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Article: Non-Association of Driver Alterations in PTEN with Differential Gene Expression and Gene Methylation in IDH1 Wildtype Glioblastomas.

Mallik, Mrinmay Kumar / Majumdar, Kaushik / Mujtaba, Shiraz

2023 Volume 13, Issue 2

Abstract: During oncogenesis, alterations in driver genes called driver alterations (DAs) modulate the transcriptome, methylome and proteome through oncogenic signaling pathways. These modulatory effects of any DA may be analyzed by examining differentially ... ...

Abstract	During oncogenesis, alterations in driver genes called driver alterations (DAs) modulate the transcriptome, methylome and proteome through oncogenic signaling pathways. These modulatory effects of any DA may be analyzed by examining differentially expressed mRNAs (DEMs), differentially methylated genes (DMGs) and differentially expressed proteins (DEPs) between tumor samples with and without that DA. We aimed to analyze these modulations with 12 common driver genes in Isocitrate Dehydrogenase 1 wildtype glioblastomas (IDH1-W-GBs). Using Cbioportal, groups of tumor samples with and without DAs in these 12 genes were generated from the IDH1-W-GBs available from "The Cancer Genomics Atlas Firehose Legacy Study Group" (TCGA-FL-SG) on Glioblastomas (GBs). For all 12 genes, samples with and without DAs were compared for DEMs, DMGs and DEPs. We found that DAs in
Language	English
Publishing date	2023-01-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2651993-8
ISSN	2076-3425
ISSN	2076-3425
DOI	10.3390/brainsci13020186
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Article ; Online: Cardiac Children Hospital Early Warning ScoreVersus the Inadequate Oxygen Delivery Index for the Detection of Early Warning Signs of Deterioration.

Khalil, Mujtaba / Abbas, Qalab / Azhar, Mohammad Kumael / Aamir, Faiqa Binte / Hashmi, Shiraz / Ali, Sadaqat / Faiz, Tahira / Malik, Mahim Akmal

Critical care explorations

2023 Volume 5, Issue 1, Page(s) e0833

Abstract: To assess the utility of the Cardiac Children's Hospital Early Warning Score (C-CHEWS) in the early detection of deterioration.: Design: Single-center longitudinal pilot study.: Setting: Pediatric cardiac ICU (PCICU), Aga Khan University.: ... ...

Abstract	To assess the utility of the Cardiac Children's Hospital Early Warning Score (C-CHEWS) in the early detection of deterioration. Design: Single-center longitudinal pilot study. Setting: Pediatric cardiac ICU (PCICU), Aga Khan University. Interventions: C-CHEWS and Inadequate Oxygen Delivery (IDO Patients: A total of 60 children (0 d to 18 yr old). Measurements and main results: A single-center longitudinal pilot study was conducted at PCICU. All postoperative extubated patients were assessed and scored between 0 and 11, and these scores were then correlated with the IDO Conclusions: The C-CHEWS tool provides a standardized assessment and approach to deteriorating congenital cardiac surgery patients in recognizing early postoperative deterioration.
Language	English
Publishing date	2023-01-23
Publishing country	United States
Document type	Journal Article
ISSN	2639-8028
ISSN (online)	2639-8028
DOI	10.1097/CCE.0000000000000833
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Article ; Online: The Biological Significance of Targeting Acetylation-Mediated Gene Regulation for Designing New Mechanistic Tools and Potential Therapeutics.

O'Garro, Chenise / Igbineweka, Loveth / Ali, Zonaira / Mezei, Mihaly / Mujtaba, Shiraz

Biomolecules

2021 Volume 11, Issue 3

Abstract: The molecular interplay between nucleosomal packaging and the chromatin landscape regulates the transcriptional programming and biological outcomes of downstream genes. An array of epigenetic modifications plays a pivotal role in shaping the chromatin ... ...

Abstract	The molecular interplay between nucleosomal packaging and the chromatin landscape regulates the transcriptional programming and biological outcomes of downstream genes. An array of epigenetic modifications plays a pivotal role in shaping the chromatin architecture, which controls DNA access to the transcriptional machinery. Acetylation of the amino acid lysine is a widespread epigenetic modification that serves as a marker for gene activation, which intertwines the maintenance of cellular homeostasis and the regulation of signaling during stress. The biochemical horizon of acetylation ranges from orchestrating the stability and cellular localization of proteins that engage in the cell cycle to DNA repair and metabolism. Furthermore, lysine acetyltransferases (KATs) modulate the functions of transcription factors that govern cellular response to microbial infections, genotoxic stress, and inflammation. Due to their central role in many biological processes, mutations in KATs cause developmental and intellectual challenges and metabolic disorders. Despite the availability of tools for detecting acetylation, the mechanistic knowledge of acetylation-mediated cellular processes remains limited. This review aims to integrate molecular and structural bases of KAT functions, which would help design highly selective tools for understanding the biology of KATs toward developing new disease treatments.
MeSH term(s)	Acetylation ; DNA Repair/genetics ; DNA Repair/physiology ; Epigenesis, Genetic/genetics ; Epigenesis, Genetic/physiology ; Gene Expression Regulation/genetics ; Gene Expression Regulation/physiology ; Humans ; Lysine Acetyltransferases/genetics ; Lysine Acetyltransferases/metabolism
Chemical Substances	Lysine Acetyltransferases (EC 2.3.1.32)
Language	English
Publishing date	2021-03-18
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom11030455
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Article: Dichotomy in the Epigenetic Mark Lysine Acetylation is Critical for the Proliferation of Prostate Cancer Cells.

Pathak, Ravi / Philizaire, Marc / Mujtaba, Shiraz

Cancers

2015 Volume 7, Issue 3, Page(s) 1622–1642

Abstract: The dynamics of lysine acetylation serve as a major epigenetic mark, which regulates cellular response to inflammation, DNA damage and hormonal changes. Microarray assays reveal changes in gene expression, but cannot predict regulation of a protein ... ...

Abstract	The dynamics of lysine acetylation serve as a major epigenetic mark, which regulates cellular response to inflammation, DNA damage and hormonal changes. Microarray assays reveal changes in gene expression, but cannot predict regulation of a protein function by epigenetic modifications. The present study employs computational tools to inclusively analyze microarray data to understand the potential role of acetylation during development of androgen-independent PCa. The data revealed that the androgen receptor interacts with 333 proteins, out of which at least 92 proteins were acetylated. Notably, the number of cellular proteins undergoing acetylation in the androgen-dependent PCa was more as compared to the androgen-independent PCa. Specifically, the 32 lysine-acetylated proteins in the cellular models of androgen-dependent PCa were mainly involved in regulating stability as well as pre- and post-processing of mRNA. Collectively, the data demonstrate that protein lysine acetylation plays a crucial role during the transition of androgen-dependent to -independent PCa, which importantly, could also serve as a functional axis to unravel new therapeutic targets.
Language	English
Publishing date	2015-08-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers7030854
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Article ; Online: Dichotomy in the Epigenetic Mark Lysine Acetylation is Critical for the Proliferation of Prostate Cancer Cells

Ravi Pathak / Marc Philizaire / Shiraz Mujtaba

Cancers, Vol 7, Iss 3, Pp 1622-

2015 Volume 1642

Abstract	The dynamics of lysine acetylation serve as a major epigenetic mark, which regulates cellular response to inflammation, DNA damage and hormonal changes. Microarray assays reveal changes in gene expression, but cannot predict regulation of a protein function by epigenetic modifications. The present study employs computational tools to inclusively analyze microarray data to understand the potential role of acetylation during development of androgen-independent PCa. The data revealed that the androgen receptor interacts with 333 proteins, out of which at least 92 proteins were acetylated. Notably, the number of cellular proteins undergoing acetylation in the androgen-dependent PCa was more as compared to the androgen-independent PCa. Specifically, the 32 lysine-acetylated proteins in the cellular models of androgen-dependent PCa were mainly involved in regulating stability as well as pre- and post-processing of mRNA. Collectively, the data demonstrate that protein lysine acetylation plays a crucial role during the transition of androgen-dependent to -independent PCa, which importantly, could also serve as a functional axis to unravel new therapeutic targets.
Keywords	prostate cancer ; androgen ; androgen receptor ; lysine acetylation ; deacetylation and molecular interactions ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282 ; Internal medicine ; RC31-1245 ; Medicine ; R
Subject code	612 ; 570
Language	English
Publishing date	2015-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: SET domain-mediated lysine methylation in lower organisms regulates growth and transcription in hosts.

Nwasike, Chukwuazam / Ewert, Sinead / Jovanovic, Srdan / Haider, Shozeb / Mujtaba, Shiraz

Annals of the New York Academy of Sciences

2016 Volume 1376, Issue 1, Page(s) 18–28

Abstract: Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain-mediated lysine methylation, one of the major epigenetic marks, has been found to regulate chromatin-mediated gene transcription. Published studies have established further that methylation is not ... ...

Abstract	Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain-mediated lysine methylation, one of the major epigenetic marks, has been found to regulate chromatin-mediated gene transcription. Published studies have established further that methylation is not restricted to nuclear proteins but is involved in many cellular processes, including growth, differentiation, immune regulation, and cancer progression. The biological complexity of lysine methylation emerges from its capacity to cause gene activation or gene repression owing to the specific position of methylated-lysine moieties on the chromatin. Accumulating evidence suggests that despite the absence of chromatin, viruses and prokaryotes also express SET proteins, although their functional roles remain relatively less investigated. One possibility could be that SET proteins in lower organisms have more than one biological function, for example, in regulating growth or in manipulating host transcription machinery in order to establish infection. Thus, elucidating the role of an SET protein in host-pathogen interactions requires a thorough understanding of their functions. This review discusses the biological role of lysine methylation in prokaryotes and lower eukaryotes, as well as the underlying structural complexity and functional diversity of SET proteins.
MeSH term(s)	Amino Acid Sequence ; Animals ; Host-Pathogen Interactions/genetics ; Humans ; Lysine/metabolism ; Methylation ; Prokaryotic Cells/metabolism ; Protein Domains ; Transcription, Genetic
Chemical Substances	Lysine (K3Z4F929H6)
Language	English
Publishing date	2016-07
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	211003-9
ISSN	1749-6632 ; 0077-8923
ISSN (online)	1749-6632
ISSN	0077-8923
DOI	10.1111/nyas.13017
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Article ; Online: Anti-viral opportunities during transcriptional activation of latent HIV in the host chromatin.

Mujtaba, Shiraz / Zhou, Ming-Ming

Methods (San Diego, Calif.)

2010 Volume 53, Issue 1, Page(s) 97–101

Abstract: Human immunodeficiency virus (HIV) when integrated into a host chromosome exists in a transcriptionally inactive but replication-competent state. Such latent infection represents a major challenge to HIV eradication efforts because a permanent virus ... ...

Abstract	Human immunodeficiency virus (HIV) when integrated into a host chromosome exists in a transcriptionally inactive but replication-competent state. Such latent infection represents a major challenge to HIV eradication efforts because a permanent virus reservoir resided in the infected cell is able to spike the viral load on immune suppression or during interruption of highly active anti-retroviral therapy. Understanding the molecular mechanisms that control HIV proviral latency and its reactivation could provide new perspectives on host factors as therapeutic targets for abolishing cellular reservoirs of dormant HIV. Although the control of HIV latency is multifactorial, chromatin structure and the chromatin-associated transcriptional machinery are known to be important factors. For instance, transcription initiation of the HIV provirus involves a complex molecular interplay between chromatin-associated proteins and the virus-encoded trans-activator, Tat. The first part of this review discusses our current understanding of the elements involved in HIV transcriptional activation and viral mRNA elongation, mainly post-translational modifications of HIV Tat and its interactions with host chromatin-modifying enzymes and chromatin-remodeling complexes. The second part highlights new experimental therapeutic approaches aimed at administrating activators of HIV gene expression to reduce or eliminate the pool of latently HIV-infected cells.
MeSH term(s)	Acetylation ; Anti-HIV Agents/pharmacology ; Anti-HIV Agents/therapeutic use ; Binding Sites ; Chromatin/genetics ; Chromatin/metabolism ; Drug Design ; HIV Infections/drug therapy ; HIV Infections/virology ; HIV-1/drug effects ; HIV-1/genetics ; HIV-1/physiology ; Host-Pathogen Interactions ; Humans ; Protein Interaction Mapping/methods ; Transcriptional Activation ; Virus Integration ; Virus Latency ; p300-CBP Transcription Factors/antagonists & inhibitors ; p300-CBP Transcription Factors/metabolism ; tat Gene Products, Human Immunodeficiency Virus/chemistry ; tat Gene Products, Human Immunodeficiency Virus/metabolism
Chemical Substances	Anti-HIV Agents ; Chromatin ; tat Gene Products, Human Immunodeficiency Virus ; p300-CBP Transcription Factors (EC 2.3.1.48) ; p300-CBP-associated factor (EC 2.3.1.48)
Language	English
Publishing date	2010-09-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2010.09.001
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Article: Anti-viral opportunities during transcriptional activation of latent HIV in the host chromatin

Mujtaba, Shiraz / Zhou, Ming-Ming

Methods. 2011 Jan., v. 53, no. 1

2011

Abstract	Human immunodeficiency virus (HIV) when integrated into a host chromosome exists in a transcriptionally inactive but replication-competent state. Such latent infection represents a major challenge to HIV eradication efforts because a permanent virus reservoir resided in the infected cell is able to spike the viral load on immune suppression or during interruption of highly active anti-retroviral therapy. Understanding the molecular mechanisms that control HIV proviral latency and its reactivation could provide new perspectives on host factors as therapeutic targets for abolishing cellular reservoirs of dormant HIV. Although the control of HIV latency is multifactorial, chromatin structure and the chromatin-associated transcriptional machinery are known to be important factors. For instance, transcription initiation of the HIV provirus involves a complex molecular interplay between chromatin-associated proteins and the virus-encoded trans-activator, Tat. The first part of this review discusses our current understanding of the elements involved in HIV transcriptional activation and viral mRNA elongation, mainly post-translational modifications of HIV Tat and its interactions with host chromatin-modifying enzymes and chromatin-remodeling complexes. The second part highlights new experimental therapeutic approaches aimed at administrating activators of HIV gene expression to reduce or eliminate the pool of latently HIV-infected cells.
Keywords	HIV infections ; Human immunodeficiency virus ; antiretroviral agents ; chromatin ; disease reservoirs ; enzymes ; gene expression ; latent period ; messenger RNA ; post-translational modification ; proviruses ; therapeutics ; transcription (genetics) ; transcriptional activation ; viral load
Language	English
Dates of publication	2011-01
Size	p. 97-101.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2010.09.001
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Article ; Online: Structural insights into FRS2α PTB domain recognition by neurotrophin receptor TrkB.

Zeng, Lei / Kuti, Miklos / Mujtaba, Shiraz / Zhou, Ming-Ming

Proteins

2014 Volume 82, Issue 7, Page(s) 1534–1541

Abstract: The fibroblast growth factor receptor (FGFR) substrate 2 (FRS2) family proteins function as scaffolding adapters for receptor tyrosine kinases (RTKs). The FRS2α proteins interact with RTKs through the phosphotyrosine-binding (PTB) domain and transfer ... ...

Abstract	The fibroblast growth factor receptor (FGFR) substrate 2 (FRS2) family proteins function as scaffolding adapters for receptor tyrosine kinases (RTKs). The FRS2α proteins interact with RTKs through the phosphotyrosine-binding (PTB) domain and transfer signals from the activated receptors to downstream effector proteins. Here, we report the nuclear magnetic resonance structure of the FRS2α PTB domain bound to phosphorylated TrkB. The structure reveals that the FRS2α-PTB domain is comprised of two distinct but adjacent pockets for its mutually exclusive interaction with either nonphosphorylated juxtamembrane region of the FGFR, or tyrosine phosphorylated peptides TrkA and TrkB. The new structural insights suggest rational design of selective small molecules through targeting of the two conjunct pockets in the FRS2α PTB domain.
MeSH term(s)	Adaptor Proteins, Signal Transducing/chemistry ; Adaptor Proteins, Signal Transducing/metabolism ; Binding Sites ; Humans ; Membrane Glycoproteins/chemistry ; Membrane Glycoproteins/metabolism ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein-Tyrosine Kinases/chemistry ; Protein-Tyrosine Kinases/metabolism ; Receptor, trkB
Chemical Substances	Adaptor Proteins, Signal Transducing ; FRS2 protein, human ; Membrane Glycoproteins ; Membrane Proteins ; Protein-Tyrosine Kinases (EC 2.7.10.1) ; Receptor, trkB (EC 2.7.10.1) ; tropomyosin-related kinase-B, human (EC 2.7.10.1)
Language	English
Publishing date	2014-01-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.24523
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Article ; Online: The biology of lysine acetylation integrates transcriptional programming and metabolism.

Patel, Jigneshkumar / Pathak, Ravi R / Mujtaba, Shiraz

Nutrition & metabolism

2011 Volume 8, Page(s) 12

Abstract: The biochemical landscape of lysine acetylation has expanded from a small number of proteins in the nucleus to a multitude of proteins in the cytoplasm. Since the first report confirming acetylation of the tumor suppressor protein p53 by a lysine ... ...

Abstract	The biochemical landscape of lysine acetylation has expanded from a small number of proteins in the nucleus to a multitude of proteins in the cytoplasm. Since the first report confirming acetylation of the tumor suppressor protein p53 by a lysine acetyltransferase (KAT), there has been a surge in the identification of new, non-histone targets of KATs. Added to the known substrates of KATs are metabolic enzymes, cytoskeletal proteins, molecular chaperones, ribosomal proteins and nuclear import factors. Emerging studies demonstrate that no fewer than 2000 proteins in any particular cell type may undergo lysine acetylation. As described in this review, our analyses of cellular acetylated proteins using DAVID 6.7 bioinformatics resources have facilitated organization of acetylated proteins into functional clusters integral to cell signaling, the stress response, proteolysis, apoptosis, metabolism, and neuronal development. In addition, these clusters also depict association of acetylated proteins with human diseases. These findings not only support lysine acetylation as a widespread cellular phenomenon, but also impel questions to clarify the underlying molecular and cellular mechanisms governing target selectivity by KATs. Present challenges are to understand the molecular basis for the overlapping roles of KAT-containing co-activators, to differentiate between global versus dynamic acetylation marks, and to elucidate the physiological roles of acetylated proteins in biochemical pathways. In addition to discussing the cellular 'acetylome', a focus of this work is to present the widespread and dynamic nature of lysine acetylation and highlight the nexus that exists between epigenetic-directed transcriptional regulation and metabolism.
Language	English
Publishing date	2011-03-03
Publishing country	England
Document type	Journal Article
ISSN	1743-7075
ISSN (online)	1743-7075
DOI	10.1186/1743-7075-8-12
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