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Radhakrishna U, Ratnamala U, Jhala DD, Uppala LV, Vedangi A, Saiyed N, Patel M, Shah SR, Rawal RM, Jemec GBE, Mazza T, Mazzoccoli G, Damiani G. Deregulated Long Non-Coding RNAs (lncRNA) as Promising Biomarkers in Hidradenitis Suppurativa. J Clin Med 2024; 13:3016. [PMID: 38792557 DOI: 10.3390/jcm13103016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/26/2024] Open
Abstract
Background/Objectives: In recent times, epigenetics alterations in Hidradenitis suppurativa (HS) have been explored and exploited translationally to guide investigation of new therapeutic approaches. On the other hand, long noncoding RNAs (LncRNAs), main regulators of the epigenetic status of the human genome, have been scarcely investigated, notwithstanding their potential relevance in broad pathogenesis comprehension. Here, we aim to explore the methylation pattern of lncRNAs in HS. Methods: In this case-control study, 24 HS patients and age-, sex- and BMI-matched controls were analyzed to characterize the methylome of lncRNA genes in peripheral blood cells. Gene ontology analysis (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction (PPI) network, and MCODE analysis were performed. Results: A set of fifteen lncRNA genes exhibited significantly differential methylation patterns, with ten of them showing hypomethylation and five displaying hypermethylation at specific CpG sites. The hypomethylated lncRNA genes were DLEU2, MESTIT1, CASC2, TUG1, KCNQ1DN, PSORS1C3, PCA3, DSCR8, RFPL1S, and PVT1, while the hypermethylated ones were HAR1A, FAM66B, SNHG9, HCG9, and HCP5. These lncRNA genes have been linked to various important biological processes, including cell proliferation, apoptosis, inflammation, chronic inflammatory skin diseases, and wound healing. Their altered methylation status suggests potential roles in regulating these processes, and may contribute to HS pathogenesis and healing mechanisms. Conclusions: This study revealed an interesting dysregulation pattern of definite lncRNAs in the methylome which is linked to both the development of HS and its comorbidities. Epigenetically altered lncRNAs genes could represent useful biomarkers, and could help in guiding innovative treatment strategies.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Uppala Ratnamala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad 380009, India
| | - Devendrasinh D Jhala
- Department of Zoology, School of Sciences, Gujarat University, Ahmedabad 380009, India
| | - Lavanya V Uppala
- Peter Kiewit Institute, College of Information Science & Technology, The University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Aaren Vedangi
- Department of Clinical Research, KIMS ICON Hospital, ICON Krishi Institute Medical Sciences, Sheelanagar, Visakhapatnam 530012, India
| | - Nazia Saiyed
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, Royal Oak, MI 48073, USA
| | | | - Sushma R Shah
- Department of Obstetrics and Gynecology, BJ Medical College Institute of Medical Post-Graduate Studies and Research, Ahmedabad 380016, India
| | - Rakesh M Rawal
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad 380009, India
| | - Gregor B E Jemec
- Department of Dermatology, Zealand University Hospital, 4000 Roskilde, Denmark
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", Opera di Padre Pio da Pietrelcina, Cappuccini Avenue, 71013 San Giovanni Rotondo, Italy
| | - Gianluigi Mazzoccoli
- Division of Internal Medicine and Chronobiology Laboratory, Department of Medical Sciences, IRCCS "Casa Sollievo della Sofferenza", Opera di Padre Pio da Pietrelcina, 71013 San Giovanni Rotondo, Italy
| | - Giovanni Damiani
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy
- Italian Center of Precision Medicine and Chronic Inflammation, University of Milan, 20122 Milan, Italy
- Fondazione IRCCS Ca' Granda, Ospedale maggiore Policlinico, 20122 Milan, Italy
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Radhakrishna U, Ratnamala U, Jhala DD, Uppala LV, Vedangi A, Saiyed N, Patel M, Vadsaria N, Shah SR, Rawal RM, Mercuri SR, McGonagle D, Jemec GBE, Damiani G. Hidradenitis suppurativa associated telomere-methylome dysregulations in blood. J Eur Acad Dermatol Venereol 2024; 38:393-403. [PMID: 37872100 DOI: 10.1111/jdv.19586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/03/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Hidradenitis suppurativa (HS) is a chronic debilitating disease with a significant burden of both organic and psychological comorbidities. It has been shown that certain telomere-related genes (TRGs) affect a wide range of diseases, including HS and its associated comorbidities, but their exact role in HS pathogenesis is still unknown. OBJECTIVES To determine whether TRG methylomes can be used as biomarkers in HS. METHODS Using the Illumina HumanMethylation450 BeadChip array, we examined methylation variations associated with TRGs in HS cases and age-, sex- and ethnicity-matched healthy controls. The study utilized integrated bioinformatics statistical methods, such as a false discovery rate (FDR), the area under the receiver operating characteristic curve (AUC) and principal component analysis. RESULTS There were a total of 585 different differentially methylated CpG sites identified in 585 TRGs associated with HS (474 hypomethylated and 111 hypermethylated) (FDR p-value < 0.05). A number of these CpGs have been identified as being involved in increased pain sensitivity including EPAS1, AHR, CSNK1D, DNMT1, IKBKAP, NOS3, PLCB1 and PRDM16 genes; GABRB3 as a potential alcohol addiction marker; DDB1, NSMCE2 and HNRNPA2B1 associated with cancers. Pathway analysis identified 67 statistically significant pathways, including DNA repair, telomere maintenance, mismatch repair and cell cycle control (p < 0.001). CONCLUSION The disruption of TRGs leads to the shortening of telomeres, which is associated with HS progression, ageing, cellular senescence and an increased risk of various diseases, including cancer and associated comorbidities, such as metabolic syndrome, cardiovascular disease and inflammatory disorders. Further research is necessary to better understand the underlying mechanisms and establish causal links between TRGs and HS. The present study is the first effort to comprehend potential pathomechanisms of sporadic HS cases concentrating on PBMC methylome since ours.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Uppala Ratnamala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | | | - Lavanya V Uppala
- College of Information Science & Technology, Peter Kiewit Institute, the University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Aaren Vedangi
- Department of Clinical Research, KIMS ICON Hospital, A Unit of ICON Krishi Institute Medical Sciences, Visakhapatnam, India
| | - Nazia Saiyed
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | | | | | - Sushma R Shah
- Department of Obstetrics and Gynecology, BJ Medical College Institute of Medical Post-Graduate Studies and Research, Ahmedabad, India
| | - Rakesh M Rawal
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Santo R Mercuri
- Unit of Dermatology and Cosmetology, IRCCS San Raffaele Hospital, Milano, Italy
| | - Dennis McGonagle
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Gregor B E Jemec
- Department of Dermatology, Zealand University Hospital, Roskilde, Denmark
| | - Giovanni Damiani
- Unit of Dermatology and Cosmetology, IRCCS San Raffaele Hospital, Milano, Italy
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Italian Center of Precision Medicine and Chronic Inflammation, University of Milan, Milan, Italy
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Radhakrishna U, Sadhasivam S, Radhakrishnan R, Forray A, Muvvala SB, Metpally RP, Patel S, Rawal RM, Vishweswaraiah S, Bahado-Singh RO, Nath SK. Placental cytochrome P450 methylomes in infants exposed to prenatal opioids: exploring the effects of neonatal opioid withdrawal syndrome on health horizons. Front Genet 2024; 14:1292148. [PMID: 38264209 PMCID: PMC10805101 DOI: 10.3389/fgene.2023.1292148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/24/2023] [Indexed: 01/25/2024] Open
Abstract
Background: Neonatal opioid withdrawal syndrome (NOWS), arises due to increased opioid use during pregnancy. Cytochrome P450 (CYP) enzymes play a pivotal role in metabolizing a wide range of substances in the human body, including opioids, other drugs, toxins, and endogenous compounds. The association between CYP gene methylation and opioid effects is unexplored and it could offer promising insights. Objective: To investigate the impact of prenatal opioid exposure on disrupted CYPs in infants and their anticipated long-term clinical implications. Study Design: DNA methylation levels of CYP genes were analyzed in a cohort of 96 placental tissues using Illumina Infinium MethylationEPIC (850 k) BeadChips. This involved three groups of placental tissues: 32 from mothers with infants exposed to opioids prenatally requiring pharmacologic treatment for NOWS, 32 from mothers with prenatally opioid-exposed infants not needing NOWS treatment, and 32 from unexposed control mothers. Results: The study identified 20 significantly differentially methylated CpG sites associated with 17 distinct CYP genes, with 14 CpGs showing reduced methylation across 14 genes (CYP19A1, CYP1A2, CYP4V2, CYP1B1, CYP24A1, CYP26B1, CYP26C1, CYP2C18, CYP2C9, CYP2U1, CYP39A1, CYP2R1, CYP4Z1, CYP2D7P1 and), while 8 exhibited hypermethylation (CYP51A1, CYP26B1, CYP2R1, CYP2U1, CYP4X1, CYP1A2, CYP2W1, and CYP4V2). Genes such as CYP1A2, CYP26B1, CYP2R1, CYP2U1, and CYP4V2 exhibited both increased and decreased methylation. These genes are crucial for metabolizing eicosanoids, fatty acids, drugs, and diverse substances. Conclusion: The study identified profound methylation changes in multiple CYP genes in the placental tissues relevant to NOWS. This suggests that disruption of DNA methylation patterns in CYP transcripts might play a role in NOWS and may serve as valuable biomarkers, suggesting a future pathway for personalized treatment. Further research is needed to confirm these findings and explore their potential for diagnosis and treatment.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, Royal Oak, MI, United States
| | - Senthilkumar Sadhasivam
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rupa Radhakrishnan
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ariadna Forray
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Srinivas B. Muvvala
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Raghu P. Metpally
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, United States
| | - Saumya Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Science, Gujarat University, Ahmedabad, India
| | - Rakesh M. Rawal
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, Royal Oak, MI, United States
| | - Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, Royal Oak, MI, United States
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
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Radhakrishna U, Ratnamala U, Jhala DD, Uppala LV, Vedangi A, Patel M, Vadsaria N, Shah S, Saiyed N, Rawal RM, Mercuri SR, Jemec GBE, Damiani G. Hidradenitis suppurativa presents a methylome dysregulation capable to explain the pro-inflammatory microenvironment: Are these DNA methylations potential therapeutic targets? J Eur Acad Dermatol Venereol 2023; 37:2109-2123. [PMID: 37338327 DOI: 10.1111/jdv.19286] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/27/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Hidradenitis suppurativa (HS) is a chronic, systemic, inflammatory skin condition with elusive pathogenesis that affects therapeutic intervention directly. OBJECTIVE To characterize epigenetic variations in cytokines genes contributing to HS. METHODS Epigenome-wide DNA methylation profiling with the Illumina Epic array was performed on blood DNA samples from 24 HS patients and 24 age- and sex-matched controls to explore DNA methylation changes in cytokine genes. RESULTS We identified 170 cytokine genes including 27 hypermethylated CpG sites and 143 genes with hypomethylated sites respectively. Hypermethylated genes, including LIF, HLA-DRB1, HLA-G, MTOR, FADD, TGFB3, MALAT1 and CCL28; hypomethylated genes, including NCSTN, SMAD3, IGF1R, IL1F9, NOD2, NOD1, YY1, DLL1 and BCL2 may contribute to the pathogenesis of HS. These genes were enriched in the 117 different pathways (FDR p-values ≤ 0.05), including IL-4/IL-13 pathways and Wnt/β-catenin signalling. CONCLUSIONS The lack of wound healing, microbiome dysbiosis and increased tumour susceptibility are all sustained by these dysfunctional methylomes, hopefully, capable to be targeted in the next future. Since methylome describes and summarizes genetic and environmental contributions, these data may represent a further step towards a feasible precision medicine also for HS patients.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynaecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Uppala Ratnamala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Devendrasinh D Jhala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
- Department of Zoology, School of Sciences, Gujarat University, Ahmedabad, India
| | - Lavanya V Uppala
- College of Information Science & Technology, The University of Nebraska at Omaha, Peter Kiewit Institute, Omaha, Nebraska, USA
| | - Aaren Vedangi
- Department of Clinical Research, KIMS ICON Hospital, A Unit of ICON Krishi Institute Medical Sciences, Visakhapatnam, India
| | | | | | - Sushma Shah
- Department of Obstetrics and Gynaecology, B.J. Medical College, Ahmedabad, India
| | - Nazia Saiyed
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Rakesh M Rawal
- College of Information Science & Technology, The University of Nebraska at Omaha, Peter Kiewit Institute, Omaha, Nebraska, USA
| | - Santo Raffaele Mercuri
- Unit of Clinical Dermatology, Università Vita-Salute San Raffaele, Milan, Italy
- Italian Center of Precisione Medicine and Chronic Inflammation, Milan, Italy
| | - Gregor B E Jemec
- Department of Dermatology, Zealand University Hospital, Roskilde, Denmark
| | - Giovanni Damiani
- Unit of Clinical Dermatology, Università Vita-Salute San Raffaele, Milan, Italy
- Italian Center of Precisione Medicine and Chronic Inflammation, Milan, Italy
- Clinical Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
- Young Dermatologists Italian Network, Milan, Italy
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Vishweswaraiah S, Yilmaz A, Saiyed N, Khalid A, Koladiya PR, Pan X, Macias S, Robinson AC, Mann D, Green BD, Kerševičiūte I, Gordevičius J, Radhakrishna U, Graham SF. Integrative Analysis Unveils the Correlation of Aminoacyl-tRNA Biosynthesis Metabolites with the Methylation of the SEPSECS Gene in Huntington's Disease Brain Tissue. Genes (Basel) 2023; 14:1752. [PMID: 37761892 PMCID: PMC10530570 DOI: 10.3390/genes14091752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The impact of environmental factors on epigenetic changes is well established, and cellular function is determined not only by the genome but also by interacting partners such as metabolites. Given the significant impact of metabolism on disease progression, exploring the interaction between the metabolome and epigenome may offer new insights into Huntington's disease (HD) diagnosis and treatment. Using fourteen post-mortem HD cases and fourteen control subjects, we performed metabolomic profiling of human postmortem brain tissue (striatum and frontal lobe), and we performed DNA methylome profiling using the same frontal lobe tissue. Along with finding several perturbed metabolites and differentially methylated loci, Aminoacyl-tRNA biosynthesis (adj p-value = 0.0098) was the most significantly perturbed metabolic pathway with which two CpGs of the SEPSECS gene were correlated. This study improves our understanding of molecular biomarker connections and, importantly, increases our knowledge of metabolic alterations driving HD progression.
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Affiliation(s)
- Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (S.V.); (U.R.)
| | - Ali Yilmaz
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
| | - Nazia Saiyed
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
| | - Abdullah Khalid
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
| | - Purvesh R. Koladiya
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
| | - Xiaobei Pan
- Advanced Asset Technology Centre, Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5DL, UK; (X.P.); (S.M.); (B.D.G.)
| | - Shirin Macias
- Advanced Asset Technology Centre, Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5DL, UK; (X.P.); (S.M.); (B.D.G.)
| | - Andrew C. Robinson
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Neuroscience, The University of Manchester, Salford Royal Hospital, Salford M6 8HD, UK; (A.C.R.); (D.M.)
| | - David Mann
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Neuroscience, The University of Manchester, Salford Royal Hospital, Salford M6 8HD, UK; (A.C.R.); (D.M.)
| | - Brian D. Green
- Advanced Asset Technology Centre, Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5DL, UK; (X.P.); (S.M.); (B.D.G.)
| | - Ieva Kerševičiūte
- VUGENE, LLC, 625 Kenmoor Ave Suite 301 PMB 96578, Grand Rapids, MI 49546, USA; (I.K.); (J.G.)
| | - Juozas Gordevičius
- VUGENE, LLC, 625 Kenmoor Ave Suite 301 PMB 96578, Grand Rapids, MI 49546, USA; (I.K.); (J.G.)
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (S.V.); (U.R.)
| | - Stewart F. Graham
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (S.V.); (U.R.)
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Rochester, MI 48309, USA
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Radhakrishna U, Nath SK, Uppala LV, Veerappa A, Forray A, Muvvala SB, Metpally RP, Crist RC, Berrettini WH, Mausi LM, Vishweswaraiah S, Bahado-Singh RO. Placental microRNA methylome signatures may serve as biomarkers and therapeutic targets for prenatally opioid-exposed infants with neonatal opioid withdrawal syndrome. Front Genet 2023; 14:1215472. [PMID: 37434949 PMCID: PMC10332887 DOI: 10.3389/fgene.2023.1215472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/01/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction: The neonate exposed to opioids in utero faces a constellation of withdrawal symptoms postpartum commonly called neonatal opioid withdrawal syndrome (NOWS). The incidence of NOWS has increased in recent years due to the opioid epidemic. MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in gene regulation. Epigenetic variations in microRNAs (miRNAs) and their impact on addiction-related processes is a rapidly evolving area of research. Methods: The Illumina Infinium Methylation EPIC BeadChip was used to analyze DNA methylation levels of miRNA-encoding genes in 96 human placental tissues to identify miRNA gene methylation profiles as-sociated with NOWS: 32 from mothers whose prenatally opioid-exposed infants required pharmacologic management for NOWS, 32 from mothers whose prenatally opioid-exposed infants did not require treat-ment for NOWS, and 32 unexposed controls. Results: The study identified 46 significantly differentially methylated (FDR p-value ≤ 0.05) CpGs associated with 47 unique miRNAs, with a receiver operating characteristic (ROC) area under the curve (AUC) ≥0.75 including 28 hypomethylated and 18 hypermethylated CpGs as potentially associated with NOWS. These dysregulated microRNA methylation patterns may be a contributing factor to NOWS pathogenesis. Conclusion: This is the first study to analyze miRNA methylation profiles in NOWS infants and illustrates the unique role miRNAs might have in diagnosing and treating the disease. Furthermore, these data may provide a step toward feasible precision medicine for NOWS babies as well.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Lavanya V. Uppala
- College of Information Science and Technology, Peter Kiewit Institute, The University of Nebraska at Omaha, Omaha, NE, United States
| | - Avinash Veerappa
- Department of Genetics, Cell Biology and Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Ariadna Forray
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Srinivas B. Muvvala
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Raghu P. Metpally
- Department of Molecular and Functional Genomics, Danville, PA, United States
| | - Richard C. Crist
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Wade H. Berrettini
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
- Geisinger Clinic, Danville, PA, United States
| | - Lori M. Mausi
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
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Radhakrishna U, Ratnamala U, Jhala DD, Vadsaria N, Patel M, Uppala LV, Vedangi A, Saiyed N, Rawal RM, Damiani G, Jemec GBE. Cytochrome P450 Genes Mediated by DNA Methylation Are Involved in the Resistance to Hidradenitis Suppurativa. J Invest Dermatol 2023; 143:670-673.e19. [PMID: 36155054 DOI: 10.1016/j.jid.2022.08.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 10/14/2022]
Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics & Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA.
| | - Uppala Ratnamala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Devendrasinh D Jhala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Nikita Vadsaria
- Department of Bioinformatics, Gujarat University, Ahmedabad, India
| | | | - Lavanya V Uppala
- College of Information Science & Technology, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Aaren Vedangi
- Department of Clinical Research, KIMS ICON Hospital, Visakapatnam, India
| | - Nazia Saiyed
- Department of Obstetrics & Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Rakesh M Rawal
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Giovanni Damiani
- Clinical Dermatology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Gregor B E Jemec
- Department of Dermatology, Zealand University Hospital, Roskilde, Denmark
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Ratnamala U, Jain NK, Jhala DD, Prasad PV, Saiyed N, Nair S, Radhakrishna U. An Updated Mutation Spectrum of the γ-Secretase Complex: Novel NCSTN Gene Mutation in an Indian Family with Hidradenitis Suppurativa and Acne Conglobata. Indian J Dermatol 2023; 68:141-147. [PMID: 37275792 PMCID: PMC10238988 DOI: 10.4103/ijd.ijd_995_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023] Open
Abstract
Background Hidradenitis suppurativa (HS) is a complex, chronic inflammatory skin disorder whose pathophysiology is poorly understood. Genetic studies have shown that HS is predisposed by mutations in the γ-secretase gene, but only a proportion of familial and partial sporadic cases have been shown to possess such mutations. HS has high genetic heterogeneity and is thought to be triggered by a combination of genetics and environmental factors. Aims The study aimed to investigate the genetic causes of HS in a large cohort of patients and to update the mutation spectrum of γ-secretase complex genes. Methods We conducted mutational screening of 95 sporadic HS cases and one large family with both HS and acne conglobata (AC) to identify mutations in the coding and splice junction region of γ-secretase complex genes (nicastrin (NCSTN), presenilin 1 (PSEN1), presenilin enhancer 2 (PSENEN), and aph-1 homolog B, gamma-secretase subunit (APH1B)). Results Our study identified a nucleotide substitution of 1876C>T in the NCSTN gene, which caused a stop codon (p.Arg626X) in the affected members of a large family with HS and AC. No pathogenic variants were detected in 95 sporadic cases of HS, indicating there is possible genetic heterogeneity. Conclusion We report a new family with a nonsense mutation in the NCSTN gene that supports the role of the γ-secretase complex genes in HS with AC. The updated γ-secretase mutation spectrum for HS now includes 78 mutations.
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Affiliation(s)
- Uppala Ratnamala
- From the Department of Life Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Nayan K. Jain
- From the Department of Life Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | | | | | - Nazia Saiyed
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Sreelatha Nair
- Department of Medical Genetics, Lifeline Super Speciality Hospital, Adoor, Pathanamthitta, Kerala, India
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI, USA
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9
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Bahado-Singh RO, Vishweswaraiah S, Turkoglu O, Graham SF, Radhakrishna U. Alzheimer's Precision Neurology: Epigenetics of Cytochrome P450 Genes in Circulating Cell-Free DNA for Disease Prediction and Mechanism. Int J Mol Sci 2023; 24:ijms24032876. [PMID: 36769199 PMCID: PMC9917756 DOI: 10.3390/ijms24032876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Precision neurology combines high-throughput technologies and statistical modeling to identify novel disease pathways and predictive biomarkers in Alzheimer's disease (AD). Brain cytochrome P450 (CYP) genes are major regulators of cholesterol, sex hormone, and xenobiotic metabolism, and they could play important roles in neurodegenerative disorders. Increasing evidence suggests that epigenetic factors contribute to AD development. We evaluated cytosine ('CpG')-based DNA methylation changes in AD using circulating cell-free DNA (cfDNA), to which neuronal cells are known to contribute. We investigated CYP-based mechanisms for AD pathogenesis and epigenetic biomarkers for disease detection. We performed a case-control study using 25 patients with AD and 23 cognitively healthy controls using the cfDNA of CYP genes. We performed a logistic regression analysis using the MetaboAnalyst software computer program and a molecular pathway analysis based on epigenetically altered CYP genes using the Cytoscape program. We identified 130 significantly (false discovery rate correction q-value < 0.05) differentially methylated CpG sites within the CYP genes. The top two differentially methylated genes identified were CYP51A1 and CYP2S1. The significant molecular pathways that were perturbed in AD cfDNA were (i) androgen and estrogen biosynthesis and metabolism, (ii) C21 steroid hormone biosynthesis and metabolism, and (iii) arachidonic acid metabolism. Existing evidence suggests a potential role of each of these biochemical pathways in AD pathogenesis. Next, we randomly divided the study group into discovery and validation sub-sets, each consisting of patients with AD and control patients. Regression models for AD prediction based on CYP CpG methylation markers were developed in the discovery or training group and tested in the independent validation group. The CYP biomarkers achieved a high predictive accuracy. After a 10-fold cross-validation, the combination of cg17852385/cg23101118 + cg14355428/cg22536554 achieved an AUC (95% CI) of 0.928 (0.787~1.00), with 100% sensitivity and 92.3% specificity for AD detection in the discovery group. The performance remained high in the independent validation or test group, achieving an AUC (95% CI) of 0.942 (0.905~0.979) with a 90% sensitivity and specificity. Our findings suggest that the epigenetic modification of CYP genes may play an important role in AD pathogenesis and that circulating CYP-based cfDNA biomarkers have the potential to accurately and non-invasively detect AD.
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Affiliation(s)
- Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA
- Corewell Health William Beaumont University Hospital, Royal Oak, MI 48073, USA
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA
- Corewell Health William Beaumont University Hospital, Royal Oak, MI 48073, USA
| | - Onur Turkoglu
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA
- Corewell Health William Beaumont University Hospital, Royal Oak, MI 48073, USA
| | - Stewart F. Graham
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA
- Corewell Health William Beaumont University Hospital, Royal Oak, MI 48073, USA
- Correspondence: (S.F.G.); (U.R.)
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA
- Correspondence: (S.F.G.); (U.R.)
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10
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Swierkowska J, Vishweswaraiah S, Mrugacz M, Radhakrishna U, Gajecka M. Differential methylation of microRNA encoding genes may contribute to high myopia. Front Genet 2023; 13:1089784. [PMID: 36685896 PMCID: PMC9847511 DOI: 10.3389/fgene.2022.1089784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/08/2022] [Indexed: 01/05/2023] Open
Abstract
Introduction: High myopia (HM), an eye disorder with a refractive error ≤-6.0 diopters, has multifactorial etiology with environmental and genetic factors involved. Recent studies confirm the impact of alterations in DNA methylation and microRNAs (miRNAs) on myopia. Here, we studied the combined aspects evaluating to the role of methylation of miRNA encoding genes in HM. Materials and Methods: From the genome-wide DNA methylation data of 18 Polish children with HM and 18 matched controls, we retrieved differentially methylated CG dinucleotides localized in miRNA encoding genes. Putative target genes of the highest-ranked miRNAs were obtained from the miRDB and included in overrepresentation analyses in the ConsensusPathDB. Expression of target genes was assessed using the RNA sequencing data of retinal ARPE-19 cell line. Results: We identified differential methylation of CG dinucleotides in promoter regions of MIR3621, MIR34C, MIR423 (increased methylation level), and MIR1178, MIRLET7A2, MIR885, MIR548I3, MIR6854, MIR675, MIRLET7C, MIR99A (decreased methylation level) genes. Several targets of these miRNAs, e.g. GNAS, TRAM1, CTNNB1, EIF4B, TENM3 and RUNX were previously associated with myopia/HM/refractive error in Europeans in genome-wide association studies. Overrepresentation analyses of miRNAs' targets revealed enrichment in pathways/processes related to eye structure/function, such as axon guidance, transcription, focal adhesion, and signaling pathways of TGF-β, insulin, MAPK and EGF-EGFR. Conclusion: Differential methylation of indicated miRNA encoding genes might influence their expression and contribute to HM pathogenesis via disrupted regulation of transcription of miRNAs' target genes. Methylation of genes encoding miRNAs may be a new direction in research on both the mechanisms determining HM and non-invasive indicators in diagnostics.
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Affiliation(s)
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Malgorzata Mrugacz
- Department of Ophthalmology and Eye Rehabilitation, Medical University of Bialystok, Bialystok, Poland
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland,*Correspondence: Marzena Gajecka,
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11
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Shao X, Vishweswaraiah S, Čuperlović-Culf M, Yilmaz A, Greenwood CMT, Surendra A, McGuinness B, Passmore P, Kehoe PG, Maddens ME, Bennett SAL, Green BD, Radhakrishna U, Graham SF. Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential. Commun Biol 2022; 5:1279. [PMID: 36418427 PMCID: PMC9684551 DOI: 10.1038/s42003-022-03965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
Dementia with Lewy bodies (DLB) is a common form of dementia with known genetic and environmental interactions. However, the underlying epigenetic mechanisms which reflect these gene-environment interactions are poorly studied. Herein, we measure genome-wide DNA methylation profiles of post-mortem brain tissue (Broadmann area 7) from 15 pathologically confirmed DLB brains and compare them with 16 cognitively normal controls using Illumina MethylationEPIC arrays. We identify 17 significantly differentially methylated CpGs (DMCs) and 17 differentially methylated regions (DMRs) between the groups. The DMCs are mainly located at the CpG islands, promoter and first exon regions. Genes associated with the DMCs are linked to "Parkinson's disease" and "metabolic pathway", as well as the diseases of "severe intellectual disability" and "mood disorders". Overall, our study highlights previously unreported DMCs offering insights into DLB pathogenesis with the possibility that some of these could be used as biomarkers of DLB in the future.
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Affiliation(s)
- Xiaojian Shao
- grid.24433.320000 0004 0449 7958National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Sangeetha Vishweswaraiah
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA
| | - Miroslava Čuperlović-Culf
- grid.24433.320000 0004 0449 7958National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada ,grid.28046.380000 0001 2182 2255Ottawa Institute of Systems Biology, Ottawa, Ontario Canada ,grid.28046.380000 0001 2182 2255Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Ali Yilmaz
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
| | - Celia M. T. Greenwood
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Canada ,grid.14709.3b0000 0004 1936 8649Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
| | - Anuradha Surendra
- grid.24433.320000 0004 0449 7958National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Bernadette McGuinness
- grid.4777.30000 0004 0374 7521Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Peter Passmore
- grid.4777.30000 0004 0374 7521Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Patrick G. Kehoe
- grid.5337.20000 0004 1936 7603Dementia Research Group, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael E. Maddens
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
| | - Steffany A. L. Bennett
- grid.28046.380000 0001 2182 2255Ottawa Institute of Systems Biology, Ottawa, Ontario Canada ,grid.28046.380000 0001 2182 2255Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Brian D. Green
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, Northern Ireland, UK
| | - Uppala Radhakrishna
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
| | - Stewart F. Graham
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
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12
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Radhakrishna U, Uppala R, Jhala DD, Vadsaria N, Patel M, Uppala LV, Vishweswaraiah S, Vedangi A, Saiyed N, Damiani G, Jemec GBE. Methylated miRNAs may serve as potential biomarkers and therapeutic targets for hidradenitis suppurativa. J Eur Acad Dermatol Venereol 2022; 36:2199-2213. [PMID: 35921387 DOI: 10.1111/jdv.18473] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/12/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Hidradenitis suppurativa (HS) is a chronic inflammatory disease influenced by genetics, non-genetic, and environmental factors that modulate miRNA expression. Currently, no miRNA data are available for HS. In this study, we profiled DNA methylation patterns of miRNA genes associated with HS susceptibility. OBJECTIVES Identify miRNA gene methylation profiles associated with HS susceptibility. This study examined the methylation patterns of DNAs from 24 healthy controls and 24 patients with HS using Illumina Infinium MethylationEPIC BeadChip array analysis. methylation patterns of miRNA genes were analyzed using Ingenuity Pathway Analysis (IPA) to explore the inversely correlated pathways regulated by miRNAs. RESULTS We identified 60 CpG sites representing 65 unique microRNA genes including 54 hypomethylated and 6 hypermethylated CpGs as potentially associated with HS. Some of these CpGs were found to be critical for skin function, such as miR-29, miR-200, miR-205, miR-548, and miR-132. The miR-192 is implicated in non-alcoholic fatty liver disease. The miR-200c gene was identified as a vital determinant in regulating skin repair after injury and may contribute to age-associated alterations in wound repair. miR-132 was significantly upregulated during the inflammation phase of wound repair, enhancing the activity of STAT3 and ERK pathways that promote keratinocyte proliferation. CONCLUSIONS Epigenetically altered microRNA genes are implicated in wound healing, inflammation, keratinocyte proliferation, and wound modulation. This is the first study to analyze methylation profiles of miRNA genes in the HS population, highlighting the unique role that miRNAs might play in diagnosing and treating HS.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Ratnamala Uppala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | - Devendrasinh D Jhala
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, India
| | | | - Maulik Patel
- Bioinformatics, Gujarat University, Ahmedabad, India
| | - Lavanya V Uppala
- College of Information Science & Technology, the University of Nebraska at Omaha, Peter Kiewit Institute, Omaha, NE, 68182, USA
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Aaren Vedangi
- Department of Clinical Research, KIMS ICON, Hospital, A unit of ICON Krishi Institute Medical Sciences, Sheelanagar, Visakapatnam-530012
| | - Nazia Saiyed
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Giovanni Damiani
- Department of Clinical Research, KIMS ICON, Hospital, A unit of ICON Krishi Institute Medical Sciences, Sheelanagar, Visakapatnam-530012.,Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Gregor B E Jemec
- Department of Dermatology, Zealand University Hospital, Roskilde, Denmark
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13
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Swierkowska J, Karolak JA, Vishweswaraiah S, Mrugacz M, Radhakrishna U, Gajecka M. Decreased Levels of DNA Methylation in the PCDHA Gene Cluster as a Risk Factor for Early-Onset High Myopia in Young Children. Invest Ophthalmol Vis Sci 2022; 63:31. [PMID: 36036911 PMCID: PMC9434983 DOI: 10.1167/iovs.63.9.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Purpose High myopia (HM), an eye disorder with at least –6.0 diopters refractive error, has a complex etiology with environmental, genetic, and likely epigenetic factors involved. To complement the DNA methylation assessment in children with HM, we analyzed genes that had significantly lower DNA methylation levels. Methods The DNA methylation pattern was studied based on the genome-wide methylation data of 18 Polish children with HM paired with 18 controls. Genes overlapping CG dinucleotides with decreased methylation level in HM cases were assessed by enrichment analyses. From those, genes with CG dinucleotides in promoter regions were further evaluated based on exome sequencing (ES) data of 16 patients with HM from unrelated Polish families, Sanger sequencing data of the studied children, and the RNA sequencing data of human retinal ARPE-19 cells. Results The CG dinucleotide with the most decreased methylation level in cases was identified in a promoter region of PCDHA10 that overlaps intronic regions of PCDHA1–9 of the PCDHA gene cluster in myopia 5q31 locus. Also, two single nucleotide variants, rs200661444, detected in our ES, and rs246073, previously found as associated with a refractive error in a genome-wide association study, were revealed within this gene cluster. Additionally, genes previously linked to ocular phenotypes, myopia-related traits, or loci, including ADAM20, ZFAND6, ETS1, ABHD13, SBSPON, SORBS2, LMOD3, ATXN1, and FARP2, were found to have decreased methylation. Conclusions Alterations in the methylation pattern of specific CG dinucleotides may be associated with early-onset HM, so this could be used to develop noninvasive biomarkers of HM in children and adolescents.
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Affiliation(s)
| | - Justyna A Karolak
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States
| | - Malgorzata Mrugacz
- Department of Ophthalmology and Eye Rehabilitation, Medical University of Bialystok, Bialystok, Poland
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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14
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Bahado-Singh RO, Radhakrishna U, Gordevičius J, Aydas B, Yilmaz A, Jafar F, Imam K, Maddens M, Challapalli K, Metpally RP, Berrettini WH, Crist RC, Graham SF, Vishweswaraiah S. Artificial Intelligence and Circulating Cell-Free DNA Methylation Profiling: Mechanism and Detection of Alzheimer's Disease. Cells 2022; 11:cells11111744. [PMID: 35681440 PMCID: PMC9179874 DOI: 10.3390/cells11111744] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Despite extensive efforts, significant gaps remain in our understanding of Alzheimer’s disease (AD) pathophysiology. Novel approaches using circulating cell-free DNA (cfDNA) have the potential to revolutionize our understanding of neurodegenerative disorders. Methods: We performed DNA methylation profiling of cfDNA from AD patients and compared them to cognitively normal controls. Six Artificial Intelligence (AI) platforms were utilized for the diagnosis of AD while enrichment analysis was used to elucidate the pathogenesis of AD. Results: A total of 3684 CpGs were significantly (adj. p-value < 0.05) differentially methylated in AD versus controls. All six AI algorithms achieved high predictive accuracy (AUC = 0.949−0.998) in an independent test group. As an example, Deep Learning (DL) achieved an AUC (95% CI) = 0.99 (0.95−1.0), with 94.5% sensitivity and specificity. Conclusion: We describe numerous epigenetically altered genes which were previously reported to be differentially expressed in the brain of AD sufferers. Genes identified by AI to be the best predictors of AD were either known to be expressed in the brain or have been previously linked to AD. We highlight enrichment in the Calcium signaling pathway, Glutamatergic synapse, Hedgehog signaling pathway, Axon guidance and Olfactory transduction in AD sufferers. To the best of our knowledge, this is the first reported genome-wide DNA methylation study using cfDNA to detect AD.
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Affiliation(s)
- Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA; (R.O.B.-S.); (A.Y.); (S.F.G.)
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
- Correspondence: (U.R.); (S.V.); Tel.: +1-248-551-2574 (U.R.); +1-248-551-2569 (S.V.)
| | - Juozas Gordevičius
- Vugene, LLC, 625 Kenmoor Ave Suite 301 PMB 96578, Grand Rapids, MI 49546, USA;
| | - Buket Aydas
- Department of Care Management Analytics, Blue Cross Blue Shield of Michigan, Detroit, MI 48226, USA;
| | - Ali Yilmaz
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA; (R.O.B.-S.); (A.Y.); (S.F.G.)
- Department of Alzheimer’s Disease Research, Beaumont Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA
| | - Faryal Jafar
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Khaled Imam
- Department of Internal Medicine, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (K.I.); (M.M.)
| | - Michael Maddens
- Department of Internal Medicine, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (K.I.); (M.M.)
| | - Kshetra Challapalli
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Raghu P. Metpally
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA 17821, USA; (R.P.M.); (W.H.B.)
| | - Wade H. Berrettini
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA 17821, USA; (R.P.M.); (W.H.B.)
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Richard C. Crist
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Stewart F. Graham
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA; (R.O.B.-S.); (A.Y.); (S.F.G.)
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
- Department of Alzheimer’s Disease Research, Beaumont Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
- Correspondence: (U.R.); (S.V.); Tel.: +1-248-551-2574 (U.R.); +1-248-551-2569 (S.V.)
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15
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Bahado-Singh R, Vlachos KT, Aydas B, Gordevicius J, Radhakrishna U, Vishweswaraiah S. Precision Oncology: Artificial Intelligence and DNA Methylation Analysis of Circulating Cell-Free DNA for Lung Cancer Detection. Front Oncol 2022; 12:790645. [PMID: 35600397 PMCID: PMC9114890 DOI: 10.3389/fonc.2022.790645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/04/2022] [Indexed: 12/12/2022] Open
Abstract
Background Lung cancer (LC) is a leading cause of cancer-deaths globally. Its lethality is due in large part to the paucity of accurate screening markers. Precision Medicine includes the use of omics technology and novel analytic approaches for biomarker development. We combined Artificial Intelligence (AI) and DNA methylation analysis of circulating cell-free tumor DNA (ctDNA), to identify putative biomarkers for and to elucidate the pathogenesis of LC. Methods Illumina Infinium MethylationEPIC BeadChip array analysis was used to measure cytosine (CpG) methylation changes across the genome in LC. Six different AI platforms including support vector machine (SVM) and Deep Learning (DL) were used to identify CpG biomarkers and for LC detection. Training set and validation sets were generated, and 10-fold cross validation performed. Gene enrichment analysis using g:profiler and GREAT enrichment was used to elucidate the LC pathogenesis. Results Using a stringent GWAS significance threshold, p-value <5x10-8, we identified 4389 CpGs (cytosine methylation loci) in coding genes and 1812 CpGs in non-protein coding DNA regions that were differentially methylated in LC. SVM and three other AI platforms achieved an AUC=1.00; 95% CI (0.90-1.00) for LC detection. DL achieved an AUC=1.00; 95% CI (0.95-1.00) and 100% sensitivity and specificity. High diagnostic accuracies were achieved with only intragenic or only intergenic CpG loci. Gene enrichment analysis found dysregulation of molecular pathways involved in the development of small cell and non-small cell LC. Conclusion Using AI and DNA methylation analysis of ctDNA, high LC detection rates were achieved. Further, many of the genes that were epigenetically altered are known to be involved in the biology of neoplasms in general and lung cancer in particular.
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Affiliation(s)
- Ray Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Kyriacos T Vlachos
- Department of Biomedical Sciences, Wayne State School of Medicine, Basic Medical Sciences, Detroit, MI, United States
| | - Buket Aydas
- Department of Healthcare Analytics, Meridian Health Plans, Detroit, MI, United States
| | | | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Beaumont Research Institute, Royal Oak, MI, United States
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Vishweswaraiah S, Akyol S, Yilmaz A, Ugur Z, Gordevičius J, Oh KJ, Brundin P, Radhakrishna U, Labrie V, Graham SF. Methylated Cytochrome P450 and the Solute Carrier Family of Genes Correlate With Perturbations in Bile Acid Metabolism in Parkinson’s Disease. Front Neurosci 2022; 16:804261. [PMID: 35431771 PMCID: PMC9009246 DOI: 10.3389/fnins.2022.804261] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/18/2022] [Indexed: 12/15/2022] Open
Abstract
Parkinson’s disease (PD) is second most prevalent neurodegenerative disorder following Alzheimer’s disease. Parkinson’s disease is hypothesized to be caused by a multifaceted interplay between genetic and environmental factors. Herein, and for the first time, we describe the integration of metabolomics and epigenetics (genome-wide DNA methylation; epimetabolomics) to profile the frontal lobe from people who died from PD and compared them with age-, and sex-matched controls. We identified 48 metabolites to be at significantly different concentrations (FDR q < 0.05), 4,313 differentially methylated sites [5’-C-phosphate-G-3’ (CpGs)] (FDR q < 0.05) and increased DNA methylation age in the primary motor cortex of people who died from PD. We identified Primary bile acid biosynthesis as the major biochemical pathway to be perturbed in the frontal lobe of PD sufferers, and the metabolite taurine (p-value = 5.91E-06) as being positively correlated with CpG cg14286187 (SLC25A27; CYP39A1) (FDR q = 0.002), highlighting previously unreported biochemical changes associated with PD pathogenesis. In this novel multi-omics study, we identify regulatory mechanisms which we believe warrant future translational investigation and central biomarkers of PD which require further validation in more accessible biomatrices.
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Affiliation(s)
| | | | - Ali Yilmaz
- Beaumont Health, Royal Oak, MI, United States
| | - Zafer Ugur
- Beaumont Health, Royal Oak, MI, United States
| | | | | | | | | | | | - Stewart F. Graham
- Beaumont Health, Royal Oak, MI, United States
- *Correspondence: Stewart F. Graham,
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Bahado-Singh RO, Vishweswaraiah S, Aydas B, Radhakrishna U. Artificial intelligence and placental DNA methylation: newborn prediction and molecular mechanisms of autism in preterm children. J Matern Fetal Neonatal Med 2021; 35:8150-8159. [PMID: 34404318 DOI: 10.1080/14767058.2021.1963704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Autism Spectrum Disorder (ASD) represents a heterogeneous group of disorders with a complex genetic and epigenomic etiology. DNA methylation is the most extensively studied epigenomic mechanism and correlates with altered gene expression. Artificial intelligence (AI) is a powerful tool for group segregation and for handling the large volume of data generated in omics experiments. METHODS We performed genome-wide methylation analysis for differential methylation of cytosine nucleotide (CpG) was performed in 20 postpartum placental tissue samples from preterm births. Ten newborns went on to develop autism (Autistic Disorder subtype) and there were 10 unaffected controls. AI including Deep Learning (AI-DL) platforms were used to identify and rank cytosine methylation markers for ASD detection. Ingenuity Pathway Analysis (IPA) to identify genes and molecular pathways that were dysregulated in autism. RESULTS We identified 4870 CpG loci comprising 2868 genes that were significantly differentially methylated in ASD compared to controls. Of these 431 CpGs met the stringent EWAS threshold (p-value <5 × 10-8) along with ≥10% methylation difference between CpGs in cases and controls. DL accurately predicted autism with an AUC (95% CI) of 1.00 (1-1) and sensitivity and specificity of 100% using a combination of 5 CpGs [cg13858611 (NRN1), cg09228833 (ZNF217), cg06179765 (GPNMB), cg08814105 (NKX2-5), cg27092191 (ZNF267)] CpG markers. IPA identified five prenatally dysregulated molecular pathways linked to ASD. CONCLUSIONS The present study provides substantial evidence that epigenetic differences in placental tissue are associated with autism development and raises the prospect of early and accurate detection of the disorder.
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Affiliation(s)
- Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Buket Aydas
- Department of Healthcare Analytics, Meridian Health Plans, Detroit, MI, USA
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
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Kim SK, Vishweswaraiah S, Macknis J, Yilmaz A, Lalwani A, Mishra NK, Guda C, Ogunyemi D, Radhakrishna U, Bahado-Singh RO. New-onset postpartum preeclampsia: epigenetic mechanism and prediction. J Matern Fetal Neonatal Med 2021; 35:7179-7187. [PMID: 34374309 DOI: 10.1080/14767058.2021.1946504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVE Placental cytosine (CpG) methylation was measured to predict new-onset postpartum preeclampsia (NOPP) and interrogate its molecular pathogenesis. METHODS NOPP was defined as patients with a new diagnosis of postpartum preeclampsia developing ≥48 h to ≤6 weeks after delivery with no prior hypertensive disorders. Placental tissue was obtained from 12 NOPP cases and 12 normotensive controls. Genome-wide individual cytosine (CpG) methylation level was measured with the Infinium MethylationEPIC BeadChip array. Significant differential methylation (NOPP vs. controls) for individual CpG loci was defined as false discovery rate (FDR) p value <.05. Gene functional enrichment using Qiagen's ingenuity pathway analysis (IPA) was performed to help elucidate the molecular pathogenesis of NOPP. A logistic regression model for NOPP prediction based on the methylation level in a combination of CpG loci was generated. The area under the receiver operating characteristic curves (AUC [95% CI]) sensitivity, and specificity for NOPP prediction based on the CpG methylation level was calculated for each locus. RESULTS There were 537 (in 540 separate genes) significantly (FDR p<.05 with a ≥ 2.0-fold methylation difference) differentially methylated CpG loci between the groups. A total of 143 individual CpG markers had excellent individual predictive accuracy for NOPP prediction (AUC ≥0.80), of which 14 markers had outstanding accuracy (AUC ≥0.90). A logistic regression model based on five CpG markers yielded an AUC (95% CI)=0.99 (0.95-0.99) with sensitivity 95% and specificity 93% for NOPP prediction. IPA revealed dysregulation of critical pathways (e.g., angiogenesis, chronic inflammation, and epithelial-mesenchymal transition) known to be linked to classic preeclampsia, in addition to other previously undescribed genes/pathways. CONCLUSIONS There was significant placental epigenetic dysregulation in NOPP. NOPP shared both common and unique molecular pathways with classic preeclampsia. Finally, we have identified novel potential biomarkers for the early post-partum prediction of NOPP.
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Affiliation(s)
- Sun Kwon Kim
- Department of Obstetrics and Gynecology, Beaumont Health System, Royal Oak, MI, USA.,Department of Obstetrics and Gynecology, Henry Ford Health System, Detroit, MI, USA
| | | | | | - Ali Yilmaz
- Department of Obstetrics and Gynecology, Beaumont Health System, Royal Oak, MI, USA
| | - Ashna Lalwani
- Department of Obstetrics and Gynecology, Beaumont Health System, Royal Oak, MI, USA
| | - Nitish K Mishra
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Dotun Ogunyemi
- Department of Obstetrics and Gynecology, Beaumont Health System, Royal Oak, MI, USA.,School of Medicine, California University of Science & Medicine, San Bernardino, CA, USA
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Beaumont Health System, Royal Oak, MI, USA
| | - Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, Beaumont Health System, Royal Oak, MI, USA
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Bahado-Singh RO, Vishweswaraiah S, Aydas B, Radhakrishna U. Placental DNA methylation changes and the early prediction of autism in full-term newborns. PLoS One 2021; 16:e0253340. [PMID: 34260616 PMCID: PMC8279352 DOI: 10.1371/journal.pone.0253340] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022] Open
Abstract
Autism spectrum disorder (ASD) is associated with abnormal brain development during fetal life. Overall, increasing evidence indicates an important role of epigenetic dysfunction in ASD. The placenta is critical to and produces neurotransmitters that regulate fetal brain development. We hypothesized that placental DNA methylation changes are a feature of the fetal development of the autistic brain and importantly could help to elucidate the early pathogenesis and prediction of these disorders. Genome-wide methylation using placental tissue from the full-term autistic disorder subtype was performed using the Illumina 450K array. The study consisted of 14 cases and 10 control subjects. Significantly epigenetically altered CpG loci (FDR p-value <0.05) in autism were identified. Ingenuity Pathway Analysis (IPA) was further used to identify molecular pathways that were over-represented (epigenetically dysregulated) in autism. Six Artificial Intelligence (AI) algorithms including Deep Learning (DL) to determine the predictive accuracy of CpG markers for autism detection. We identified 9655 CpGs differentially methylated in autism. Among them, 2802 CpGs were inter- or non-genic and 6853 intragenic. The latter involved 4129 genes. AI analysis of differentially methylated loci appeared highly accurate for autism detection. DL yielded an AUC (95% CI) of 1.00 (1.00-1.00) for autism detection using intra- or intergenic markers by themselves or combined. The biological functional enrichment showed, four significant functions that were affected in autism: quantity of synapse, microtubule dynamics, neuritogenesis, and abnormal morphology of neurons. In this preliminary study, significant placental DNA methylation changes. AI had high accuracy for the prediction of subsequent autism development in newborns. Finally, biologically functional relevant gene pathways were identified that may play a significant role in early fetal neurodevelopmental influences on later cognition and social behavior.
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Affiliation(s)
- Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States of America
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States of America
| | - Buket Aydas
- Department of Healthcare Analytics, Meridian Health Plans, Detroit, MI, United States of America
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States of America
- * E-mail:
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Radhakrishna U, Vishweswaraiah S, Uppala LV, Szymanska M, Macknis J, Kumar S, Saleem-Rasheed F, Aydas B, Forray A, Muvvala SB, Mishra NK, Guda C, Carey DJ, Metpally RP, Crist RC, Berrettini WH, Bahado-Singh RO. Placental DNA methylation profiles in opioid-exposed pregnancies and associations with the neonatal opioid withdrawal syndrome. Genomics 2021; 113:1127-1135. [PMID: 33711455 DOI: 10.1016/j.ygeno.2021.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/29/2020] [Accepted: 03/02/2021] [Indexed: 12/11/2022]
Abstract
Opioid abuse during pregnancy can result in Neonatal Opioid Withdrawal Syndrome (NOWS). We investigated genome-wide methylation analyses of 96 placental tissue samples, including 32 prenatally opioid-exposed infants with NOWS who needed therapy (+Opioids/+NOWS), 32 prenatally opioid-exposed infants with NOWS who did not require treatment (+Opioids/-NOWS), and 32 prenatally unexposed controls (-Opioids/-NOWS, control). Statistics, bioinformatics, Artificial Intelligence (AI), including Deep Learning (DL), and Ingenuity Pathway Analyses (IPA) were performed. We identified 17 dysregulated pathways thought to be important in the pathophysiology of NOWS and reported accurate AI prediction of NOWS diagnoses. The DL had an AUC (95% CI) =0.98 (0.95-1.0) with a sensitivity and specificity of 100% for distinguishing NOWS from the +Opioids/-NOWS group and AUCs (95% CI) =1.00 (1.0-1.0) with a sensitivity and specificity of 100% for distinguishing NOWS versus control and + Opioids/-NOWS group versus controls. This study provides strong evidence of methylation dysregulation of placental tissue in NOWS development.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA.
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Lavanya V Uppala
- College of Information Science & Technology, University of Nebraska at Omaha, Peter Kiewit Institute, Omaha, NE, USA
| | - Marta Szymanska
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | | | - Sandeep Kumar
- Department of Pathology, Beaumont Health System, Royal Oak, MI, USA
| | - Fozia Saleem-Rasheed
- Department of Newborn Medicine, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - Buket Aydas
- Department of Healthcare Analytics, Meridian Health Plans, Detroit, MI, USA
| | - Ariadna Forray
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | | | - Nitish K Mishra
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center Omaha, NE, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center Omaha, NE, USA
| | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Raghu P Metpally
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Richard C Crist
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wade H Berrettini
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Geisinger Clinic, Danville, PA, USA
| | - Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
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Damiani G, Grossi E, Berti E, Conic RRZ, Radhakrishna U, Pacifico A, Bragazzi NL, Piccinno R, Linder D. Artificial neural networks allow response prediction in squamous cell carcinoma of the scalp treated with radiotherapy. J Eur Acad Dermatol Venereol 2020; 34:1369-1373. [PMID: 31968143 DOI: 10.1111/jdv.16210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/07/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Epithelial neoplasms of the scalp account for approximately 2% of all skin cancers and for about 10-20% of the tumours affecting the head and neck area. Radiotherapy is suggested for localized cutaneous squamous cell carcinomas (cSCC) without lymph node involvement, multiple or extensive lesions, for patients refusing surgery, for patients with a poor general medical status, as adjuvant for incompletely excised lesions and/or as a palliative treatment. To date, prognostic risk factors in scalp cSCC patients are poorly characterized. OBJECTIVE To identify patterns of patients with higher risk of postradiotherapy recurrence. METHODS A retrospective observational study was performed on scalp cSCC patients with histological diagnosis who underwent conventional radiotherapy (50-120 kV) (between 1996 and 2008, follow-up from 1 to 140 months, median 14 months). Out of the 79 enrolled patients, 22 (27.8%) had previously undergone a surgery. Two months after radiotherapy, 66 (83.5%) patients achieved a complete remission, 6 (7.6%) a partial remission, whereas 2 (2.5%) proved non-responsive to the treatment and 5 cases were lost to follow-up. Demographical and clinical data were preliminarily analysed with classical descriptive statistics and with principal component analysis. All data were then re-evaluated with a machine learning-based approach using a 4th generation artificial neural networks (ANNs)-based algorithm. RESULTS Artificial neural networks analysis revealed four scalp cSCC profiles among radiotherapy responsive patients, not previously described: namely, (i) stage T2 cSCC type, aged 70-80 years; (ii) frontal cSCC type, aged <70 years; (iii) non-recurrent nodular or nodulo-ulcerated, stage T3 cSCC type, of the vertex and treated with >60 Grays (Gy); and (iv) flat, occipital, stage T1 cSCC type, treated with 50-59 Gy. The model uncovering these four predictive profiles displayed 85.7% sensitivity, 97.6% specificity and 91.7% overall accuracy. CONCLUSIONS Patient profiling/phenotyping with machine learning may be a new, helpful method to stratify patients with scalp cSCCs who may benefit from a RT-treatment.
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Affiliation(s)
- G Damiani
- Clinical Dermatology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Young Dermatologists Italian Network, Centro Studi GISED, Bergamo, Italy
| | - E Grossi
- Fondazione Villa Santa Maria, Tavernerio, Como, Italy
| | - E Berti
- Phototherapy Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Dermatology Unit, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico di Milano, Università degli Studi di Milano, Milan, Italy
| | - R R Z Conic
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - U Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - A Pacifico
- Clinical Dermatology Department, IRCCS S. Gallicano Dermatological Institute, Rome, Italy
| | - N L Bragazzi
- School of Public Health, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - R Piccinno
- Phototherapy Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Dermatology Unit, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico di Milano, Università degli Studi di Milano, Milan, Italy
| | - D Linder
- Ben Gurion University of the Negev, Beer Sheva, Israel
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Bahado-Singh R, Vishweswaraiah S, Mishra NK, Guda C, Radhakrishna U. Placental DNA methylation changes in detection of tetralogy of Fallot. Ultrasound Obstet Gynecol 2020; 55:768-775. [PMID: 30977211 DOI: 10.1002/uog.20292] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVES To determine whether the methylation level of cytosine nucleotides in placental DNA can be used to predict tetralogy of Fallot (TOF) and provide insights into the developmental mechanism of this condition. METHODS Tissue sections were obtained from formalin-fixed paraffin-embedded specimens of placental tissue obtained at birth from eight cases with non-chromosomal, non-syndromic TOF and 10 unaffected newborns. The Illumina Infinium HumanMethylation450 BeadChip assay was used to measure cytosine ('CpG' or 'cg') methylation levels at loci throughout the placental genome. Differential methylation was assessed by comparing the β-values (a measure of the extent of cytosine methylation) for individual CpG loci in fetuses with TOF vs in controls. The most discriminating CpG sites were determined based on a preset cut-off of ≥ 2.0-fold change in the methylation level. The predictive accuracy of CpG loci with significant methylation changes for TOF was determined by the area under the receiver-operating-characteristics curve (AUC). A false-discovery-rate (FDR) P-value < 0.05 was used to define a statistically significant difference in the methylation level. Ingenuity Pathway Analysis (IPA) (Qiagen) was used to identify gene pathways that were significantly overexpressed, and thus altered, in TOF cases compared with controls. RESULTS We found a total of 165 significantly differentially methylated CpG loci in TOF cases compared with controls, in 165 separate genes. These biomarkers demonstrated from fair to excellent individual predictive accuracy for TOF detection, with AUCs ≥ 0.75 (FDR P-value < 0.001 for all). The following CpG loci (gene) had the highest predictive accuracy: cg05273049 (ARHGAP22; AUC = 1.00; 95% CI, 1.00-1.00), cg02540011 (CDK5; AUC = 0.96; 95% CI, 0.87-1.00), cg08404201 (TRIM27; AUC = 0.95; 95% CI, 0.84-1.00) and cg00687252 (IER3; AUC = 0.95; 95% CI, 0.84-1.00). IPA revealed over-representation (dysregulation) of 14 gene pathways involved in normal cardiac development, including cardiomyocyte differentiation via bone morphogenetic protein receptors, cardiac hypertrophy signaling and role of nuclear factor of activated T cells in cardiac hypertrophy. Cardiac hypertrophy is an important feature of TOF. CONCLUSIONS Analysis of placental DNA cytosine methylation changes yielded accurate markers for TOF detection and provided mechanistic information on TOF development. Our work appears to confirm the central role of epigenetic changes and of the placenta in the development of TOF. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- R Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - S Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - N K Mishra
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - C Guda
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - U Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
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Bahado-Singh RO, Vishweswaraiah S, Aydas B, Yilmaz A, Saiyed NM, Mishra NK, Guda C, Radhakrishna U. Precision cardiovascular medicine: artificial intelligence and epigenetics for the pathogenesis and prediction of coarctation in neonates. J Matern Fetal Neonatal Med 2020; 35:457-464. [PMID: 32019381 DOI: 10.1080/14767058.2020.1722995] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Advances in omics and computational Artificial Intelligence (AI) have been said to be key to meeting the objectives of precision cardiovascular medicine. The focus of precision medicine includes a better assessment of disease risk and understanding of disease mechanisms. Our objective was to determine whether significant epigenetic changes occur in isolated, non-syndromic CoA. Further, we evaluated the AI analysis of DNA methylation for the prediction of CoA.Methods: Genome-wide DNA methylation analysis of newborn blood DNA was performed in 24 isolated, non-syndromic CoA cases and 16 controls using the Illumina HumanMethylation450 BeadChip arrays. Cytosine nucleotide (CpG) methylation changes in CoA in each of 450,000 CpG loci were determined. Ingenuity pathway analysis (IPA) was performed to identify molecular and disease pathways that were epigenetically dysregulated. Using methylation data, six artificial intelligence (AI) platforms including deep learning (DL) was used for CoA detection.Results: We identified significant (FDR p-value ≤ .05) methylation changes in 65 different CpG sites located in 75 genes in CoA subjects. DL achieved an AUC (95% CI) = 0.97 (0.80-1) with 95% sensitivity and 98% specificity. Gene ontology (GO) analysis yielded epigenetic alterations in important cardiovascular developmental genes and biological processes: abnormal morphology of cardiovascular system, left ventricular dysfunction, heart conduction disorder, thrombus formation, and coronary artery disease.Conclusion: In an exploratory study we report the use of AI and epigenomics to achieve important objectives of precision cardiovascular medicine. Accurate prediction of CoA was achieved using a newborn blood spot. Further, we provided evidence of a significant epigenetic etiology in isolated CoA development.
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Affiliation(s)
- Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Buket Aydas
- Department of Mathematics & Computer Science, Albion College, Albion, Michigan, USA
| | - Ali Yilmaz
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Nazia M Saiyed
- Nirma Institute of Science, Nirma University, Ahmedabad, India
| | - Nitish K Mishra
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
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Radhakrishna U, Singh RB, Taylor RW, Vishweswaraiah S, Aydas B, Szymanska M, Wharton K, Yilmaz A. 615: Artificial Intelligence accurately predicts outcomes in Preterm PROM. Am J Obstet Gynecol 2020. [DOI: 10.1016/j.ajog.2019.11.631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Vishweswaraiah S, Singh RB, Talbot C, Aydas B, Southekal S, Mishra NK, Friedman P, Yilmaz A, Guda C, Radhakrishna U. 614: Artificial Intelligence and epigenomic analysis of cell-free fetal DNA for Congenital Heart Defect (CHD) detection. Am J Obstet Gynecol 2020. [DOI: 10.1016/j.ajog.2019.11.630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bahado-Singh RO, Vishweswaraiah S, Aydas B, Mishra NK, Yilmaz A, Guda C, Radhakrishna U. Artificial intelligence analysis of newborn leucocyte epigenomic markers for the prediction of autism. Brain Res 2019; 1724:146457. [DOI: 10.1016/j.brainres.2019.146457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 01/05/2023]
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Radhakrishna U, Albayrak S, Zafra R, Baraa A, Vishweswaraiah S, Veerappa AM, Mahishi D, Saiyed N, Mishra NK, Guda C, Ali-Fehmi R, Bahado-Singh RO. Placental epigenetics for evaluation of fetal congenital heart defects: Ventricular Septal Defect (VSD). PLoS One 2019; 14:e0200229. [PMID: 30897084 PMCID: PMC6428297 DOI: 10.1371/journal.pone.0200229] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 03/11/2019] [Indexed: 12/19/2022] Open
Abstract
Ventricular Septal Defect (VSD), the most common congenital heart defect, is characterized by a hole in the septum between the right and left ventricles. The pathogenesis of VSD is unknown in most clinical cases. There is a paucity of data relevant to epigenetic changes in VSD. The placenta is a fetal tissue crucial in cardiac development and a potentially useful surrogate for evaluating the development of heart tissue. To understand epigenetic mechanisms that may play a role in the development of VSD, genome-wide DNA methylation assay on placentas of 8 term subjects with isolated VSD and no known or suspected genetic syndromes and 10 unaffected controls was performed using the Illumina HumanMethylation450 BeadChip assay. We identified a total of 80 highly accurate potential CpGs in 80 genes for detection of VSD; area under the receiver operating characteristic curve (AUC ROC) 1.0 with significant 95% CI (FDR) p-values < 0.05 for each individual locus. The biological processes and functions for many of these differentially methylated genes are previously known to be associated with heart development or disease, including cardiac ventricle development (HEY2, ISL1), heart looping (SRF), cardiac muscle cell differentiation (ACTC1, HEY2), cardiac septum development (ISL1), heart morphogenesis (SRF, HEY2, ISL1, HEYL), Notch signaling pathway (HEY2, HEYL), cardiac chamber development (ISL1), and cardiac muscle tissue development (ACTC1, ISL1). In addition, we identified 8 microRNAs that have the potential to be biomarkers for the detection of VSD including: miR-191, miR-548F1, miR-148A, miR-423, miR-92B, miR-611, miR-2110, and miR-548H4. To our knowledge this is the first report in which placental analysis has been used for determining the pathogenesis of and predicting VSD.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States of America
- * E-mail:
| | - Samet Albayrak
- Department of Obstetrics and Gynaecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Rita Zafra
- Department of Obstetrics and Gynaecology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Alosh Baraa
- Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States of America
| | - Avinash M. Veerappa
- Department of Studies in Genetics and Genomics, Laboratory of Genomic Sciences, University of Mysore, Mysore, India
| | - Deepthi Mahishi
- Department of Studies in Genetics and Genomics, Laboratory of Genomic Sciences, University of Mysore, Mysore, India
| | - Nazia Saiyed
- Biotechnology, Nirma Institute of Science, Nirma University, Ahmedabad, India
| | - Nitish K. Mishra
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Centre Omaha, Nebraska, United States of America
| | - Chittibabu Guda
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Centre Omaha, Nebraska, United States of America
| | - Rouba Ali-Fehmi
- Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States of America
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Kwon Kim S, Vishweswaraiah S, Macknis J, Lalwani A, Mishra NK, Guda C, Ogunyemi D, Radhakrishna U, Bahado-Singh R. 511: New-onset postpartum preeclampsia: Mechanisms and Prediction. Am J Obstet Gynecol 2019. [DOI: 10.1016/j.ajog.2018.11.533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Radhakrishna U, Vishweswaraiah S, Veerappa AM, Zafra R, Albayrak S, Sitharam PH, Saiyed NM, Mishra NK, Guda C, Bahado-Singh R. Newborn blood DNA epigenetic variations and signaling pathway genes associated with Tetralogy of Fallot (TOF). PLoS One 2018; 13:e0203893. [PMID: 30212560 PMCID: PMC6136787 DOI: 10.1371/journal.pone.0203893] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/29/2018] [Indexed: 12/31/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common Critical Congenital Heart Defect (CCHD). The etiology of TOF is unknown in most cases. Preliminary data from our group and others suggest that epigenetic changes may play an important role in CHD. Epidemiologically, a significant percentage of CHD including TOF fail to be diagnosed in the prenatal and early newborn period which can negatively affect health outcomes. We performed genome-wide methylation assay in newborn blood in 24 non-syndromic TOF cases and 24 unaffected matched controls using Illumina Infinium HumanMethylation450 BeadChips. We identified 64 significantly differentially methylated CpG sites in TOF cases, of which 25 CpG sites had high predictive accuracy for TOF, based on the area under the receiver operating characteristics curve (AUC ROC) ≥ 0.90). The CpG methylation difference between TOF and controls was ≥10% in 51 CpG targets suggesting biological significance. Gene ontology analysis identified significant biological processes and functions related to these differentially methylated genes, including: CHD development, cardiomyopathy, diabetes, immunological, inflammation and other plausible pathways in CHD development. Multiple genes known or plausibly linked to heart development and post-natal heart disease were found to be differentially methylated in the blood DNA of newborns with TOF including: ABCB1, PPP2R5C, TLR1, SELL, SCN3A, CREM, RUNX and LHX9. We generated novel and highly accurate putative molecular markers for TOF detection using leucocyte DNA and thus provided information on pathogenesis of TOF.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States of America
- * E-mail:
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States of America
| | - Avinash M. Veerappa
- Department of Studies in Genetics and Genomics, Laboratory of Genomic Sciences, University of Mysore, Mysore, Karnataka, India
| | - Rita Zafra
- Department of Obstetrics and Gynecology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Samet Albayrak
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Prajna H. Sitharam
- Department of Studies in Genetics and Genomics, Laboratory of Genomic Sciences, University of Mysore, Mysore, Karnataka, India
| | - Nazia M. Saiyed
- Biotechnology, Nirma Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Nitish K. Mishra
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center Omaha, Omaha, Nebraska, United States of America
| | - Chittibabu Guda
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center Omaha, Omaha, Nebraska, United States of America
| | - Ray Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, United States of America
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Bahado-Singh RO, Vishweswaraia S, Radhakrishna U. P2‐275: NON‐INVASIVE EPIGENOMIC DETECTION OF ALZHEIMER'S DISEASE AND ELUCIDATION OF ITS PATHOPHYSIOLOGY. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ray O. Bahado-Singh
- Department of Obstetrics and GynecologyOakland University William Beaumont School of MedicineRoyal OakMIUSA
| | - Sangeetha Vishweswaraia
- Department of Obstetrics and GynecologyOakland University William Beaumont School of MedicineRoyal OakMIUSA
| | - Uppala Radhakrishna
- Department of Obstetrics and GynecologyOakland University William Beaumont School of MedicineRoyal OakMIUSA
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Sheth FJ, Radhakrishna U, Morris MA, Blouin JL, Sheth JJ, Multani A, Antonarakis SE. Cytogenetic, Molecular and FISH Analysis of an Isodicentric Chromosome 21 idic(21)(q22.3) in a Mildly-Affected Patient with Down Syndrome. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2007.11885998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Frenny J Sheth
- FRIGE HOUSE (Foundation for Research in Genetics and Endocrinology), Genetic Centre, 15, Kapidway, Jodhpur Gam Road, Satellite, Ahmedabad 380 015. Gujarat, India
| | | | | | | | - Jayesh J Sheth
- FRIGE HOUSE (Foundation for Research in Genetics and Endocrinology), Genetic Centre, 15, Kapidway, Jodhpur Gam Road, Satellite, Ahmedabad 380 015. Gujarat, India
| | - Asha Multani
- Department of Cell Biology, University of Texas, Houston, Texas, USA
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Ratnamala U, Jhala D, Jain NK, Saiyed NM, Raveendrababu M, Rao MV, Mehta TY, Al-Ali FM, Raval K, Nair S, Chandramohan NK, Kuracha MR, Nath SK, Radhakrishna U. Expanding the spectrum ofγ-secretase gene mutation-associated phenotypes: two novel mutations segregating with familial hidradenitis suppurativa (acne inversa) and acne conglobata. Exp Dermatol 2016; 25:314-6. [DOI: 10.1111/exd.12911] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Uppala Ratnamala
- Department of Pharmacology; Creighton University; Omaha NE USA
- Department of Life Sciences; Gujarat University; Ahmedabad India
| | - Devendrasinh Jhala
- Department of Zoology; School of Science; Gujarat University; Ahmedabad India
| | - Nayan K. Jain
- Department of Life Sciences; Gujarat University; Ahmedabad India
| | - Nazia M. Saiyed
- Department of Biotechnology; Institute of Science; Nirma University; Ahmedabad India
| | - Meda Raveendrababu
- Department of Zoology; School of Science; Gujarat University; Ahmedabad India
| | - Mandava V. Rao
- Department of Zoology; School of Science; Gujarat University; Ahmedabad India
| | - Timir Y. Mehta
- Samarpan Medical & Research Organization on Skin; Modasa India
| | - Faiza M. Al-Ali
- Dermatology Centre; Rashid Hospital; Dubai Health Authority; Dubai UAE
| | - Kavi Raval
- Department of Radiology; Sinai-Grace Hospital; Detroit MI USA
| | - Sreelatha Nair
- Department of Fetal Medicine; Lifeline Genetics and Research Centre; Lifeline Hospital; Adoor India
| | | | | | - Swapan K. Nath
- Arthritis and Immunology Research Program; Oklahoma Medical Research Foundation; Oklahoma City OK USA
| | - Uppala Radhakrishna
- Green Cross Voluntary Blood Bank; Ahmedabad India
- Obstetrics and Gynecology; Oakland University William Beaumont School of Medicine; Royal Oak MI USA
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Bahado-Singh RO, Zaffra R, Albayarak S, Chelliah A, Bolinjkar R, Turkoglu O, Radhakrishna U. Epigenetic markers for newborn congenital heart defect (CHD). J Matern Fetal Neonatal Med 2015; 29:1881-7. [PMID: 26429603 DOI: 10.3109/14767058.2015.1069811] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Our objective was to determine whether there were significant differences in genome-wide DNA methylation in newborns with major congenital heart defect (CHD) compared to controls. We also evaluated methylation of cytosines in CpG motifs for the detection of these CHDs. METHODS Genome-wide DNA methylation analysis was performed on DNA from 60 newborns with various CHDs, including hypoplastic left heart syndrome, ventricular septal deficit, atrial septal defect, pulmonary stenosis, coarctation of the aorta and Tetralogy of Fallot, and 32 controls. RESULTS Highly significant differences in cytosine methylation were seen in a large number of genes throughout the genome for all CHD categories. Gene ontology analysis of CHD overall indicated over-represented biological processes involving cell development and differentiation, and anatomical structure morphogenesis. Methylation of individual cytosines in CpG motifs had high diagnostic accuracy for the detection of CHD. For example, for coarctation one predictive model based on levels of particular cytosine nucleotides achieved a sensitivity of 100% and specificity of 93.8% (AUC = 0.974, p < 0.00001). CONCLUSION Profound differences in cytosine methylation were observed in hundreds of genes in newborns with different types of CHD. There appears to be the potential for development of accurate genetic biomarkers for CHD detection in newborns.
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Affiliation(s)
- Ray O Bahado-Singh
- a Department of Obstetrics and Gynecology , William Beaumont School of Medicine, Oakland University , Royal Oak , MI , USA and
| | - Rita Zaffra
- b Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Samet Albayarak
- b Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Anushka Chelliah
- b Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Rashmi Bolinjkar
- b Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Onur Turkoglu
- a Department of Obstetrics and Gynecology , William Beaumont School of Medicine, Oakland University , Royal Oak , MI , USA and
| | - Uppala Radhakrishna
- a Department of Obstetrics and Gynecology , William Beaumont School of Medicine, Oakland University , Royal Oak , MI , USA and
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Affiliation(s)
- Uppala Radhakrishna
- Department of Surgery-Transplant, Nebraska Medical Center Omaha, NE, USA, and Green Cross Voluntary Blood Bank Pathology and RIA Laboratory, Ahmedabad, India
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Radhakrishna U, Nath SK, McElreavey K, Ratnamala U, Sun C, Maiti AK, Gagnebin M, Béna F, Newkirk HL, Sharp AJ, Everman DB, Murray JC, Schwartz CE, Antonarakis SE, Butler MG. Genome-wide linkage and copy number variation analysis reveals 710 kb duplication on chromosome 1p31.3 responsible for autosomal dominant omphalocele. J Med Genet 2012; 49:270-6. [PMID: 22499347 DOI: 10.1136/jmedgenet-2012-100826] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Omphalocele is a congenital birth defect characterised by the presence of internal organs located outside of the ventral abdominal wall. The purpose of this study was to identify the underlying genetic mechanisms of a large autosomal dominant Caucasian family with omphalocele. METHODS AND FINDINGS A genetic linkage study was conducted in a large family with an autosomal dominant transmission of an omphalocele using a genome-wide single nucleotide polymorphism (SNP) array. The analysis revealed significant evidence of linkage (non-parametric NPL = 6.93, p=0.0001; parametric logarithm of odds (LOD) = 2.70 under a fully penetrant dominant model) at chromosome band 1p31.3. Haplotype analysis narrowed the locus to a 2.74 Mb region between markers rs2886770 (63014807 bp) and rs1343981 (65757349 bp). Molecular characterisation of this interval using array comparative genomic hybridisation followed by quantitative microsphere hybridisation analysis revealed a 710 kb duplication located at 63.5-64.2 Mb. All affected individuals who had an omphalocele and shared the haplotype were positive for this duplicated region, while the duplication was absent from all normal individuals of this family. Multipoint linkage analysis using the duplication as a marker yielded a maximum LOD score of 3.2 at 1p31.3 under a dominant model. The 710 kb duplication at 1p31.3 band contains seven known genes including FOXD3, ALG6, ITGB3BP, KIAA1799, DLEU2L, PGM1, and the proximal portion of ROR1. Importantly, this duplication is absent from the database of genomic variants. CONCLUSIONS The present study suggests that development of an omphalocele in this family is controlled by overexpression of one or more genes in the duplicated region. To the authors' knowledge, this is the first reported association of an inherited omphalocele condition with a chromosomal rearrangement.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
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Klopocki E, Lohan S, Doelken SC, Stricker S, Ockeloen CW, Soares Thiele de Aguiar R, Lezirovitz K, Mingroni Netto RC, Jamsheer A, Shah H, Kurth I, Habenicht R, Warman M, Devriendt K, Kordass U, Hempel M, Rajab A, Mäkitie O, Naveed M, Radhakrishna U, Antonarakis SE, Horn D, Mundlos S. Duplications of BHLHA9 are associated with ectrodactyly and tibia hemimelia inherited in non-Mendelian fashion. J Med Genet 2011; 49:119-25. [PMID: 22147889 DOI: 10.1136/jmedgenet-2011-100409] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Split-hand/foot malformation (SHFM)-also known as ectrodactyly-is a congenital disorder characterised by severe malformations of the distal limbs affecting the central rays of hands and/or feet. A distinct entity termed SHFLD presents with SHFM and long bone deficiency. Mouse models suggest that a defect of the central apical ectodermal ridge leads to the phenotype. Although six different loci/mutations (SHFM1-6) have been associated with SHFM, the underlying cause in a large number of cases is still unresolved. METHODS High resolution array comparative genomic hybridisation (CGH) was performed in patients with SHFLD to detect copy number changes. Candidate genes were further evaluated for expression and function during limb development by whole mount in situ hybridisation and morpholino knock-down experiments. RESULTS Array CGH showed microduplications on chromosome 17p13.3, a locus previously associated with SHFLD. Detailed analysis of 17 families revealed that this copy number variation serves as a susceptibility factor for a highly variable phenotype with reduced penetrance, particularly in females. Compared to other known causes for SHFLD 17p duplications appear to be the most frequent cause of SHFLD. A ~11.8 kb minimal critical region was identified encompassing a single gene, BHLHA9, a putative basic loop helix transcription factor. Whole mount in situ hybridisation showed expression restricted to the limb bud mesenchyme underlying the apical ectodermal ridge in mouse and zebrafish embryos. Knock down of bhlha9 in zebrafish resulted in shortening of the pectoral fins. CONCLUSIONS Genomic duplications encompassing BHLHA9 are associated with SHFLD and non-Mendelian inheritance characterised by a high degree of non-penetrance with sex bias. Knock-down of bhlha9 in zebrafish causes severe reduction defects of the pectoral fin, indicating a role for this gene in limb development.
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Affiliation(s)
- Eva Klopocki
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Ratnamala U, Lyle R, Rawal R, Singh R, Vishnupriya S, Himabindu P, Rao V, Aggarwal S, Paluru P, Bartoloni L, Young TL, Paoloni-Giacobino A, Morris MA, Nath SK, Antonarakis SE, Radhakrishna U. Refinement of the X-linked nonsyndromic high-grade myopia locus MYP1 on Xq28 and exclusion of 13 known positional candidate genes by direct sequencing. Invest Ophthalmol Vis Sci 2011; 52:6814-9. [PMID: 21357393 DOI: 10.1167/iovs.10-6815] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Myopia is a common vision problem affecting almost one third of the world's population. It can occur as an isolated genetic condition or be associated with other anomalies and/or syndromes. Seventeen myopia loci have been identified on various chromosomes; however, no specific gene mutations have yet been identified. METHODS Two large multigeneration Asian Indian pedigrees (UR006 and UR077) with isolated, nonsyndromic myopia were studied, in which the condition appeared to segregate as an X-linked recessive trait (MYP1; MIM 310460). The degree of myopia was variable in both families, ranging from -6 to -23 D (mean, -8.48 D) with the majority >7.0 D. To map the myopia locus in these families, polymorphic microsatellite markers covering the entire X chromosome were used in linkage analyses performed on 42 genomic DNA samples (13 affected and 29 normal) from both families. RESULTS Marker DXYS154, which is located within the pseudoautosomal region in distal Xq28 (PAR2; pseudoautosomal region 2), gave a combined maximum LOD score of 5.3 at = 0 under an autosomal recessive model. Other markers in the region (near but not within the PAR2 region) that showed no recombination with the phenotype in both the families included DXS1108, DXS8087, and F8i13. CONCLUSIONS Observation of recombination in family UR006 refined the disease locus to a ∼1.25-Mb region flanked by the proximal marker DXS1073 and distal marker DXYS154. Mutation search in exons and splice junctions of candidate genes CTAG2, GAB3, MPP1, F8Bver, FUNDC2, VBP1, RAB39B, CLIC2, TMLHE, SYBL, IL9R, SPRY3, and CXYorf1 did not detect a pathogenic or predisposing variant.
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Affiliation(s)
- Uppala Ratnamala
- Department of Pharmacology, Creighton University, Omaha, Nebraska, USA
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Rydzanicz M, Nath SK, Sun C, Podfigurna-Musielak M, Frajdenberg A, Mrugacz M, Winters D, Ratnamala U, Radhakrishna U, Bejjani BA, Gajecka M. Identification of novel suggestive loci for high-grade myopia in Polish families. Mol Vis 2011; 17:2028-39. [PMID: 21850178 PMCID: PMC3154124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 07/18/2011] [Indexed: 10/31/2022] Open
Abstract
PURPOSE Myopia is the most common human eye disorder with complex genetic and environmental causes. To date, several myopia loci have been identified in families of different geographic origin. However, no causative gene(s) have yet been identified. The aim of this study was the characterization of Polish families with high-grade myopia, including genetic analysis. METHODS Forty-two multiplex Polish families with non-syndromic high-grade myopia participated in the study. All family members underwent detailed ophthalmic examination and high-grade myopia was defined as ≤-6.0 diopters (D) based on the spherical refractive error. A genome-wide single nucleotide polymorphism (SNP)-based high-density linkage scan was performed using Affymetrix Human SNP Array 6.0 on a selected family (HM-32) with multiple affected individuals. RESULTS Nonparametric linkage analysis identified three novel loci in family HM-32 at chromosome 7p22.1-7p21.1 ([NPL] 8.26; p=0.006), chromosome 7p12.3-7p11.2 ([NPL] 8.23; p=0.006), and chromosome 12p12.3-12p12.1 ([NPL] 8.02; p=0.006), respectively. The effect of linkage disequilibrium on linkage due to dense SNP map was addressed by systematically pruning SNPs from the linkage panel. CONCLUSIONS Haplotype analysis with informative crossovers in affected individuals defined a 12.2; 10.9; and 9.5 Mb genomic regions for high-grade myopia spanned between SNP markers rs11977885/rs10950639, rs11770622/rs9719399, and rs4763417/rs10842388 on chromosomes 7p22.1-7p21.1, 7p12.3-7p11.2, and 12p12.3-12p12.1, respectively.
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Affiliation(s)
| | - Swapan K. Nath
- Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Celi Sun
- Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | | | - Agata Frajdenberg
- Department of Ophthalmology, Marcinkowski University of Medical Sciences, Poznan, Poland,Namsos Hospital, Department of Ophthalmology, Namsos, Norway,University Hospital in Linköping, Department of Ophthalmology, Linköping, Sweden
| | - Malgorzata Mrugacz
- Department of Pediatric Ophthalmology, Medical University of Bialystok, Bialystok, Poland
| | - Daniel Winters
- School of Molecular Biosciences, Washington State University, Spokane, WA
| | - Uppala Ratnamala
- Department of Surgery-Transplant, University of Nebraska Medical Center, Omaha, NE
| | - Uppala Radhakrishna
- Department of Surgery-Transplant, University of Nebraska Medical Center, Omaha, NE
| | | | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland,Basic Medical Sciences Program, WWAMI, Spokane, WA
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Al-Ali FMS, Ratnamala U, Mehta TY, Naveed M, Al-Ali MT, Al-Khaja N, Sheth JJ, Master DC, Maiti AK, Chetan GK, Nath SK, Radhakrishna U. Hidradenitis suppurativa (or Acne inversa) with autosomal dominant inheritance is not linked to chromosome 1p21.1-1q25.3 region. Exp Dermatol 2010; 19:851-3. [PMID: 20698881 DOI: 10.1111/j.1600-0625.2010.01088.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition characterized by swollen, painful, inflamed lesions in the axillae, groin, armpits and other parts of the body that contain apocrine glands. The aetiology of HS is unknown, and earlier reports indicate genetic locus responsible for this phenotype on chromosome 1p21.1-1q25.3, but no causative gene(s) have yet been identified. We studied two large multigeneration pedigrees (UR251 and UR252), in which the condition appeared to segregate as an autosomal dominant trait with 100% penetrance. No skipping of generations was observed in either family. Pedigrees consist of 96 individuals, including 25 affected individuals. Because of squamous cell carcinoma, a few deaths were reported in family UR0251. The locus on chromosome 1p21.1-1p25.3, known from previous studies is associated with HS, was excluded in both families by linkage and haplotype analyses. Further studies are in progress to identify the region that is associated with the phenotype in these families.
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Foster JM, Radhakrishna U, Govindarajan V, Carreau JH, Gatalica Z, Sharma P, Nath SK, Loggie BW. Clinical implications of novel activating EGFR mutations in malignant peritoneal mesothelioma. World J Surg Oncol 2010; 8:88. [PMID: 20942962 PMCID: PMC2970593 DOI: 10.1186/1477-7819-8-88] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 10/13/2010] [Indexed: 12/21/2022] Open
Abstract
Background There is a paucity of information about the molecular perturbations involved in MPM tumor formation. We previously reported that EGFR-TK mutations in MPM were predictive of achieving optimal surgical cytoreduction, but the status of EGFR pathway activation potential of these mutations was not known. Here we present the mutant EGFR activating potential and the matured survival data of the EGFR mutant(mut+) relative to wild type EGFR(mut-) mesothelioma. Methods Twenty-nine patients were evaluated and their tumors were probed for mutations in the catalytic TK-domain. Twenty-five patients were treated with cytoreductive surgery and complete clinical data was available for comparison of the mut+ and mut- groups. A COS-7 cell expression model was used to determine mutation activating profiles and response to erlotinib. Results Functional mutations were found in 31%(9/29) of patients; 7 of these mutations were novel and another was the L858R mutation. All missense mutations were found to be activating mutations and responsive to erlotinib. Of the 25 patients managed surgically, there were 7 mut+ and 18 mut-. Two of 7 (29%) mut+ developed progressive disease and died with a median follow-up time of 22 months; while 13/18 (72%) mut- developed progressive disease and 10/18 (56%) died with median TTP of 12 months and median survival of 14 months. Conclusions The novel EGFR mutations identified are activating mutations responsive to erlotinib. The mut+ subset have a 'relative' improved outcome. Erlotinib may have a role in MPM and exploration for mutations in a larger patient cohort is warranted.
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Affiliation(s)
- Jason M Foster
- Department of Surgery, Creighton Cancer Center, Creighton University, Omaha, NE, USA.
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Bashamboo A, Ferraz-de-Souza B, Lourenço D, Lin L, Sebire NJ, Montjean D, Bignon-Topalovic J, Mandelbaum J, Siffroi JP, Christin-Maitre S, Radhakrishna U, Rouba H, Ravel C, Seeler J, Achermann JC, McElreavey K. Human male infertility associated with mutations in NR5A1 encoding steroidogenic factor 1. Am J Hum Genet 2010; 87:505-12. [PMID: 20887963 DOI: 10.1016/j.ajhg.2010.09.009] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Revised: 09/05/2010] [Accepted: 09/15/2010] [Indexed: 10/19/2022] Open
Abstract
One in seven couples worldwide are infertile, and male factor infertility accounts for approximately 30%-50% of these cases. Although many genes are known to be essential for gametogenesis, there are surprisingly few monogenic mutations that have been conclusively demonstrated to cause human spermatogenic failure. A nuclear receptor, NR5A1 (also called steroidogenic factor 1), is a key transcriptional regulator of genes involved in the hypothalamic-pituitary-steroidogenic axis, and it is expressed in the steroidogenic tissue of the developing and adult human gonad. Mutations of NR5A1 have been reported in 46,XY disorders of sex development and in 46,XX primary ovarian insufficiency. To test the hypothesis that mutations in NR5A1 cause male infertility, we sequenced NR5A1 in 315 men with idiopathic spermatogenic failure. We identified seven men with severe spermatogenic failure who carried missense mutations in NR5A1. Functional studies indicated that these mutations impaired NR5A1 transactivational activity. We did not observe these mutations in more than 4000 control alleles, including the entire coding sequence of 359 normospermic men and 370 fertile male controls. NR5A1 mutations are found in approximately 4% of men with otherwise unexplained severe spermatogenic failure.
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Gajecka M, Radhakrishna U, Winters D, Nath SK, Rydzanicz M, Ratnamala U, Ewing K, Molinari A, Pitarque JA, Lee K, Leal SM, Bejjani BA. Localization of a gene for keratoconus to a 5.6-Mb interval on 13q32. Invest Ophthalmol Vis Sci 2008; 50:1531-9. [PMID: 19011015 DOI: 10.1167/iovs.08-2173] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Keratoconus (KTCN) is a noninflammatory thinning and anterior protrusion of the cornea that results in steepening and distortion of the cornea, altered refractive powers, and reduced visual acuity. Several loci responsible for a familial form of KTCN have been mapped, however; no mutations in any genes have been identified for any of these loci. There is also evidence that VSX1 and SOD1 may be involved in the etiology of KTCN. The purpose of this study was to verify the available data and to identify a new keratoconus susceptibility locus. METHODS KTCN without other ocular or systemic features was diagnosed in 18 families. VSX1 and SOD1 sequencing was performed on affected individuals and control subjects. Genomewide linkage analysis was then performed in all families using polymorphic microsatellite markers with an average spacing of 5 cM. Next, single-nucleotide polymorphism (SNP) arrays, fluorescence in situ hybridization (FISH) analysis, and a comparative genomic hybridization array were used in one family to assess a candidate region on 13q32. RESULTS All previously reported KTCN loci were excluded. VSX1 and SOD1 were sequenced, and no potentially functional variants were found. One KTCN family yielded a maximum multipoint parametric LOD score of 4.1 and multipoint nonparametric linkage (NPL) LOD score of 3.2. Multipoint linkage and haplotype analysis narrowed the locus to a 5.6-Mb region between the SNPs rs9516572 and rs3825523 on 13q32. CONCLUSIONS The results exclude VSX1 and SOD1 as potential disease-causing genes in these families and localize a novel gene for keratoconus to a 5.6-Mb interval on 13q32.
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Affiliation(s)
- Marzena Gajecka
- Basic Medical Sciences Program, Washington, Wyoming, Alaska, Montana, and Idaho, Washington State University, Spokane, Washington 99210-1495, USA
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Radhakrishna U, Mehta TY, Solanki JV, Nath SK. Genetic analysis of three large Indian pedigrees with autosomal dominant hidradenitis suppurativa. Exp Dermatol 2008. [DOI: 10.1111/j.0906-6705.2006.0436e.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Orten DJ, Fischer SM, Sorensen JL, Radhakrishna U, Cremers CW, Marres HA, Van Camp G, Welch KO, Smith RJ, Kimberling WJ. Branchio-oto-renal syndrome (BOR): novel mutations in theEYA1gene, and a review of the mutational genetics of BOR. Hum Mutat 2008; 29:537-44. [DOI: 10.1002/humu.20691] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Mehenni H, Resta N, Guanti G, Mota-Vieira L, Lerner A, Peyman M, Chong KA, Aissa L, Ince A, Cosme A, Costanza MC, Rossier C, Radhakrishna U, Burt RW, Picard D. Molecular and clinical characteristics in 46 families affected with Peutz-Jeghers syndrome. Dig Dis Sci 2007; 52:1924-33. [PMID: 17404884 DOI: 10.1007/s10620-006-9435-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Accepted: 05/12/2006] [Indexed: 01/24/2023]
Abstract
Germline mutations of the tumor suppressor gene LKB1/STK11 are responsible for the Peutz-Jeghers syndrome (PJS), an autosomal-dominant disorder characterized by mucocutaneous pigmentation, hamartomatous polyps, and an increased risk of associated malignancies. In this study, we assessed the presence of pathogenic mutations in the LKB1/STK11 gene in 46 unrelated PJS families, and also carried genotype-phenotype correlation in regard of the development of cancer in 170 PJS patients belonging to these families. All LKB1/STK11 variants detected with single-strand conformational polymorphism were confirmed by direct sequencing, and those without LKB1/STK11 mutation were further submitted to Southern blot analysis for detection of deletions/rearrangements. Statistical analysis for genotype-phenotype correlation was performed. In 59% (27/46) of unrelated PJS cases, pathogenic mutations in the LKB1/STK11 gene, including 9 novel mutations, were identified. The new mutations were 2 splice site deletion-insertions, 2 missenses, 1 nonsense, and 4 abnormal splice sites. Genotype-phenotype analysis did not yield any significant differences between patients carrying mutations in LKB1/STK11 versus those without mutations, even with respect to primary biliary adenocarcinoma. This study presents the molecular characterization and cancer occurrence of a large cohort of PJS patients, increases the mutational spectrum of LKB1/STK11 allelic variants worldwide, and provides a new insight useful for clinical diagnosis and genetic counseling of PJS families.
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Affiliation(s)
- Hamid Mehenni
- Centre Médico-Chirurgical Rond-Point-Plainpalais et Département de biologie cellulaire, Unité de recherche des maladies prédisposant aux cancers gastro-intestinaux, Université de Genève, Genève, Switzerland.
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Beiraghi S, Nath SK, Gaines M, Mandhyan DD, Hutchings D, Ratnamala U, McElreavey K, Bartoloni L, Antonarakis GS, Antonarakis SE, Radhakrishna U. Autosomal dominant nonsyndromic cleft lip and palate: significant evidence of linkage at 18q21.1. Am J Hum Genet 2007; 81:180-8. [PMID: 17564975 PMCID: PMC1950911 DOI: 10.1086/518944] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 04/05/2007] [Indexed: 01/10/2023] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common congenital facial defects, with an incidence of 1 in 700-1,000 live births among individuals of European descent. Several linkage and association studies of NSCL/P have suggested numerous candidate genes and genomic regions. A genomewide linkage analysis of a large multigenerational family (UR410) with NSCL/P was performed using a single-nucleotide-polymorphism array. Nonparametric linkage (NPL) analysis provided significant evidence of linkage for marker rs728683 on chromosome 18q21.1 (NPL=43.33 and P=.000061; nonparametric LOD=3.97 and P=.00001). Parametric linkage analysis with a dominant mode of inheritance and reduced penetrance resulted in a maximum LOD score of 3.61 at position 47.4 Mb on chromosome 18q21.1. Haplotype analysis with informative crossovers defined a 5.7-Mb genomic region spanned by proximal marker rs1824683 (42,403,918 bp) and distal marker rs768206 (48,132,862 bp). Thus, a novel genomic region on 18q21.1 was identified that most likely harbors a high-risk variant for NSCL/P in this family; we propose to name this locus "OFC11" (orofacial cleft 11).
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Affiliation(s)
- Soraya Beiraghi
- Division of Pediatric Dentistry, University of Minnesota, Minneapolis, MN, USA
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Naveed M, Nath SK, Gaines M, Al-Ali MT, Al-Khaja N, Hutchings D, Golla J, Deutsch S, Bottani A, Antonarakis SE, Ratnamala U, Radhakrishna U. Genomewide linkage scan for split-hand/foot malformation with long-bone deficiency in a large Arab family identifies two novel susceptibility loci on chromosomes 1q42.2-q43 and 6q14.1. Am J Hum Genet 2007; 80:105-11. [PMID: 17160898 PMCID: PMC1785322 DOI: 10.1086/510724] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Accepted: 11/06/2006] [Indexed: 11/04/2022] Open
Abstract
Split-hand/foot malformation with long-bone deficiency (SHFLD) is a rare, severe limb deformity characterized by tibia aplasia with or without split-hand/split-foot deformity. Identification of genetic susceptibility loci for SHFLD has been unsuccessful because of its rare incidence, variable phenotypic expression and associated anomalies, and uncertain inheritance pattern. SHFLD is usually inherited as an autosomal dominant trait with reduced penetrance, although recessive inheritance has also been postulated. We conducted a genomewide linkage analysis, using a 10K SNP array in a large consanguineous family (UR078) from the United Arab Emirates (UAE) who had disease transmission consistent with an autosomal dominant inheritance pattern. The study identified two novel SHFLD susceptibility loci at 1q42.2-q43 (nonparametric linkage [NPL] 9.8, P=.000065) and 6q14.1 (NPL 7.12, P=.000897). These results were also supported by multipoint parametric linkage analysis. Maximum multipoint LOD scores of 3.20 and 3.78 were detected for genomic locations 1q42.2-43 and 6q14.1, respectively, with the use of an autosomal dominant mode of inheritance with reduced penetrance. Haplotype analysis with informative crossovers enabled mapping of the SHFLD loci to a region of approximately 18.38 cM (8.4 Mb) between single-nucleotide polymorphisms rs1124110 and rs535043 on 1q42.2-q43 and to a region of approximately 1.96 cM (4.1 Mb) between rs623155 and rs1547251 on 6q14.1. The study identified two novel loci for the SHFLD phenotype in this UAE family.
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Affiliation(s)
- Mohammed Naveed
- Center for Arab Genomic Studies (CAGS), Dubai, United Arab Emirates
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Lyle R, Radhakrishna U, Blouin JL, Gagos S, Everman DB, Gehrig C, Delozier-Blanchet C, Solanki JV, Patel UC, Nath SK, Gurrieri F, Neri G, Schwartz CE, Antonarakis SE. Split-hand/split-foot malformation 3 (SHFM3) at 10q24, development of rapid diagnostic methods and gene expression from the region. Am J Med Genet A 2006; 140:1384-95. [PMID: 16691619 DOI: 10.1002/ajmg.a.31247] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Split-hand/split-foot malformation (SHFM, also called ectrodactyly) is a clinically variable and genetically heterogeneous group of limb malformations. Several SHFM loci have been mapped, including SHFM1 (7q21), SHFM2 (Xq26), SHFM3 (10q24), SHFM4 (3q27) and SHFM5 (2q31). To date, mutations in a gene (TP63) have only been identified for SHFM4. SHFM3 has been shown by pulsed-field gel electrophoresis to be caused by an approximately 500 kb DNA rearrangement at 10q24. This region contains a number of candidate genes for SHFM3, though which gene(s) is (are) involved in the pathogenesis of SHFM3 is not known. Our aim in this study was to improve the diagnosis of SHFM3, and to begin to understand which genes are involved in SHFM3. Here we show, using two different techniques, FISH and quantitative PCR that SHFM3 is caused by a minimal 325 kb duplication containing only two genes (BTRC and POLL). The data presented provide improved methods for diagnosis and begin to elucidate the pathogenic mechanism of SHFM3. Expression analysis of 13 candidate genes within and flanking the duplicated region shows that BTRC (present in three copies) and SUFU (present in two copies) are overexpressed in SHFM3 patients compared to controls. Our data suggest that SHFM3 may be caused by overexpression of BTRC and SUFU, both of which are involved in beta-catenin signalling.
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Affiliation(s)
- Robert Lyle
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland
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Radhakrishna U, Ratnamala U, Gaines M, Beiraghi S, Hutchings D, Golla J, Husain SA, Gambhir PS, Sheth JJ, Sheth FJ, Chetan GK, Naveed M, Solanki JV, Patel UC, Master DC, Memon R, Antonarakis GS, Antonarakis SE, Nath SK. Genomewide scan for nonsyndromic cleft lip and palate in multigenerational Indian families reveals significant evidence of linkage at 13q33.1-34. Am J Hum Genet 2006; 79:580-5. [PMID: 16909398 PMCID: PMC1559556 DOI: 10.1086/507487] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Accepted: 07/07/2006] [Indexed: 11/03/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (CL-P) is a common congenital anomaly with incidence ranging from 1 in 300 to 1 in 2,500 live births. We analyzed two Indian pedigrees (UR017 and UR019) with isolated, nonsyndromic CL-P, in which the anomaly segregates as an autosomal dominant trait. The phenotype was variable, ranging from unilateral to bilateral CL-P. A genomewide linkage scan that used approximately 10,000 SNPs was performed. Nonparametric linkage (NPL) analysis identified 11 genomic regions (NPL>3.5; P<.005) that could potentially harbor CL-P susceptibility variations. Among those, the most significant evidence was for chromosome 13q33.1-34 at marker rs1830756 (NPL=5.57; P=.00024). This was also supported by parametric linkage; MOD score (LOD scores maximized over genetic model parameters) analysis favored an autosomal dominant model. The maximum LOD score was 4.45, and heterogeneity LOD was 4.45 (alpha =100%). Haplotype analysis with informative crossovers enabled the mapping of the CL-P locus to a region of approximately 20.17 cM (7.42 Mb) between SNPs rs951095 and rs726455. Thus, we have identified a novel genomic region on 13q33.1-34 that harbors a high-risk variant for CL-P in these Indian families.
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Ravel C, El Houate B, Chantot S, Lourenço D, Dumaine A, Rouba H, Bandyopadahyay A, Radhakrishna U, Das B, Sengupta S, Mandelbaum J, Siffroi JP, McElreavey K. Haplotypes, mutations and male fertility: the story of the testis-specific ubiquitin protease USP26. Mol Hum Reprod 2006; 12:643-6. [PMID: 16888075 DOI: 10.1093/molehr/gal063] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Recently, mutations in the X-linked ubiquitin protease 26 (USP26) gene have been proposed to be associated with male infertility. In particular a 371insACA, 494T>C and 1423C>T haplotype, which results in a T123-124ins, L165S and H475Y amino acid change respectively, has been reported to be associated with Sertoli cell-only syndrome (SCOS) and an absence of sperm in the ejaculate. Here, we demonstrate that two of these changes actually correspond to the ancestral sequence of the gene and that the USP26 haplotype is present in significant frequencies in sub-Saharan African and South and East Asian populations, including in individuals with known fertility. This indicates that the allele is not associated with infertility. The pattern of frequency distribution of the derived haplotype (371delACA, 494T), which is present at high frequencies in most non-African populations could be interpreted as either a result of migration followed by simple genetic drift or alternatively as positive selection acting on the derived alleles. The latter hypothesis seems likely, because there is evidence of strong positive selection acting on the USP26 gene.
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Affiliation(s)
- C Ravel
- Reproduction, Fertility and Populations, Institut Pasteur, 25 rue du Dr Roux, Paris, France
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