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  1. Fulltext Revisiting the Roles of Pro-Metastatic EpCAM in Cancer
    Mohtar MA, Syafruddin SE, Nasir SN, Low TY
    Biomolecules, 2020 02 07;10(2).
    PMID: 32046162 DOI: 10.3390/biom10020255
    Epithelial cell adhesion molecule (EpCAM) is a cell surface protein that was discovered as a tumour marker of epithelial origins nearly four decades ago. EpCAM is expressed at basal levels in the basolateral membrane of normal epithelial cells. However, EpCAM expression is upregulated in solid epithelial cancers and stem cells. EpCAM can also be found in disseminated tumour cells and circulating tumour cells. Various OMICs studies have demonstrated that EpCAM plays roles in several key biological processes such as cell adhesion, migration, proliferation and differentiation. Additionally, EpCAM can be detected in the bodily fluid of cancer patients suggesting that EpCAM is a pathophysiologically relevant anti-tumour target as well as being utilized as a diagnostic/prognostic agent for a variety of cancers. This review will focus on the structure-features of EpCAM protein and discuss recent evidence on the pathological and physiological roles of EpCAM in modulating cell adhesion and signalling pathways in cancers as well as deliberating the clinical implication of EpCAM as a therapeutic target.
  2. Connecting Proteomics to Next-Generation Sequencing: Proteogenomics and Its Current Applications in Biology
    Low TY, Mohtar MA, Ang MY, Jamal R
    Proteomics, 2019 05;19(10):e1800235.
    PMID: 30431238 DOI: 10.1002/pmic.201800235
    Understanding the relationship between genotypes and phenotypes is essential to disentangle biological mechanisms and to unravel the molecular basis of diseases. Genes and proteins are closely linked in biological systems. However, genomics and proteomics have developed separately into two distinct disciplines whereby crosstalk among scientists from the two domains is limited and this constrains the integration of both fields into a single data modality of useful information. The emerging field of proteogenomics attempts to address this by building bridges between the two disciplines. In this review, how genomics and transcriptomics data in different formats can be utilized to assist proteogenomics application is briefly discussed. Subsequently, a much larger part of this review focuses on proteogenomics research articles that are published in the last five years that answer two important questions. First, how proteogenomics can be applied to tackle biological problems is discussed, covering genome annotation and precision medicine. Second, the latest developments in analytical technologies for data acquisition and the bioinformatics tools to interpret and visualize proteogenomics data are covered.
  3. The anterior gradient-2 interactome
    Delom F, Mohtar MA, Hupp T, Fessart D
    Am. J. Physiol., Cell Physiol., 2020 01 01;318(1):C40-C47.
    PMID: 31644305 DOI: 10.1152/ajpcell.00532.2018
    The anterior gradient-2 (AGR2) is an endoplasmic reticulum (ER)-resident protein belonging to the protein disulfide isomerase family that mediates the formation of disulfide bonds and assists the protein quality control in the ER. In addition to its role in proteostasis, extracellular AGR2 is responsible for various cellular effects in many types of cancer, including cell proliferation, survival, and metastasis. Various OMICs approaches have been used to identify AGR2 binding partners and to investigate the functions of AGR2 in the ER and outside the cell. Emerging data showed that AGR2 exists not only as monomer, but it can also form homodimeric structure and thus interact with different partners, yielding different biological outcomes. In this review, we summarize the AGR2 "interactome" and discuss the pathological and physiological role of such AGR2 interactions.
  4. Fulltext Impact of Chemotherapy on Extracellular Vesicles: Understanding the Chemo-EVs
    Ab Razak NS, Ab Mutalib NS, Mohtar MA, Abu N
    Front Oncol, 2019;9:1113.
    PMID: 31803605 DOI: 10.3389/fonc.2019.01113
    Chemotherapy is the standard go-to treatment for cancer besides surgery and radiation. It has recently come to light that the interaction between chemotherapy and the immune system is important in maintaining tumor immunity as well as influencing the efficacy of the therapy. However, ample preclinical studies have shown that in addition to direct cytotoxic effects on cancer cells, a fraction of chemotherapeutic agents may promote immunogenic cell death, and alter the inflammatory milieu of the tumor microenvironment. Extracellular vesicles (EV) have been shown to interact with the tumor microenvironment by delivering alterative signals to the surrounding cells; as a result, this results in interference with each cell's capability to eradicate tumors or gives advantages to cancer cells so as to survive therapy. Chemotherapy-induced extracellular vesicles (chemo-EVs) have been theorized to be carrying different cargo loads than non-chemotherapy-induced EVs. Aside from chemoresistance, there is growing evidence to suggest that chemo-EVs could dictate tumor behavior, especially in terms of metastasis, immune response, and cancer stemness. This mini-review attempts to summarize and evaluate recent developments on the role of chemo-EVs in other aspects of tumor-related processes.
  5. Fulltext More Than Meets the Eye: Revisiting the Roles of Heat Shock Factor 4 in Health and Diseases
    Syafruddin SE, Ling S, Low TY, Mohtar MA
    Biomolecules, 2021 Mar 31;11(4).
    PMID: 33807297 DOI: 10.3390/biom11040523
    Cells encounter a myriad of endogenous and exogenous stresses that could perturb cellular physiological processes. Therefore, cells are equipped with several adaptive and stress-response machinery to overcome and survive these insults. One such machinery is the heat shock response (HSR) program that is governed by the heat shock factors (HSFs) family in response towards elevated temperature, free radicals, oxidants, and heavy metals. HSF4 is a member of this HSFs family that could exist in two predominant isoforms, either the transcriptional repressor HSFa or transcriptional activator HSF4b. HSF4 is constitutively active due to the lack of oligomerization negative regulator domain. HSF4 has been demonstrated to play roles in several physiological processes and not only limited to regulating the classical heat shock- or stress-responsive transcriptional programs. In this review, we will revisit and delineate the recent updates on HSF4 molecular properties. We also comprehensively discuss the roles of HSF4 in health and diseases, particularly in lens cell development, cataract formation, and cancer pathogenesis. Finally, we will posit the potential direction of HSF4 future research that could enhance our knowledge on HSF4 molecular networks as well as physiological and pathophysiological functions.
  6. Fulltext Cholesterol accumulation in ccRCC: the role of ccRCC-initiating VHL-HIFα pathway
    Mohtar MA, Hasanah Mohd Yusuf SN, Syafruddin SE
    EBioMedicine, 2024 May;103:105112.
    PMID: 38599011 DOI: 10.1016/j.ebiom.2024.105112
  7. Fulltext In vitro inhibitory and cytotoxic activity of MFM 501, a novel codonopsinine derivative, against Methicillin-Resistant Staphylococcus aureus clinical isolates
    Johari SA, Mohtar M, Mohammad SA, Sahdan R, Shaameri Z, Hamzah AS, et al.
    Biomed Res Int, 2015;2015:823829.
    PMID: 25710030 DOI: 10.1155/2015/823829
    28 new pyrrolidine types of compounds as analogues for natural polyhydroxy alkaloids of codonopsinine were evaluated for their anti-MRSA activity using MIC and MBC value determination assay against a panel of S. aureus isolates. One pyrrolidine compound, MFM 501, exhibited good inhibitory activity with MIC value of 15.6 to 31.3 μg/mL against 55 S. aureus isolates (43 MRSA and 12 MSSA isolates). The active compound also displayed MBC values between 250 and 500 μg/mL against 58 S. aureus isolates (45 MRSA and 13 MSSA isolates) implying that MFM 501 has a bacteriostatic rather than bactericidal effect against both MRSA and MSSA isolates. In addition, MFM 501 showed no apparent cytotoxicity activity towards three normal cell lines (WRL-68, Vero, and 3T3) with IC50 values of >625 µg/mL. Selectivity index (SI) of MFM 501 gave a value of >10 suggesting that MFM 501 is significant and suitable for further in vivo investigations. These results suggested that synthetically derived intermediate compounds based on natural products may play an important role in the discovery of new anti-infective agents against MRSA.
  8. Inhibitory and resistance-modifying potential of plant-based alkaloids against methicillin-resistant Staphylococcus aureus (MRSA)
    Mohtar M, Johari SA, Li AR, Isa MM, Mustafa S, Ali AM, et al.
    Curr Microbiol, 2009 Aug;59(2):181-6.
    PMID: 19475447 DOI: 10.1007/s00284-009-9416-9
    Increased prevalence of methicillin-resistant Staphylococcus aureus (MRSA) has become a major threat to the health sector worldwide due to their virulence, limited therapeutic options and their distribution in both hospital and community settings. Discovery and development of new anti-MRSA agents as alternatives to the very few antibiotics left in the armamentarium are, thus, urgently required. Recently, an efflux mechanism in MRSA has been identified as one of the main contributors of resistance towards various structurally unrelated antibiotics. The potential of reserpine (a phytoalkaloid) as efflux pump inhibitor (EPI) against various microbes remains limited as the concentration needed for inhibition is toxic to humans. This study therefore aimed to evaluate 13 alkaloid compounds as potential inhibitory agents and/or potential EPIs against a panel of three MRSA isolates which not only differ in their susceptibility to vancomycin (amongst the last drugs available to treat serious MRSA infection), but also exhibited active efflux activity. Results indicated berberine's moderate inhibitiory activity against two MRSA isolates scoring a minimum inhibitory concentration (MIC) value of 125 microg/ml. Notable efflux inhibitory activity (ranging from two- to eightfold Ethidium Bromide MIC reduction) meanwhile was detected from quinine, piperine and harmaline using reserpine as the positive control. Findings from this study support the opinion that a vast number of potential phytocompounds with pharmacological potential await discovery. Therapeutic application of these compounds, however, warrants further investigation to ascertain their pharmacodynamics and safety aspects.
  9. Antimicrobial compounds from Alpinia conchigera
    Aziz AN, Ibrahim H, Rosmy Syamsir D, Mohtar M, Vejayan J, Awang K
    J Ethnopharmacol, 2013 Feb 13;145(3):798-802.
    PMID: 23266278 DOI: 10.1016/j.jep.2012.12.024
    The rhizome of Alpinia conchigerahas been used as a condiment in the northern states of Peninsular Malaysia and occasionally in folk medicine in the east coast to treat fungal infections. In some states of Peninsular Malaysia, the rhizomes are consumed as a post-partum medicine and the young shoots are prepared into a vegetable dish. This study aimed to investigate the chemical constituents of the pseudostems and rhizomes of Malaysian Alpinia conchigera and to evaluate the antimicrobial activity of the dichloromethane (DCM) extracts of the pseudostems, rhizomes and the isolated compounds against three selected fungi and five strains of Staphylococcus aureus.
  10. Secretion of pro-oncogenic AGR2 protein in cancer
    Moidu NA, A Rahman NS, Syafruddin SE, Low TY, Mohtar MA
    Heliyon, 2020 Sep;6(9):e05000.
    PMID: 33005802 DOI: 10.1016/j.heliyon.2020.e05000
    Anterior gradient-2 (AGR2) protein mediates the formation, breakage and isomerization of disulphide bonds during protein maturation in the endoplasmic reticulum (ER) and contributes to the homoeostasis of the secretory pathway. AGR2 promotes tumour development and metastasis and its elevated expression is almost completely restricted to malignant tumours. Interestingly, this supposedly ER-resident protein can be localised to other compartments of cancer cells and can also be secreted into the extracellular milieu. There are emerging evidences that describe the gain-of-function activities of the extracellular AGR2, particularly in cancer development. Here, we reviewed studies detailing the expression, pathological and physiological roles associated with AGR2 and compared the duality of localization, intracellular and extracellular, with special emphasis on the later. We also discussed the possible mechanisms of AGR2 secretion as well as deliberating the functional impacts of AGR2 in cancer settings. Last, we deliberate the current therapeutic strategies and posit the potential use AGR2, as a prognosis and diagnosis marker in cancer.
  11. Fulltext CRISPR Gene-Editing Models Geared Toward Therapy for Hereditary and Developmental Neurological Disorders
    Wong PK, Cheah FC, Syafruddin SE, Mohtar MA, Azmi N, Ng PY, et al.
    Front Pediatr, 2021;9:592571.
    PMID: 33791256 DOI: 10.3389/fped.2021.592571
    Hereditary or developmental neurological disorders (HNDs or DNDs) affect the quality of life and contribute to the high mortality rates among neonates. Most HNDs are incurable, and the search for new and effective treatments is hampered by challenges peculiar to the human brain, which is guarded by the near-impervious blood-brain barrier. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), a gene-editing tool repurposed from bacterial defense systems against viruses, has been touted by some as a panacea for genetic diseases. CRISPR has expedited the research into HNDs, enabling the generation of in vitro and in vivo models to simulate the changes in human physiology caused by genetic variation. In this review, we describe the basic principles and workings of CRISPR and the modifications that have been made to broaden its applications. Then, we review important CRISPR-based studies that have opened new doors to the treatment of HNDs such as fragile X syndrome and Down syndrome. We also discuss how CRISPR can be used to generate research models to examine the effects of genetic variation and caffeine therapy on the developing brain. Several drawbacks of CRISPR may preclude its use at the clinics, particularly the vulnerability of neuronal cells to the adverse effect of gene editing, and the inefficiency of CRISPR delivery into the brain. In concluding the review, we offer some suggestions for enhancing the gene-editing efficacy of CRISPR and how it may be morphed into safe and effective therapy for HNDs and other brain disorders.
  12. Fulltext The Sequence-specific Peptide-binding Activity of the Protein Sulfide Isomerase AGR2 Directs Its Stable Binding to the Oncogenic Receptor EpCAM
    Mohtar MA, Hernychova L, O'Neill JR, Lawrence ML, Murray E, Vojtesek B, et al.
    Mol Cell Proteomics, 2018 04;17(4):737-763.
    PMID: 29339412 DOI: 10.1074/mcp.RA118.000573
    AGR2 is an oncogenic endoplasmic reticulum (ER)-resident protein disulfide isomerase. AGR2 protein has a relatively unique property for a chaperone in that it can bind sequence-specifically to a specific peptide motif (TTIYY). A synthetic TTIYY-containing peptide column was used to affinity-purify AGR2 from crude lysates highlighting peptide selectivity in complex mixtures. Hydrogen-deuterium exchange mass spectrometry localized the dominant region in AGR2 that interacts with the TTIYY peptide to within a structural loop from amino acids 131-135 (VDPSL). A peptide binding site consensus of Tx[IL][YF][YF] was developed for AGR2 by measuring its activity against a mutant peptide library. Screening the human proteome for proteins harboring this motif revealed an enrichment in transmembrane proteins and we focused on validating EpCAM as a potential AGR2-interacting protein. AGR2 and EpCAM proteins formed a dose-dependent protein-protein interaction in vitro Proximity ligation assays demonstrated that endogenous AGR2 and EpCAM protein associate in cells. Introducing a single alanine mutation in EpCAM at Tyr251 attenuated its binding to AGR2 in vitro and in cells. Hydrogen-deuterium exchange mass spectrometry was used to identify a stable binding site for AGR2 on EpCAM, adjacent to the TLIYY motif and surrounding EpCAM's detergent binding site. These data define a dominant site on AGR2 that mediates its specific peptide-binding function. EpCAM forms a model client protein for AGR2 to study how an ER-resident chaperone can dock specifically to a peptide motif and regulate the trafficking a protein destined for the secretory pathway.
  13. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT
    Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M
    Mass Spectrom Rev, 2021 07;40(4):309-333.
    PMID: 32491218 DOI: 10.1002/mas.21636
    Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
  14. Fulltext Integration of RNA-Seq and proteomics data identifies glioblastoma multiforme surfaceome signature
    Syafruddin SE, Nazarie WFWM, Moidu NA, Soon BH, Mohtar MA
    BMC Cancer, 2021 Jul 23;21(1):850.
    PMID: 34301218 DOI: 10.1186/s12885-021-08591-0
    BACKGROUND: Glioblastoma multiforme (GBM) is a highly lethal, stage IV brain tumour with a prevalence of approximately 2 per 10,000 people globally. The cell surface proteins or surfaceome serve as information gateway in many oncogenic signalling pathways and are important in modulating cancer phenotypes. Dysregulation in surfaceome expression and activity have been shown to promote tumorigenesis. The expression of GBM surfaceome is a case in point; OMICS screening in a cell-based system identified that this sub-proteome is largely perturbed in GBM. Additionally, since these cell surface proteins have 'direct' access to drugs, they are appealing targets for cancer therapy. However, a comprehensive GBM surfaceome landscape has not been fully defined yet. Thus, this study aimed to define GBM-associated surfaceome genes and identify key cell-surface genes that could potentially be developed as novel GBM biomarkers for therapeutic purposes.

    METHODS: We integrated the RNA-Seq data from TCGA GBM (n = 166) and GTEx normal brain cortex (n = 408) databases to identify the significantly dysregulated surfaceome in GBM. This was followed by an integrative analysis that combines transcriptomics, proteomics and protein-protein interaction network data to prioritize the high-confidence GBM surfaceome signature.

    RESULTS: Of the 2381 significantly dysregulated genes in GBM, 395 genes were classified as surfaceome. Via the integrative analysis, we identified 6 high-confidence GBM molecular signature, HLA-DRA, CD44, SLC1A5, EGFR, ITGB2, PTPRJ, which were significantly upregulated in GBM. The expression of these genes was validated in an independent transcriptomics database, which confirmed their upregulated expression in GBM. Importantly, high expression of CD44, PTPRJ and HLA-DRA is significantly associated with poor disease-free survival. Last, using the Drugbank database, we identified several clinically-approved drugs targeting the GBM molecular signature suggesting potential drug repurposing.

    CONCLUSIONS: In summary, we identified and highlighted the key GBM surface-enriched repertoires that could be biologically relevant in supporting GBM pathogenesis. These genes could be further interrogated experimentally in future studies that could lead to efficient diagnostic/prognostic markers or potential treatment options for GBM.

  15. Fulltext Two Sides of the Same Coin: The Roles of KLF6 in Physiology and Pathophysiology
    Syafruddin SE, Mohtar MA, Wan Mohamad Nazarie WF, Low TY
    Biomolecules, 2020 09 28;10(10).
    PMID: 32998281 DOI: 10.3390/biom10101378
    The Krüppel-like factors (KLFs) family of proteins control several key biological processes that include proliferation, differentiation, metabolism, apoptosis and inflammation. Dysregulation of KLF functions have been shown to disrupt cellular homeostasis and contribute to disease development. KLF6 is a relevant example; a range of functional and expression assays suggested that the dysregulation of KLF6 contributes to the onset of cancer, inflammation-associated diseases as well as cardiovascular diseases. KLF6 expression is either suppressed or elevated depending on the disease, and this is largely due to alternative splicing events producing KLF6 isoforms with specialised functions. Hence, the aim of this review is to discuss the known aspects of KLF6 biology that covers the gene and protein architecture, gene regulation, post-translational modifications and functions of KLF6 in health and diseases. We put special emphasis on the equivocal roles of its full-length and spliced variants. We also deliberate on the therapeutic strategies of KLF6 and its associated signalling pathways. Finally, we provide compelling basic and clinical questions to enhance the knowledge and research on elucidating the roles of KLF6 in physiological and pathophysiological processes.
  16. Fulltext The Study of Drag Reduction on Ships Inspired by Simplified Shark Skin Imitation
    Ibrahim MD, Amran SNA, Yunos YS, Rahman MRA, Mohtar MZ, Wong LK, et al.
    Appl Bionics Biomech, 2018;2018:7854321.
    PMID: 29853998 DOI: 10.1155/2018/7854321
    The skin of a fast swimming shark reveals riblet structures that help reduce the shark's skin friction drag, enhancing its efficiency and speed while moving in the water. Inspired by the structure of the shark skin denticles, our team has carried out a study as an effort in improving the hydrodynamic design of marine vessels through hull design modification which was inspired by this riblet structure of shark skin denticle. Our study covers on macroscaled design modification. This is an attempt to propose an alternative for a better economical and practical modification to obtain a more optimum cruising characteristics for marine vessels. The models used for this study are constructed using computer-aided design (CAD) software, and computational fluid dynamic (CFD) simulations are then carried out to predict the effectiveness of the hydrodynamic effects of the biomimetic shark skins on those models. Interestingly, the numerical calculated results obtained show that the presence of biomimetic shark skin implemented on the vessels give about 3.75% reduction of drag coefficient as well as reducing up to 3.89% in drag force experienced by the vessels. Theoretically, as force drag can be reduced, it can lead to a more efficient vessel with a better cruising speed. This will give better impact to shipping or marine industries around the world. However, it can be suggested that an experimental procedure is best to be conducted to verify the numerical result that has been obtained for further improvement on this research.
  17. Fulltext In Vitro Evaluations and In Vivo Toxicity and Efficacy Studies of MFM501 against MRSA
    Johari SA, Mohtar M, Syed Mohamad SA, Mohammat MF, Sahdan R, Mohamed A, et al.
    Biomed Res Int, 2017;2017:8032865.
    PMID: 28536702 DOI: 10.1155/2017/8032865
    Previously we have discovered a synthetically derived pyrrolidone alkaloid, MFM501, exhibiting good inhibitory activity against 53 MRSA and MSSA isolates with low cytotoxicity against three normal cell-lines with IC50 values at >625 µg/ml. Time-kill assay, scanning electron microscopy (SEM) analysis, in vivo oral acute toxicity test, and mice peritonitis model were carried out in this study. In the time-kill study, MFM501 showed a less than 3 log10 decrease in bacterial colony concentration value (CFU/ml) which represented a bacteriostatic action while displaying a time-dependent inhibitory mechanism. Following that, SEM analysis suggested that MFM501 may exert its inhibitory activity via cytoplasmic membrane disruption. Moreover, MFM501 showed no toxicity effect on treated mice at an estimated median acute lethal dose (LD50) value of more than 300 mg/kg and less than 2000 mg/kg. For the efficacy test, a mean effective dose (ED50) of 87.16 mg/kg was obtained via a single dose oral administration. Our data demonstrated that MFM501 has the potential to be developed further as a new, safe, and effective oral-delivered antibacterial agent against MRSA isolates.
  18. Chemical constituents and antimicrobial activity of the leaf and rhizome oils of Alpinia pahangensis Ridl., an endemic wild ginger from peninsular Malaysia
    Awang K, Ibrahim H, Rosmy Syamsir D, Mohtar M, Mat Ali R, Azah Mohamad Ali N
    Chem Biodivers, 2011 Apr;8(4):668-73.
    PMID: 21480512 DOI: 10.1002/cbdv.201000225
    The essential oils from the leaves and rhizomes of Alpinia pahangensis Ridl., collected from Pahang, Peninsular Malaysia, were obtained by hydrodistillation, and their chemical compositions were determined by GC and GC/MS analyses. The major components of the rhizome oil were γ-selinene (11.60%), β-pinene (10.87%), (E,E)-farnesyl acetate (8.65%), and α-terpineol (6.38%), while those of the leaf oil were β-pinene (39.61%), α-pinene (7.55%), and limonene (4.89%). The investigation of the antimicrobial activity of the essential oils using the broth microdilution technique revealed that the rhizome oil of A. pahangensis inhibited five Staphylococcus aureus strains with minimum inhibitory concentration (MIC) values between 0.08 and 0.31 μg/μl, and four selected fungi with MIC values between 1.25 and 2.50 μg/μl.
  19. Cancer Cell-Derived PDGFB Stimulates mTORC1 Activation in Renal Carcinoma
    Abuhamad AY, Mohamad Zamberi NN, Vanharanta S, Mohd Yusuf SNH, Mohtar MA, Syafruddin SE
    Int J Mol Sci, 2023 Mar 29;24(7).
    PMID: 37047421 DOI: 10.3390/ijms24076447
    Clear cell renal cell carcinoma (ccRCC) is a hypervascular tumor that is characterized by bi-allelic inactivation of the VHL tumor suppressor gene and mTOR signalling pathway hyperactivation. The pro-angiogenic factor PDGFB, a transcriptional target of super enhancer-driven KLF6, can activate the mTORC1 signalling pathway in ccRCC. However, the detailed mechanisms of PDGFB-mediated mTORC1 activation in ccRCC have remained elusive. Here, we investigated whether ccRCC cells are able to secrete PDGFB into the extracellular milieu and stimulate mTORC1 signalling activity. We found that ccRCC cells secreted PDGFB extracellularly, and by utilizing KLF6- and PDGFB-engineered ccRCC cells, we showed that the level of PDGFB secretion was positively correlated with the expression of intracellular KLF6 and PDGFB. Moreover, the reintroduction of either KLF6 or PDGFB was able to sustain mTORC1 signalling activity in KLF6-targeted ccRCC cells. We further demonstrated that conditioned media of PDGFB-overexpressing ccRCC cells was able to re-activate mTORC1 activity in KLF6-targeted cells. In conclusion, cancer cell-derived PDGFB can mediate mTORC1 signalling pathway activation in ccRCC, further consolidating the link between the KLF6-PDGFB axis and the mTORC1 signalling pathway activity in ccRCC.
  20. dCas9 Tells Tales: Probing Gene Function and Transcription Regulation in Cancer
    Mohamad Zamberi NN, Abuhamad AY, Low TY, Mohtar MA, Syafruddin SE
    CRISPR J, 2024 Apr;7(2):73-87.
    PMID: 38635328 DOI: 10.1089/crispr.2023.0078
    Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing is evolving into an essential tool in the field of biological and medical research. Notably, the development of catalytically deactivated Cas9 (dCas9) enzyme has substantially broadened its traditional boundaries in gene editing or perturbation. The conjugation of dCas9 with various molecular effectors allows precise control over transcriptional processes, epigenetic modifications, visualization of chromosomal dynamics, and several other applications. This expanded repertoire of CRISPR-Cas9 applications has emerged as an invaluable molecular tool kit that empowers researchers to comprehensively interrogate and gain insights into health and diseases. This review delves into the advancements in Cas9 protein engineering, specifically on the generation of various dCas9 tools that have significantly enhanced the CRISPR-based technology capability and versatility. We subsequently discuss the multifaceted applications of dCas9, especially in interrogating the regulation and function of genes that involve in supporting cancer pathogenesis. In addition, we also delineate the designing and utilization of dCas9-based tools as well as highlighting its current constraints and transformative potentials in cancer research.
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