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Molecular Genetics and Biological Mechanism of Upper Gastrointestinal Diseases
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Molecular Genetics and Biological Mechanism of Upper Gastrointestinal Diseases

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

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 12966

Special Issue Editors

Prof. Dr. Ines Gockel

E-Mail Website
Guest Editor
Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
Interests: moleculargenetic analyses of upper gastrointestinal diseases;esophageal and gastric cancer; intraoperative imaging (hyperspectral imaging and ICG); robotics;minimally invasive visceral surgery
Special Issues, Collections and Topics in MDPI journals
Dr. Johannes Schumacher

E-Mail Website
Guest Editor
Institute of Human Genetics, University Hospital of Marburg, Marburg, Germany
Interests: schizophrenia; bipolar disorder; genome-wide association study
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Moleculargenetic decryptions of upper gastrointestinal disorders have evolved to an emerging field with increasing attention. This holds for benign and malignant diseases and also far beyond prediction and prevention. Extensive and holistic analyses of the moleculargenetic background in multifactorial upper gastrointestinal diseases, including genetic germline risk variants and somatic mutations, as well as corresponding functional consequences—although still developing and in progress—have already led to a relevant rise in our current understanding. This new knowledge has the ability of early prediction and the possibility of developing targeted therapies, as well as the identification of genetic profiles to predict drug resistance.

In this Special Issue of IJMS, we are presenting the state-of-the-art of moleculargenetic and biological aspects of upper gastrointestinal diseases by internationally prominent and renowned authors.

Prof. Dr. Ines Gockel
Dr. Johannes Schumacher
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.

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Keywords

  • molecular genetic analyses of upper gastrointestinal diseases
  • esophageal cancer
  • squamous cell carcinoma of the esophagus
  • Barrett’s adenocarcinoma
  • achalasia
  • GERD (gastroesophageal reflux disease)
  • gastric cancer
  • molecular subtypes of esophageal and gastric cancer
  • multifactorial upper gastrointestinal diseases
  • somatic mutations

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Related Special Issue

Published Papers (4 papers)

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Research

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14 pages, 1914 KiB  
Article
TP53 Targeted Deep Sequencing of Cell-Free DNA in Esophageal Squamous Cell Carcinoma Using Low-Quality Serum: Concordance with Tumor Mutation
by Dariush Nasrollahzadeh, Gholamreza Roshandel, Tiffany Myriam Delhomme, Patrice Hodonou Avogbe, Matthieu Foll, Farrokh Saidi, Hossein Poustchi, Masoud Sotoudeh, Reza Malekzadeh, Paul Brennan, James Mckay, Pierre Hainaut and Behnoush Abedi-Ardekani
Int. J. Mol. Sci. 2021, 22(11), 5627; https://doi.org/10.3390/ijms22115627 - 26 May 2021
Cited by 7 | Viewed by 3355
Abstract
Circulating cell-free DNA (cfDNA) is emerging as a potential tumor biomarker. CfDNA-based biomarkers may be applicable in tumors without an available non-invasive screening method among at-risk populations. Esophageal squamous cell carcinoma (ESCC) and residents of the Asian cancer belt are examples of those [...] Read more.
Circulating cell-free DNA (cfDNA) is emerging as a potential tumor biomarker. CfDNA-based biomarkers may be applicable in tumors without an available non-invasive screening method among at-risk populations. Esophageal squamous cell carcinoma (ESCC) and residents of the Asian cancer belt are examples of those malignancies and populations. Previous epidemiological studies using cfDNA have pointed to the need for high volumes of good quality plasma (i.e., >1 mL plasma with 0 or 1 cycles of freeze-thaw) rather than archival serum, which is often the main available source of cfDNA in retrospective studies. Here, we have investigated the concordance of TP53 mutations in tumor tissue and cfDNA extracted from archival serum left-over from 42 cases and 39 matched controls (age, gender, residence) in a high-risk area of Northern Iran (Golestan). Deep sequencing of TP53 coding regions was complemented with a specialized variant caller (Needlestack). Overall, 23% to 31% of mutations were concordantly detected in tumor and serum cfDNA (based on two false discovery rate thresholds). Concordance was positively correlated with high cfDNA concentration, smoking history (p-value = 0.02) and mutations with a high potential of neoantigen formation (OR; 95%CI = 1.9 (1.11–3.29)), suggesting that tumor DNA release in the bloodstream might reflect the effects of immune and inflammatory context on tumor cell turnover. We identified TP53 mutations in five controls, one of whom was subsequently diagnosed with ESCC. Overall, the results showed that cfDNA mutations can be reliably identified by deep sequencing of archival serum, with a rate of success comparable to plasma. Nonetheless, 70% non-identifiable mutations among cancer patients and 12% mutation detection in controls are the main challenges in applying cfDNA to detect tumor-related variants when blindly targeting whole coding regions of the TP53 gene in ESCC. Full article
(This article belongs to the Special Issue Molecular Genetics and Biological Mechanism of Upper Gastrointestinal Diseases)
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17 pages, 10667 KiB  
Article
The Transition from Gastric Intestinal Metaplasia to Gastric Cancer Involves POPDC1 and POPDC3 Downregulation
by Rachel Gingold-Belfer, Gania Kessler-Icekson, Sara Morgenstern, Lea Rath-Wolfson, Romy Zemel, Doron Boltin, Zohar Levi and Michal Herman-Edelstein
Int. J. Mol. Sci. 2021, 22(10), 5359; https://doi.org/10.3390/ijms22105359 - 19 May 2021
Cited by 9 | Viewed by 2958
Abstract
Intestinal metaplasia (IM) is an intermediate step in the progression from premalignant to malignant stages of gastric cancer (GC). The Popeye domain containing (POPDC) gene family encodes three transmembrane proteins, POPDC1, POPDC2, and POPDC3, initially described in muscles and later in [...] Read more.
Intestinal metaplasia (IM) is an intermediate step in the progression from premalignant to malignant stages of gastric cancer (GC). The Popeye domain containing (POPDC) gene family encodes three transmembrane proteins, POPDC1, POPDC2, and POPDC3, initially described in muscles and later in epithelial and other cells, where they function in cell–cell interaction, and cell migration. POPDC1 and POPDC3 downregulation was described in several tumors, including colon and gastric cancers. We questioned whether IM-to-GC transition involves POPDC gene dysregulation. Gastric endoscopic biopsies of normal, IM, and GC patients were examined for expression levels of POPDC1-3 and several suggested IM biomarkers, using immunohistochemistry and qPCR. Immunostaining indicated lower POPDC1 and POPDC3 labeling in IM compared with normal tissues. Significantly lower POPDC1 and POPDC3 mRNA levels were measured in IM and GC biopsies and in GC-derived cell lines. The reduction in focal IM was smaller than in extensive IM that resembled GC tissues. POPDC1 and POPDC3 transcript levels were highly correlated with each other and inversely correlated with LGR5, OLFM4, CDX2, and several mucin transcripts. The association of POPDC1 and POPDC3 downregulation with IM-to-GC transition implicates a role in tumor suppression and highlights them as potential biomarkers for GC progression and prospective treatment targets. Full article
(This article belongs to the Special Issue Molecular Genetics and Biological Mechanism of Upper Gastrointestinal Diseases)
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11 pages, 1622 KiB  
Article
MicroRNA Expression Profiles in Superficial Esophageal Squamous Cell Carcinoma before Endoscopic Submucosal Dissection: A Pilot Study
by Shintaro Fujihara, Hideki Kobara, Noriko Nishiyama, Kayo Hirose, Hisakazu Iwama and Tsutomu Masaki
Int. J. Mol. Sci. 2021, 22(9), 4789; https://doi.org/10.3390/ijms22094789 - 30 Apr 2021
Cited by 9 | Viewed by 2108
Abstract
Esophageal squamous cell carcinoma (ESCC) has a poor prognosis when diagnosed at an advanced stage, and early detection and treatment are essential to improve survival. However, intraobserver and interobserver variation make the diagnosis of superficial ESCC difficult, and suitable biomarkers are urgently needed. [...] Read more.
Esophageal squamous cell carcinoma (ESCC) has a poor prognosis when diagnosed at an advanced stage, and early detection and treatment are essential to improve survival. However, intraobserver and interobserver variation make the diagnosis of superficial ESCC difficult, and suitable biomarkers are urgently needed. Here, we compared the microRNA (miRNA) expression profiles of superficial ESCC tissues and adjacent normal tissues obtained immediately before esophageal endoscopic submucosal dissection. We found that ESCC and normal tissues differed in their miRNA expression profiles. In particular, miR-21-5p and miR-146b-5p were significantly upregulated and miR-210-3p was significantly downregulated in tumor tissues compared with normal tissues. We also detected significant associations between miRNA expression and ESCC invasion depth and lymphovascular invasion. The same differential expression of miR-21-5p, miR-146b-5p, and miR-210-3p was detected in ESCC cell lines compared with normal esophageal epithelial cells in vitro. However, transfection of ESCC cells with miR-210-3p and miR-21-5p mimics or inhibitors had partial effects on cell proliferation and invasion in vitro. These results indicate that miRNA expression is significantly deregulated in superficial ESCC, and suggest that the potential contribution of differentially expressed miRNAs to the malignant phenotype should be further investigated. Full article
(This article belongs to the Special Issue Molecular Genetics and Biological Mechanism of Upper Gastrointestinal Diseases)
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Review

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23 pages, 1738 KiB  
Review
Overview of Epstein–Barr-Virus-Associated Gastric Cancer Correlated with Prognostic Classification and Development of Therapeutic Options
by Valli De Re, Giulia Brisotto, Ombretta Repetto, Mariangela De Zorzi, Laura Caggiari, Stefania Zanussi, Lara Alessandrini, Vincenzo Canzonieri, Gianmaria Miolo, Fabio Puglisi, Claudio Belluco, Agostino Steffan and Renato Cannizzaro
Int. J. Mol. Sci. 2020, 21(24), 9400; https://doi.org/10.3390/ijms21249400 - 10 Dec 2020
Cited by 19 | Viewed by 3622
Abstract
Gastric cancer (GC) is a deadly disease with poor prognosis that is characterized by heterogeneity. New classifications based on histologic features, genotypes, and molecular phenotypes, for example, the Cancer Genome Atlas subtypes and those by the Asian Cancer Research Group, help understand the [...] Read more.
Gastric cancer (GC) is a deadly disease with poor prognosis that is characterized by heterogeneity. New classifications based on histologic features, genotypes, and molecular phenotypes, for example, the Cancer Genome Atlas subtypes and those by the Asian Cancer Research Group, help understand the carcinogenic differences in GC and have led to the identification of an Epstein–Barr virus (EBV)-related GC subtype (EBVaGC), providing new indications for tailored treatment and prognostic factors. This article provides a review of the features of EBVaGC and an update on the latest insights from EBV-related research with a particular focus on the strict interaction between EBV infection and the gastric tumor environment, including the host immune response. This information may help increase our knowledge of EBVaGC pathogenesis and the mechanisms that sustain the immune response of patients since this mechanism has been demonstrated to offer a survival advantage in a proportion of patients with GC. Full article
(This article belongs to the Special Issue Molecular Genetics and Biological Mechanism of Upper Gastrointestinal Diseases)
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