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Article: Homeobox Gene Expression Dysregulation as Potential Diagnostic and Prognostic Biomarkers in Bladder Cancer.

Chin, Fee-Wai / Chan, Soon-Choy / Veerakumarasivam, Abhi

2023 Volume 13, Issue 16

Abstract: Homeobox genes serve as master regulatory transcription factors that regulate gene expression during embryogenesis. A homeobox gene may have either tumor-promoting or tumor-suppressive properties depending on the specific organ or cell lineage where it ... ...

Abstract	Homeobox genes serve as master regulatory transcription factors that regulate gene expression during embryogenesis. A homeobox gene may have either tumor-promoting or tumor-suppressive properties depending on the specific organ or cell lineage where it is expressed. The dysregulation of homeobox genes has been reported in various human cancers, including bladder cancer. The dysregulated expression of homeobox genes has been associated with bladder cancer clinical outcomes. Although bladder cancer has high risk of tumor recurrence and progression, it is highly challenging for clinicians to accurately predict the risk of tumor recurrence and progression at the initial point of diagnosis. Cystoscopy is the routine surveillance method used to detect tumor recurrence. However, the procedure causes significant discomfort and pain that results in poor surveillance follow-up amongst patients. Therefore, the development of reliable non-invasive biomarkers for the early detection and monitoring of bladder cancer is crucial. This review provides a comprehensive overview of the diagnostic and prognostic potential of homeobox gene expression dysregulation in bladder cancer.
Language	English
Publishing date	2023-08-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics13162641
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mainstreaming responsible conduct of research education in Malaysia.

Chau, De-Ming / Chai, Lay Ching / Cheema, Manraj Singh / Veerakumarasivam, Abhi

Forensic sciences research

2021 Volume 6, Issue 4, Page(s) 338–340

Language	English
Publishing date	2021-11-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2885963-7
ISSN	2471-1411 ; 2096-1790
ISSN (online)	2471-1411
ISSN	2096-1790
DOI	10.1080/20961790.2021.1987619
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Article ; Online: The role of the university in recovering from COVID-19 and preparing for future crises-perspectives and experiences from Sunway University, Malaysia.

Renganathan, Elil / Guinto, Renzo / Mahmood, Jemilah / Lacey-Hall, Oliver / Veerakumarasivam, Abhi / Poppema, Sibrandes

Frontiers in public health

2023 Volume 11, Page(s) 1072823

Abstract: This article is part of the Research Topic 'Health Systems Recovery in the Context of COVID-19 and Protracted Conflict'. Universities, as engines of knowledge creation and dissemination and as incubators of disciplined yet original thinking, have a key ... ...

Abstract	This article is part of the Research Topic 'Health Systems Recovery in the Context of COVID-19 and Protracted Conflict'. Universities, as engines of knowledge creation and dissemination and as incubators of disciplined yet original thinking, have a key role to play in tackling the most complex challenges that societies and our planet face, from infectious diseases to the climate emergency. This commentary presents the perspectives from Sunway University, a young private university in Malaysia that made a strong commitment to the sustainable development goals (SDGs) prior to the pandemic, and its experiences in promoting research, innovation, and learning as part of COVID-19 recovery and in preparation for future crises such as the climate emergency. Some of the university's initiatives include embracing the planetary health approach, reviving essential public health functions, exploring pandemic resilience, addressing 'infodemics' and promoting science diplomacy. The example of Sunway University provides some insights on the opportunities and challenges that academic institutions face as they seek to reorient the paradigm of education, research, and service away from disciplinary siloes and towards a more integrated, preventive, accessible and translational approach.
MeSH term(s)	Humans ; COVID-19/prevention & control ; Universities ; Malaysia ; Public Health
Language	English
Publishing date	2023-04-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2023.1072823
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Article: Dithiocarbazate Ligand-Based Cu(II), Ni(II), and Zn(II) Complexes: Synthesis, Structural Investigations, Cytotoxicity, DNA Binding, and Molecular Docking Studies.

Yusof, Enis Nadia Md / Azam, Mohammad / Sirat, Siti Syaida / Ravoof, Thahira B S A / Page, Alister J / Veerakumarasivam, Abhi / Karunakaran, Thiruventhan / Razali, Mohd Rizal

Bioinorganic chemistry and applications

2022 Volume 2022, Page(s) 2004052

Abstract: S-4-methylbenzyl- ...

Abstract	S-4-methylbenzyl-
Language	English
Publishing date	2022-07-31
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2213020-2
ISSN	1687-479X ; 1565-3633
ISSN (online)	1687-479X
ISSN	1565-3633
DOI	10.1155/2022/2004052
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Article: Differential Protein Expression Patterns of HOXA13 and HOXB13 Are Associated with Bladder Cancer Progression.

Chin, Fee-Wai / Hussin, Huzlinda / Chau, De-Ming / Ong, Teng-Aik / Yunus, Rosna / Abdul Razack, Azad Hassan / Yusoff, Khatijah / Chan, Soon-Choy / Veerakumarasivam, Abhi

Diagnostics (Basel, Switzerland)

2023 Volume 13, Issue 16

Abstract: Bladder cancer is a common urological cancer and has the highest recurrence rate of any cancer. The aim of our study was to profile and characterize the protein expression of homeobox A13 ( ...

Abstract	Bladder cancer is a common urological cancer and has the highest recurrence rate of any cancer. The aim of our study was to profile and characterize the protein expression of homeobox A13 (
Language	English
Publishing date	2023-08-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics13162636
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Article ; Online: Mainstreaming responsible conduct of research education in Malaysia

De-Ming Chau / Lay Ching Chai / Manraj Singh Cheema / Abhi Veerakumarasivam

Forensic Sciences Research, Vol 6, Iss 4, Pp 338-

2021 Volume 340

Keywords	Criminal law and procedure ; K5000-5582 ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Taylor & Francis Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The location of the inferior alveolar nerve in the malaysian population: Implications for dental implant planning.

Kumar, Sujaysen R / Patil, Pravinkumar G / Choy, Chan S / Veerakumarasivam, Abhi

Indian journal of dental research : official publication of Indian Society for Dental Research

2020 Volume 31, Issue 2, Page(s) 197–202

Abstract: Background: The location of the inferior alveolar nerve (IAN) is generally constant in fully grown mandibles. If we know its average distance from the lower border of the mandible, available bone length from the crest of the edentulous ridge can be ... ...

Abstract	Background: The location of the inferior alveolar nerve (IAN) is generally constant in fully grown mandibles. If we know its average distance from the lower border of the mandible, available bone length from the crest of the edentulous ridge can be estimated by physical measurement of the whole length of mandible in that area. This study aimed to measure the superio-inferior distance of the inferior alveolar nerve (SIDIAN) from the base of the mandible in posterior regions on the right and left side based on cone-beam-computed tomography (CBCT) scans and to evaluate gender and ethnicity-related variations in the Malaysian population. Materials and methods: A total of 100 CBCT-Digital Imaging and Communications in Medicine files of the patients of 3 ethnic populations (Malay, Chinese and Indian) between the ages of 18 and 80 years were selected for the study. The files were imported onto the iCAT software. The measurements of the SIDIAN to the lower border of the mandible in molar regions were done on both sides. The data was analysed using t-test, one-way analysis of variance test, and correlation coefficient test via the SPSS software. Results: Statistically significant positive correlations were identified between the SIDIAN from the lower border of the mandible in the first and second molar regions within the same side as well as between both sides of the mandible (r ≈ 0.8). There were no statistically significant differences between genders. However, there were statistically significant differences on both molar regions and on both sides in all three ethnic groups (P < 0.05). In general, the SIDIAN from the lower border of the mandible was greatest amongst Chinese and smallest amongst Indians. Conclusions: The strong positive correlations on both sides of the mandible indicate the presence of symmetry. Ethnicity-related variations exist in terms of the location of the IAN in the mandible.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Cone-Beam Computed Tomography ; Dental Implants ; Female ; Humans ; Male ; Mandible ; Mandibular Nerve ; Middle Aged ; Molar ; Young Adult
Chemical Substances	Dental Implants
Language	English
Publishing date	2020-05-20
Publishing country	India
Document type	Journal Article
ZDB-ID	1354886-4
ISSN	1998-3603 ; 0970-9290
ISSN (online)	1998-3603
ISSN	0970-9290
DOI	10.4103/ijdr.IJDR_553_17
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Article ; Online: Analysis of PPI networks of transcriptomic expression identifies hub genes associated with Newcastle disease virus persistent infection in bladder cancer.

Ahmad, Umar / Abdullah, Syahril / Chau, De Ming / Chia, Suet Lin / Yusoff, Khatijah / Chan, Soon Choy / Ong, Teng Aik / Razack, Azad Hassan / Veerakumarasivam, Abhi

Scientific reports

2023 Volume 13, Issue 1, Page(s) 7323

Abstract: Bladder cancer cells can acquire persistent infection of oncolytic Newcastle disease virus (NDV) but the molecular mechanism(s) remain unelucidated. This poses a major barrier to the effective clinical translation of oncolytic NDV virotherapy of cancers. ...

Abstract	Bladder cancer cells can acquire persistent infection of oncolytic Newcastle disease virus (NDV) but the molecular mechanism(s) remain unelucidated. This poses a major barrier to the effective clinical translation of oncolytic NDV virotherapy of cancers. To improve our understanding of the molecular mechanism(s) associated with the development of NDV persistent infection in bladder cancer, we used mRNA expression profiles of persistently infected bladder cancer cells to construct PPI networks. Based on paths and modules in the PPI network, the bridges were found mainly in the upregulated mRNA-pathways of p53 signalling, ECM-receptor interaction, and TGF-beta signalling and downregulated mRNA-pathways of antigen processing and presentation, protein processing in endoplasmic reticulum, completement and coagulation cascades in persistent TCCSUPPi cells. In persistent EJ28Pi cells, connections were identified mainly through upregulated mRNA-pathways of renal carcinoma, viral carcinogenesis, Ras signalling and cell cycle and the downregulated mRNA-pathways of Wnt signalling, HTLV-I infection and pathways in cancers. These connections were mainly dependent on RPL8-HSPA1A/HSPA4 in TCCSUPPi cells and EP300, PTPN11, RAC1-TP53, SP1, CCND1 and XPO1 in EJ28Pi cells. Oncomine validation showed that the top hub genes identified in the networks that include RPL8, THBS1, F2 from TCCSUPPi and TP53 and RAC1 from EJ28Pi are involved in the development and progression of bladder cancer. Protein-drug interaction networks identified several putative drug targets that could be used to disrupt the linkages between the modules and prevent bladder cancer cells from acquiring NDV persistent infection. This novel PPI network analysis of differentially expressed mRNAs of NDV persistently infected bladder cancer cell lines provide an insight into the molecular mechanisms of NDV persistency of infection in bladder cancers and the future screening of drugs that can be used together with NDV to enhance its oncolytic efficacy.
MeSH term(s)	Animals ; Humans ; Newcastle disease virus/genetics ; Transcriptome ; Cell Line, Tumor ; Persistent Infection ; Oncolytic Viruses/genetics ; Oncolytic Virotherapy ; Urinary Bladder Neoplasms/genetics ; RNA, Messenger/genetics ; Newcastle Disease
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2023-05-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-20521-z
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Article ; Online: Persistent Newcastle disease virus infection in bladder cancer cells is associated with putative pro-survival and anti-viral transcriptomic changes.

Chan, Lee-Chin / Kalyanasundram, Jeevanathan / Leong, Sze-Wei / Masarudin, Mas Jaffri / Veerakumarasivam, Abhi / Yusoff, Khatijah / Chan, Soon-Choy / Chia, Suet-Lin

BMC cancer

2021 Volume 21, Issue 1, Page(s) 625

Abstract: Background: Newcastle disease virus (NDV) is an oncolytic virus with excellent selectivity against cancer cells, both in vitro and in vivo. Unfortunately, prolonged in vitro NDV infection results in the development of persistent infection in the cancer ... ...

Abstract	Background: Newcastle disease virus (NDV) is an oncolytic virus with excellent selectivity against cancer cells, both in vitro and in vivo. Unfortunately, prolonged in vitro NDV infection results in the development of persistent infection in the cancer cells which are then able to resist NDV-mediated oncolysis. However, the mechanism of persistency of infection remains poorly understood. Methods: In this study, we established persistently NDV-infected EJ28 bladder cancer cells, designated as EJ28P. Global transcriptomic analysis was subsequently carried out by microarray analysis. Differentially expressed genes (DEGs) between EJ28 and EJ28P cells identified by the edgeR program were further analysed by Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA) analyses. In addition, the microarray data were validated by RT-qPCR. Results: Persistently NDV-infected EJ28 bladder cancer cells were successfully established and confirmed by flow cytometry. Microarray analysis identified a total of 368 genes as differentially expressed in EJ28P cells when compared to the non-infected EJ28 cells. GSEA revealed that the Wnt/β-catenin and KRAS signalling pathways were upregulated while the TGF-β signalling pathway was downregulated. Findings from this study suggest that the upregulation of genes that are associated with cell growth, pro-survival, and anti-apoptosis may explain the survivability of EJ28P cells and the development of persistent infection of NDV. Conclusions: This study provides insights into the transcriptomic changes that occur and the specific signalling pathways that are potentially involved in the development and maintenance of NDV persistency of infection in bladder cancer cells. These findings warrant further investigation and is crucial towards the development of effective NDV oncolytic therapy against cancer.
MeSH term(s)	Cell Line, Tumor ; Cell Survival/genetics ; Cell Survival/immunology ; Down-Regulation/immunology ; Gene Expression Regulation, Neoplastic/immunology ; Humans ; Newcastle disease virus/immunology ; Oncolytic Virotherapy/methods ; Oncolytic Viruses/immunology ; Proto-Oncogene Proteins p21(ras)/metabolism ; Transforming Growth Factor beta/metabolism ; Up-Regulation/immunology ; Urinary Bladder/immunology ; Urinary Bladder/pathology ; Urinary Bladder Neoplasms/immunology ; Urinary Bladder Neoplasms/therapy ; Wnt Signaling Pathway/genetics ; Wnt Signaling Pathway/immunology ; beta Catenin/metabolism
Chemical Substances	CTNNB1 protein, human ; KRAS protein, human ; Transforming Growth Factor beta ; beta Catenin ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
Language	English
Publishing date	2021-05-27
Publishing country	England
Document type	Journal Article
ISSN	1471-2407
ISSN (online)	1471-2407
DOI	10.1186/s12885-021-08345-y
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Article ; Online: Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel.

Tan, Jaymi / Chow, Yock Ping / Zainul Abidin, Norziha / Chang, Kian Meng / Selvaratnam, Veena / Tumian, Nor Rafeah / Poh, Yang Ming / Veerakumarasivam, Abhi / Laffan, Michael Arthur / Wong, Chieh Lee

BMC medical genomics

2022 Volume 15, Issue 1, Page(s) 10

Abstract: Background: The Philadelphia (Ph)-negative myeloproliferative neoplasms (MPNs), namely essential thrombocythaemia (ET), polycythaemia vera (PV) and primary myelofibrosis (PMF), are a group of chronic clonal haematopoietic disorders that have the ... ...

Abstract	Background: The Philadelphia (Ph)-negative myeloproliferative neoplasms (MPNs), namely essential thrombocythaemia (ET), polycythaemia vera (PV) and primary myelofibrosis (PMF), are a group of chronic clonal haematopoietic disorders that have the propensity to advance into bone marrow failure or acute myeloid leukaemia; often resulting in fatality. Although driver mutations have been identified in these MPNs, subtype-specific markers of the disease have yet to be discovered. Next-generation sequencing (NGS) technology can potentially improve the clinical management of MPNs by allowing for the simultaneous screening of many disease-associated genes. Methods: The performance of a custom, in-house designed 22-gene NGS panel was technically validated using reference standards across two independent replicate runs. The panel was subsequently used to screen a total of 10 clinical MPN samples (ET n = 3, PV n = 3, PMF n = 4). The resulting NGS data was then analysed via a bioinformatics pipeline. Results: The custom NGS panel had a detection limit of 1% variant allele frequency (VAF). A total of 20 unique variants with VAFs above 5% (4 of which were putatively novel variants with potential biological significance) and one pathogenic variant with a VAF of between 1 and 5% were identified across all of the clinical MPN samples. All single nucleotide variants with VAFs ≥ 15% were confirmed via Sanger sequencing. Conclusions: The high fidelity of the NGS analysis and the identification of known and novel variants in this study cohort support its potential clinical utility in the management of MPNs. However, further optimisation is needed to avoid false negatives in regions with low sequencing coverage, especially for the detection of driver mutations in MPL.
MeSH term(s)	High-Throughput Nucleotide Sequencing ; Humans ; Janus Kinase 2/genetics ; Mutation ; Myeloproliferative Disorders/diagnosis ; Myeloproliferative Disorders/genetics ; Polycythemia Vera/diagnosis ; Polycythemia Vera/genetics
Chemical Substances	Janus Kinase 2 (EC 2.7.10.2)
Language	English
Publishing date	2022-01-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2411865-5
ISSN	1755-8794 ; 1755-8794
ISSN (online)	1755-8794
ISSN	1755-8794
DOI	10.1186/s12920-021-01145-0
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