Search results for: MCF-7 human breast cancer cell line

Authors: Mohsin Ali Baloch, Saira Baloch

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Objective: To analyze hematological changes in patients of oral cancer with history of smokable and chewable tobacco use, and to compare them with healthy controls. Study Design: Descriptive type of study survey. Setting: This study was conducted at the Department of Oral and Maxillofacial Surgery, LUMHS, Jamshoro. Study Period: One year July, 2013 to July, 2014. Subject and Methods: Histopathologically confirmed hundred cases of oral cancer with the history of smokable and non-smokable tobacco were selected to analyze the hematological variation. Inclusion Criteria: Histopathologically diagnosed patients of oral squamous cell carcinoma, with history of smokable and non-smokable tobacco. Exclusion Criteria: Patient with any systemic medically compromising problem, terminally ill patients, radio or chemotherapeutically treated patients, patients with metastasis to lungs or any distant metastasis, patients with the history of more than one well-defined etiological factor involved. Results: There were 73% patients of oral cancer reported with anemic. Significantly lower values of Hb, platelet, and higher mean values of ESR, TLC, and were observed in both groups of oral cancer patients; tobacco smokers and tobacco chewers as compared to non-smokers healthy controls. There was more decline in the level of haemoglobin and incline in the level of ESR observed in tobacco chewer oral cancer patients as compared to tobacco smokers patients, while TLC was more observed in smokers. Conclusion: Oral cancer patients with a history of chewable/smokable tobacco have likely worse hematological profile, which increases the anesthetic and surgical challenges for maxillofacial surgeons, which have a significant impact on treatment planning as well.

Keywords: oral cancer, hematological variations, tobacco, smokers

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Authors: Mitra Shokrollahi, Mia Stanic, Anisha Hundal, Janet N. Y. Chan, Defne Urman, Chris A. Jordan, Anne Hakem, Roderic Espin, Jun Hao, Rehna Krishnan, Philipp G. Maass, Brendan C. Dickson, Manoor P. Hande, Miquel A. Pujana, Razqallah Hakem, Karim Mekhail

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Current models suggest that DNA double-strand breaks (DSBs) can move to the nuclear periphery for repair. It is unclear to what extent human DSBs display such repositioning. Here we show that the human nuclear envelope localizes to DSBs in a manner depending on DNA damage response (DDR) kinases and cytoplasmic microtubules acetylated by α-tubulin acetyltransferase-1 (ATAT1). These factors collaborate with the linker of nucleoskeleton and cytoskeleton complex (LINC), nuclear pore complex (NPC) protein NUP153, the nuclear lamina and kinesins KIF5B and KIF13B to generate DSB-capturing nuclear envelope tubules (dsbNETs). dsbNETs are partly supported by nuclear actin filaments and the circadian factor PER1 and reversed by kinesin KIFC3. Although dsbNETs promote repair and survival, they are also co-opted during poly (ADP-ribose) polymerase (PARP) inhibition to restrain BRCA1-deficient breast cancer cells and are hyper-induced in cells expressing the aging-linked lamin A mutant progerin. In summary, our results advance understanding of nuclear structure-function relationships, uncover a nuclear-cytoplasmic DDR and identify dsbNETs as critical factors in genome organization and stability.

Keywords: DNA damage response, genome stability, nuclear envelope, cancer, age-related disorders

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Authors: Suharni Mohamad Suharni Mohamad, Nurul Izzati Hamzan Nurul Izzati Hamzan, Norhayu Abdul Rahman Norhayu Abdul Rahman, Siti Suraiya Md Noor Siti Suraiya Md Noor

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Human papillomavirus (HPV) is an important risk factor for development of oral cancer. HPV16 is the most common type found in HPV-positive squamous cell carcinoma. In the present study, we established a real-time loop-mediated isothermal amplification (real-time LAMP) for detection of HPV16. A set of six primers was specially designed to recognize eight distinct sequences of HPV16-E6. Detection and quantification was achieved by real-time monitoring using a real-time turbidimeter based on threshold time required for turbidity in the LAMP reaction. LAMP reagents (MgSO4, dNTPs, Bst polymerase concentrations) and various incubation times and temperatures were optimized. The sensitivity was determined using 10-fold serial dilutions of HPV16 standard strain. The specificity of was evaluated using other HPV genotypes. The optimized method was established with specifically designed primers by real-time detection in approximately 30 min at 65°C. The limit of detection of HPV16 using the LAMP assay was 10 pg/ml that could be detected in 30 min. The LAMP assay was 10 times more sensitive than the conventional PCR in detecting HPV16. No cross-reactivity with other HPV genotypes was observed. This quantitative real-time LAMP assay may improve diagnostic potential for the detection and quantification of HPV16 in clinical samples and epidemiological studies due to its rapidity, simplicity, high sensitivity and specificity. This assay will be further evaluated with HPV DNAs of saliva from patients with oral squamous cell carcinoma. Acknowledgement: This study was financially supported by the ScienceFund Grant, Ministry of Science, Technology and Innovation (305/PPSG/6113219).

Keywords: Oral Squamous Cell Carcinoma (OSCC), Human Papillomavirus 16 (HPV16), Loop-Mediated Isothermal Amplification (LAMP), rapid detection

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Authors: Yudi Zhao, Ziyun Zhou, Yueting Yao, Shuying Dai, Zhiling Yan, Longyu Yang, Chuanyin Li, Li Shi, Yufeng Yao

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HPV16 E4 gene plays an important role in viral genome amplification and release. Therefore, a variation of the E4 gene nucleic acid sequence may affect the carcinogenicity of HPV16. In order to understand the relationship between the variation of HPV16 E4 gene and cervical cancer, this study was to amplify and sequence the DNA sequences of E4 genes in 118 HPV16-positive cervical cancer patients and 151 HPV16-positive asymptomatic individuals. After obtaining E4 gene sequences, the phylogenetic trees were constructed by the Neighbor-joining method for gene variation analysis. The results showed that: 1) The distribution of HPV16 variants between the case group and the control group differed greatly (P = 0.015)，and the Asian-American（AA）variant was likely to relate to the occurrence of cervical cancer. 2) DNA sequence analysis showed that there were significant differences in the distribution of 8 variants between the case group and the control group (P < 0.05). And 3) In European (EUR) variant, two variations, C3384T (L18L) and A3449G (P39P), were associated with the initiation and development of cervical cancer. The results suggested that the variation of HPV16 E4 gene may be a contributor affecting the occurrence as well as the development of cervical cancer, and different HPV16 variants may have different carcinogenic capability.

Keywords: cervical cancer, HPV16, E4 gene, variations

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Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

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In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

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Authors: Mehrnaz Mostafavi

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Lung cancer is one of the most harmful forms of cancer. The long-term survival rate of lung cancer patients treated by conventional modalities such as surgical resection, radiation, and chemotherapy remains far from satisfactory. Systemic drug delivery is rarely successful because only a limited amount of the chemotherapeutic drug targets lung tumor sites, even when administered at a high dose. Targeted delivery of drug molecules to organs or special sites is one of the most challenging research areas in pharmaceutical sciences. By developing colloidal delivery systems such as liposomes, micelles and nanoparticles a new frontier was opened for improving drug delivery. Nanoparticles with their special characteristics such as small particle size, large surface area and the capability of changing their surface properties have numerous advantages compared with other delivery systems. Targeted nanoparticle delivery to the lungs is an emerging area of interest.Multimodal or combination therapy represents a promising new method to fight disease. Therefore, a combination of different therapeutic strategies may be the best alternative to improve treatment outcomes for lung cancer. Photothermal therapy was proposed as a novel approach to treatment. In this work, photothermal therapy with gold nanoparticles and near infrared laser (NIR) irradiation was investigated.Four types of small (<100nm), NIR absorbing gold nanoparticles (nanospheres, nanorods) were synthesized using wet chemical methods and characterized by transmission electron microscopy, dynamic light scattering and UV-vis spectroscopy. Their synthesis and properties were evaluated, to determine their feasibility as a photothermal agent for clinical applications. In vitro cellular uptake studies of the nanoparticles into lung cancer cell lines was measured using light scattering microscopy.Small gold nanorods had good photothermal properties and the greatest cellular uptake, and were used in photothermal studies. Under 4W laser irradiation, an increase in temperature of 10°C and decrease in cell viability of up to 80% were obtained.

Keywords: photothermal, therapy, cancer, gold nanorods

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Authors: T. Scattolin, E. Cavarzerani, F. Visentin, F. Rizzolio

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Organopalladium compounds have recently attracted attention for their high stability even under physiological conditions and, above all, for their remarkable in vitro cytotoxicity towards cisplatin-resistant cell lines. Among the organopalladium derivatives, those bearing at least one N-heterocyclic carbene ligand (NHC) and the Pd(II)-η³-allyl fragment have exhibited IC₅₀ values in the micro and sub-micromolar range towards several cancer cell lines in vitro and in some cases selectivity towards cancerous vs. non-tumorigenic cells. Herein, a selection of allyl and indenyl palladates were synthesized using a solvent-free method consisting of grinding the corresponding palladium precursors with different saturated and unsaturated azolium salts. All compounds have been fully characterized by NMR, XRD and elemental analyses. The intramolecular H, Cl interaction has been elucidated and quantified using the Voronoi Deformation Density scheme. Most of the complexes showed excellent cytotoxicity towards ovarian cancer cell lines, with I₅₀ values comparable to or even lower than cisplatin. Interestingly, the potent anticancer activity was also confirmed in a high-serous ovarian cancer (HGSOC) patient-derived tumoroid, with a clear superiority of this class of compounds over classical platinum-based agents. Finally, preliminary enzyme inhibition studies of the synthesized palladate complexes against the model TrxR show that the compounds have high activity comparable to or even higher than auranofin and classical Au(I) NHC complexes. Based on such promising data, further in vitro and in vivo experiments and in-depth mechanistic studies are ongoing in our laboratories.

Keywords: anticancer activity, palladium complexes, organoids, indenyl and allyl ligands

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Authors: Farhan Sohail, Gul Shahnaz Irshad Hussain, Shoaib Sarwar, Ibrahim Javed, Zajif Hussain, Akhtar Nadhman

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The present study was aimed to develop a hybrid nanocarrier (NC) system with enhanced membrane permeability, bioavailability and targeted delivery of Docetaxel (DTX) in breast cancer. Hybrid NC’s based on folic acid (FA) grafted thiolated chitosan (TCS) enveloped liposomes were prepared with DTX and evaluated in-vitro and in-vivo for their enhanced permeability and bioavailability. Physicochemical characterization of NC’s including particle size, morphology, zeta potential, FTIR, DSC, PXRD, encapsulation efficiency and drug release from NC’s was determined in vitro. Permeation enhancement and p-gp inhibition were performed through everted sac method on freshly excised rat intestine which indicated that permeation was enhanced 5 times as compared to pure DTX and the hybrid NC’s were strongly able to inhibit the p-gp activity as well. In-vitro cytotoxicity and tumor targeting was done using MDA-MB-231 cell line. The stability study of the formulations performed for 3 months showed the improved stability of FA-TCS enveloped liposomes in terms of its particles size, zeta potential and encapsulation efficiency as compared to TCS NP’s and liposomes. The pharmacokinetic study was performed in vivo using rabbits. The oral bioavailability and AUC0-96 was increased 10.07 folds with hybrid NC’s as compared to positive control. Half-life (t1/2) was increased 4 times (58.76 hrs) as compared to positive control (17.72 hrs). Conclusively, it is suggested that FA-TCS enveloped liposomes have strong potential to enhance permeability and bioavailability of hydrophobic drugs after oral administration and tumor targeting.

Keywords: docetaxel, coated liposome, permeation enhancement, oral bioavailability

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Authors: Safee Chaudhary, Mahnoor Naseer Gondal, Hira Anees Awan, Abdul Rehman, Ammar Arif, Risham Hussain, Huma Khawar, Zainab Arshad, Muhammad Faizyab Ali Chaudhary, Waleed Ahmed, Muhammad Umer Sultan, Bibi Amina, Salaar Khan, Muhammad Moaz Ahmad, Osama Shiraz Shah, Hadia Hameed, Muhammad Farooq Ahmad Butt, Muhammad Ahmad, Sameer Ahmed, Fayyaz Ahmed, Omer Ishaq, Waqar Nabi, Wim Vanderbauwhede, Bilal Wajid, Huma Shehwana, Muhammad Tariq, Amir Faisal

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Cancer is a manifestation of multifactorial deregulations in biomolecular pathways. These deregulations arise from the complex multi-scale interplay between cellular and extracellular factors. Such multifactorial aberrations at gene, protein, and extracellular scales need to be investigated systematically towards decoding the underlying mechanisms and orchestrating therapeutic interventions for patient treatment. In this work, we propose ‘TISON’, a next-generation web-based multiscale modeling platform for clinical systems oncology. TISON’s unique modeling abstraction allows a seamless coupling of information from biomolecular networks, cell decision circuits, extra-cellular environments, and tissue geometries. The platform can undertake multiscale sensitivity analysis towards in silico biomarker identification and drug evaluation on cellular phenotypes in user-defined tissue geometries. Furthermore, integration of cancer expression databases such as The Cancer Genome Atlas (TCGA) and Human Proteome Atlas (HPA) facilitates in the development of personalized therapeutics. TISON is the next-evolution of multiscale cancer modeling and simulation platforms and provides a ‘zero-code’ model development, simulation, and analysis environment for application in clinical settings.

Keywords: systems oncology, cancer systems biology, cancer therapeutics, personalized therapeutics, cancer modelling

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Authors: Abdulkader Helwan

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Iris cancer, so called intraocular melanoma is a cancer that starts in the iris; the colored part of the eye that surrounds the pupil. There is a need for an accurate and cost-effective iris cancer detection system since the available techniques used currently are still not efficient. The combination of the image processing and artificial neural networks has a great efficiency for the diagnosis and detection of the iris cancer. Image processing techniques improve the diagnosis of the cancer by enhancing the quality of the images, so the physicians diagnose properly. However, neural networks can help in making decision; whether the eye is cancerous or not. This paper aims to develop an intelligent system that stimulates a human visual detection of the intraocular melanoma, so called iris cancer. The suggested system combines both image processing techniques and neural networks. The images are first converted to grayscale, filtered, and then segmented using prewitt edge detection algorithm to detect the iris, sclera circles and the cancer. The principal component analysis is used to reduce the image size and for extracting features. Those features are considered then as inputs for a neural network which is capable of deciding if the eye is cancerous or not, throughout its experience adopted by many training iterations of different normal and abnormal eye images during the training phase. Normal images are obtained from a public database available on the internet, “Mile Research”, while the abnormal ones are obtained from another database which is the “eyecancer”. The experimental results for the proposed system show high accuracy 100% for detecting cancer and making the right decision.

Keywords: iris cancer, intraocular melanoma, cancerous, prewitt edge detection algorithm, sclera

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Authors: Danni Cheng

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Background: Preclinical and epidemiological studies have reported potential protective effects of low-density lipoprotein cholesterol (LDL-C) lowering drugs on head and neck squamous cell cancer (HNSCC) survival, but the causality was not consistent. Genetic variants associated with LDL-C lowering drug targets can predict the effects of their therapeutic inhibition on disease outcomes. Objective: We aimed to evaluate the causal association of genetically proxied cholesterol-lowering drug targets and circulating lipid traits with cancer survival in HNSCC patients stratified by human papillomavirus (HPV) status using two-sample Mendelian randomization (MR) analyses. Method: Single-nucleotide polymorphisms (SNPs) in gene region of LDL-C lowering drug targets (HMGCR, NPC1L1, CETP, PCSK9, and LDLR) associated with LDL-C levels in genome-wide association study (GWAS) from the Global Lipids Genetics Consortium (GLGC) were used to proxy LDL-C lowering drug action. SNPs proxy circulating lipids (LDL-C, HDL-C, total cholesterol, triglycerides, apoprotein A and apoprotein B) were also derived from the GLGC data. Genetic associations of these SNPs and cancer survivals were derived from 1,120 HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) and 2,570 non-HPV-driven HNSCC patients in VOYAGER program. We estimated the causal associations of LDL-C lowering drugs and circulating lipids with HNSCC survival using the inverse-variance weighted method. Results: Genetically proxied HMGCR inhibition was significantly associated with worse overall survival (OS) in non-HPV-drive HNSCC patients (inverse variance-weighted hazard ratio (HR IVW), 2.64[95%CI,1.28-5.43]; P = 0.01) but better OS in HPV-positive OPSCC patients (HR IVW,0.11[95%CI,0.02-0.56]; P = 0.01). Estimates for NPC1L1 were strongly associated with worse OS in both total HNSCC (HR IVW,4.17[95%CI,1.06-16.36]; P = 0.04) and non-HPV-driven HNSCC patients (HR IVW,7.33[95%CI,1.63-32.97]; P = 0.01). A similar result was found that genetically proxied PSCK9 inhibitors were significantly associated with poor OS in non-HPV-driven HNSCC (HR IVW,1.56[95%CI,1.02 to 2.39]). Conclusion: Genetically proxied long-term HMGCR inhibition was significantly associated with decreased OS in non-HPV-driven HNSCC and increased OS in HPV-positive OPSCC. While genetically proxied NPC1L1 and PCSK9 had associations with worse OS in total and non-HPV-driven HNSCC patients. Further research is needed to understand whether these drugs have consistent associations with head and neck tumor outcomes.

Keywords: Mendelian randomization analysis, head and neck cancer, cancer survival, cholesterol, statin

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Authors: H. Chassaigne, S. Gioria, J. Lobo Vicente, D. Carpi, P. Barboro, G. Tomasi, A. Kinsner-Ovaskainen, F. Rossi

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Emerging approaches in the area of exposure to nanomaterials and assessment of human health effects combine the use of in vitro systems and analytical techniques to study the perturbation of the proteome and/or the metabolome. We investigated the modification in the cytoplasmic compartment of the Balb/3T3 cell line exposed to gold nanoparticles. On one hand, the proteomic approach is quite standardized even if it requires precautions when dealing with in vitro systems. On the other hand, metabolomic analysis is challenging due to the chemical diversity of cellular metabolites that complicate data elaboration and interpretation. Differentially expressed proteins were found to cover a range of functions including stress response, cell metabolism, cell growth and cytoskeleton organization. In addition, de-regulated metabolites were annotated using the HMDB database. The "omics" fields hold huge promises in the interaction of nanoparticles with biological systems. The combination of proteomics and metabolomics data is possible however challenging.

Keywords: data processing, gold nanoparticles, in vitro systems, metabolomics, proteomics

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Authors: Azza T. Tahera, Eman M. Ahmeda, Nadia A. Khalila, Yassin M. Nissanb

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New 3-(pyridin-4-yl)-[1,2,4] triazolo [4,3-b] pyridazine derivatives 2a-i, 4a,b and 6a,b were designed, synthesized and evaluated as cytotoxic agents. All compounds were investigated for their in vitro cytotoxicity at a single dose 10-5M concentration towards 60 cancer cell lines according to USA NCI protocol. The preliminary screening results showed that the majority of tested compounds exhibited remarkable activity against SR (leukemia) cell panel. Molecular docking for all synthesized compounds was performed on the active site of c-Met kinase. The most active compounds, 2f and 4a were further evaluated at a seven dose level screening and their IC50 as a c-Met kinase inhibitors were determined in vitro.

Keywords: triazolopyridazines, pyridazines, cytotoxic activity, cell panel

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Authors: Arati Inamdar, Siddharth Bhattacharyya, Kester Haye

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Collision tumors are rare entities characterized by neoplasms of two different cell populations with distinct separating boundaries. Such tumors could be benign, malignant, or a combination of both. The exact mechanism of origin for collision tumors is predicted to be tumor heterogeneity or concurrent occurrence of neoplasm in the same organ. We present two cases of plasmacytoma presenting as a collision tumor, one with a tumor of hematological origin and another with a non-hematological origin, namely Chronic Lymphocytic Leukemia and Adenocarcinoma of the colon, respectively. The immunohistochemical stains and flowcytometry analysis performed on the specimens aided incorrect diagnosis. Interestingly, neoplastic cells of plasmacytoma in the first case demonstrated strong cytokeratin along with weak Epithelial Specific Antigen/ Epithelial cell adhesion molecule Monoclonal Antibody (MOC31) positivity, indicating that the tumor may influence the microenvironment of the tumor in the vicinity. Furthermore, the next-generation sequencing studies performed on the specimen with plasmacytoma and chronic lymphocytic lymphoma demonstrated BReast CAncer gene (BRCA2) and Tumor Necrosis Factor Alpha Induced Protein 3 (TNFAIP3) as a disease associated variants suggestive of risk for multiple tumors including collision tumors. Our reports highlight the unique collision tumors involving plasmacytoma, which have never been reported previously, as well as provide necessary insights about the underline genetic aberrations and tumor heterogeneity through sequencing studies and allow clonality assessment for subsequent tumors.

Keywords: BRCA2, collision tumor, chronic lymphocytic leukemia, plasmacytoma

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Authors: Sarim Ahmad

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The Single Cell Gel Electrophoresis Assay (SCGE, known as comet assay) is a potential, uncomplicated, sensitive and state-of-the-art technique for quantitating DNA damage at individual cell level and repair from in vivo and in vitro samples of eukaryotic cells and some prokaryotic cells, being popular in its widespread use in various areas including human biomonitoring, genotoxicology, ecological monitoring and as a tool for research into DNA damage or repair in different cell types in response to a range of DNA damaging agents, cancer risk and therapy. The method involves the encapsulation of cells in a low-melting-point agarose suspension, lysis of the cells in neutral or alkaline (pH > 13) conditions, and electrophoresis of the suspended lysed cells, resulting in structures resembling comets as observed by fluorescence microscopy; the intensity of the comet tail relative to the head reflects the number of DNA breaks. The likely basis for this is that loops containing a break lose their supercoiling and become free to extend towards the anode. This is followed by visual analysis with staining of DNA and calculating fluorescence to determine the extent of DNA damage. This can be performed by manual scoring or automatically by imaging software. The assay can, therefore, predict an individual’s tumor sensitivity to radiation and various chemotherapeutic drugs and further assess the oxidative stress within tumors and to detect the extent of DNA damage in various cancerous and precancerous lesions of oral cavity.

Keywords: comet assay, single cell gel electrophoresis, DNA damage, early detection test

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Authors: Denis Mustafov, Emmanouil Karteris, Maria Braoudaki

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Glioblastoma multiform (GBM) is a heterogenous primary brain tumour that kills most affected patients. To the authors best knowledge, despite all research efforts there is no early diagnostic biomarker for GBM. MicroRNAs (miRNAs) are short non-coding RNA molecules which are deregulated in many cancers. The aim of this research was to determine miRNAs with a diagnostic impact and to potentially identify promising therapeutic targets for glioblastoma multiform. In silico analysis was performed to identify deregulated miRNAs with diagnostic relevance for glioblastoma. The expression profiles of the chosen miRNAs were then validated in vitro in the human glioblastoma cell lines A172 and U-87MG. Briefly, RNA extraction was carried out using the Trizol method, whilst miRNA extraction was performed using the mirVANA miRNA isolation kit. Quantitative Real-Time Polymerase Chain Reaction was performed to verify their expression. The presence of five target proteins within the A172 cell line was evaluated by Western blotting. The expression of the CORO1C protein within 32 GBM cases was examined via immunohistochemistry. The miRNAs identified in silico included miR-21-5p, miR-34a and miR-128a. These miRNAs were shown to target deregulated GBM genes, such as CDK6, E2F3, BMI1, JAG1, and CORO1C. miR-34a and miR-128a showed low expression profiles in comparison to a control miR-RNU-44 in both GBM cell lines suggesting tumour suppressor properties. Opposing, miR-21-5p demonstrated greater expression indicating that it could potentially function as an oncomiR. Western blotting revealed expression of all five proteins within the A172 cell line. In silico analysis also suggested that CORO1C is a target of miR-128a and miR-34a. Immunohistochemistry demonstrated that 75% of the GBM cases showed moderate to high expression of CORO1C protein. Greater understanding of the deregulated expression of miR-128a and the upregulation of CORO1C in GBM could potentially lead to the identification of a promising diagnostic biomarker signature for glioblastomas.

Keywords: non-coding RNAs, gene expression, brain tumours, immunohistochemistry

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Authors: Babak Bahri, Fatemeh Yassaee Meybodi, Changiz Eslahchi

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In the pursuit of effective cancer therapies, the exploration of combinatorial drug regimens is crucial to leverage synergistic interactions between drugs, thereby improving treatment efficacy and overcoming drug resistance. However, identifying synergistic drug pairs poses challenges due to the vast combinatorial space and limitations of experimental approaches. This study introduces ClusterSyn, a machine learning (ML)-powered framework for classifying anti-cancer drug synergy scores. ClusterSyn employs a two-step approach involving drug clustering and synergy score prediction using a fully connected deep neural network. For each cell line in the training dataset, a drug graph is constructed, with nodes representing drugs and edge weights denoting synergy scores between drug pairs. Drugs are clustered using the Markov clustering (MCL) algorithm, and vectors representing the similarity of drug pairs to each cluster are input into the deep neural network for synergy score prediction (synergy or antagonism). Clustering results demonstrate effective grouping of drugs based on synergy scores, aligning similar synergy profiles. Subsequently, neural network predictions and synergy scores of the two drugs on others within their clusters are used to predict the synergy score of the considered drug pair. This approach facilitates comparative analysis with clustering and regression-based methods, revealing the superior performance of ClusterSyn over state-of-the-art methods like DeepSynergy and DeepDDS on diverse datasets such as Oniel and Almanac. The results highlight the remarkable potential of ClusterSyn as a versatile tool for predicting anti-cancer drug synergy scores.

Keywords: drug synergy, clustering, prediction, machine learning., deep learning

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Authors: Sumrina Kousar

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Objective: The aim of this study was to observe the effect of fortification of expressed human breast milk with olive oil and skimmed milk in improving weight gain in very low birth weight neonates and shortening their length of hospital stay. Study Design and place: A randomized controlled trial was carried out at the Combined Military Hospital Lahore from March 2018 to March 2019. Methods: Neonates admitted with very low birth weight and gestational age of < 34 weeks were included in the study. Sixty babies were enrolled using non-probability consecutive sampling; a random number table was used to allocate them into a fortification group and a control group. The control group received expressed milk alone, while olive oil 1 ml twice daily and skimmed milk 1 gram in every third feed were added to expressed milk in the fortification group. Data was analyzed on SPSS 20. Proportions were compared by applying the chi-square test. An independent sample t-test was applied for comparing means. A p-value of ≤ 0.05 was considered significant. Results: The study comprised of 60 neonates, with 30 in each of the groups. Weight gain was 24.83±5.63 in the fortification group and 11.72±3.95 in the control group (p =< 0.001). Mean hospital stay was 20.5716.511 in the fortification group and 27.678.89 in the control group (p =< 0.043). Conclusion: Olive oil and skimmed milk fortification of breast milk was effective for weight gain and reducing the length of hospital stay in very low birth weight neonates.

Keywords: fortification, olive oil, skimmed milk, weight gain

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Authors: Kirti Hira, A. Sajeli Begum, S. Mahibalan, Poorna Chandra Rao

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Introduction: Cancer is one of the leading causes of death worldwide. Although existing therapy effectively kills cancer cells, they do affect normal growing cells leading to many undesirable side effects. Hence there is need to develop effective as well as safe drug molecules to combat cancer, which is possible through phyto-research. The currently available plant-derived blockbuster drugs are the example for this. In view of this, an investigation was done to identify cytotoxic lead molecules from Hedyotis umbellata (Family Rubiaceae), a widely distributed weed in India. Materials and Methods: The methanolic extract of the whole plant of H. umbellata (MHU), prepared through Soxhlet extraction method was further fractionated with diethyl ether and n-butanol, successively. MHU, ether fraction (EMHU) and butanol fraction (BMHU) were lyophilized and were tested for the cytotoxic effect using 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay against non-small cell lung cancer (NSCLC) A549 cell lines. The potentially active EMHU was subjected to chromatographic purification using normal-phase silica columns, in order to isolate the responsible bioactive compounds. The isolated pure compounds were tested for their cytotoxic effect by MTT assay against A549 cells. Compound-3, which was found to be most active, was characterized using IR, 1H- and 13C-NMR and MS analysis. The study was further extended to decipher the mechanism of action of cytotoxicity of compound-3 against A549 cells through various in vitro cellular models. Cell cycle analysis was done using flow cytometry following PI (Propidium Iodide) staining. Protein analysis was done using Western blot technique. Results: Among MHU, EMHU, and BMHU, the non-polar fraction EMHU demonstrated a significant dose-dependent cytotoxic effect with IC50 of 67.7μg/ml. Chromatography of EMHU yielded seven compounds. MTT assay of isolated compounds explored compound-3 as potentially active one, which inhibited the growth of A549 cells with IC50value of 14.2μM. Further, compound-3 was identified as cedrelopsin, a coumarin derivative having molecular weight of 260. Results of in vitro mechanistic studies explained that cedrelopsin induced cell cycle arrest at G2/M phase and down-regulated the expression of G2/M regulatory proteins such as cyclin B1, cdc2, and cdc25C, dose dependently. This is the first report that explores the cytotoxic mechanism of cedrelopsin. Conclusion: Thus a potential small lead molecule, cedrelopsin isolated from H. umbellata, showing antiproliferative effect mediated by G2/M arrest in A549 cells was discovered. The effect of cedrelopsin against other cancer cell lines followed by in vivo studies can be performed in future to develop a new drug candidate.

Keywords: A549, cedrelopsin, G2/M phase, Hedyotis umbellata

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Authors: Mónica P. Cala, Juan S. Carreño, Roland J.W. Meesters

Abstract:

Recently, collection of biological fluids on special filter papers has become a popular micro-sampling technique. Especially, the dried blood spot (DBS) micro-sampling technique has gained much attention and is momently applied in various life sciences reserach areas. As a result of this popularity, DBS are not only intensively competing with the venous blood sampling method but are at this moment widely applied in numerous bioanalytical assays. In particular, in the screening of inherited metabolic diseases, pharmacokinetic modeling and in therapeutic drug monitoring. Recently, microsampling techniques were also introduced in “omics” areas, whereunder metabolomics. For a metabolic profiling study we applied micro-sampling of biological fluids (blood and plasma) from healthy controls and from women with breast cancer. From blood samples, dried blood and plasma samples were prepared by spotting 8uL sample onto pre-cutted 5-mm paper disks followed by drying of the disks for 100 minutes. Dried disks were then extracted by 100 uL of methanol. From liquid blood and plasma samples 40 uL were deproteinized with methanol followed by centrifugation and collection of supernatants. Supernatants and extracts were evaporated until dryness by nitrogen gas and residues derivated by O-methyxyamine and MSTFA. As internal standard C17:0-methylester in heptane (10 ppm) was used. Deconvolution and alignment of and full scan (m/z 50-500) MS data were done by AMDIS and SpectConnect (http://spectconnect.mit.edu) software, respectively. Statistical Data analysis was done by Principal Component Analysis (PCA) using R software. The results obtained from our preliminary study indicate that the use of dried blood/plasma on paper disks could be a powerful new tool in metabolic profiling. Many of the metabolites observed in plasma (liquid/dried) were also positively identified in whole blood samples (liquid/dried). Whole blood could be a potential substitute matrix for plasma in Metabolomic profiling studies as well also micro-sampling techniques for the collection of samples in clinical studies. It was concluded that the separation of the different sample methodologies (liquid vs. dried) as observed by PCA was due to different sample treatment protocols applied. More experiments need to be done to confirm obtained observations as well also a more rigorous validation .of these micro-sampling techniques is needed. The novelty of our approach can be found in the application of different biological fluid micro-sampling techniques for metabolic profiling.

Keywords: biofluids, breast cancer, metabolic profiling, micro-sampling

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Authors: Hossein Pourbashash

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Recent experimental studies have shown that HIV can be transmitted directly from cell to cell when structures called virological synapses form during interactions between T cells. In this article, we describe a new within-host model of HIV infection that incorporates two mechanisms: infection by free virions and the direct cell-to-cell transmission. We conduct the local and global stability analysis of the model. We show that if the basic reproduction number R0 1, the virus is cleared and the disease dies out; if R0 > 1, the virus persists in the host. We also prove that the unique positive equilibrium attracts all positive solutions under additional assumptions on the parameters.

Keywords: HIV virus model, cell-to-cell transmission, global stability, Lyapunov function, second compound matrices

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Authors: H. Akbari Khorami, P. Wild, N. Djilali

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This paper reports on the response of a fiber-optic sensing probe to small concentrations of hydrogen peroxide (H2O2) vapor at room temperature. H2O2 has extensive applications in industrial and medical environments. Conversely, H2O2 can be a health hazard by itself. For example, H2O2 induces cellular damage in human cells and its presence can be used to diagnose illnesses such as asthma and human breast cancer. Hence, development of reliable H2O2 sensor is of vital importance to detect and measure this species. Ferric ferrocyanide, referred to as Prussian blue (PB), was deposited on the tip of a multimode optical fiber through the single source precursor technique and served as an indicator of H2O2 in a spectroscopic manner. Sensing tests were performed in H2O2-H2O vapor mixtures with different concentrations of H2O2. The results of sensing tests show the sensor is able to detect H2O2 concentrations in the range of 50.6 ppm to 229.5 ppm. Furthermore, the sensor response to H2O2 concentrations is linear in a log-log scale with the adjacent R-square of 0.93. This sensing behavior allows us to detect and quantify the concentration of H2O2 in the vapor phase.

Keywords: chemical deposition, fiber-optic sensor, hydrogen peroxide vapor, prussian blue

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Authors: Feng Guo

Abstract:

Human brain organoids, 3D brain tissue cultures derived from human pluripotent stem cells, hold promising potential in modeling neuroinflammation for a variety of neurological diseases. However, challenges remain in generating standardized human brain organoids that can recapitulate key physiological features of a human brain. Here, this study presents a series of organoids-on-a-chip systems to generate better human brain organoids and model neuroinflammation. By employing 3D printing and microfluidic 3D cell culture technologies, the study’s systems enable the reliable, scalable, and reproducible generation of human brain organoids. Compared with conventional protocols, this study’s method increased neural progenitor proliferation and reduced heterogeneity of human brain organoids. As a proof-of-concept application, the study applied this method to model substance use disorders.

Keywords: human brain organoids, microfluidics, organ-on-a-chip, neuroinflammation

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Authors: Wen-Hsi Lee, C.G. Kao

Abstract:

In this study, Cu paste was prepared and printed with narrow line screen printing process on polycrystalline Si solar cell which has already finished the back Al printing and deposition of double anti-reflection coatings (DARCs). Then, two-step firing process was applied to sinter the front electrode and obtain the ohmic contact between front electrode and solar cell. The first step was in air atmosphere. In this process, PbO-based glass frit etched the DARCs and Ag recrystallized at the surface of Si, constructing the preliminary contact. The second step was in reducing atmosphere. In this process, CuO reduced to Cu and sintered. Besides, Ag nanoparticles recrystallized in the glass layer at interface due to the interactions between H2, Ag and PbO-based glass frit and the volatility of Pb, constructing the ohmic contact between electrode and solar cell. By experiment and analysis, reaction mechanism in each stage was surmised, and it was also proven that ohmic contact and good sheet resistance for front electrode could both be obtained by applying newly-invented paste and process.

Keywords: front electrode, solar cell, ohmic contact, screen printing, paste

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Authors: Varun Agarwal

Abstract:

Introduction: With the advent of personalized medicine, histopathological review of whole slide images (WSIs) for cancer diagnosis presents an exceedingly time-consuming, complex task. Specifically, detecting metastatic regions in WSIs of sentinel lymph node biopsies necessitates a full-scanned, holistic evaluation of the image. Thus, digital pathology, low-level image manipulation algorithms, and machine learning provide significant advancements in improving the efficiency and accuracy of WSI analysis. Using Camelyon16 data, this paper proposes a deep learning pipeline to automate and ameliorate breast cancer metastasis localization and WSI classification. Methodology: The model broadly follows five stages -region of interest detection, WSI partitioning into image tiles, convolutional neural network (CNN) image-segment classifications, probabilistic mapping of tumor localizations, and further processing for whole WSI classification. Transfer learning is applied to the task, with the implementation of Inception-ResNetV2 - an effective CNN classifier that uses residual connections to enhance feature representation, adding convolved outputs in the inception unit to the proceeding input data. Moreover, in order to augment the performance of the transfer learning CNN, a stack of convolutional denoising autoencoders (CDAE) is applied to produce embeddings that enrich image representation. Through a saliency-detection algorithm, visual training segments are generated, which are then processed through a denoising autoencoder -primarily consisting of convolutional, leaky rectified linear unit, and batch normalization layers- and subsequently a contrast-normalization function. A spatial pyramid pooling algorithm extracts the key features from the processed image, creating a viable feature map for the CNN that minimizes spatial resolution and noise. Results and Conclusion: The simplified and effective architecture of the fine-tuned transfer learning Inception-ResNetV2 network enhanced with the CDAE stack yields state of the art performance in WSI classification and tumor localization, achieving AUC scores of 0.947 and 0.753, respectively. The convolutional feature retention and compilation with the residual connections to inception units synergized with the input denoising algorithm enable the pipeline to serve as an effective, efficient tool in the histopathological review of WSIs.

Keywords: breast cancer, convolutional neural networks, metastasis mapping, whole slide images

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Authors: Haonan Hu, Shuge Lei, Dasheng Sun, Huabin Zhang, Kehong Yuan, Jian Dai, Jijun Tang

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This paper focuses on the classification task of breast ultrasound images and conducts research on the reliability measurement of classification results. A dual-channel evaluation framework was developed based on the proposed inference reliability and predictive reliability scores. For the inference reliability evaluation, human-aligned and doctor-agreed inference rationals based on the improved feature attribution algorithm SP-RISA are gracefully applied. Uncertainty quantification is used to evaluate the predictive reliability via the test time enhancement. The effectiveness of this reliability evaluation framework has been verified on the breast ultrasound clinical dataset YBUS, and its robustness is verified on the public dataset BUSI. The expected calibration errors on both datasets are significantly lower than traditional evaluation methods, which proves the effectiveness of the proposed reliability measurement.

Keywords: medical imaging, ultrasound imaging, XAI, uncertainty measurement, trustworthy AI

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Authors: Urvi Panwar, Kanchan Mishra, Kanjaksha Ghosh, ShankerLal Kothari

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Background: Day-by-day the increasing prevalence of neurodegenerative diseases have become a global issue to manage them by medical sciences. The adult neural stem cells are rare and require an invasive and painful procedure to obtain it from central nervous system. Mesenchymal stem cell (MSCs) therapies have shown remarkable application in treatment of various cell injuries and cell loss. MSCs can be derived from various sources like adult tissues, human bone marrow, umbilical cord blood and cord tissue. MSCs have similar proliferation and differentiation capability, but the human umbilical cord-derived mesenchymal stem cells (hUCMSCs) are proved to be more beneficial with respect to cell procurement, differentiation to other cells, preservation, and transplantation. Material and method: Human umbilical cord is easily obtainable and non-controversial comparative to bone marrow and other adult tissues. The umbilical cord can be collected after delivery of baby, and its tissue can be cultured using explant culture method. Cell culture medium such as DMEMF12+10% FBS and DMEMF12+Neural growth factors (bFGF, human noggin, B27) with antibiotics (Streptomycin/Gentamycin) were used to culture and differentiate mesenchymal stem cells into neural cells, respectively. The characterisations of MSCs were done with Flow Cytometer for surface markers CD90, CD73 and CD105 and colony forming unit assay. The differentiated various neural cells will be characterised by fluorescence markers for neurons, astrocytes, and oligodendrocytes; quantitative PCR for genes Nestin and NeuroD1 and Western blotting technique for gap43 protein. Result and discussion: The high quality and number of MSCs were isolated from human umbilical cord via explant culture method. The obtained MSCs were differentiated into neural cells like neurons, astrocytes and oligodendrocytes. The differentiated neural cells can be used to treat neural injuries and neural cell loss by delivering cells by non-invasive administration via cerebrospinal fluid (CSF) or blood. Moreover, the MSCs can also be directly delivered to different injured sites where they differentiate into neural cells. Therefore, human umbilical cord is demonstrated to be an inexpensive and easily available source for MSCs. Moreover, the hUCMSCs can be a potential source for neural cell therapies and neural cell regeneration for neural cell injuries and neural cell loss. This new way of research will be helpful to treat and manage neural cell damages and neurodegenerative diseases like Alzheimer and Parkinson. Still the study has a long way to go but it is a promising approach for many neural disorders for which at present no satisfactory management is available.

Keywords: bone marrow, cell therapy, explant culture method, flow cytometer, human umbilical cord, mesenchymal stem cells, neurodegenerative diseases, neuroprotective, regeneration

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Authors: Adjebli Ahmed, Messis Abdelaziz, Ayeche Riad, Tighilet Karim, Talbi Melissa, Smaili Yanis, Lehri Mokrane, Louardiane Mustapha

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Colorectal cancer is one of the most common types of cancer worldwide, and its incidence has been increasing in recent years. Data and fecal samples from colorectal cancer patients were collected at the Amizour Public Hospital's oncology department (Bejaia, Algeria). Microbiological and cohort study were conducted at the Biological Engineering of Cancers laboratory at the Faculty of Medicine of the University of Bejaia. All the data showed that patients aged between 50 and 70 years were the most affected by colorectal cancer, while the age categories of [30-40] and [40-50] were the least affected. Males were more likely to be at risk of contracting colorectal cancer than females. The most common types of colorectal cancer among the studied population were sigmoid cancer, rectal cancer, transverse colon cancer, and ascending colon cancer. The hereditary factor was found to be more dominant than other risk factors. Bacterial identification revealed the presence of certain pathogenic and opportunistic bacterial genera, such as E. coli, K. pneumoniae, Shigella sp, and Streptococcus group D. These results led us to conclude that dysbiosis of the intestinal microbiome is strongly present in colorectal cancer patients at the EPH of Amizour.

Keywords: microbiome, colorectal cancer, risk factors, bacterial identification

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Authors: Mehmet Savsar

Abstract:

Several factors affect productivity of Food Processing Assembly Lines (FPAL). Engineers and line managers usually do not recognize some of these factors and underutilize their production/assembly lines. In this paper, a special food processing assembly line is studied in detail, and procedures are presented to illustrate how productivity and efficiency of such lines can be increased. The assembly line considered produces ten different types of freshly prepared salads on the same line, which is called mixed model assembly line. Problems causing delays and inefficiencies on the line are identified. Line balancing and related tools are used to increase line efficiency and minimize balance delays. The procedure and the approach utilized in this paper can be useful for the operation managers and industrial engineers dealing with similar assembly lines in food processing industry.

Keywords: assembly lines, line balancing, production efficiency, bottleneck

Procedia PDF Downloads 385

Authors: Siva Chander Chabattula, Piyush Kumar Gupta, Debashis Chakraborty, Rama Shanker Verma

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Green nanoparticles have gotten a lot of attention because of their potential applications in tissue regeneration, bioimaging, wound healing, and cancer therapy. The physical and chemical methods to synthesize metal oxide nanoparticles have an environmental impact, necessitating the development of an environmentally friendly green strategy for nanoparticle synthesis. In this study, we used Annona muricata plant leaf extract to synthesize Zinc Oxide nanoparticles (Am-ZnO NPs), which were evaluated using UV/Visible spectroscopy, FTIR spectroscopy, X-Ray Diffraction, DLS, and Zeta potential. Nanoparticles had an optical absorbance of 355 nm and a net negative surface charge of ~ - 2.59 mV. Transmission Electron Microscope characterizes the Shape and size of the nanoparticles. The obtained Am-ZnO NPs are biocompatible and hemocompatible in nature. These nanoparticles caused an anti-cancer therapeutic effect in MIA PaCa2 and MOLT4 cancer cells by inducing oxidative stress, and a change in mitochondrial membrane potential leads to programmed cell death. Further, we observed a reduction in the size of lung cancer spheroids (act as tumor micro-environment) with doxorubicin as a positive control.

Keywords: Biomaterials, nanoparticle, anticancer activity, ZnO nanoparticles

Procedia PDF Downloads 201