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Fulltext An evaluation of dose equivalence between synchrotron microbeam radiation therapy and conventional broad beam radiation using clonogenic and cell impedance assays

Ibahim MJ, Crosbie JC, Yang Y, Zaitseva M, Stevenson AW, Rogers PA, et al.

PLoS One, 2014;9(6):e100547.
PMID: 24945301 DOI: 10.1371/journal.pone.0100547

High-dose synchrotron microbeam radiation therapy (MRT) has shown the potential to deliver improved outcomes over conventional broadbeam (BB) radiation therapy. To implement synchrotron MRT clinically for cancer treatment, it is necessary to undertake dose equivalence studies to identify MRT doses that give similar outcomes to BB treatments.
An evaluation of novel real-time technology as a tool for measurement of radiobiological and radiation-induced bystander effects

Ibahim MJ, Crosbie JC, Paiva P, Yang Y, Zaitseva M, Rogers PA

Radiat Environ Biophys, 2016 May;55(2):185-94.
PMID: 26994995 DOI: 10.1007/s00411-016-0641-x

The xCELLigence real-time cell impedance system uses a non-invasive and label-free method to create a cell index that is a composite measure of cell proliferation. The aim of this study was to evaluate xCELLigence against clonogenic assay (gold standard) for measuring radiobiological effects and radiation-induced bystander effects (RIBE). A radiobiological study was conducted by irradiating EMT6.5, 4T1.2 and NMUMG cell lines with different radiation doses, while a RIBE study was done using transfer of conditioned media (CM) harvested from donor to the same type of recipient cell (EMT6.5, 4T1.2, NMUMG, HACAT and SW48). CM was harvested using two protocols which differed in the dose chosen and the exposure to the recipient cells. Results showed that xCELLigence measured a radiobiological effect which correlated with the clonogenic assay. For the RIBE study, no statistically significant differences were observed between xCELLigence or clonogenic survival in control or recipient cells incubated with CM in protocol one. However, there was a significant increase in cell index slope using CM from EMT-6.5 cells irradiated at 7.5 Gy compared with the control group under the second protocol. No other evidence of RIBE was detected by either xCELLigence or clonogenic assay. In conclusion, xCELLigence methods can measure radiobiological effects and the results correlate with clonogenic assay. We observed a lack of RIBE in all tested cell lines with the clonogenic assay; however, we observed a RIBE effect in EMT6.5 cells under one particular protocol that showed RIBE is cell type dependent, is not universally observed and can be detected in different assays.
Fulltext Stability and Reproducibility of Radiomic Features Based Various Segmentation Technique on MR Images of Hepatocellular Carcinoma (HCC)

Haniff NSM, Abdul Karim MK, Osman NH, Saripan MI, Che Isa IN, Ibahim MJ

Diagnostics (Basel), 2021 Aug 30;11(9).
PMID: 34573915 DOI: 10.3390/diagnostics11091573

Hepatocellular carcinoma (HCC) is considered as a complex liver disease and ranked as the eighth-highest mortality rate with a prevalence of 2.4% in Malaysia. Magnetic resonance imaging (MRI) has been acknowledged for its advantages, a gold technique for diagnosing HCC, and yet the false-negative diagnosis from the examinations is inevitable. In this study, 30 MR images from patients diagnosed with HCC is used to evaluate the robustness of semi-automatic segmentation using the flood fill algorithm for quantitative features extraction. The relevant features were extracted from the segmented MR images of HCC. Four types of features extraction were used for this study, which are tumour intensity, shape feature, textural feature and wavelet feature. A total of 662 radiomic features were extracted from manual and semi-automatic segmentation and compared using intra-class relation coefficient (ICC). Radiomic features extracted using semi-automatic segmentation utilized flood filling algorithm from 3D-slicer had significantly higher reproducibility (average ICC = 0.952 ± 0.009, p < 0.05) compared with features extracted from manual segmentation (average ICC = 0.897 ± 0.011, p > 0.05). Moreover, features extracted from semi-automatic segmentation were more robust compared to manual segmentation. This study shows that semi-automatic segmentation from 3D-Slicer is a better alternative to the manual segmentation, as they can produce more robust and reproducible radiomic features.
Fulltext Hyperparameter Tuning and Pipeline Optimization via Grid Search Method and Tree-Based AutoML in Breast Cancer Prediction

Radzi SFM, Karim MKA, Saripan MI, Rahman MAA, Isa INC, Ibahim MJ

J Pers Med, 2021 Sep 29;11(10).
PMID: 34683118 DOI: 10.3390/jpm11100978

Automated machine learning (AutoML) has been recognized as a powerful tool to build a system that automates the design and optimizes the model selection machine learning (ML) pipelines. In this study, we present a tree-based pipeline optimization tool (TPOT) as a method for determining ML models with significant performance and less complex breast cancer diagnostic pipelines. Some features of pre-processors and ML models are defined as expression trees and optimal gene programming (GP) pipelines, a stochastic search system. Features of radiomics have been presented as a guide for the ML pipeline selection from the breast cancer data set based on TPOT. Breast cancer data were used in a comparative analysis of the TPOT-generated ML pipelines with the selected ML classifiers, optimized by a grid search approach. The principal component analysis (PCA) random forest (RF) classification was proven to be the most reliable pipeline with the lowest complexity. The TPOT model selection technique exceeded the performance of grid search (GS) optimization. The RF classifier showed an outstanding outcome amongst the models in combination with only two pre-processors, with a precision of 0.83. The grid search optimized for support vector machine (SVM) classifiers generated a difference of 12% in comparison, while the other two classifiers, naïve Bayes (NB) and artificial neural network-multilayer perceptron (ANN-MLP), generated a difference of almost 39%. The method's performance was based on sensitivity, specificity, accuracy, precision, and receiver operating curve (ROC) analysis.
Eosinophil-Associated Gene Pathways but not Eosinophil Numbers are Differentially Regulated between Synchrotron Microbeam Radiation Treatment and Synchrotron Broad-Beam Treatment by 48 Hours Postirradiation

Ibahim MJ, Yang Y, Crosbie JC, Stevenson A, Cann L, Paiva P, et al.

Radiat Res, 2016 Jan;185(1):60-8.
PMID: 26720800 DOI: 10.1667/RR14115.1

Synchrotron microbeam radiation treatment (MRT) is a preclinical radiotherapy technique with considerable clinical promise, although some of the underlying radiobiology of MRT is still not well understood. In recently reported studies, it has been suggested that MRT elicits a different tumor immune profile compared to broad-beam treatment (BB). The aim of this study was to investigate the effects of synchrotron MRT and BB on eosinophil-associated gene pathways and eosinophil numbers within and around the tumor in the acute stage, 48 h postirradiation. Balb/C mice were inoculated with EMT6.5 mouse mammary tumors and irradiated with microbeam radiation (112 and 560 Gy) and broad-beam radiation (5 and 9 Gy) at equivalent doses determined from a previous in vitro study. After tumors were collected 24 and 48 h postirradiation, RNA was extracted and quantitative PCR performed to assess eosinophil-associated gene expression. Immunohistochemistry was performed to detect two known markers of eosinophils: eosinophil-associated ribonucleases (EARs) and eosinophil major basic protein (MBP). We identified five genes associated with eosinophil function and recruitment (Ear11, Ccl24, Ccl6, Ccl9 and Ccl11) and all of them, except Ccl11, were differentially regulated in synchrotron microbeam-irradiated tumors compared to broad-beam-irradiated tumors. However, immunohistochemical localization demonstrated no significant differences in the number of EAR- and MBP-positive eosinophils infiltrating the primary tumor after MRT compared to BB. In conclusion, our work demonstrates that the effects of MRT on eosinophil-related gene pathways are different from broad-beam radiation treatment at doses previously demonstrated to be equivalent in an in vitro study. However, a comparison of the microenvironments of tumors, which received MRT and BB, 48 h after exposure showed no difference between them with respect to eosinophil accumulation. These findings contribute to our understanding of the role of differential effects of MRT on the tumor immune response.
Effect of iterative reconstruction algorithm levels on noise index and figure-of-merit in CT pulmonary angiography examinations

Harun HH, Karim MKA, Abbas Z, Sabarudin A, Muniandy SC, Ibahim MJ

J Xray Sci Technol, 2020;28(5):893-903.
PMID: 32741801 DOI: 10.3233/XST-200699

PURPOSE: To evaluate the influence of iterative reconstruction (IR) levels on Computed Tomography (CT) image quality and to establish Figure of Merit (FOM) value for CT Pulmonary Angiography (CTPA) examinations.
METHODS: Images of 31 adult patients who underwent CTPA examinations in our institution from March to April 2019 were retrospectively collected. Other data, such as scanning parameters, radiation dose and body habitus information from the subjects were also recorded. Six different levels of IR were applied to the volume data of the subjects. Five circles of the region of interest (ROI) were drawn in five different arteries namely, pulmonary trunk, right pulmonary artery, left pulmonary artery, ascending aorta and descending aorta. The mean Signal-to-noise ratio (SNR) was obtained, and the FOM was calculated in a fraction of the SNR2 divided by volume-weighted CT dose index (CTDIvol) and SNR2 divided by the size-specific dose estimates (SSDE).
RESULTS: Overall, we observed that the mean value of CTDIvol and SSDE were 13.79±7.72 mGy and 17.25±8.92 mGy, respectively. Notably, SNR values significantly increase with increase of the IR level (p
Fulltext Role of ErbB1 in the Underlying Mechanism of Lapatinib-Induced Diarrhoea: A Review

Raja Sharin RNFS, Khan J, Ibahim MJ, Muhamad M, Bowen J, Wan Mohamad Zain WNI

Biomed Res Int, 2022;2022:4165808.
PMID: 35800225 DOI: 10.1155/2022/4165808

Lapatinib, an orally administered small-molecule tyrosine kinase inhibitor (SM-TKI), is an effective treatment for ErbB2-positive breast cancer. However, its efficacy as one of the targeted cancer therapies has been hampered by several adverse effects, especially gastrointestinal toxicity, commonly manifested as diarrhoea. Although it can be generally tolerated, diarrhoea is reported as the most common and most impactful on a patient's quality of life and associated with treatment interruption. Severe diarrhoea can result in malabsorption, leading to dehydration, fatigue, and even death. ErbB1 is an epidermal growth factor profoundly expressed in normal gut epithelium while lapatinib is a dual ErbB1/ErbB2 tyrosine kinase inhibitor. Thus, ErbB1 inhibition by lapatinib may affect gut homeostasis leading to diarrhoea. Nevertheless, the underlying mechanisms remain unclear. This review article provides evidence of the possible mechanisms of lapatinib-induced diarrhoea that may be related to/or modulated by ErbB1. Insight regarding the involvement of ErbB1 in the pathophysiological changes such as inflammation and intestinal permeability as the underlying cause of diarrhoea is covered in this article.
Fulltext Stability and Reproducibility of Radiomic Features Based on Various Segmentation Techniques on Cervical Cancer DWI-MRI

Ramli Z, Karim MKA, Effendy N, Abd Rahman MA, Kechik MMA, Ibahim MJ, et al.

Diagnostics (Basel), 2022 Dec 12;12(12).
PMID: 36553132 DOI: 10.3390/diagnostics12123125

Cervical cancer is the most common cancer and ranked as 4th in morbidity and mortality among Malaysian women. Currently, Magnetic Resonance Imaging (MRI) is considered as the gold standard imaging modality for tumours with a stage higher than IB2, due to its superiority in diagnostic assessment of tumour infiltration with excellent soft-tissue contrast. In this research, the robustness of semi-automatic segmentation has been evaluated using a flood-fill algorithm for quantitative feature extraction, using 30 diffusion weighted MRI images (DWI-MRI) of cervical cancer patients. The relevant features were extracted from DWI-MRI segmented images of cervical cancer. First order statistics, shape features, and textural features were extracted and analysed. The intra-class relation coefficient (ICC) was used to compare 662 radiomic features extracted from manual and semi-automatic segmentations. Notably, the features extracted from the semi-automatic segmentation and flood filling algorithm (average ICC = 0.952 0.009, p > 0.05) were significantly higher than the manual extracted features (average ICC = 0.897 0.011, p > 0.05). Henceforth, we demonstrate that the semi-automatic segmentation is slightly expanded to manual segmentation as it produces more robust and reproducible radiomic features.
Assessing the bioefficacy of a commercial temephos formulation (Temebate®) for controlling Aedes albopictus larvae in different land use localities in Malaysia

Wan-Norafikah O, Aliah-Diyanah S, Atiqah-Izzah Z, Chen CD, Sofian-Azirun M, Lailatul-Nadhirah A, et al.

Exp Parasitol, 2023 Nov;254:108627.
PMID: 37802180 DOI: 10.1016/j.exppara.2023.108627

Temephos is the World Health Organization (WHO) recommended larvicide and is still being utilized worldwide to control larvae of dengue vectors; Aedes aegypti and Aedes albopictus. The efficacy of a commercial temephos product; Temebate® to exterminate the local populations of Ae. albopictus larvae originated from different land use particularly dengue-risk and dengue-free housing localities as well as agrarian localities including oil palm plantations, rubber estates and paddy fields was assessed to verify its bioefficacy in these localities. Field populations of Ae. albopictus larvae were attained via a larval survey at each study locality. Each Ae. albopictus larval population was subjected to a 24-h larval bioassay using Temebate® at operational dosage of 1 mg/L. Almost all Ae. albopictus larval populations demonstrated mortalities between 7.00% and 100.00% by the end of the first 4 h of Temebate® exposure with the resistance ratios between 0.94 and 8.33. After 24 h of Temebate® exposure, all sixteen Ae. albopictus larval populations exhibited increased mortalities with ten of them showing 100% mortalities. These results confirmed the relevance of Temebate® to be continuously used by the residents of these localities as their control efforts against dengue vectors. Nevertheless, Temebate® application by consumers in dengue-risk localities need to be carefully monitored to prevent further development of temephos resistance among Ae. albopictus populations and substantiated with other vector control approaches.
A single targeted gamma-ray irradiation induced an acute modulation of immune cells and related cytokines in EMT6 mouse-bearing tumour model

Hasan N, Hasani NAH, Omar E, Sham FR, Fuad SBSA, Karim MKA, et al.

Cancer Biomark, 2023;38(1):61-75.
PMID: 37522193 DOI: 10.3233/CBM-220268

BACKGROUND: A complicated interplay between radiation doses, tumour microenvironment (TME), and host immune system is linked to the active participation of immune response.
OBJECTIVE: The effects of single targeted 2 Gy and 8 Gy gamma-ray irradiations on the immune cell population (lymphocytes, B-cells, T-cells, neutrophils, eosinophils, and macrophages) in EMT6 mouse-bearing tumour models was investigated.
METHODS: The effects of both irradiation doses in early (96 hours) and acute phase (5 to 11 days) post-irradiation on immune parameters were monitored in blood circulation and TME using flow cytometry. Simultaneously, selected cytokines related to immune cells within the TME were measured using multiplex ELISA.
RESULTS: A temporary reduction in systemic total white blood count (TWBC) resulted from an early phase (96 hours) of gamma-ray irradiation at 2 Gy and 8 Gy compared to sham control group. No difference was obtained in the acute phase. Neutrophils dominated among other immune cells in TME in sham control group. Eosinophils in TME was significantly increased after 8 Gy treatment in acute phase compared to sham control (p< 0.005). Furthermore, the increment of tumour necrosis (TNF)-α, eotaxin and interleukin (IL)-7 (p< 0.05) in both treatment groups and phases were associated with anti-tumour activities within TME by gamma-ray irradiation.
CONCLUSION: The temporary changes in immune cell populations within systemic circulation and TME induced by different doses of gamma-ray irradiation correlated with suppression of several pro-tumorigenic cytokines in mouse-bearing EMT6 tumour models.
Fulltext Acquired radioresistance in EMT6 mouse mammary carcinoma cell line is mediated by CTLA-4 and PD-1 through JAK/STAT/PI3K pathway

Sham NFR, Hasani NAH, Hasan N, Karim MKA, Fuad SBSA, Hasbullah HH, et al.

Sci Rep, 2023 Feb 22;13(1):3108.
PMID: 36813833 DOI: 10.1038/s41598-023-29925-x

Cancer recurrence is often associated with the acquisition of radioresistance by cancer tissues due to failure in radiotherapy. The underlying mechanism leading to the development of acquired radioresistance in the EMT6 mouse mammary carcinoma cell line and the potential pathway involved was investigated by comparing differential gene expressions between parental and acquired radioresistance cells. EMT6 cell line was exposed to 2 Gy/per cycle of gamma-ray and the survival fraction between EMT6-treated and parental cells was compared. EMT6RR_MJI (acquired radioresistance) cells was developed after 8 cycles of fractionated irradiation. The development of EMT6RR_MJI cells was confirmed with further irradiation at different doses of gamma-ray, and both the survival fraction and migration rates were measured. Higher survival fraction and migration rates were obtained in EMT6RR_MJI cells after exposure to 4 Gy and 8 Gy gamma-ray irradiations compared to their parental cells. Gene expression between EMT6RR_MJI and parental cells was compared, and 16 genes identified to possess more than tenfold changes were selected and validated using RT-PCR. Out of these genes, 5 were significantly up-regulated i.e., IL-6, PDL-1, AXL, GAS6 and APCDD1. Based on pathway analysis software, the development of acquired radioresistance in EMT6RR_MJI was hypothesized through JAK/STAT/PI3K pathway. Presently, CTLA-4 and PD-1 were determined to be associated with JAK/STAT/PI3K pathway, where both their expressions were significantly increased in EMT6RR_MJI compared to parental cells in the 1st, 4th and 8th cycle of radiation. As a conclusion, the current findings provided a mechanistic platform for the development of acquired radioresistance in EMT6RR_MJI through overexpression of CTLA-4 and PD-1, and novel knowledge on therapeutic targets for recurrent radioresistant cancers.
Fulltext Development of custom lead shield and strainer for targeted irradiation for mice in the gamma cell chamber

Hasan N, Sham NFR, Karim MKA, Fuad SBSA, Hasani NAH, Omar E, et al.

Sci Rep, 2021 Jul 15;11(1):14559.
PMID: 34267293 DOI: 10.1038/s41598-021-93964-5

We presented a development of a custom lead shield and mouse strainer for targeted irradiation from the gamma-cell chamber. This study was divided into two parts i.e., to (i) fabricate the shield and strainer from a lead (Pb) and (ii) optimize the irradiation to the mice-bearing tumour model with 2 and 8 Gy absorbed doses. The lead shielding was fabricated into a cuboid shape with a canal on the top and a hole on the vertical side for the beam path. Respective deliveries doses of 28 and 75 Gy from gamma-cell were used to achieve 2 and 8 Gy absorbed doses at the tumour sites.

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