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Proteins and Mutations: Inherited Diseases, Drug Resistance and Pharmacogenomics

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

Deadline for manuscript submissions: 31 May 2024 | Viewed by 2309

Special Issue Editors

Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
Interests: structural bioinformatics and its applications to drug discovery
Pharmacogenomics and Drug Metabolism Research Group, Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
Interests: study of genomic variation as predictive or prognostic markers in the context of drug therapies

Special Issue Information

Dear Colleagues,

Genetic variations that result in changes in amino acids can have striking effects on proteins. These effects can lead to inherited diseases; cause drug resistance in both communicable and non-communicable diseases; and play an important role in pathogenicity and infectivity, among many other biological phenomena. Hence, deciphering the impact of mutations, particularly missense mutations, on protein structure and function would help to understand their effects, which would ultimately guide the design of safer and more effective therapies or the safer use of current treatments. In this context, this Special Issue aims to cover different aspects of mutations and their structural as well as functional effects on proteins, and welcomes contributions from, but not limited to, biochemical, computational, and structural studies in the form of original research articles or up-to-date reviews.

Prof. Dr. Ozlem Tastan Bishop
Prof. Dr. Carlo R. Largiadèr
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.

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Keywords

  • allostery
  • cancer
  • drug metabolism
  • drug resistance
  • drug and vaccine development
  • infectious diseases
  • missense mutations
  • pathogenicity
  • pharmacogenomics
  • rare diseases

Published Papers (2 papers)

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Research

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21 pages, 3369 KiB  
Article
An Activated Dendritic-Cell-Related Gene Signature Indicative of Disease Prognosis and Chemotherapy and Immunotherapy Response in Colon Cancer Patients
by Yiben Ouyang, Mingqian Yu, Tiange Liu, Mengying Suo, Jingyi Qiao, Liqiang Wang and Na Li
Int. J. Mol. Sci. 2023, 24(21), 15959; https://doi.org/10.3390/ijms242115959 - 03 Nov 2023
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Abstract
Accumulating evidence has underscored the prognostic value of tumor-infiltrating immune cells in the tumor microenvironment of colon cancer (CC). In this retrospective study, based on publicly available transcriptome profiles and clinical data from the Gene Expression Omnibus and The Cancer Genome Atlas databases, [...] Read more.
Accumulating evidence has underscored the prognostic value of tumor-infiltrating immune cells in the tumor microenvironment of colon cancer (CC). In this retrospective study, based on publicly available transcriptome profiles and clinical data from the Gene Expression Omnibus and The Cancer Genome Atlas databases, we derived and verified an activated dendritic cell (aDC)-related gene signature (aDCRS) for predicting the survival outcomes and chemotherapy and immunotherapy response of CC patients. We quantified the infiltration abundance of 22 immune cell subtypes via the “CIBERSORT” R script. Univariate Cox proportional hazards (PHs) regression was used to identify aDC as the most robust protective cell type for CC prognosis. After selecting differentially expressed genes (DEGs) significantly correlated with aDC infiltration, we performed univariate Cox-PH regression, LASSO regression, and stepwise multivariate Cox-PH regression successively to screen out prognosis-related genes from selected DEGs for constructing the aDCRS. Receiver operating characteristic (ROC) curves and Kaplan–Meier (KM) analysis were employed to assess the discriminatory ability and risk-stratification capacity. The “oncoPredict” package, Cancer Treatment Response gene signature DataBase, and Tumor Immune Dysfunction and Exclusion algorithm were utilized to estimate the practicability of the aDCRS in predicting response to chemotherapy and immune checkpoint blockade. Gene set enrichment analysis and single-cell RNA sequencing analysis were also implemented. Furthermore, an aDCRS-based nomogram was constructed and validated via ROC curves, calibration plots and decision curve analysis. In conclusion, aDCRS and an aDCRS-based nomogram will facilitate precise prognosis prediction and individualized therapeutic interventions, thus improving the survival outcomes of CC patients in the future. Full article
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15 pages, 1937 KiB  
Review
Challenges of Diagnosing Mendelian Susceptibility to Mycobacterial Diseases in South Africa
by Denise Scholtz, Tracey Jooste, Marlo Möller, Ansia van Coller, Craig Kinnear and Brigitte Glanzmann
Int. J. Mol. Sci. 2023, 24(15), 12119; https://doi.org/10.3390/ijms241512119 - 28 Jul 2023
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Abstract
Inborn errors of immunity (IEI) are genetic disorders with extensive clinical presentations. They can range from increased susceptibility to infections to significant immune dysregulation that results in immune impairment. While IEI cases are individually rare, they collectively represent a significant burden of disease, [...] Read more.
Inborn errors of immunity (IEI) are genetic disorders with extensive clinical presentations. They can range from increased susceptibility to infections to significant immune dysregulation that results in immune impairment. While IEI cases are individually rare, they collectively represent a significant burden of disease, especially in developing countries such as South Africa, where infectious diseases like tuberculosis (TB) are endemic. This is particularly alarming considering that certain high penetrance mutations that cause IEI, such as Mendelian Susceptibility to Mycobacterial Disease (MSMD), put individuals at higher risk for developing TB and other mycobacterial diseases. MSMD patients in South Africa often present with different clinical phenotypes than those from the developed world, therefore complicating the identification of disease-associated variants in this setting with a high burden of infectious diseases. The lack of available data, limited resources, as well as variability in clinical phenotype are the reasons many MSMD cases remain undetected or misdiagnosed. This article highlights the challenges in diagnosing MSMD in South Africa and proposes the use of transcriptomic analysis as a means of potentially identifying dysregulated pathways in affected African populations. Full article
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