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Genomic Analysis of Common Disease, 2nd Edition
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Genomic Analysis of Common Disease, 2nd Edition

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Medicine".

Deadline for manuscript submissions: closed (31 August 2025) | Viewed by 5345

Special Issue Editor

Dr. Golder N. Wilson

E-Mail Website
Guest Editor
1. Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX, USA
2. KinderGenome Genetics Private Practice, 5347 W Mockingbird, Dallas, TX 75209, USA
Interests: genomics; syndromology; connective tissue dysplasias; Ehlers–Danlos syndrome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The ability of NextGen or massive parallel sequencing technology to screen all genes in the human genome for mutations is transforming the reductive one disease–one responsible gene paradigm to one of multifactorial (polygenic–environmental) causation. The multiple DNA changes defined by all-gene screening are particularly applicable to common diseases like intellectual disability (autism), diabetes, cardiomyopathy/arrhythmias, connective tissue dysplasias, and many cancers where changes in gene networks lead to spectra of disease. A combined genomic analysis of microarray and whole exome sequencing can define the respective duplication/deficiency of chromosome regions (copy number variants) and of gene sequence alterations (DNA sequence variants), the former being common in patients with intellectual disability (autism), and the latter being common in diseases affecting older children and adults. This Special Issue will begin with a brief introduction of genomics and an article contrasting its results when applied to patients with increased joint laxity (hypermobility). Patients with developmental disability and joint laxity from hypotonia of surrounding muscles will have a mixture of copy number and sequence variants, and those with laxity from dysplastic connective tissue in Ehlers–Danlos syndrome will have sequence variants in a different but overlapping network of genes. Accompanying articles that describe DNA results from genomic analysis of other common conditions ranging from cardiovascular diseases to cancer will be explored as well.

Dr. Golder N. Wilson
Guest Editor

Manuscript Submission Information

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Keywords

  • genomic analysis
  • microarray analysis
  • whole exome sequencing
  • pathogenic mutations
  • copy number variants
  • DNA sequence variation
  • intellectual disability
  • autism
  • connective tissue dysplasia

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Published Papers (6 papers)

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Editorial

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3 pages, 168 KB  
Editorial
Introduction to Special Issue: Genomic Analysis of Common Disease
by Golder N. Wilson
Curr. Issues Mol. Biol. 2025, 47(2), 112; https://doi.org/10.3390/cimb47020112 - 10 Feb 2025
Viewed by 755
Abstract
The development of NextGen or massive parallel sequencing [...] Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)

Research

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38 pages, 4420 KB  
Article
Uncovering the Tumorigenic Blueprint of PFOS and PFOA Through Multi-Organ Transcriptomic Analysis of Biomarkers, Mechanisms, and Therapeutic Targets
by Krisha Mathur, Aleezah Khaliq, Stephanie Park, Nathan Chu, Vaishnavi M. Burra, Norah Kanukolanu, Ellen Costello and Sivanesan Dakshanamurthy
Curr. Issues Mol. Biol. 2025, 47(9), 763; https://doi.org/10.3390/cimb47090763 - 15 Sep 2025
Viewed by 337
Abstract
Per- and polyfluoroalkyl substances (PFASs), called forever chemicals, persist in the environment and bioaccumulate, posing significant health risks. While epidemiological studies have linked exposure to specific PFAS types, perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS), to an increased incidence of various cancers, [...] Read more.
Per- and polyfluoroalkyl substances (PFASs), called forever chemicals, persist in the environment and bioaccumulate, posing significant health risks. While epidemiological studies have linked exposure to specific PFAS types, perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS), to an increased incidence of various cancers, specific tumorigenesis mechanisms are unknown. Here, we investigated the potential molecular markers and signatures of perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) tumorigenesis. We performed a comprehensive transcriptomic analysis across multiple species and tissue types (N = 529) using PFOS and PFOA-exposed RNA-Seq samples. Conserved signatures demonstrate significant disruptions in seven key carcinogenic characteristics including metabolic reprogramming, epigenetic modifications, immune suppression, oxidative stress, and genomic instability. Tumorigenic markers such as SERPINE1, FN1, PLIN2, ALDOA, TRIB3, and TSC22D3 and their associated pathways may act independently or synergistically to promote a pro-tumorigenic environment. Additionally, PPARα, LARP1, ACOX1, MYC, and MYCN were identified as key upstream regulators supporting disruptions in lipid metabolism, oxidative stress, and uncontrolled cell proliferation. In liver samples, low concentrations of PFOS and PFOA were sufficient to exhibit tumorigenic signatures associated with tumorigenesis initiation and development. Inferred mechanisms of ccRCC initiation and development were linked to lipid metabolism dysregulation and immunosuppressive signaling. In prostate and testicular xenograft tumor models, carcinogenic mechanisms for tumor progression and promotion were hypothesized. Receptor-mediated signaling and protein synthesis was disrupted in prostate cancer and epigenetic alterations and ECM remodeling observed in testicular cancer. We also explored potential therapeutic rescue strategies, including chemopreventive agents for early intervention. All our findings provide hypotheses for PFOS/PFOA-induced tumorigenesis; however, experimental studies are required to establish translational relevance. All the R codes developed in this study are publicly available. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)
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12 pages, 814 KB  
Article
TP53 IVS3 16 bp Variant and Breast Cancer Risk in Western Mexican Women: A Case–Control Study
by Mariana Araiza-Guzmán, Bricia M. Gutiérrez-Zepeda, Ana M. Saldaña-Cruz, Ingrid B. Montoya-Delgado, Diana Rubio-Delgado, Pablo Benítez-Villa, Diana M. Hernández-Corona, Adrian Daneri-Navarro, Alicia del Toro-Arreola, Jazmin Márquez-Pedroza, Antonio Quintero-Ramos and Betsabé Contreras-Haro
Curr. Issues Mol. Biol. 2025, 47(9), 744; https://doi.org/10.3390/cimb47090744 - 11 Sep 2025
Viewed by 272
Abstract
Background: Mutations in the TP53 gene can alter its tumor suppressor functions, thereby promoting oncogenic activity. The TP53 IVS3 16 bp genetic variant overlaps with nucleotide sequences that can alter regulatory structures, potentially affecting its function. The aim of the present study was [...] Read more.
Background: Mutations in the TP53 gene can alter its tumor suppressor functions, thereby promoting oncogenic activity. The TP53 IVS3 16 bp genetic variant overlaps with nucleotide sequences that can alter regulatory structures, potentially affecting its function. The aim of the present study was to evaluate the association between TP53 IVS3 16 bp genetic variant and the risk of breast cancer (BC) in women from western Mexico. Methods: The study included 220 women diagnosed with BC and 198 cancer-free controls. Clinical and demographic data were collected through structured questionnaires and verified with medical records. Genotyping of the TP53 IVS3 16 bp genetic variant was performed using polymerase chain reaction (PCR) and visualized on 6% polyacrylamide gels. Results: Compared to controls, women with BC more frequently reported a family history of the disease and menopausal status (p < 0.05). Genotypic analysis revealed that carriers of the D/I genotype and the combined D/I + I/I genotypes were associated with a reduced risk of BC in codominant (OR = 0.53; 95% CI 0.32–0.88) and dominant (OR = 0.57; 95% CI 0.35–0.93) models. Conclusions: The D/I and D/I + I/I genotypes in codominant and dominant models showed a lower risk against BC. More studies are needed to confirm these findings. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)
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12 pages, 1531 KB  
Article
Association of DROSHA Variants with Susceptibility and Outcomes in Childhood Acute Lymphoblastic Leukemia
by Ioannis Kyriakidis, Iordanis Pelagiadis, Charalampos Pontikoglou, Helen A. Papadaki and Eftichia Stiakaki
Curr. Issues Mol. Biol. 2025, 47(6), 473; https://doi.org/10.3390/cimb47060473 - 19 Jun 2025
Cited by 1 | Viewed by 606
Abstract
MicroRNAs are key regulators of lymphoid differentiation, exhibiting a pivotal role in acute lymphoblastic leukemia (ALL) biology and prognosis. The initial steps of canonical miRNA biogenesis involve the microprocessor complex processing the primary miRNA transcripts into precursor miRNAs via Drosha. DROSHA polymorphisms have [...] Read more.
MicroRNAs are key regulators of lymphoid differentiation, exhibiting a pivotal role in acute lymphoblastic leukemia (ALL) biology and prognosis. The initial steps of canonical miRNA biogenesis involve the microprocessor complex processing the primary miRNA transcripts into precursor miRNAs via Drosha. DROSHA polymorphisms have been implicated in pediatric ALL and linked with cancer risk. This study investigated the role of rs642321, rs3805500, and rs10035440 DROSHA polymorphisms in ALL susceptibility, relapse, and outcomes in children and adolescents of Greek descent. The study included 252 children and adolescents (115 ALL cases and 137 controls). Genotyping was performed using RT-qPCR and the TaqMan Genotyping Assay. Homozygotes for the minor allele in DROSHA rs642321 were nominally associated with ALL susceptibility (TT vs. CC+CT; OR 4.5; 95% CI: 1.2–21.2; padj = 0.034). Likewise, homozygotes for the minor allele in rs3805500 were linked with ALL risk (GG vs. AA+AG; OR 2.7; 95% CI: 1.3–6.1; padj = 0.012). A suggestive association was observed between the rs3805500 AG genotype and both relapsed (OR 5.8; 95% CI: 1.6–24.3; padj = 0.011) and deceased cases (OR 5; 95% CI: 1.1–26.3; padj = 0.038). Patients with the rs3805500 AG and GG genotypes showed a trend toward poorer overall survival rates. In summary, certain haplotypes of DROSHA polymorphisms may be modestly associated with the occurrence of childhood ALL and its outcomes, although these findings require validation in larger, independent cohorts. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)
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20 pages, 1887 KB  
Article
Microarray Analysis Reveals Sepsis Is a Syndrome with Hyperactivity of TH17 Immunity, with Over-Presentation of the Treg Cell Cytokine TGF-β
by Yu-Ju Chen, Jang-Jih Lu, Chih-Pei Lin and Wan-Chung Hu
Curr. Issues Mol. Biol. 2025, 47(6), 435; https://doi.org/10.3390/cimb47060435 - 9 Jun 2025
Viewed by 842
Abstract
Currently, there are two major theories regarding the pathogenesis of sepsis: hyperimmune and hypoimmune. The hyperimmune theory suggests that a cytokine storm causes the symptoms of sepsis. On the contrary, the hypoimmune theory suggests that immunosuppression causes the manifestations of sepsis. By conducting [...] Read more.
Currently, there are two major theories regarding the pathogenesis of sepsis: hyperimmune and hypoimmune. The hyperimmune theory suggests that a cytokine storm causes the symptoms of sepsis. On the contrary, the hypoimmune theory suggests that immunosuppression causes the manifestations of sepsis. By conducting a microarray analysis on peripheral leukocytes from patients with sepsis, this study found that hyperactivity of TH17 immunity was noted in sepsis patients. Innate immunity-related genes are significantly upregulated, including CD14, TLR1,2,4,5,8, HSP70, CEBP proteins, AP1 (JUNB and FOSL2), TGFB1, IL6, TGFA, CSF2 receptor, TNFRSF1A, S100A binding proteins, CCR2, FPR2, amyloid proteins, pentraxin, defensins, CLEC5A, whole complement machinery, CPD, NCF, MMP, neutrophil elastase, caspases, IgG and IgA Fc receptors (CD64, CD32), ALOX5, PTGS, LTB4R, LTA4H, and ICAM1. The majority of adaptive immunity genes were downregulated, including MHC-related genes, TCR genes, granzymes/perforin, CD40, CD8, CD3, TCR signaling, BCR signaling, T and B cell-specific transcription factors, NK killer receptors, and TH17 helper-specific transcription factors (STAT3, RORA, and REL), as well as Treg-related genes, including TGFB1, IL15, STAT5B, SMAD2/4, CD36, and thrombospondin. The findings of this study show that Th17 with Treg over-presentation play an important role in the pathophysiology of sepsis. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)
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Other

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11 pages, 1472 KB  
Case Report
The Novel Association of a Single Nucleotide Variant in the COL3A1 Gene with Diffuse Coronary Aneurysms
by Charlene Norgan Radler, Kevin Ku, Alison Hodge, Tianci Wang, Peyton Moore and Mohanakrishnan Sathyamoorthy
Curr. Issues Mol. Biol. 2025, 47(2), 82; https://doi.org/10.3390/cimb47020082 - 27 Jan 2025
Viewed by 1968
Abstract
The COL3A1 gene, encoding the pro-alpha chain of type III collagen, has been implicated in a range of collagen-mediated diseases such as Ehlers–Danlos syndrome and aortic aneurysms. In this report, we present evidence for the first time associating a single nucleotide variant p.P517R [...] Read more.
The COL3A1 gene, encoding the pro-alpha chain of type III collagen, has been implicated in a range of collagen-mediated diseases such as Ehlers–Danlos syndrome and aortic aneurysms. In this report, we present evidence for the first time associating a single nucleotide variant p.P517R in exon 22 of COL3A1 with the development of diffuse coronary aneurysms in a human subject without prior atherosclerotic cardiovascular disease, connective tissue disorder, or phenotypic characteristics diagnostic for vascular Ehlers–Danlos syndrome. Computational modeling of this specific variant in AlphaFold and in silico analyses predict deleterious alterations in the structure and function of the COL3A1 gene product, alpha 1 chain of type III collagen. This novel phenotype-to-genotype correlation should prompt further investigation into the mechanistic basis of this association. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)
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