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Ozyerli-Goknar E, Kala EY, Aksu AC, Bulut I, Cingöz A, Nizamuddin S, Biniossek M, Seker-Polat F, Morova T, Aztekin C, Kung SHY, Syed H, Tuncbag N, Gönen M, Philpott M, Cribbs AP, Acilan C, Lack NA, Onder TT, Timmers HTM, Bagci-Onder T. Epigenetic-focused CRISPR/Cas9 screen identifies (absent, small, or homeotic)2-like protein (ASH2L) as a regulator of glioblastoma cell survival. Cell Commun Signal 2023; 21:328. [PMID: 37974198 PMCID: PMC10652464 DOI: 10.1186/s12964-023-01335-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/26/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Glioblastoma is the most common and aggressive primary brain tumor with extremely poor prognosis, highlighting an urgent need for developing novel treatment options. Identifying epigenetic vulnerabilities of cancer cells can provide excellent therapeutic intervention points for various types of cancers. METHOD In this study, we investigated epigenetic regulators of glioblastoma cell survival through CRISPR/Cas9 based genetic ablation screens using a customized sgRNA library EpiDoKOL, which targets critical functional domains of chromatin modifiers. RESULTS Screens conducted in multiple cell lines revealed ASH2L, a histone lysine methyltransferase complex subunit, as a major regulator of glioblastoma cell viability. ASH2L depletion led to cell cycle arrest and apoptosis. RNA sequencing and greenCUT&RUN together identified a set of cell cycle regulatory genes, such as TRA2B, BARD1, KIF20B, ARID4A and SMARCC1 that were downregulated upon ASH2L depletion. Mass spectrometry analysis revealed the interaction partners of ASH2L in glioblastoma cell lines as SET1/MLL family members including SETD1A, SETD1B, MLL1 and MLL2. We further showed that glioblastoma cells had a differential dependency on expression of SET1/MLL family members for survival. The growth of ASH2L-depleted glioblastoma cells was markedly slower than controls in orthotopic in vivo models. TCGA analysis showed high ASH2L expression in glioblastoma compared to low grade gliomas and immunohistochemical analysis revealed significant ASH2L expression in glioblastoma tissues, attesting to its clinical relevance. Therefore, high throughput, robust and affordable screens with focused libraries, such as EpiDoKOL, holds great promise to enable rapid discovery of novel epigenetic regulators of cancer cell survival, such as ASH2L. CONCLUSION Together, we suggest that targeting ASH2L could serve as a new therapeutic opportunity for glioblastoma. Video Abstract.
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Affiliation(s)
- Ezgi Ozyerli-Goknar
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Freiburg, Heidelberg, Germany
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Ezgi Yagmur Kala
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Ali Cenk Aksu
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Ipek Bulut
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Ahmet Cingöz
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Sheikh Nizamuddin
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Freiburg, Heidelberg, Germany
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Martin Biniossek
- Institute for Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Fidan Seker-Polat
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
| | - Tunc Morova
- Koç University School of Medicine, Istanbul, Türkiye
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Can Aztekin
- Koç University School of Medicine, Istanbul, Türkiye
| | - Sonia H Y Kung
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Hamzah Syed
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Biostatistics, Bioinformatics and Data Management Lab, KUTTAM, Istanbul, Türkiye
| | - Nurcan Tuncbag
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Department of Chemical and Biological Engineering, Koç University, Istanbul, Türkiye
| | - Mehmet Gönen
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Department of Industrial Engineering, Koç University, Istanbul, Türkiye
| | - Martin Philpott
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Ceyda Acilan
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
| | - Nathan A Lack
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Tamer T Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
| | - H T Marc Timmers
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Freiburg, Heidelberg, Germany
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Tugba Bagci-Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Rumelifeneri Yolu, Sarıyer, Istanbul, 34450, Türkiye.
- Koç University School of Medicine, Istanbul, Türkiye.
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Sequeira JJ, Nizamuddin S, van Driem G, Mustak MS. TAS2R38 bitter taste perception in the Koṅkaṇī Sārasvata Brahmin population. Genes Genomics 2023; 45:1409-1422. [PMID: 37336804 DOI: 10.1007/s13258-023-01409-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND The TAS2R38 gene carries markers for phenylthiocarbamide (PTC) sensitivity. Various studies have investigated the genotype-phenotype association pattern for bitter tasting ability and other factors in different populations. However, a paucity of such information for endogamous Indian populations is the reason behind this study. OBJECTIVE To study the association of phenylthiocarbamide (PTC) sensitivity with TAS2R38 gene variations in Koṅkaṇī Sārasvata Brahmin population. METHODS We studied the association of the alleles rs714598, rs1726866, rs10246939 with PTC sensitivity and other factors in the Koṅkaṇī Sārasvata Brahmin population. DNA was extracted from 114 individuals belonging to the Koṅkaṇī Sārasvata Brahmin community. The TAS2R38 gene was sequenced to find the genotype distribution pattern. The association between genotype and phenotype was checked using the Chi-Square test and multifactorial logistical regression. RESULTS We observed a 58.8% frequency of the AVI haplotype, which is the most prevalent in European populations. A higher number of non-taster haplotypes and diplotypes were observed in Koṅkaṇī Sārasvata Brahmins, with the allele rs10246939 showing a significant association with PTC bitter taste sensitivity in both allelic (p = 8.6 × 10-4; Allele-G, OR = 3.57 [95% CI = 1.66-7.69]) and genotype-based (p = 6.9 × 10-4; genotype-AG, OR = 3.11 [95% CI = 0.73-13.20]; genotype-GG, OR = 40 [95% CI = 3.58-447.03]) tests. CONCLUSION Our results are in line with earlier studies, which report an association between PTC sensitivity and the TAS2R38 gene in different populations. In the global context, Koṅkaṇī Sārasvata Brahmins, who are mostly distributed along the southwestern coast of India, show a PTC sensitivity pattern slightly similar to that of West Eurasian populations. Our findings suggest ancestry specific selection in TAS2R38 gene variations for taste sensitivity at global level.
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Affiliation(s)
- Jaison Jeevan Sequeira
- Department of Applied Zoology, Mangalore University, Mangalagangotri, Mangaluru, 574199, India
| | - Sheikh Nizamuddin
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Urology, Medical Center-University of Freiburg, 79016, Freiburg, Germany
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Länggassstrasse 49, 3012, Bern, Switzerland
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalagangotri, Mangaluru, 574199, India.
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Mustak MS, Das R, Mishra A, Nizamuddin S. Editorial: Individual and population-specific variation in cancer susceptibility, prevalence, and disease presentation. Front Genet 2023; 14:1287610. [PMID: 37928240 PMCID: PMC10622754 DOI: 10.3389/fgene.2023.1287610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 09/29/2023] [Indexed: 11/07/2023] Open
Affiliation(s)
| | - Ranajit Das
- Yenepoya Research Centre, Yenepoya University, Mangalore, India
| | | | - Sheikh Nizamuddin
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
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Fotouhi O, Nizamuddin S, Falk S, Schilling O, Knüchel-Clarke R, Biniossek ML, Timmers HTM. Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6A. Cancers (Basel) 2023; 15:3117. [PMID: 37370727 DOI: 10.3390/cancers15123117] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
The UTX/KDM6A histone H3K27 demethylase plays an important role in development and is frequently mutated in cancers such as urothelial cancer. Despite many studies on UTX proteins, variations in mRNA splicing have been overlooked. Using Nanopore sequencing, we present a comprehensive analysis of UTX/KDM6A splicing events in human cell lines and in tissue samples from bladder cancer cases and normal epithelia. We found that the central region of UTX mRNAs encoded by exons 12 to 17 undergoes extensive alternative splicing. Up to half of all stable mRNAs (8-48% in bladder tissues and 18-58% in cell lines) are represented by the UTX canonical isoform lacking exon 14 encoding a nuclear localization sequence, and hence exon 14-containing UTX isoforms exclusively localize to the nucleus, unlike the cytonuclear localization of the canonical isoform. Chromatin association was also higher for exon-14-containing isoforms compared to the canonical UTX. Using quantitative mass spectrometry, we found that all UTX isoforms integrated into the MLL3 and MLL4, PR-DUB and MiDAC complexes. Interestingly, one of the novel UTX isoforms, which lacks exons 14 and 16, fails to interact with PR-DUB and MiDAC complex members. In conclusion, UTX mRNAs undergo extensive alternative splicing, which controls the subcellular localization of UTX and its interactions with other chromatin regulatory complexes.
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Affiliation(s)
- Omid Fotouhi
- Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sheikh Nizamuddin
- Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stephanie Falk
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Oliver Schilling
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, 79106 Freiburg, Germany
| | - Ruth Knüchel-Clarke
- Institute of Pathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - H T Marc Timmers
- Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Khan MI, C.S P, Mustak MS, Nizamuddin S. Maternal Transmission of the PAX7 Single Nucleotide Polymorphisms among Indian Cleft Trios. Glob Med Genet 2023; 10:6-11. [PMID: 36703778 PMCID: PMC9873478 DOI: 10.1055/s-0042-1760383] [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] [Indexed: 01/26/2023] Open
Abstract
Cleft lip and/or cleft palate (CL/P) is one of the most common congenital anomalies of the human face with a complex etiology involving multiple genetic and environmental factors. Several studies have shown the association of the paired box 7 ( PAX7 ) gene with CL/P in different populations worldwide. However, the current literature reveals no reported case-parent trio studies to evaluate the association between the PAX7 gene and the risk of nonsyndromic cleft lip and/or palate (NSCL/P) in the Indian population. Hence, the purpose of this study was to assess the PAX7 gene single nucleotide polymorphisms (SNPs) in the etiology of NSCL/P among the Indian cleft trios. Forty Indian case-parent trios of NSCL/P were included. The cases and their parents' genomic DNA were extracted. The SNPs rs9439714, rs1339062, rs6695765, rs742071, and rs618941of the PAX7 gene were genotyped using the Agena Bio MassARRAY analysis. The allelic transmission disequilibrium test was performed using PLINK software while pair-wise linkage disequilibrium by the Haploview program. The SNP rs9439714 showed evidence of association ( p -value = 0.02, odds ratio = 3) with NSCL/P. Considering the parent-of-origin effects, the SNPs rs9439714 and rs618941 showed an excess maternal transmission of allele C at rs9439714 ( p -value = 0.05) and G allele at rs618941 ( p -value = 0.04). The results of the present study suggested that the SNPs rs9439714 and rs618941 showed an excess maternal transmission of alleles suggestive of the possible role of the PAX7 gene involvement in the etiology of NSCL/P in the Indian population.
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Affiliation(s)
- Mahamad Irfanulla Khan
- Department of Orthodontics and Dentofacial Orthopedics, The Oxford Dental College, Bangalore, Karnataka, India,Address for correspondence Mahamad Irfanulla Khan, BDS, MDS Department of Orthodontics and Dentofacial Orthopedics, The Oxford Dental CollegeBangalore, Karnataka, 560068India
| | - Prashanth C.S
- Department of Orthodontics and Dentofacial Orthopedics, DAPM R.V Dental College, Bangalore, Karnataka, India
| | - Mohammed S. Mustak
- Department of Applied Zoology Mangalore University, Mangalore, Karnataka, India
| | - Sheikh Nizamuddin
- Department of Urology, Medical Center-University of Freiburg, Germany,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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Dreijerink KMA, Ozyerli-Goknar E, Koidl S, Van der Lelij E, Van den Heuvel P, Kooijman J, Biniossek M, Rodenburg K, Nizamuddin S, Timmers M. LBODP106 Multi-omics Analyses Of MEN1 Missense Mutations Identify Disruption Of Menin-MLL And Menin-JunD Interactions As Critical Requirements For Molecular Pathogenicity. J Endocr Soc 2022. [PMCID: PMC9628758 DOI: 10.1210/jendso/bvac150.1788] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Loss-of-function mutations of the multiple endocrine neoplasia type 1 (MEN1) gene are causal to the MEN1 endocrine tumor syndrome, but they are also commonly found in sporadic pancreatic neuroendocrine tumors and other types of cancers. The MEN1 gene product, menin, is involved in transcriptional and chromatin regulation, most prominently as an integral component of KMT2A/MLL1 and KMT2B/MLL2 containing COMPASS-like histone H3K4 methyltransferase complexes. In a mutually exclusive fashion, menin also interacts with the JunD subunit of the AP-1 and ATF/CREB transcription factors. After in silico screening of 253 disease-related MEN1 missense mutations, we selected a set of nine menin mutations in surface-exposed residues. The protein interactomes of these mutants were assessed by quantitative mass spectrometry, which indicated that seven of the nine mutants disrupt interactions with both MLL1/2 and JunD complexes. Interestingly, we identified three missense mutations, R52G, E255K and E359K, which predominantly reduce the interaction with MLL1 compared to JunD. This observation was supported by a pronounced loss of binding of the R52G, E255K and E359K mutant proteins at unique MLL1 genomic binding sites with less effect on unique JunD sites. These findings support the general importance of the menin-MLL1 and menin-JunD interactions in MEN1 gene-associated pathogenic conditions. Presentation: No date and time listed
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Affiliation(s)
| | - Ezgi Ozyerli-Goknar
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Stefanie Koidl
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | | | - Priscilla Van den Heuvel
- School of Life Sciences, and Research Group of Technologies of Analyses in Life Sciences (ATLS), Avans University of Applied Sciences, Breda, Netherlands
| | - Jeffrey Kooijman
- School of Life Sciences, and Research Group of Technologies of Analyses in Life Sciences (ATLS), Avans University of Applied Sciences, Breda, Netherlands
| | - Martin Biniossek
- Institute for Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Kees Rodenburg
- School of Life Sciences, and Research Group of Technologies of Analyses in Life Sciences (ATLS), Avans University of Applied Sciences, Breda, Netherlands
| | - Sheikh Nizamuddin
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Marc Timmers
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
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Dreijerink KMA, Ozyerli-Goknar E, Koidl S, van der Lelij EJ, van den Heuvel P, Kooijman JJ, Biniossek ML, Rodenburg KW, Nizamuddin S, Timmers HTM. Multi-omics analyses of MEN1 missense mutations identify disruption of menin-MLL and menin-JunD interactions as critical requirements for molecular pathogenicity. Epigenetics Chromatin 2022; 15:29. [PMID: 35941657 PMCID: PMC9361535 DOI: 10.1186/s13072-022-00461-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background Loss-of-function mutations of the multiple endocrine neoplasia type 1 (MEN1) gene are causal to the MEN1 tumor syndrome, but they are also commonly found in sporadic pancreatic neuroendocrine tumors and other types of cancers. The MEN1 gene product, menin, is involved in transcriptional and chromatin regulation, most prominently as an integral component of KMT2A/MLL1 and KMT2B/MLL2 containing COMPASS-like histone H3K4 methyltransferase complexes. In a mutually exclusive fashion, menin also interacts with the JunD subunit of the AP-1 and ATF/CREB transcription factors. Results Here, we applied and in silico screening approach for 253 disease-related MEN1 missense mutations in order to select a set of nine menin mutations in surface-exposed residues. The protein interactomes of these mutants were assessed by quantitative mass spectrometry, which indicated that seven of the nine mutants disrupt interactions with both MLL1/MLL2 and JunD complexes. Interestingly, we identified three missense mutations, R52G, E255K and E359K, which predominantly reduce the MLL1 and MLL2 interactions when compared with JunD. This observation was supported by a pronounced loss of binding of the R52G, E255K and E359K mutant proteins at unique MLL1 genomic binding sites with less effect on unique JunD sites. Conclusions Our results underline the effects of MEN1 gene mutations in both familial and sporadic tumors of endocrine origin on the interactions of menin with the MLL1 and MLL2 histone H3K4 methyltransferase complexes and with JunD-containing transcription factors. Menin binding pocket mutants R52G, E255K and E359K have differential effects on MLL1/MLL2 and JunD interactions, which translate into differential genomic binding patterns. Our findings encourage future studies addressing the pathophysiological relevance of the separate MLL1/MLL2- and JunD-dependent functions of menin mutants in MEN1 disease model systems.
Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00461-8.
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Affiliation(s)
| | - Ezgi Ozyerli-Goknar
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Urology, Medical Center -University of Freiburg, Freiburg, Germany
| | - Stefanie Koidl
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Urology, Medical Center -University of Freiburg, Freiburg, Germany
| | | | - Priscilla van den Heuvel
- School of Life Sciences, and Research Group of Technologies of Analyses in Life Sciences (ATLS), Avans University of Applied Sciences, Breda, The Netherlands
| | - Jeffrey J Kooijman
- School of Life Sciences, and Research Group of Technologies of Analyses in Life Sciences (ATLS), Avans University of Applied Sciences, Breda, The Netherlands.,Oncolines B.V., Oss, The Netherlands
| | - Martin L Biniossek
- Institute for Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Kees W Rodenburg
- School of Life Sciences, and Research Group of Technologies of Analyses in Life Sciences (ATLS), Avans University of Applied Sciences, Breda, The Netherlands
| | - Sheikh Nizamuddin
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Urology, Medical Center -University of Freiburg, Freiburg, Germany
| | - H T Marc Timmers
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Department of Urology, Medical Center -University of Freiburg, Freiburg, Germany.
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Gupta G, Deval R, Rai N, Nizamuddin S, Upadhyay S, Pasupuleti N, Ng HKT, Singh PK, Rao V. Genome-wide association study for suicide in high–risk isolated historical population from North East India. Journal of Affective Disorders Reports 2022. [DOI: https://doi.org/10.1016/j.jadr.2022.100327] [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: 01/16/2023] Open
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Gupta G, Deval R, Rai N, Nizamuddin S, Upadhyay S, Pasupuleti N, Ng HKT, Singh PK, Rao V. Genome-wide association study for suicide in high–risk isolated historical population from North East India. Journal of Affective Disorders Reports 2022. [DOI: https:/doi.org/10.1016/j.jadr.2022.100327] [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: 01/17/2023] Open
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Tiwari JK, Negi S, Kashyap M, Nizamuddin S, Singh A, Khattri A. Pan-Cancer Analysis Shows Enrichment of Macrophages, Overexpression of Checkpoint Molecules, Inhibitory Cytokines, and Immune Exhaustion Signatures in EMT-High Tumors. Front Oncol 2022; 11:793881. [PMID: 35096592 PMCID: PMC8790577 DOI: 10.3389/fonc.2021.793881] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/13/2021] [Indexed: 01/06/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a highly dynamic process that occurs under normal circumstances; however, EMT is also known to play a central role in tumor progression and metastasis. Furthermore, role of tumor immune microenvironment (TIME) in shaping anticancer immunity and inducing the EMT is also well recognized. Understanding the key features of EMT is critical for the development of effective therapeutic interventions. Given the central role of EMT in immune escape and cancer progression and treatment, we have carried out a pan-cancer TIME analysis of The Cancer Genome Atlas (TCGA) dataset in context to EMT. We have analyzed infiltration of various immune cells, expression of multiple checkpoint molecules and cytokines, and inflammatory and immune exhaustion gene signatures in 22 cancer types from TCGA dataset. A total of 16 cancer types showed a significantly increased (p < 0.001) infiltration of macrophages in EMT-high tumors (mesenchymal samples). Furthermore, out of the 17 checkpoint molecules we analyzed, 11 showed a significant overexpression (p < 0.001) in EMT-high samples of at least 10 cancer types. Analysis of cytokines showed significant enrichment of immunosuppressive cytokines-TGFB1 and IL10-in the EMT-high group of almost all cancer types. Analysis of various gene signatures showed enrichment of inflammation, exhausted CD8+ T cells, and activated stroma signatures in EMT-high tumors. In summary, our pan-cancer EMT analysis of TCGA dataset shows that the TIME of EMT-high tumors is highly immunosuppressive compared to the EMT-low (epithelial) tumors. The distinctive features of EMT-high tumors are as follows: (i) the enrichment of tumor-associated macrophages, (ii) overexpression of immune checkpoint molecules, (iii) upregulation of immune inhibitory cytokines TGFB1 and IL10, and (iv) enrichment of inflammatory and exhausted CD8+ T-cell signatures. Our study shows that TIMEs of different EMT groups differ significantly, and this would pave the way for future studies analyzing and targeting the TIME regulators for anticancer immunotherapy.
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Affiliation(s)
- Jayesh Kumar Tiwari
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Shloka Negi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Manju Kashyap
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción, Chile
| | - Sheikh Nizamuddin
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amar Singh
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, United States
| | - Arun Khattri
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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11
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Khan M, Prashanth CS, Mustak M, Nizamuddin S, Tejasvi A. Parental transmission effects of the PAX7 Polymorphisms among non-syndromic cleft lip palate: A case-parent trio study. J Indian Acad Oral Med Radiol 2022. [DOI: 10.4103/jiaomr.jiaomr_50_22] [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: 11/04/2022] Open
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12
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Capponi S, Stöffler N, Penney EB, Grütz K, Nizamuddin S, Vermunt MW, Castelijns B, Fernandez-Cerado C, Legarda GP, Velasco-Andrada MS, Muñoz EL, Ang MA, Diesta CCE, Creyghton MP, Klein C, Bragg DC, De Rijk P, Timmers HTM. Dissection of TAF1 neuronal splicing and implications for neurodegeneration in X-linked dystonia-parkinsonism. Brain Commun 2021; 3:fcab253. [PMID: 34746789 PMCID: PMC8567410 DOI: 10.1093/braincomms/fcab253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 04/27/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 11/29/2022] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a monogenic neurodegenerative disorder of the basal ganglia, which presents as a combination of hyperkinetic movements and parkinsonian features. The underlying genetic mechanism involves the insertion of a SINE-VNTR-Alu retrotransposon within the TAF1 gene. Interestingly, alterations of TAF1 have been involved in multiple neurological diseases. In XDP, the SINE-VNTR-Alu insertion in TAF1 has been proposed to result in alternative splicing defects, including the decreased incorporation of a neuron-specific microexon annotated as 34′. This mechanism has become controversial as recent studies failed to provide support. In order to resolve this conundrum, we examined the alternative splicing patterns of TAF1 mRNAs in XDP and control brains. The impact of the disease-associated SINE-VNTR-Alu on alternative splicing of microexon 34′ was further investigated in cellular assays. Subsequently, microexon 34′ incorporation was explored by RT-PCR and Nanopore long-read sequencing of TAF1 mRNAs from XDP and control brains tissues. Using cell-based splicing assays, we demonstrate that presence of the disease-associated SINE-VNTR-Alu does not affect the inclusion of microexon 34′. In addition, we show that (1) microexon 34′-containing TAF1 mRNAs are detected at similar levels in XDP as in controls and that (2) the architecture of TAF1 transcripts is remarkably similar between XDP and controls brains. These results indicate that microexon 34′ incorporation into TAF1 mRNA is not affected in XDP brains. Our findings shift the current paradigm of XDP by discounting alternative splicing of TAF1 microexon 34′ as the molecular basis for this disease.
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Affiliation(s)
- Simona Capponi
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Nadja Stöffler
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Ellen B Penney
- The Collaborative Center for X-Linked Dystonia Parkinsonism (CCXDP), Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Karen Grütz
- Institute of Neurogenetics, University of Lübeck, Lübeck 23538, Germany
| | - Sheikh Nizamuddin
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Marit W Vermunt
- Erasmus University Medical Center, Department of Developmental Biology, Rotterdam 3015 GD, The Netherlands
| | - Bas Castelijns
- Erasmus University Medical Center, Department of Developmental Biology, Rotterdam 3015 GD, The Netherlands
| | | | - G Paul Legarda
- Sunshine Care Foundation, Roxas City, 5800 Capiz, Philippines
| | | | - Edwin L Muñoz
- Department of Pathology, College of Medicine, University of the Philippines, 1000 Manila, Philippines
| | - Mark A Ang
- Department of Pathology, College of Medicine, University of the Philippines, 1000 Manila, Philippines
| | - Cid Czarina E Diesta
- Department of Neurosciences, Makati Medical Center, 1229 Makati City, Philippines
| | - Menno P Creyghton
- Erasmus University Medical Center, Department of Developmental Biology, Rotterdam 3015 GD, The Netherlands
| | - Christine Klein
- Institute of Neurogenetics and Department of Neurology, University of Lübeck, 23538 Lübeck, Germany
| | - D Cristopher Bragg
- The Collaborative Center for X-Linked Dystonia Parkinsonism (CCXDP), Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB - University of Antwerp, B-2610 Antwerp, Belgium
| | - H T Marc Timmers
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
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13
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Badarukhiya JA, Tupperwar N, Nizamuddin S, Mulpur AK, Thangaraj K. Novel FCN2 Variants and Haplotypes are Associated with Rheumatic Heart Disease. DNA Cell Biol 2021; 40:1338-1348. [PMID: 34529517 DOI: 10.1089/dna.2021.0478] [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] [Indexed: 11/13/2022] Open
Abstract
Ficolins are pattern recognition molecules that are involved in innate immune defense. Ficonin-2 (FCN2) has a specific affinity for lipoteichoic acid present in the cell wall of Streptococcus pyogenes, an etiological agent for rheumatic heart disease (RHD). We have estimated FCN2 serum levels and analyzed the functional variants of FCN2 in 400 RHD patients, 617 healthy controls, and 581 individuals belonged to various ethnic populations, who are inhabited in various geographical regions of India. Our study revealed that the FCN2 -986A and +6359T alleles were the risk factors for RHD susceptibility (p = 0.0007 for -986G>A; p = 0.0004 for +6359C>T). The haplotype AGGT (p = 0.0024) was observed to be a risk factor for RHD susceptibility, and the haplotype GGAC (p = 0.002) was found to confer protection against RHD. The level of serum FCN2 was significantly higher in controls (p < 0.0001) and in controls with GGAC haplotypes (p < 0.0001). The frequency of the risk alleles -986A and +6359T was found to be more prevalent in Northern and North-Western (Indo-European) India. The protective GGAC haplotype was found more prevalent in Eastern (Tibeto-Burman) and South-Western (Dravidian) India. Alleles -986A and +6359T were in positive correlation with the prevalence of RHD (regression coefficient = 1.84 and 1.94, respectively), whereas GGAC haplotype was in negative correlation with prevalence of RHD (regression coefficient = -1.71). In conclusion, we found that low level of serum ficolin-2 is significantly associated with RHD. Further, FCN2 -986A and +6359T alleles and AGGT haplotype are associated with increased susceptibility to RHD, while GGAC haplotype is associated with moderate protection against RHD.
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Affiliation(s)
| | - Nitin Tupperwar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sheikh Nizamuddin
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anil Kumar Mulpur
- Department of Cardiothoracic Surgery, Sunshine Hospitals, Hyderabad, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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14
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Nizamuddin S, Koidl S, Bhuiyan T, Werner TV, Biniossek ML, Bonvin AMJJ, Lassmann S, Timmers HT. Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN. Nucleic Acids Res 2021; 49:e49. [PMID: 33524153 PMCID: PMC8136828 DOI: 10.1093/nar/gkab038] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/08/2021] [Accepted: 01/16/2021] [Indexed: 11/14/2022] Open
Abstract
Genome-wide localization of chromatin and transcription regulators can be detected by a variety of techniques. Here, we describe a novel method ‘greenCUT&RUN’ for genome-wide profiling of transcription regulators, which has a very high sensitivity, resolution, accuracy and reproducibility, whilst assuring specificity. Our strategy begins with tagging of the protein of interest with GFP and utilizes a GFP-specific nanobody fused to MNase to profile genome-wide binding events. By using a GFP-nanobody the greenCUT&RUN approach eliminates antibody dependency and variability. Robust genomic profiles were obtained with greenCUT&RUN, which are accurate and unbiased towards open chromatin. By integrating greenCUT&RUN with nanobody-based affinity purification mass spectrometry, ‘piggy-back’ DNA binding events can be identified on a genomic scale. The unique design of greenCUT&RUN grants target protein flexibility and yields high resolution footprints. In addition, greenCUT&RUN allows rapid profiling of mutants of chromatin and transcription proteins. In conclusion, greenCUT&RUN is a widely applicable and versatile genome-mapping technique.
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Affiliation(s)
- Sheikh Nizamuddin
- Department of Urology, Medical Center-University of Freiburg, 79016 Freiburg, Germany.,German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefanie Koidl
- Department of Urology, Medical Center-University of Freiburg, 79016 Freiburg, Germany.,German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Tanja Bhuiyan
- Department of Urology, Medical Center-University of Freiburg, 79016 Freiburg, Germany.,German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Tamara V Werner
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center-University of Freiburg, 79016 Freiburg, Germany
| | - Martin L Biniossek
- Institute for Molecular Medicine and Cell Research, Medical Center-University of Freiburg, 79016 Freiburg, Germany
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Silke Lassmann
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center-University of Freiburg, 79016 Freiburg, Germany
| | - HThMarc Timmers
- Department of Urology, Medical Center-University of Freiburg, 79016 Freiburg, Germany.,German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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15
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Torumkuney D, Anwar S, Nizamuddin S, Malik N, Morrissey I. Results from the Survey of Antibiotic Resistance (SOAR) 2015-17 in Pakistan: data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints. J Antimicrob Chemother 2021; 75:i76-i87. [PMID: 32337594 DOI: 10.1093/jac/dkaa085] [Citation(s) in RCA: 2] [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: 12/17/2022] Open
Abstract
OBJECTIVES To determine antibiotic susceptibility of community-acquired respiratory tract infection (CA-RTI) isolates of Streptococcus pneumoniae and Haemophilus influenzae collected in 2015-17 from Pakistan. METHODS MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints. RESULTS A total of 94 S. pneumoniae and 122 H. influenzae isolates were collected. Susceptibility to penicillin was noted in 23.4% of the S. pneumoniae isolates by CLSI oral/EUCAST low-dose IV breakpoints, although by CLSI IV and EUCAST high-dose breakpoints all isolates were characterized as susceptible. Susceptibility to trimethoprim/sulfamethoxazole (10.6%), macrolides (33%) and cefaclor (28.7%) was low but higher susceptibility was observed to ceftriaxone (100%), amoxicillin and amoxicillin/clavulanic acid (98.9%), cefuroxime (oral, 97.9%), cefpodoxime (96.8%), fluoroquinolones (93.6%-96.8%) and cefdinir (76.6%) by CLSI breakpoints. However, using EUCAST breakpoints, susceptibility to cefpodoxime (70.2%) and cefuroxime (oral, 61.7%) was reduced. H. influenzae isolates were almost all β-lactamase negative (96.7%). Using CLSI breakpoints, ≥93.4% of isolates were susceptible to all antibiotics tested except fluoroquinolones (75.4%-77.1%) and trimethoprim/sulfamethoxazole (41%). The proportion of isolates susceptible using EUCAST breakpoints was similar or identical for penicillins, trimethoprim/sulfamethoxazole and the cephalosporins that have EUCAST breakpoints; the proportion of isolates susceptible using EUCAST breakpoints was similar or identical to that using CSLI breakpoints except for cefuroxime (oral), where only 1.6% of isolates were considered susceptible. Susceptibility of H. influenzae to fluoroquinolones was also lower by EUCAST breakpoints (33.6%-34.4%). The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified. CONCLUSIONS Antibiotic susceptibility in these important respiratory tract pathogens varied in Pakistan based on different breakpoints. These data are important for empirical therapy choices in the treatment of CA-RTIs.
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Affiliation(s)
- D Torumkuney
- GlaxoSmithKline, 980 Great West Road, Brentford, Middlesex TW8 9GS, UK
| | - S Anwar
- Liaquat National Hospital and Medical College, Microbiology Department, Stadium Road, Karachi, Pakistan
| | - S Nizamuddin
- Shaukat Khanum Memorial Cancer Hospital and Research Centre, Section of Microbiology, Department of Pathology, 7A Block R3, Johar Town, Lahore, Pakistan
| | - N Malik
- Shaukat Khanum Memorial Cancer Hospital and Research Centre, Section of Microbiology, Department of Pathology, 7A Block R3, Johar Town, Lahore, Pakistan
| | - I Morrissey
- IHMA Europe Sàrl, Route de l'Ile-au-Bois 1A, 1870 Monthey/VS, Switzerland
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16
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Abstract
Targeting protein-protein interactions (PPIs) with small-molecule inhibitors has become a hotbed of modern drug development. In this review, we describe a new class of PPI inhibitors that block menin from binding to MLL proteins. Menin is encoded by the MEN1 tumor suppressor, but acts as an essential cofactor for MLL/KMT2A-rearranged leukemias. The most promising menin-MLL inhibitors belong to the thienopyrimidine class and have recently entered phase I/II clinical trials for treating acute leukemias characterized by MLL/KMT2A translocations or NPM1 mutations. As single agents, thienopyrimidine compounds eradicate leukemia in a xenograft models of primary leukemic cells belonging to the MLL-rearranged or NPM1-mutant subtypes. These compounds are well tolerated with few or no side effects, which is remarkable given the tumor-suppressor function of menin. The menin-MLL inhibitors highlight how leukemia patients could benefit from a targeted epigenetic therapy with novel PPI inhibitors obtained by directed chemical evolution.
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Affiliation(s)
- Ezgi Ozyerli‐Goknar
- German Cancer Consortium (DKTK) partner site Freiburg German Cancer Research Center (DKFZ) Medical Center-University of Freiburg, Department of UrologyBreisacherstrasse 6679016FreiburgGermany
| | - Sheikh Nizamuddin
- German Cancer Consortium (DKTK) partner site Freiburg German Cancer Research Center (DKFZ) Medical Center-University of Freiburg, Department of UrologyBreisacherstrasse 6679016FreiburgGermany
| | - H. T. Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg German Cancer Research Center (DKFZ) Medical Center-University of Freiburg, Department of UrologyBreisacherstrasse 6679016FreiburgGermany
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17
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Nizamuddin S, Dubey S, Singh S, Sharma S, Machha P, Thangaraj K. CYP2C9 Variations and Their Pharmacogenetic Implications Among Diverse South Asian Populations. Pharmgenomics Pers Med 2021; 14:135-147. [PMID: 33536773 PMCID: PMC7850565 DOI: 10.2147/pgpm.s272015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/01/2020] [Indexed: 11/23/2022]
Abstract
Introduction Allelic frequency distribution of drug metabolizing enzyme genes among populations is important to identify risk groups for adverse drug reaction and to select representative populations for clinical trials. Although India emerged as an important hub for clinical trials, information about the pharmacogenetic diversity for this region is still lacking. Here, we investigated genetic diversity of cytochrome-P450-2C9 (CYP2C9) gene which metabolizes wide range of drugs and is highly expressed in the human liver. Methods In total, 1278 individuals from 36 diverse Indian populations, 210 individuals from in-house data-repository and 489 other South Asian samples from the 1000 Genomes Project were selected. Variants observed in CYP2C9 gene were subjected to various statistical analyses. Results High frequency of CYP2C9*3 (~13%) and CYP2C9*3/*3 (~1%) was observed among South Asians, compared to 21 populations living outside the Indian subcontinent. The allelic/genotypic frequency does not correlate with geographical location or linguistic affiliation, except populations speaking Tibeto-Burmans language, who have lower frequency of CYP2C9*3 and CYP2C9*3/*3. Since, South Asians practice strict endogamy, presence of unique mutation and high frequency of homozygous genotypes not surprising. CYP2C9*3 has been associated with therapeutic response.The effect of CYP2C9*3/*3 is more pronounced compared to heterozygous and wild type homozygous genotypes as evident in many in vitro studies. As South Asians have high frequency, it would be interesting to explore potential of CYP2C9*3 as a marker for personalized therapy. Our study revealed several rare functional variants, which form eight novel and rare haplotypes of CYP2C9 (CYP2C9*63–*70). Of which, CYP2C9*64, *65, *66, *68, *69 and *70 haplotypes are South Asian-specific. Conclusion Overall, we find high genetic heterogeneity within South Asians and identified South Asian-specific putative functional CYP2C9 haplotypes. High frequency of CYP2C9*3 and CYP2C9*3/*3 was observed in South Asian populations. Taken together, current study greatly enriches the knowledge of naturally occurring CYP2C9 variants and its diversity in South Asia, which are relevant to further CYP2C9-related functional research and for personalized medicine.
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Affiliation(s)
- Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India.,German Cancer Consortium (DKTK) c/o Zentrale Klinische Forschung (ZKF), University Medical Center, Freiburg, Germany
| | - Shivendra Dubey
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Saurav Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Pratheusa Machha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India.,AcSIR (Academy of Scientific and Innovative Research), CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India.,AcSIR (Academy of Scientific and Innovative Research), CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India.,DBT-Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
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18
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Rosenthal VD, Bat-Erdene I, Gupta D, Belkebir S, Rajhans P, Zand F, Myatra SN, Afeef M, Tanzi VL, Muralidharan S, Gurskis V, Al-Abdely HM, El-Kholy A, AlKhawaja SAA, Sen S, Mehta Y, Rai V, Hung NV, Sayed AF, Guerrero-Toapanta FM, Elahi N, Morfin-Otero MDR, Somabutr S, De-Carvalho BM, Magdarao MS, Velinova VA, Quesada-Mora AM, Anguseva T, Ikram A, Aguilar-de-Moros D, Duszynska W, Mejia N, Horhat FG, Belskiy V, Mioljevic V, Di-Silvestre G, Furova K, Gamar-Elanbya MO, Gupta U, Abidi K, Raka L, Guo X, Luque-Torres MT, Jayatilleke K, Ben-Jaballah N, Gikas A, Sandoval-Castillo HR, Trotter A, Valderrama-Beltrán SL, Leblebicioglu H, Riera F, López M, Maurizi D, Desse J, Pérez I, Silva G, Chaparro G, Golschmid D, Cabrera R, Montanini A, Bianchi A, Vimercati J, Rodríguez-del-Valle M, Domínguez C, Saul P, Chediack V, Piastrelini M, Cardena L, Ramasco L, Olivieri M, Gallardo P, Juarez P, Brito M, Botta P, Alvarez G, Benchetrit G, Caridi M, Stagnaro J, Bourlot I, García M, Arregui N, Saeed N, Abdul-Aziz S, ALSayegh S, Humood M, Mohamed-Ali K, Swar S, Magray T, Aguiar-Portela T, Sugette-de-Aguiar T, Serpa-Maia F, Fernandes-Alves-de-Lima L, Teixeira-Josino L, Sampaio-Bezerra M, Furtado-Maia R, Romário-Mendes A, Alves-De-Oliveira A, Vasconcelos-Carneiro A, Anjos-Lima JD, Pinto-Coelho K, Maciel-Canuto M, Rocha-Batista M, Moreira T, Rodrigues-Amarilo N, Lima-de-Barros T, Guimarães KA, Batista C, Santos C, de-Lima-Silva F, Santos-Mota E, Karla L, Ferreira-de-Souza M, Luzia N, de-Oliveira S, Takeda C, Azevedo-Ferreira-Lima D, Faheina J, Coelho-Oliveira L, do-Nascimento S, Machado-Silva V, Bento-Ferreira, Olszewski J, Tenorio M, Silva-Lemos A, Ramos-Feijó C, Cardoso D, Correa-Barbosa M, Assunção-Ponte G, Faheina J, da-Silva-Escudero D, Servolo-Medeiros E, Andrade-Oliveira-Reis M, Kostadinov E, Dicheva V, Petrov M, Guo C, Yu H, Liu T, Song G, Wang C, Cañas-Giraldo L, Marin-Tobar D, Trujillo-Ramirez E, Andrea-Rios P, Álvarez-Moreno C, Linares C, González-Rubio P, Ariza-Ayala B, Gamba-Moreno L, Gualtero-Trujill S, Segura-Sarmiento S, Rodriguez-Pena J, Ortega R, Olarte N, Pardo-Lopez Y, Luis Marino Otela-Baicue A, Vargas-Garcia A, Roncancio E, Gomez-Nieto K, Espinosa-Valencia M, Barahona-Guzman N, Avila-Acosta C, Raigoza-Martinez W, Villamil-Gomez W, Chapeta-Parada E, Mindiola-Rochel A, Corchuelo-Martinez A, Martinez A, Lagares-Guzman A, Rodriguez-Ferrer M, Yepes-Gomez D, Muñoz-Gutierrez G, Arguello-Ruiz A, Zuniga-Chavarria M, Maroto-Vargas L, Valverde-Hernández M, Solano-Chinchilla A, Calvo-Hernandez I, Chavarria-Ugalde O, Tolari G, Rojas-Fermin R, Diaz-Rodriguez C, Huascar S, Ortiz M, Bovera M, Alquinga N, Santacruz G, Jara E, Delgado V, Salgado-Yepez E, Valencia F, Pelaez C, Gonzalez-Flores H, Coello-Gordon E, Picoita F, Arboleda M, Garcia M, Velez J, Valle M, Unigarro L, Figueroa V, Marin K, Caballero-Narvaez H, Bayani V, Ahmed S, Alansary A, Hassan A, Abdel-Halim M, El-Fattah M, Abdelaziz-Yousef R, Hala A, Abdelhady K, Ahmed-Fouad H, Mounir-Agha H, Hamza H, Salah Z, Abdel-Aziz D, Ibrahim S, Helal A, AbdelMassih A, Mahmoud AR, Elawady B, El-sherif R, Fattah-Radwan Y, Abdel-Mawla T, Kamal-Elden N, Kartsonaki M, Rivera D, Mandal S, Mukherjee S, Navaneet P, Padmini B, Sorabjee J, Sakle A, Potdar M, Mane D, Sale H, Abdul-Gaffar M, Kazi M, Chabukswar S, Anju M, Gaikwad D, Harshe A, Blessymole S, Nair P, Khanna D, Chacko F, Rajalakshmi A, Mubarak A, Kharbanda M, Kumar S, Mathur P, Saranya S, Abubakar F, Sampat S, Raut V, Biswas S, Kelkar R, Divatia J, Chakravarthy M, Gokul B, Sukanya R, Pushparaj L, Thejasvini A, Rangaswamy S, Saini N, Bhattacharya C, Das S, Sanyal S, Chaudhury B, Rodrigues C, Khanna G, Dwivedy A, Binu S, Shetty S, Eappen J, Valsa T, Sriram A, Todi S, Bhattacharyya M, Bhakta A, Ramachandran B, Krupanandan R, Sahoo P, Mohanty N, Sahu S, Misra S, Ray B, Pattnaik S, Pillai H, Warrier A, Ranganathan L, Mani A, Rajagopal S, Abraham B, Venkatraman R, Ramakrishnan N, Devaprasad D, Siva K, Divekar D, Satish Kavathekar M, Suryawanshi M, Poojary A, Sheeba J, Patil P, Kukreja S, Varma K, Narayanan S, Sohanlal T, Agarwal A, Agarwal M, Nadimpalli G, Bhamare S, Thorat S, Sarda O, Nadimpalli P, Nirkhiwale S, Gehlot G, Bhattacharya S, Pandya N, Raphel A, Zala D, Mishra S, Patel M, Aggarwal D, Jawadwal B, Pawar N, Kardekar S, Manked A, Tamboli A, Manked A, Khety Z, Singhal T, Shah S, Kothari V, Naik R, Narain R, Sengupta S, Karmakar A, Mishra S, Pati B, Kantroo V, Kansal S, Modi N, Chawla R, Chawla A, Roy I, Mukherjee S, Bej M, Mukherjee P, Baidya S, Durell A, Vadi S, Saseedharan S, Anant P, Edwin J, Sen N, Sandhu K, Pandya N, Sharma S, Sengupta S, Palaniswamy V, Sharma P, Selvaraj M, Saurabh L, Agarwal M, Punia D, Soni D, Misra R, Harsvardhan R, Azim A, Kambam C, Garg A, Ekta S, Lakhe M, Sharma C, Singh G, Kaur A, Singhal S, Chhabra K, Ramakrishnan G, Kamboj H, Pillai S, Rani P, Singla D, Sanaei A, Maghsudi B, Sabetian G, Masjedi M, Shafiee E, Nikandish R, Paydar S, Khalili H, Moradi A, Sadeghi P, Bolandparvaz S, Mubarak S, Makhlouf M, Awwad M, Ayyad O, Shaweesh A, Khader M, Alghazawi A, Hussien N, Alruzzieh M, Mohamed Y, ALazhary M, Abdul Aziz O, Alazmi M, Mendoza J, De Vera P, Rillorta A, de Guzman M, Girvan M, Torres M, Alzahrani N, Alfaraj S, Gopal U, Manuel M, Alshehri R, Lessing L, Alzoman H, Abdrahiem J, Adballah H, Thankachan J, Gomaa H, Asad T, AL-Alawi M, Al-Abdullah N, Demaisip N, Laungayan-Cortez E, Cabato A, Gonzales J, Al Raey M, Al-Darani S, Aziz M, Al-Manea B, Samy E, AlDalaton M, Alaliany M, Alabdely H, Helali N, Sindayen G, Malificio A, Al-Dossari H, Kelany A, Algethami A, Mohamed D, Yanne L, Tan A, Babu S, Abduljabbar S, Al-Zaydani M, Ahmed H, Al Jarie A, Al-Qathani A, Al-Alkami H, AlDalaton M, Alih S, Alaliany M, Gasmin-Aromin R, Balon-Ubalde E, Diab H, Kader N, Hassan-Assiry I, Kelany A, Albeladi E, Aboushoushah S, Qushmaq N, Fernandez J, Hussain W, Rajavel R, Bukhari S, Rushdi H, Turkistani A, Mushtaq J, Bohlega E, Simon S, Damlig E, Elsherbini S, Abraham S, Kaid E, Al-Attas A, Hawsawi G, Hussein B, Esam B, Caminade Y, Santos A, Abdulwahab M, Aldossary A, Al-Suliman S, AlTalib A, Albaghly N, HaqlreMia M, Kaid E, Altowerqi R, Ghalilah K, Alradady M, Al-Qatri A, Chaouali M, Shyrine E, Philipose J, Raees M, AbdulKhalik N, Madco M, Acostan C, Safwat R, Halwani M, Abdul-Aal N, Thomas A, Abdulatif S, Ali-Karrar M, Al-Gosn N, Al-Hindi A, Jaha R, AlQahtani S, Ayugat E, Al-Hussain M, Aldossary A, Al-Suliman S, Al-Talib A, Albaghly N, Haqlre-Mia M, Briones S, Krishnan R, Tabassum K, Alharbi L, Madani A, Al-Hindi A, Al-Gethamy M, Alamri D, Spahija G, Gashi A, Kurian A, George S, Mohamed A, Ramapurath R, Varghese S, Abdo N, Foda-Salama M, Al-Mousa H, Omar A, Salama M, Toleb M, Khamis S, Kanj S, Zahreddine N, Kanafani Z, Kardas T, Ahmadieh R, Hammoud Z, Zeid I, Al-Souheil A, Ayash H, Mahfouz T, Kondratas T, Grinkeviciute D, Kevalas R, Dagys A, Mitrev Z, Bogoevska-Miteva Z, Jankovska K, Guroska S, Petrovska M, Popovska K, Ng C, Hoon Y, Hasan YM, Othman-Jailani M, Hadi-Jamaluddin M, Othman A, Zainol H, Wan-Yusoff W, Gan C, Lum L, Ling C, Aziz F, Zhazali R, Abud-Wahab M, Cheng T, Elghuwael I, Wan-Mat W, Abd-Rahman R, Perez-Gomez H, Kasten-Monges M, Esparza-Ahumada S, Rodriguez-Noriega E, Gonzalez-Diaz E, Mayoral-Pardo D, Cerero-Gudino A, Altuzar-Figueroa M, Perez-Cruz J, Escobar-Vazquez M, Aragon D, Coronado-Magana H, Mijangos-Mendez J, Corona-Jimenez F, Aguirre-Avalos G, Lopez-Mateos A, Martinez-Marroquin M, Montell-Garcia M, Martinez-Martinez A, Leon-Sanchez E, Gomez-Flores G, Ramirez M, Gomez M, Lozano M, Mercado V, Zamudio-Lugo I, Gomez-Gonzalez C, Miranda-Novales M, Villegas-Mota I, Reyes-Garcia C, Ramirez-Morales M, Sanchez-Rivas M, Cureno-Diaz M, Matias-Tellez B, Gonzalez-Martinez J, Juarez-Vargas R, Pastor-Salinas O, Gutierrez-Munoz V, Conde-Mercado J, Bruno-Carrasco G, Manrique M, Monroy-Colin V, Cruz-Rivera Z, Rodriguez-Pacheco J, Cruz N, Hernandez-Chena B, Guido-Ramirez O, Arteaga-Troncoso G, Guerra-Infante F, Lopez-Hurtado M, Caleco JD, Leyva-Medellin E, Salamanca-Meneses A, Cosio-Moran C, Ruiz-Rendon R, Aguilar-Angel L, Sanchez-Vargas M, Mares-Morales R, Fernandez-Alvarez L, Castillo-Cruz B, Gonzalez-Ma M, Zavala-Ramír M, Rivera-Reyna L, del-Moral-Rossete L, Lopez-Rubio C, Valadez-de-Alba M, Bat-Erdene A, Chuluunchimeg K, Baatar O, Batkhuu B, Ariyasuren Z, Bayasgalan G, Baigalmaa S, Uyanga T, Suvderdene P, Enkhtsetseg D, Suvd-Erdene D, Chimedtseye E, Bilguun G, Tuvshinbayar M, Dorj M, Khajidmaa T, Batjargal G, Naranpurev M, Bat-Erdene A, Bolormaa T, Battsetseg T, Batsuren C, Batsaikhan N, Tsolmon B, Saranbaatar A, Natsagnyam P, Nyamdawa O, Madani N, Abouqal R, Zeggwagh A, Berechid K, Dendane T, Koirala A, Giri R, Sainju S, Acharya S, Paul N, Parveen A, Raza A, Nizamuddin S, Sultan F, Imran X, Sajjad R, Khan M, Sana F, Tayyab N, Ahmed A, Zaman G, Khan I, Khurram F, Hussain A, Zahra F, Imtiaz A, Daud N, Sarwar M, Roop Z, Yusuf S, Hanif F, Shumaila X, Zeb J, Ali S, Demas S, Ariff S, Riaz A, Hussain A, Kanaan A, Jeetawi R, Castaño E, Moreno-Castillo L, García-Mayorca E, Prudencio-Leon W, Vivas-Pardo A, Changano-Rodriguez M, Castillo-Bravo L, Aibar-Yaranga K, Marquez-Mondalgo V, Mueras-Quevedo J, Meza-Borja C, Flor J, Fernandez-Camacho Y, Banda-Flores C, Pichilingue-Chagray J, Castaneda-Sabogal A, Caoili J, Mariano M, Maglente R, Santos S, de-Guzman G, Mendoza M, Javellana O, Tajanlangit A, Tapang A, Sg-Buenaflor M, Labro E, Carma R, Dy A, Fortin J, Navoa-Ng J, Cesar J, Bonifacio B, Llames M, Gata H, Tamayo A, Calupit H, Catcho V, Bergosa L, Abuy M, Barteczko-Grajek B, Rojek S, Szczesny A, Domanska M, Lipinska G, Jaroslaw J, Wieczoreka A, Szczykutowicza A, Gawor M, Piwoda M, Rydz-Lutrzykowska J, Grudzinska M, Kolat-Brodecka P, Smiechowicz K, Tamowicz B, Mikstacki A, Grams A, Sobczynski P, Nowicka M, Kretov V, Shalapuda V, Molkov A, Puzanov S, Utkin I, Tchekulaev A, Tulupova V, Vasiljevic S, Nikolic L, Ristic G, Eremija J, Kojovic J, Lekic D, Simic A, Hlinkova S, Lesnakova A, Kadankunnel S, Abdo-Ali M, Pimathai R, Wanitanukool S, Supa N, Prasan P, Luxsuwong M, Khuenkaew Y, Lamngamsupha J, Siriyakorn N, Prasanthai V, Apisarnthanarak A, Borgi A, Bouziri A, Cabadak H, Tuncer G, Bulut C, Hatipoglu C, Sebnem F, Demiroz A, Kaya A, Ersoz G, Kuyucu N, Karacorlu S, Oncul O, Gorenek L, Erdem H, Yildizdas D, Horoz O, Guclu E, Kaya G, Karabay O, Altindis M, Oztoprak N, Sahip Y, Uzun C, Erben N, Usluer G, Ozgunes I, Ozcelik M, Ceyda B, Oral M, Unal N, Cigdem Y, Bayar M, Bermede O, Saygili S, Yesiler I, Memikoglu O, Tekin R, Oncul A, Gunduz A, Ozdemir D, Geyik M, Erdogan S, Aygun C, Dilek A, Esen S, Turgut H, Sungurtekin H, Ugurcan D, Yarar V, Bilir Y, Bayram N, Devrim I, Agin H, Ceylan G, Yasar N, Oruc Y, Ramazanoglu A, Turhan O, Cengiz M, Yalcin A, Dursun O, Gunasan P, Kaya S, Senol G, Kocagoz A, Al-Rahma H, Annamma P, El-Houfi A, Vidal H, Perez F, D-Empaire G, Ruiz Y, Hernandez D, Aponte D, Salinas E, Vidal H, Navarrete N, Vargas R, Sanchez E, Ngo Quy C, Thu T, Nguyet L, Hang P, Hang T, Hanh T, Anh D. International Nosocomial Infection Control Consortium (INICC) report, data summary of 45 countries for 2012-2017: Device-associated module. Am J Infect Control 2020; 48:423-432. [PMID: 31676155 DOI: 10.1016/j.ajic.2019.08.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND We report the results of International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2012 to December 2017 in 523 intensive care units (ICUs) in 45 countries from Latin America, Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific. METHODS During the 6-year study period, prospective data from 532,483 ICU patients hospitalized in 242 hospitals, for an aggregate of 2,197,304 patient days, were collected through the INICC Surveillance Online System (ISOS). The Centers for Disease Control and Prevention-National Healthcare Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI) were applied. RESULTS Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAI rates were higher in the INICC ICUs: in the medical-surgical ICUs, the pooled central line-associated bloodstream infection rate was higher (5.05 vs 0.8 per 1,000 central line-days); the ventilator-associated pneumonia rate was also higher (14.1 vs 0.9 per 1,000 ventilator-days,), as well as the rate of catheter-associated urinary tract infection (5.1 vs 1.7 per 1,000 catheter-days). From blood cultures samples, frequencies of resistance, such as of Pseudomonas aeruginosa to piperacillin-tazobactam (33.0% vs 18.3%), were also higher. CONCLUSIONS Despite a significant trend toward the reduction in INICC ICUs, DA-HAI rates are still much higher compared with CDC-NHSN's ICUs representing the developed world. It is INICC's main goal to provide basic and cost-effective resources, through the INICC Surveillance Online System to tackle the burden of DA-HAIs effectively.
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Rani DS, Nallari P, Rani J, Nizamuddin S, Seelamneni T, Narasimhan C, Thangaraj K. A Complete Absence of Missense Mutation in Myosin Regulatory and Essential Light Chain Genes of South Indian Hypertrophic and Dilated Cardiomyopathies. Cardiology 2019; 141:156-166. [PMID: 30605904 DOI: 10.1159/000495027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 10/25/2018] [Indexed: 11/19/2022]
Abstract
BACKGROUND Myosin is a hexameric contractile protein composed of 2 heavy chains associated with 4 light chains of 2 distinct classes - 2 regulatory light chains (MYL2) and 2 essential light chains (MYL3). The myosin light chains stabilize the long alpha helical neck of the myosin head and regulate the myosin ATPase activities. OBJECTIVES Mutations in MYL2 and MYL3 are reported to be associated with cardiomyopathies. However, there is no study available on these genes in Indian cardiomyopathies, and therefore we planned to study them. METHOD For the first time we sequenced MYL2 and MYL3 genes in a total of 248 clinically well-characterized cardiomyopathies consisting of 101 hypertrophic and 147 dilated cases along with 207 healthy controls from south India. RESULTS Our study revealed a total of 10 variations - 7 in MYL2 and 3 in MYL3, of which 3 are novel variations observed exclusively in cases. However, the 15 causative missense mutations previously reported are totally absent in our study, which showed that the sequences of MYL2 and MYL3 are highly conserved in Indian cases/controls. CONCLUSIONS MYL2 and MYL3 mutations are rare and the least cause of cardiomyopathies in Indians.
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Affiliation(s)
- Deepa Selvi Rani
- CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | | | - Jhansi Rani
- CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Sheikh Nizamuddin
- CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
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Mishra A, Sundaravadivel P, Tripathi SK, Jha RK, Badrukhiya J, Basak N, Anerao I, Sharma A, Idowu AE, Mishra A, Pandey S, Kumar U, Singh S, Nizamuddin S, Tupperwar NC, Jha AN, Thangaraj K. Variations in macrophage migration inhibitory factor gene are not associated with visceral leishmaniasis in India. J Infect Public Health 2019; 12:380-387. [PMID: 30611734 DOI: 10.1016/j.jiph.2018.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 09/16/2017] [Revised: 11/24/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The host genetic factors play important role in determining the outcome of visceral leishmaniasis (VL). Macrophage migration inhibitory factor (MIF) is an important host cytokine, which is a key regulator of innate immune system. Genetic variants in MIF gene have been found to be associated with several inflammatory and infectious diseases. Role of MIF is well documented in leishmaniasis diseases, including Indian visceral leishmaniasis, where elevated level of serum MIF has been associated with VL phenotypes. However, there was no genetic study to correlate MIF variants in VL, therefore, we aimed to study the possible association of three reported MIF gene variants -794 CATT, -173G > C and non-coding RNA gene LOC284889 in Indian VL phenotype. METHODS Study subjects comprised of 214 VL patients along with ethnically and demographically matched 220 controls from VL endemic regions of Bihar state in India. RESULTS We found no significant difference between cases and controls in allelic, genotypic and haplotype frequency of the markers analysed [-794 CATT repeats (χ2=0.86; p=0.35; OR=0.85; 95% CI=0.61-1.19); -173 G>C polymorphism (χ2=1.11; p=0.29; OR=0.83; 95% CI=0.59-1.16); and LOC284889 (χ2=0.78; p=0.37; OR=0.86; 95% CI=0.61-1.20)]. CONCLUSION Since we did not find any significant differences between case and control groups, we conclude that sequencing of complete MIF gene and extensive study on innate and adaptive immunity genes may help in identifying genetic variations that are associated with VL susceptibility/resistance among Indians.
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Affiliation(s)
- Anshuman Mishra
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Vinoba Bhave Research Institute, Allahabad, India; Institute of Advanced Materials, Linkoping, Sweden
| | | | | | - Rajan Kumar Jha
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Nipa Basak
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research, India
| | - Isha Anerao
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Akshay Sharma
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ajayi Ebenezer Idowu
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Osun State University, Oshogbo, Nigeria
| | | | | | - Umesh Kumar
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sakshi Singh
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Aditya Nath Jha
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Sickle Cell Institute Chhattisgarh, Raipur, India
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Asif M, Bhat S, Nizamuddin S, Mustak MS. Association between Myocardial Infarction and Dermatoglyphics: A Cross-Sectional Study. J Cardiovasc Dis Res 2018. [DOI: 10.5530/jcdr.2018.1.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Sudhakar DVS, Nizamuddin S, Manisha G, Devi JR, Gupta NJ, Chakravarthy BN, Deenadayal M, Singh L, Thangaraj K. NR5A1 mutations are not associated with male infertility in Indian men. Andrologia 2017; 50. [PMID: 29265478 DOI: 10.1111/and.12931] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2017] [Indexed: 01/10/2023] Open
Abstract
NR5A1 or steroidogenic factor 1 (SF1) is an autosomal gene, which encodes a protein that is a member of nuclear receptor family. NR5A1 regulates the transcription of numerous genes that are expressed in hypothalamic-pituitary-gonadal axis and adrenal cortex which in turn, coordinate the gonadal development, steroidogenesis and sex differentiation. Several mutations in NR5A1 have been reported to cause gonadal dysgenesis with adrenal insufficiency in individuals with 46,XY karyotype. However, studies in the past few years have shown that NR5A1 mutations can also contribute to primary ovarian insufficiency and impaired spermatogenesis. As there is no genetic study on NR5A1 in Indian infertile men, we have sequenced the entire coding region (exons 2-7) of NR5A1 in 502 infertile men of which, 414 were non-obstructive azoospermic and 88 severe oligozoospermic, along with 427 ethnically matched fertile controls. Interestingly, none of the mutations reported to be associated with male infertility were found in our study, except one polymorphism, rs1110061. However, it was not significantly different between infertile and fertile groups (p = .76). In addition, we have identified six intronic variants; but none of them was significantly associated with male infertility.
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Affiliation(s)
- D V S Sudhakar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - S Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - G Manisha
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - J R Devi
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - N J Gupta
- Institute of Reproductive Medicine, Kolkata, India
| | | | - M Deenadayal
- Infertility Institute and Research Center, Secunderabad, India
| | - L Singh
- Genome Foundation, Hyderabad, India
| | - K Thangaraj
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
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Asif M, Bhat S, Nizamuddin S, Mustak MS. TG haplotype in the LRP8 is associated with myocardial infarction in south Indian population. Gene 2017; 642:225-229. [PMID: 29032149 DOI: 10.1016/j.gene.2017.10.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 06/14/2017] [Revised: 09/15/2017] [Accepted: 10/11/2017] [Indexed: 01/02/2023]
Abstract
Myocardial infarction (MI) is a complex multifactorial cardiovascular disease. India experiences a much greater burden of MI, also suggesting an experimental increase of this burden in the future. The absolute reasons for MI are context dependent and differ with different geographical settings. Several reports indicate that SNPs that are associated with certain diseases in other populations may not be associated with Indian population. It is, therefore, important to validate the association of SNPs. Low density lipoprotein receptor related protein 8 (LRP8) gene plays central role in human lipoprotein metabolism as it facilitates the clearance of bad cholesterol LDL, VLDL from plasma and is reported to be associated with MI in the western population. However, this gene has not been studied in the South Indian population. We aim to test the role of the LRP8 gene variants correlating with the lipid profile in MI patients in South Indian population. We sequenced regions of SNPs rs10788952, rs7546246, rs2297660 and rs5174 of LRP8 in 100 MI patients and 100 age-matched controls. Our result revealed a total of 4 variations. None of the SNPs were significantly associated with MI (p>0.973). Interestingly, haplotype based association analysis showed TG and CG of rs10788952 and rs7546246 significantly associated with MI (p<0.01 and p<0.00005) and in particular, haplotype TG was positively correlated with the risk of MI, as this increased the LDL and total cholesterol level in MI patients in south Indians. Our results suggest that haplotype TG is a risk factor for MI in South Indian population.
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Affiliation(s)
- Muhammed Asif
- Department of Anatomy, Yenepoya Medical College and Hospital, Mangalore 575018, Karnataka, India
| | - Shivarama Bhat
- Department of Anatomy, Yenepoya Medical College and Hospital, Mangalore 575018, Karnataka, India
| | - Sheikh Nizamuddin
- Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalagangothri, 574199 Mangalore, India.
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Gill GK, Mubarak NM, Nizamuddin S, Al-Salim HS, Sahu JN. Column performance of carbon nanotube packed bed for methylene blue and orange red dye removal from waste water. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1757-899x/206/1/012081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Affiliation(s)
- S. Nizamuddin
- Service d'Etudes de Réacteurs et de Mathématiques Appliqués Centre d'Etudes Nucléaires de Saclay, BP N°2, 91190 Gif-sur-Yvette, France
| | - J. Blons
- Département de Physique Nucléaire Centre d'Etudes Nucléaires de Saclay, BP N°2, 91190 Gif-sur-Yvette, France
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Zafar A, Hasan R, Nizamuddin S, Mahmood N, Mukhtar S, Ali F, Morrissey I, Barker K, Torumkuney D. Antibiotic susceptibility in Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus pyogenes in Pakistan: a review of results from the Survey of Antibiotic Resistance (SOAR) 2002-15. J Antimicrob Chemother 2016; 71 Suppl 1:i103-9. [PMID: 27048578 DOI: 10.1093/jac/dkw076] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To investigate changes in the antibiotic susceptibility of Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus pyogenes from the Survey of Antibiotic Resistance (SOAR) in community-acquired respiratory tract infections (CA-RTIs) between 2002 and 2015 in Pakistan. METHODS This is a review based on previously published studies from 2002-03, 2004-06 and 2007-09 and also new data from 2014-15. Susceptibility was determined by Etest(®) or disc diffusion according to CLSI and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints. RESULTS A total of 706 isolates from CA-RTIs comprising 381 S. pneumoniae, 230 H. influenzae and 95 S. pyogenes were collected between 2002 and 2015 and tested against a range of antibiotics. Antibiotic resistance in S. pneumoniae rose steeply from 2002 to 2009, with isolates non-susceptible to penicillin and macrolides increasing from 10% to 34.1% and from 13%-14% to 29.7%, respectively. Susceptibility to amoxicillin/clavulanic acid (and by inference amoxicillin) remained between 99.4% and 100% from 2002 to 2015. Over the years, the prevalence of susceptibility to cefuroxime was 98%-100% among S. pneumoniae. Resistance in S. pneumoniae to some older antibiotics between 2007 and 2009 was high (86.8% for trimethoprim/sulfamethoxazole and 57.2% for tetracycline). Between 2002 and 2015, ampicillin resistance (β-lactamase-positive strains) among H. influenzae has remained low (between 2.6% and 3.2%) and almost unchanged over the years (H. influenzae was not tested during 2004-06). For S. pyogenes isolates, macrolide resistance reached 22%; however, susceptibility to penicillin, amoxicillin/clavulanic acid and cefuroxime remained stable at 100%. CONCLUSIONS In S. pneumoniae from Pakistan, there has been a clear reduction in susceptibility to key antibiotics since 2002, but not to amoxicillin/clavulanic acid (amoxicillin) or cefuroxime. However, susceptibility in H. influenzae has remained stable. Local antibiotic susceptibility/resistance data are essential to support informed prescribing for CA-RTIs and other infections.
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Affiliation(s)
- A Zafar
- Aga Khan University Hospital, Department of Pathology and Laboratory Medicine, Section of Microbiology, Karachi, Pakistan
| | - R Hasan
- Aga Khan University Hospital, Department of Pathology and Laboratory Medicine, Section of Microbiology, Karachi, Pakistan
| | - S Nizamuddin
- Shaukat Khanum Memorial Cancer Hospital and Research Center, Department of Microbiology, 7A, Block R-3, Johar Town, Lahore, Pakistan
| | - N Mahmood
- Shaukat Khanum Memorial Cancer Hospital and Research Center, Department of Microbiology, 7A, Block R-3, Johar Town, Lahore, Pakistan
| | - S Mukhtar
- Shaukat Khanum Memorial Cancer Hospital and Research Center, Department of Microbiology, 7A, Block R-3, Johar Town, Lahore, Pakistan
| | - F Ali
- GlaxoSmithKline Pakistan, 35 Dockyard Road, West Wharf, Karachi 74000, Pakistan
| | - I Morrissey
- IHMA Europe Sàrl, 9a route de la Corniche, Epalinges 1066, Switzerland
| | - K Barker
- GlaxoSmithKline, 980 Great West Road, Brentford, Middlesex TW8 9GS, UK
| | - D Torumkuney
- GlaxoSmithKline, 980 Great West Road, Brentford, Middlesex TW8 9GS, UK
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Ganesan M, Nizamuddin S, Katkam SK, Kumaraswami K, Hosad UK, Lobo LL, Kutala VK, Thangaraj K. c.*84G>A Mutation in CETP Is Associated with Coronary Artery Disease in South Indians. PLoS One 2016; 11:e0164151. [PMID: 27768712 PMCID: PMC5074517 DOI: 10.1371/journal.pone.0164151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 06/28/2016] [Accepted: 09/20/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Coronary artery disease (CAD) is one of the leading causes of mortality worldwide. It is a multi-factorial disease and several studies have demonstrated that the genetic factors play a major role in CAD. Although variations in cholesteryl ester transfer protein (CETP) gene are reported to be associated with CAD, this gene has not been studied in South Indian populations. Hence we evaluated the CETP gene variations in CAD patients of South Indian origin. METHODS We sequenced all the exons, exon-intron boundaries and UTRs of CETP in 323 CAD patients along with 300 ethnically and age matched controls. Variations observed in CETP were subjected to various statistical analyses. RESULTS AND DISCUSSION Our analysis revealed a total of 13 variations. Of these, one3'UTRvariant rs1801706 (c.*84G>A) was significantly associated with CAD (genotype association test: OR = 2.16, 95% CI: 1.50-3.10, p = 1.88x10-5 and allelic association test: OR = 1.92, 95% CI: 1.40-2.63, p = 2.57x10-5). Mutant allele "A" was observed to influence the higher concentration of mRNA (p = 7.09×10-3, R2 = 0.029 and β = 0.2163). Since expression of CETP has been shown to be positively correlated with the risk of CAD, higher frequency of "A" allele (patients: 22.69% vs.controls: 13%) reveals that c.*84G>A is a risk factor for CAD in South Indians. CONCLUSIONS This is the first report of the CETP gene among South Indians CAD patients. Our results suggest that rs1801706 (c.*84G>A) is a risk factor for CAD in South Indian population.
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Affiliation(s)
- Mala Ganesan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Konda Kumaraswami
- Department of Clinical Pharmacology and Therapeutics, Nizam's Institute of Medical Sciences (NIMS), Hyderabad, India
| | | | | | - Vijay Kumar Kutala
- Department of Clinical Pharmacology and Therapeutics, Nizam's Institute of Medical Sciences (NIMS), Hyderabad, India
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Nizamuddin S, Govindaraj P, Saxena S, Kashyap M, Mishra A, Singh S, Rotti H, Raval R, Nayak J, Bhat BK, Prasanna BV, Dhumal VR, Bhale S, Joshi KS, Dedge AP, Bharadwaj R, Gangadharan GG, Nair S, Gopinath PM, Patwardhan B, Kondaiah P, Satyamoorthy K, Valiathan MS, Thangaraj K. Reply to 'Lack of replication of association of THSD7A with obesity'. Int J Obes (Lond) 2016; 40:727-8. [PMID: 26902698 DOI: 10.1038/ijo.2016.16] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- S Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - P Govindaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - S Saxena
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M Kashyap
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - A Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - S Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - H Rotti
- School of Life Sciences, Manipal University, Manipal, India
| | - R Raval
- School of Life Sciences, Manipal University, Manipal, India
| | - J Nayak
- Shri Dharmasthala Manjunatheshwara College of Ayurveda, Udupi, India
| | - B K Bhat
- Shri Dharmasthala Manjunatheshwara College of Ayurveda, Udupi, India
| | - B V Prasanna
- Shri Dharmasthala Manjunatheshwara College of Ayurveda, Udupi, India
| | - V R Dhumal
- Sinhgad College of Engineering, Pune, India
| | - S Bhale
- Sinhgad College of Engineering, Pune, India
| | - K S Joshi
- Sinhgad College of Engineering, Pune, India
| | - A P Dedge
- Sinhgad College of Engineering, Pune, India
| | - R Bharadwaj
- Foundation for Revitalization of Local Health Traditions, Bengaluru, India
| | - G G Gangadharan
- Foundation for Revitalization of Local Health Traditions, Bengaluru, India
| | - S Nair
- Department of Statistics, Manipal University, Manipal, India
| | - P M Gopinath
- School of Life Sciences, Manipal University, Manipal, India
| | - B Patwardhan
- Interdisciplinary School of Health Sciences, University of Pune, Pune, India
| | - P Kondaiah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - K Satyamoorthy
- School of Life Sciences, Manipal University, Manipal, India
| | - M S Valiathan
- School of Life Sciences, Manipal University, Manipal, India
| | - K Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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Singh S, Singh A, Rajkumar R, Sampath Kumar K, Kadarkarai Samy S, Nizamuddin S, Singh A, Ahmed Sheikh S, Peddada V, Khanna V, Veeraiah P, Pandit A, Chaubey G, Singh L, Thangaraj K. Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup. Sci Rep 2016; 6:19157. [PMID: 26754573 PMCID: PMC4709632 DOI: 10.1038/srep19157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 03/17/2015] [Accepted: 10/08/2015] [Indexed: 11/24/2022] Open
Abstract
The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.
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Affiliation(s)
- Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Raja Rajkumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | | | - Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Amita Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Vidya Peddada
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Vinee Khanna
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
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Mubarak NM, Fo YT, Al-Salim HS, Sahu JN, Abdullah EC, Nizamuddin S, Jayakumar NS, Ganesan P. Removal of Methylene Blue and Orange-G from Waste Water Using Magnetic Biochar. Int J Nanosci 2015. [DOI: 10.1142/s0219581x1550009x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study on the removal of methylene blue (MB) and orange-G dyes using magnetic biochar derived from the empty fruit bunch (EFB) was carried out. Process parameters such as pH, adsorbent dosage, agitation speed and contact time were optimized using Design-Expert Software v.6.0.8. The statistical analysis reveals that the optimum conditions for the maximum adsorption of MB are at pH 2 and pH 10, dosage 1.0 g, and agitation speed and contact time of 125 rpm and 120 min respectively. While for orange-G, at pH 2, dosage 1.0 g, and agitation speed and contact time of 125 rpm and 120 min respectively. The maximum adsorption capacity of 31.25 mg/g and 32.36 mg/g for MB and orange-G respectively. The adsorption kinetic for both dyes obeyed pseudo-second order.
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Affiliation(s)
- N. M. Mubarak
- Department of Chemical and Petroleum Engineering, Faculty of Engineering, UCSI University, Kuala Lumpur-56000, Malaysia
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Y. T. Fo
- Department of Chemical and Petroleum Engineering, Faculty of Engineering, UCSI University, Kuala Lumpur-56000, Malaysia
| | - Hikmat Said Al-Salim
- Department of Chemical and Petroleum Engineering, Faculty of Engineering, UCSI University, Kuala Lumpur-56000, Malaysia
| | - J. N. Sahu
- Petroleum and Chemical Engineering Programme Area, Faculty of Engineering, Institut Teknologi Brunei (A Technology University), Tungku Gadong, P. O. Box 2909, Brunei Darussalam
| | - E. C. Abdullah
- Malaysia – Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Semarak, 54100 Kuala Lumpur, Malaysia
| | - S. Nizamuddin
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - N. S. Jayakumar
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - P. Ganesan
- Department of Mechanical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Mattapally S, Nizamuddin S, Murthy KS, Thangaraj K, Banerjee SK. c.620C>T mutation in GATA4 is associated with congenital heart disease in South India. BMC Med Genet 2015; 16:7. [PMID: 25928801 PMCID: PMC4422155 DOI: 10.1186/s12881-015-0152-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/30/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND Congenital heart diseases (CHDs) usually refer to abnormalities in the structure and/or function of the heart that arise before birth. GATA4 plays an important role in embryonic heart development, hence the aim of this study was to find the association of GATA4 mutations with CHD among the south Indian CHD patients. METHOD GATA4 gene was sequenced in 100 CHD patients (ASD, VSD, TOF and SV) and 200 controls. Functional significance of the observed GATA4 mutations was analyzed using PolyPhen, SIFT, PMut, Plink, Haploview, ESE finder 3.0 and CONSITE. RESULTS We observed a total of 19 mutations, of which, one was in 5' UTR, 10 in intronic regions, 3 in coding regions and 5 in 3' UTR. Of the above mutations, one was associated with Atrial Septal Defect (ASD), two were found to be associated with Tetralogy of Fallot (TOF) and three (rs804280, rs4841587 and rs4841588) were strongly associated with Ventricular Septal Defect (VSD). Interestingly, one promoter mutation (-490 to 100 bp) i.e., 620 C>T (rs61277615, p-value = 0.008514), one splice junction mutation (G>A rs73203482; p-value = 9.6e-3, OR = 6.508) and one intronic mutation rs4841587 (p-value = 4.6e-3, OR = 4.758) were the most significant findings of this study. In silico analysis also proves that some of the mutations reported above are pathogenic. CONCLUSION The present study found that GATA4 genetic variations are associated with ASD, TOF and VSD in South Indian patients. In silico analysis provides further evidence that some of the observed mutations are pathogenic.
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Affiliation(s)
- Saidulu Mattapally
- Division of Pharmacology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500 007, India.
| | - Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
| | - Kona Samba Murthy
- Innova Children's Heart Hospital, Tarnaka, Hyderabad, 500017, India.
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
| | - Sanjay K Banerjee
- Division of Pharmacology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500 007, India. .,Current Address: Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI), Gurgaon, HR-122016, Haryana, India.
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Thangalazhy-Gopakumar S, Al-Nadheri WMA, Jegarajan D, Sahu JN, Mubarak NM, Nizamuddin S. Utilization of palm oil sludge through pyrolysis for bio-oil and bio-char production. Bioresour Technol 2015; 178:65-69. [PMID: 25278112 DOI: 10.1016/j.biortech.2014.09.068] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 07/10/2014] [Revised: 09/13/2014] [Accepted: 09/15/2014] [Indexed: 06/03/2023]
Abstract
In this study, pyrolysis technique was utilized for converting palm oil sludge to value added materials: bio-oil (liquid fuel) and bio-char (soil amendment). The bio-oil yield obtained was 27.4±1.7 wt.% having a heating value of 22.2±3.7 MJ/kg and a negligible ash content of 0.23±0.01 wt.%. The pH of bio-oil was in alkaline region. The bio-char yielded 49.9±0.3 wt.%, which was further investigated for sorption efficiency by adsorbing metal (Cd(2+) ions) from water. The removal efficiency of Cd(2+) was 89.4±2%, which was almost similar to the removal efficiency of a commercial activated carbon. The adsorption isotherm was well described by Langmuir model. Therefore, pyrolysis is proved as an efficient tool for palm oil sludge management, where the waste was converted into valuable products.
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Affiliation(s)
| | | | - Dinesh Jegarajan
- Department of Chemical and Petroleum Engineering, Faculty of Engineering, UCSI University, KL 56000, Malaysia
| | - J N Sahu
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, KL 50603, Malaysia; Petroleum and Chemical Engineering Programme Area, Faculty of Engineering, Institute Technology Brunei, Tungku Gadong, P.O. Box 2909, Brunei Darussalam
| | - N M Mubarak
- Department of Chemical and Petroleum Engineering, Faculty of Engineering, UCSI University, KL 56000, Malaysia; Department of Chemical Engineering, Faculty of Engineering, University of Malaya, KL 50603, Malaysia
| | - S Nizamuddin
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, KL 50603, Malaysia
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Nizamuddin S, Khan F, Khan A, Kamaal C. Assessment of hearing loss in multi-drug resistant tuberculosis (MDR-TB) patients undergoing Aminoglycoside treatment. ACTA ACUST UNITED AC 2015. [DOI: 10.18203/2320-6012.ijrms20150261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Shivanand K, Raju SA, Nizamuddin S, Jayakar B. In vivo bioavailability studies of sumatriptan succinate buccal tablets. Daru 2011; 19:224-30. [PMID: 22615661 PMCID: PMC3232104] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 06/18/2011] [Accepted: 06/19/2011] [Indexed: 12/03/2022] Open
Abstract
UNLABELLED BACK GROUND AND THE PURPOSE OF STUDY: Sumatriptan succinate is a Serotonin 5- HT1 receptor agonist, used in treatment of migraine. It is absorbed rapidly but incompletely when given orally and undergoes first-pass metabolism, resulting in a low absolute bioavailability of about 15%. The aim of this work was to design mucoadhesive bilayered buccal tablets of sumatriptan succinate to improve its bioavailability. METHODS Mucoadhesive polymers carbopol 934 (Carbopol), HPMC K4M, HPMC K15M along with ethyl cellulose as an impermeable backing layer were used for the preparation of mucoadhesive bilayered tablets. In vivo bioavailability studies was also conducted in rabbits for optimized formulation using oral solution of sumatriptan succinate as standard. RESULTS Bilayered buccal tablets (BBT) containing the mixture of Carbopol and HPMC K4M in the ratio 1:1 (T1) had the maximum percentage of in vitro drug release within 6 hrs. The optimized formulation (T1) followed non-Fickian release mechanism. The percentage relative bioavailability of sumatriptan succinate from selected bilayered buccal tablets (T1) was found to be 140.78%. CONCLUSIONS Bilayered buccal tablets of sumatriptan succinate was successfully prepared with improved bioavailability.
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Affiliation(s)
- K Shivanand
- Acharya and B M Reddy College of Pharmacy, Bangalore-560090, India,Correspondence:
| | - SA Raju
- HKE Society's College of Pharmacy, Gulbarga-585105 (Karnataka)
| | - S Nizamuddin
- Acharya and B M Reddy College of Pharmacy, Bangalore-560090, India
| | - B Jayakar
- Vinayaka Mission's College of Pharmacy, Salem (Tamil Nadu), India
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Gurupadayya BM, Ravi MC, Manohara YN, Raju SA, Nizamuddin S. Spectrophotometric estimation of famciclovir in bulk and tablet dosage form. Indian J Pharm Sci 2007. [DOI: 10.4103/0250-474x.34562] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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