to their high sequence similarity to the parent genes and their frequent absence in the reference genome. This homology can lead to errors in variant identification, as sequences derived from processed pseudogenes can be incorrectly assigned to parental genes, complicating correct variant calling. In this study, we quantified the occurrence of variant calling errors associated with pseudogenes, generated by the most popular germline variant callers, namely GATK-HC, DRAGEN, and DeepVariant, when analysing 30x human whole-genome sequencing data (n = 13,307). The results show that the presence of pseudogenes can interfere with variant calling, leading to false positive identifications of potentially clinically relevant variants. Compared to other approaches, DeepVariant was the most effective in correcting these errors. Full article
(This article belongs to the Special Issue New Breakthroughs in Molecular Diagnostic Tools for Human Diseases)
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17 pages, 982 KiB  
Article
Proteomic Analysis of Follicular Fluid in Polycystic Ovary Syndrome: Insights into Protein Composition and Metabolic Pathway Alterations
by Janusz Przewocki, Adam Łukaszuk, Grzegorz Jakiel, Izabela Wocławek-Potocka, Karolina Kłosińska, Jolanta Olszewska and Krzysztof Łukaszuk
Int. J. Mol. Sci. 2024, 25(21), 11749; https://doi.org/10.3390/ijms252111749 - 1 Nov 2024
Viewed by 1543
Abstract
This study explores the proteomic composition of follicular fluid (FF) from women undergoing oocyte retrieval for in vitro fertilisation (IVF), with a focus on the effects of polycystic ovary syndrome (PCOS). FF samples were collected from 74 patients, including 34 with PCOS and [...] Read more.
This study explores the proteomic composition of follicular fluid (FF) from women undergoing oocyte retrieval for in vitro fertilisation (IVF), with a focus on the effects of polycystic ovary syndrome (PCOS). FF samples were collected from 74 patients, including 34 with PCOS and 40 oocyte donors. Proteomic profiling using machine learning identified significant differences in protein abundance between the PCOS and control groups. Of the 484 quantified proteins, 20 showed significantly altered levels in the PCOS group. Functional annotation and pathway enrichment analysis pointed to the involvement of protease inhibitors and immune-related proteins in the pathophysiology of PCOS, suggesting that inflammation and immune dysregulation may play a key role. Additionally, HDL assembly was identified as a significant pathway, with apolipoprotein-AI (APOA1) and alpha-2-macroglobulin (A2M) as the major proteins involved. Notably, myosin light polypeptide 6 was the most downregulated protein, showing the highest absolute fold change, and may serve as a novel independent biomarker for PCOS. Full article
(This article belongs to the Special Issue New Breakthroughs in Molecular Diagnostic Tools for Human Diseases)
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22 pages, 2270 KiB  
Article
Analysis of miRNA Expression Profiles in Traumatic Brain Injury (TBI) and Their Correlation with Survival and Severity of Injury
by Francesca Consalvo, Martina Padovano, Matteo Scopetti, Donato Morena, Luigi Cipolloni, Vittorio Fineschi and Alessandro Santurro
Int. J. Mol. Sci. 2024, 25(17), 9539; https://doi.org/10.3390/ijms25179539 - 2 Sep 2024
Cited by 2 | Viewed by 1505
Abstract
Traumatic brain injury (TBI) is the leading cause of traumatic death worldwide and is a public health problem associated with high mortality and morbidity rates, with a significant socioeconomic burden. The diagnosis of brain injury may be difficult in some cases or may [...] Read more.
Traumatic brain injury (TBI) is the leading cause of traumatic death worldwide and is a public health problem associated with high mortality and morbidity rates, with a significant socioeconomic burden. The diagnosis of brain injury may be difficult in some cases or may leave diagnostic doubts, especially in mild trauma with insignificant pathological brain changes or in cases where instrumental tests are negative. Therefore, in recent years, an important area of research has been directed towards the study of new biomarkers, such as micro-RNAs (miRNAs), which can assist clinicians in the diagnosis, staging, and prognostic evaluation of TBI, as well as forensic pathologists in the assessment of TBI and in the estimation of additional relevant data, such as survival time. The aim of this study is to investigate the expression profiles (down- and upregulation) of a panel of miRNAs in subjects deceased with TBI in order to assess, verify, and define the role played by non-coding RNA molecules in the different pathophysiological mechanisms of brain damage. This study also aims to correlate the detected expression profiles with survival time, defined as the time elapsed between the traumatic event and death, and with the severity of the trauma. This study was conducted on 40 cases of subjects deceased with TBI (study group) and 10 cases of subjects deceased suddenly from non-traumatic causes (control group). The study group was stratified according to the survival time and the severity of the trauma. The selection of miRNAs to be examined was based on a thorough literature review. Analyses were performed on formalin-fixed, paraffin-embedded (FFPE) brain tissue samples, with a first step of total RNA extraction and a second step of quantification of the selected miRNAs of interest. This study showed higher expression levels in cases compared to controls for miR-16, miR-21, miR-130a, and miR-155. In contrast, lower expression levels were found in cases compared to controls for miR-23a-3p. There were no statistically significant differences in the expression levels between cases and controls for miR-19a. In cases with short survival, the expression levels of miR-16-5p and miR-21-5p were significantly higher. In cases with long survival, miR-21-5p was significantly lower. The expression levels of miR-130a were significantly higher in TBI cases with short and middle survival. In relation to TBI severity, miR-16-5p and miR-21-5p expression levels were significantly higher in the critical–fatal TBI subgroup. Conclusions: This study provides evidence for the potential of the investigated miRNAs as predictive biomarkers to discriminate between TBI cases and controls. These miRNAs could improve the postmortem diagnosis of TBI and also offer the possibility to define the survival time and the severity of the trauma. The analysis of miRNAs could become a key tool in forensic investigations, providing more precise and detailed information on the nature and extent of TBI and helping to define the circumstances of death. Full article
(This article belongs to the Special Issue New Breakthroughs in Molecular Diagnostic Tools for Human Diseases)
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16 pages, 4642 KiB  
Article
Usefulness and Limitations of PFGE Diagnosis and Nucleotide Sequencing Method in the Analysis of Food Poisoning Pathogens Found in Cooking Employees
by Mi-Na Park, Sang-Gu Yeo, Junhyuk Park, Yoomi Jung and Se-Min Hwang
Int. J. Mol. Sci. 2024, 25(7), 4123; https://doi.org/10.3390/ijms25074123 - 8 Apr 2024
Cited by 1 | Viewed by 1880
Abstract
In the case of a food poisoning outbreak, it is essential to understand the relationship between cooking workers and food poisoning. Many biological diagnostic methods have recently been developed to detect food poisoning pathogens. Among these diagnostic tools, this study presents PCR-based pulsed-field [...] Read more.
In the case of a food poisoning outbreak, it is essential to understand the relationship between cooking workers and food poisoning. Many biological diagnostic methods have recently been developed to detect food poisoning pathogens. Among these diagnostic tools, this study presents PCR-based pulsed-field gel electrophoresis and nucleotide sequencing diagnostic analysis results for diagnosing food poisoning outbreaks associated with cooking employees in Chungcheongnam-do, Republic of Korea. Pulsed-field gel electrophoresis was useful in identifying the food poisoning outbreaks caused by Staphylococcus aureus and Enteropathogenic Escherichia coli. In the case of Norovirus, nucleotide sequencing was used to identify the relationship between cooking workers and the food poisoning outbreak. However, it is difficult to determine whether cooking employees directly caused the food poisoning outbreaks based on these molecular biological diagnostic results alone. A system is needed to integrate epidemiological and diagnostic information to identify a direct correlation between the food poisoning outbreak and cooking employees. Full article
(This article belongs to the Special Issue New Breakthroughs in Molecular Diagnostic Tools for Human Diseases)
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