|
1
|
Mahmoud AH, Alhamidi RS, Ilce BY, Hamad AM, Ali N, Mahasneh A, Talaat IM, Tlili A, Hamoudi R. Identification of Genes Associated with Familial Focal Segmental Glomerulosclerosis Through Transcriptomics and In Silico Analysis, Including RPL27, TUBB6, and PFDN5. Int J Mol Sci 2024; 25:11659. [PMID: 39519211 PMCID: PMC11546068 DOI: 10.3390/ijms252111659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Revised: 10/23/2024] [Accepted: 10/27/2024] [Indexed: 11/16/2024] Open
Abstract
Focal segmental glomerulosclerosis (FSGS) is a major cause of nephrotic syndrome and often leads to progressive kidney failure. Its varying clinical presentation suggests potential genetic diversity, requiring further molecular investigation. This study aims to elucidate some of the genetic and molecular mechanisms underlying FSGS. The study focuses on the use of bioinformatic analysis of gene expression data to identify genes associated with familial FSGS. A comprehensive in silico analysis was performed using the GSE99340 data set from Gene Expression Omnibus (GEO) comparing gene expression in glomerular and tubulointerstitial tissues from FSGS patients (n = 10) and Minimal Change Disease (MCD) patients (n = 8). These findings were validated using transcriptomics data obtained using RNA sequencing from FSGS (n = 3) and control samples (n = 3) from the UAE. Further validation was conducted using qRT-PCR on an independent FFPE cohort (FSGS, n = 6; MCD, n = 7) and saliva samples (FSGS, n = 3; Control, n = 7) from the UAE. Three genes (TUBB6, RPL27, and PFDN5) showed significant differential expression (p < 0.01) when comparing FSGS and MCD with healthy controls. These genes are associated with cell junction organization and synaptic pathways of the neuron, supporting the link between FSGS and the neural system. These genes can potentially be useful as diagnostic biomarkers for FSGS and to develop new treatment options.
Collapse
Affiliation(s)
- Anfal Hussain Mahmoud
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (A.H.M.); (R.S.A.); (B.Y.I.); (A.M.H.); (N.A.); or (R.H.)
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Reem Sami Alhamidi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (A.H.M.); (R.S.A.); (B.Y.I.); (A.M.H.); (N.A.); or (R.H.)
| | - Burcu Yener Ilce
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (A.H.M.); (R.S.A.); (B.Y.I.); (A.M.H.); (N.A.); or (R.H.)
| | - Alaa Mohamed Hamad
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (A.H.M.); (R.S.A.); (B.Y.I.); (A.M.H.); (N.A.); or (R.H.)
| | - Nival Ali
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (A.H.M.); (R.S.A.); (B.Y.I.); (A.M.H.); (N.A.); or (R.H.)
| | - Amjad Mahasneh
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah P.O. Box 26666, United Arab Emirates;
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Iman M. Talaat
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (A.H.M.); (R.S.A.); (B.Y.I.); (A.M.H.); (N.A.); or (R.H.)
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Pathology Department, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (A.H.M.); (R.S.A.); (B.Y.I.); (A.M.H.); (N.A.); or (R.H.)
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Center of Excellence for Precision Medicine, Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London NW3 2QG, UK
| |
Collapse
|
|
2
|
The Role of Systems Biology in Deciphering Asthma Heterogeneity. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101562. [PMID: 36294997 PMCID: PMC9605413 DOI: 10.3390/life12101562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
Abstract
Asthma is one of the most common and lifelong and chronic inflammatory diseases characterized by inflammation, bronchial hyperresponsiveness, and airway obstruction episodes. It is a heterogeneous disease of varying and overlapping phenotypes with many confounding factors playing a role in disease susceptibility and management. Such multifactorial disorders will benefit from using systems biology as a strategy to elucidate molecular insights from complex, quantitative, massive clinical, and biological data that will help to understand the underlying disease mechanism, early detection, and treatment planning. Systems biology is an approach that uses the comprehensive understanding of living systems through bioinformatics, mathematical, and computational techniques to model diverse high-throughput molecular, cellular, and the physiologic profiling of healthy and diseased populations to define biological processes. The use of systems biology has helped understand and enrich our knowledge of asthma heterogeneity and molecular basis; however, such methods have their limitations. The translational benefits of these studies are few, and it is recommended to reanalyze the different studies and omics in conjugation with one another which may help understand the reasons for this variation and help overcome the limitations of understanding the heterogeneity in asthma pathology. In this review, we aim to show the different factors that play a role in asthma heterogeneity and how systems biology may aid in understanding and deciphering the molecular basis of asthma.
Collapse
|
|
3
|
Almansoori A, Bhamidimarri PM, Bendardaf R, Hamoudi R. In silico Analysis of Publicly Available Transcriptomics Data Identifies Putative Prognostic and Therapeutic Molecular Targets for Papillary Thyroid Carcinoma. Int J Gen Med 2022; 15:3097-3120. [PMID: 35330879 PMCID: PMC8939872 DOI: 10.2147/ijgm.s345336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/25/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Thyroid cancer is the most common endocrine malignancy. However, the molecular mechanism involved in its pathogenesis is not well characterized. PURPOSE The objective of this study is to identify key cellular pathways and differentially expressed genes along the thyroid cancer pathogenesis sequence as well as to identify potential prognostic and therapeutic targets. METHODS Publicly available transcriptomics data comprising a total of 95 samples consisting of 41 normal, 28 non-aggressive and 26 metastatic papillary thyroid carcinoma (PTC) cases were used. Transcriptomics data were normalized and filtered identifying 9394 differentially expressed genes. The genes identified were subjected to pathway analysis using absGSEA identifying PTC related pathways. Three of the genes identified were validated on 508 thyroid cancer biopsies using RNAseq and TNMplot. RESULTS Pathway analysis revealed a total of 2193 differential pathways among non-aggressive samples and 1969 among metastatic samples compared to normal tissue. Pathways for non-aggressive PTC include calcium and potassium ion transport, hormone signaling, protein tyrosine phosphatase activity and protein tyrosine kinase activity. Metastatic pathways include growth, apoptosis, activation of MAPK and regulation of serine threonine kinase activity. Genes for non-aggressive are KCNQ1, CACNA1D, KCNN4, BCL2, and PTK2B and metastatic PTC are EGFR, PTK2B, KCNN4 and BCL2. Three of the genes identified were validated using clinical biopsies showing significant overexpression in aggressive compared to non-aggressive PTC; EGFR (p < 0.05), KCNN4 (p < 0.001) and PTK2B (p < 0.001). DrugBank database search identified several FDA approved drug targets including anti-EGFR Vandetanib used to treat thyroid cancer in addition to others that may prove useful in treating PTC. CONCLUSION Transcriptomics analysis identified putative prognostic targets including EGFR, PTK2B, BCL2, KCNQ1, KCNN4 and CACNA1D. EGFR, PTK2B and KCN44 were validated using thyroid cancer clinical biopsies. The drug search identified FDA approved drugs including Vandetanib in addition to others that may prove useful in treating the disease.
Collapse
Affiliation(s)
- Asma Almansoori
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Riyad Bendardaf
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Department of Oncology, University Hospital Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, UK
| |
Collapse
|
|
4
|
Lad A, Breidenbach JD, Su RC, Murray J, Kuang R, Mascarenhas A, Najjar J, Patel S, Hegde P, Youssef M, Breuler J, Kleinhenz AL, Ault AP, Westrick JA, Modyanov NN, Kennedy DJ, Haller ST. As We Drink and Breathe: Adverse Health Effects of Microcystins and Other Harmful Algal Bloom Toxins in the Liver, Gut, Lungs and Beyond. Life (Basel) 2022; 12:life12030418. [PMID: 35330169 PMCID: PMC8950847 DOI: 10.3390/life12030418] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/19/2022] Open
Abstract
Freshwater harmful algal blooms (HABs) are increasing in number and severity worldwide. These HABs are chiefly composed of one or more species of cyanobacteria, also known as blue-green algae, such as Microcystis and Anabaena. Numerous HAB cyanobacterial species produce toxins (e.g., microcystin and anatoxin—collectively referred to as HAB toxins) that disrupt ecosystems, impact water and air quality, and deter recreation because they are harmful to both human and animal health. Exposure to these toxins can occur through ingestion, inhalation, or skin contact. Acute health effects of HAB toxins have been well documented and include symptoms such as nausea, vomiting, abdominal pain and diarrhea, headache, fever, and skin rashes. While these adverse effects typically increase with amount, duration, and frequency of exposure, susceptibility to HAB toxins may also be increased by the presence of comorbidities. The emerging science on potential long-term or chronic effects of HAB toxins with a particular emphasis on microcystins, especially in vulnerable populations such as those with pre-existing liver or gastrointestinal disease, is summarized herein. This review suggests additional research is needed to define at-risk populations who may be helped by preventative measures. Furthermore, studies are required to develop a mechanistic understanding of chronic, low-dose exposure to HAB toxins so that appropriate preventative, diagnostic, and therapeutic strategies can be created in a targeted fashion.
Collapse
Affiliation(s)
- Apurva Lad
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Joshua D. Breidenbach
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Robin C. Su
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Jordan Murray
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Rebecca Kuang
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Alison Mascarenhas
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - John Najjar
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Shivani Patel
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Prajwal Hegde
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Mirella Youssef
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Jason Breuler
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Andrew L. Kleinhenz
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - Andrew P. Ault
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Judy A. Westrick
- Lumigen Instrumentation Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, USA;
| | - Nikolai N. Modyanov
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
| | - David J. Kennedy
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
- Correspondence: (D.J.K.); (S.T.H.); Tel.: +1-419-383-6822 (D.J.K.); +1-419-383-6859 (S.T.H.)
| | - Steven T. Haller
- College of Medicine and Life Science, University of Toledo, Toledo, OH 43614, USA; (A.L.); (J.D.B.); (R.C.S.); (J.M.); (R.K.); (A.M.); (J.N.); (S.P.); (P.H.); (M.Y.); (J.B.); (A.L.K.); (N.N.M.)
- Correspondence: (D.J.K.); (S.T.H.); Tel.: +1-419-383-6822 (D.J.K.); +1-419-383-6859 (S.T.H.)
| |
Collapse
|