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Genetic Analyses of Immune Genes in Human and Animals
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Genetic Analyses of Immune Genes in Human and Animals

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (25 May 2023) | Viewed by 6777

Special Issue Editors

Dr. Hisham Atan Edinur

E-Mail Website
Guest Editor
School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
Interests: immunogenetics; population genetics; ancestry; wildlife DNA forensics
Dr. Nor Fazila Che Mat

E-Mail Website
Guest Editor
School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
Interests: immunology; virology; cancer; natural products

Special Issue Information

Dear Colleagues,

The genetics of immunity is being studied using a wide variety of approaches and organisms, including humans and animals. In recent times, considerable efforts have been devoted to understanding how immune genes perceive and decode various pathways of diseases using advanced molecular biology techniques. This includes the understanding of immune system pathways and responses, diagnosis of diseases, and identification of variants associated with disease pathogenesis. Molecular biology techniques such as the well-established Sanger sequencing and next generation sequencing are also extensively used for studying immune genes (e.g., killer cell immunoglobulin-like receptors, cytokines and human leukocyte antigens) in animals and have been shown to associate with disease susceptibility and reproductive fitness in animals. This Special Issue in Genes on “Genetic Analyses of Immune Genes in Humans and Animals” will highlight the latest immunogenetic research in humans and animals, with a special focus on but not limited to health, conservation, and ancestry. In this Special Issue, we will provide a snapshot of current research activities aiming to gain a better understanding of the role of immune genes in health and diseases.

Dr. Hisham Atan Edinur
Dr. Nor Fazila Che Mat
Guest Editors

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Keywords

  • immune genes
  • health
  • immunogenetics
  • wildlife DNA analysis
  • conservation

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Published Papers (3 papers)

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Research

20 pages, 903 KiB  
Article
Prognostic Role of Human Leukocyte Antigen Alleles and Cytokine Single-Nucleotide Polymorphisms in Patients with Chronic Myeloid Leukemia Treated with Tyrosine Kinase Inhibitor Drugs
by Samuel Kinde Birru, Ilias Doxiadis, Rawleigh Howe, Tsehayneh Kelemu, Saifu Hailu Chala, Abdulaziz Sherif, Fisihatsion Tadesse, Aster Tsegaye, Amha Gebremedhin and Claudia Lehmann
Genes 2024, 15(6), 732; https://doi.org/10.3390/genes15060732 - 2 Jun 2024
Viewed by 1744
Abstract
Tyrosine kinase inhibitor (TKI) drugs have significantly improved chronic myeloid leukemia (CML) outcomes. Neopeptides from CML cells may induce specific immune responses, which are crucial for deep molecular (DMR) and treatment-free remission (TFR). In this study of Ethiopian patients with CML (n = [...] Read more.
Tyrosine kinase inhibitor (TKI) drugs have significantly improved chronic myeloid leukemia (CML) outcomes. Neopeptides from CML cells may induce specific immune responses, which are crucial for deep molecular (DMR) and treatment-free remission (TFR). In this study of Ethiopian patients with CML (n = 162), the HLA alleles and single-nucleotide polymorphisms of five cytokines revealed significant associations with clinical outcomes. Clinically unfavorable outcomes correlated with HLA alleles A*03:01/02, A*23:17:01, B*57:01/02/03, and HLA-DRB4*01:01 (p-value = 0.0347, p-value = 0.0285, p-value = 0.037, and p-value = 0.0127, respectively), while HLA-DRB4*01:03:01 was associated with favorable outcomes (p-value = 0.0058). After assigning values for the ‘low’, ‘intermediate’, and ‘high’ gene expression of the SNPs’ respective cytokine genes, Kaplan–Meier estimates for relapse-free survival, adjusted for age, treatment duration, and relapse risk among patients after the administration of TKIs, indicated that a gene expression ratio above the overall median of TNF-α, IL-6, and the combination of TGF-β1/IL-10, IFNγ, and IL-6/IL-10 TGF-β1 was correlated with a higher likelihood of treatment failure ((RR: 3.01; 95% CI: 1.1–8.3; p-value = 0.0261) and (RR: 2.4; 95% CI: 1.1–5.2; p-value = 0.022), respectively). Multi-SNPs, surpassing single-SNPs, and HLA allele polymorphisms showed promise in predicting outcomes of patients with CML during TKI treatment, prompting further exploration into their potential utility. Full article
(This article belongs to the Special Issue Genetic Analyses of Immune Genes in Human and Animals)
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13 pages, 1011 KiB  
Article
Analysis of the Origin of Emiratis as Inferred from a Family Study Based on HLA-A, -C, -B, -DRB1, and -DQB1 Genes
by Zain Al Yafei, Abdelhafidh Hajjej, Marion Alvares, Ayeda Al Mahri, Amre Nasr, Rajaa Mirghani, Ali Al Obaidli, Mohamed Al Seiari, Steven J. Mack, Medhat Askar, Hisham A. Edinur, Wassim Y. Almawi and Gehad ElGhazali
Genes 2023, 14(6), 1159; https://doi.org/10.3390/genes14061159 - 26 May 2023
Cited by 1 | Viewed by 2313
Abstract
In this study, we investigated HLA class I and class II allele and haplotype frequencies in Emiratis and compared them to those of Asian, Mediterranean, and Sub-Saharan African populations. Methods: Two-hundred unrelated Emirati parents of patients selected for bone marrow transplantation were genotyped [...] Read more.
In this study, we investigated HLA class I and class II allele and haplotype frequencies in Emiratis and compared them to those of Asian, Mediterranean, and Sub-Saharan African populations. Methods: Two-hundred unrelated Emirati parents of patients selected for bone marrow transplantation were genotyped for HLA class I (A, B, C) and class II (DRB1, DQB1) genes using reverse sequence specific oligonucleotide bead-based multiplexing. HLA haplotypes were assigned with certainty by segregation (pedigree) analysis, and haplotype frequencies were obtained by direct counting. HLA class I and class II frequencies in Emiratis were compared to data from other populations using standard genetic distances (SGD), Neighbor-Joining (NJ) phylogenetic dendrograms, and correspondence analysis. Results: The studied HLA loci were in Hardy–Weinberg Equilibrium. We identified 17 HLA-A, 28 HLA-B, 14 HLA-C, 13 HLA-DRB1, and 5 HLA-DQB1 alleles, of which HLA-A*02 (22.2%), -B*51 (19.5%), -C*07 (20.0%), -DRB1*03 (22.2%), and -DQB1*02 (32.8%) were the most frequent allele lineages. DRB1*03~DQB1*02 (21.2%), DRB1*16~DQB1*05 (17.3%), B*35~C*04 (11.7%), B*08~DRB1*03 (9.7%), A*02~B*51 (7.5%), and A*26~C*07~B*08~DRB1*03~DQB1*02 (4.2%) were the most frequent two- and five-locus HLA haplotypes. Correspondence analysis and dendrograms showed that Emiratis were clustered with the Arabian Peninsula populations (Saudis, Omanis and Kuwaitis), West Mediterranean populations (North Africans, Iberians) and Pakistanis, but were distant from East Mediterranean (Turks, Albanians, Greek), Levantine (Syrians, Palestinians, Lebanese), Iranian, Iraqi Kurdish, and Sub-Saharan populations. Conclusions: Emiratis were closely related to Arabian Peninsula populations, West Mediterranean populations and Pakistanis. However, the contribution of East Mediterranean, Levantine Arab, Iranian, and Sub-Saharan populations to the Emiratis’ gene pool appears to be minor. Full article
(This article belongs to the Special Issue Genetic Analyses of Immune Genes in Human and Animals)
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14 pages, 6456 KiB  
Article
RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury
by Jing Zhang, Zhihui Xue, Qingbo Zhao, Keke Zhang, Ao Zhou, Liangyu Shi and Yulan Liu
Genes 2023, 14(4), 945; https://doi.org/10.3390/genes14040945 - 20 Apr 2023
Viewed by 2194
Abstract
We assessed differentially expressed (DE) mRNAs and lncRNAs in the liver of septic pigs to explore the key factors regulating lipopolysaccharide (LPS)-induced liver injury. We identified 543 DE lncRNAs and 3642 DE mRNAs responsive to LPS. Functional enrichment analysis revealed the DE mRNAs [...] Read more.
We assessed differentially expressed (DE) mRNAs and lncRNAs in the liver of septic pigs to explore the key factors regulating lipopolysaccharide (LPS)-induced liver injury. We identified 543 DE lncRNAs and 3642 DE mRNAs responsive to LPS. Functional enrichment analysis revealed the DE mRNAs were involved in liver metabolism and other pathways related to inflammation and apoptosis. We also found significantly upregulated endoplasmic reticulum stress (ERS)-associated genes, including the receptor protein kinase receptor-like endoplasmic reticulum kinase (PERK), the eukaryotic translation initiation factor 2α (EIF2S1), the transcription factor C/EBP homologous protein (CHOP), and activating transcription factor 4 (ATF4). In addition, we predicted 247 differentially expressed target genes (DETG) of DE lncRNAs. The analysis of protein-protein interactions (PPI) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway detected key DETGs that are involved in metabolic pathways, such as N-Acetylgalactosaminyltransferase 2 (GALNT2), argininosuccinate synthetase 1 (ASS1), and fructose 1,6-bisphosphatase 1 (FBP1). LNC_003307 was the most abundant DE lncRNA in the pig liver, with a marked upregulation of >10-fold after LPS stimulation. We identified three transcripts for this gene using the rapid amplification of the cDNA ends (RACE) technique and obtained the shortest transcript sequence. This gene likely derives from the nicotinamide N-methyltransferase (NNMT) gene in pigs. According to the identified DETGs of LNC_003307, we hypothesize that this gene regulates inflammation and endoplasmic reticulum stress in LPS-induced liver damage in pigs. This study provides a transcriptomic reference for further understanding of the regulatory mechanisms underlying septic hepatic injury. Full article
(This article belongs to the Special Issue Genetic Analyses of Immune Genes in Human and Animals)
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