Cancer Genomics

DETECTING NOVEL BIOMARKERS FOR OVARIAN CANCER

DETECTING NOVEL BIOMARKERS FOR OVARIAN CANCER: ROLE OF RAD51AP1

Authors: Vincent Ruttoh1,2, Emmanouil Karteris2, Dimple Chudasama2

Affiliations

  1. Kenya Medical Research Institute (KEMRI)
  2. Brunel University, London

Ovarian carcinoma is the most lethal gynecologic malignancy in developed countries with a five-year survival rate of less than 40%. This is due to the asymptomatic nature of ovarian cancer and lack of reliable assay that can be used in early diagnosis hence 80% of the cases are detected in stages III or IV when the chances of a 5-year survival has diminished. Despite advances in treatment options, the treatment outcomes for patients have remained largely unchanged over the past few decades. There is no single molecular profile that has been that has been able to overcome the limitations of CA125.

Using microarray data of multiple cancer studies and a combination of in silico networks, we first derived a unique-network for ovarian cancer and then identified the genes that are uniquely involved in this mechanism.  RAD51AP1 was one of the genes identified.  Ovarian tissue microarrays were then analyzed immunohistochemically for protein expression of RAD51AP1. Patient serum was then analyzed using quantitative RT-PCR to measure gene expression RAD51AP1.

RAD51AP1 was expressed constitutively in all serous papillary carcinoma tissues Immunohistochemical analysis of ovarian and lung cancer tissues and unaffected controls demonstrated that significant quantitative and qualitative change in RAD51AP1 protein expression between normal and cancerous tissues. Significant expression was also observed between tumour grade and RAD51AP1 protein expression. qRT-PCR results showed that RAD51AP1 was overexpressed in blood samples of ovarian cancer patients compared to healthy controls.

RAD51AP1 is a promising prognostic and/or predictive biomarker candidate. Its role in ovarian cancer oncogenesis should be studied further before being validated for clinical use.

 

Presenter: Mr. Vincent Ruttoh

Affiliation: Kenya Medical Research Institute

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THE BULK OF CANCER ASSOCIATED MUTATION

 

THE BULK OF CANCER ASSOCIATED MUTATIONS IN A CRC FAMILY ARE NOVEL SOMATIC EVENTS AND LIKELY A PRODUCT OF APOBEC3B MUTAGENESIS

Authors and affiliations

Omnia E. Yousif1, Rayan Saifeldin Yousif1, Ali  Sultan,  Suleiman H. Suleiman2, *Muntasir E. Ibrahim1

*Corresponding author: Muntasir E. Ibrahim

1.Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum. P.O. Box 102, Sudan,2.Soba University Hospital, Department of Surgery, Faculty of Medicine, University of Khartoum, Sudan,3. Weill Cornell Medical College in Qatar, Qatar

Abstract

Aim

To investigate the role of APOBEC-3B gene in familial colorectal cancer

Background

Colorectal cancer is the third most common cancer worldwide. The disease may occur due to mutations in undiscovered genetic loci in patients with no Lynch. Hitherto, new technologies like next generation sequencing (NGS) provide a persuasive tool and deciphered a wide range of culprits that contributed to tumorigenesis process. Different spheres were described as causative factors of the disease including genetic, epigenetic and infection. In this regard APOBEC family of editing proteins plays a major role in causing non-random mutations. However, much to be learned about the interaction between: APOBEC family, novel mutations and Epstein–Barr virus (EBV).

Methods

 Herein, multidisciplinary approach (NGS, qRT-PCR, in situ hyperdization and microarray) was use in order to investigate different mutations in one CRC family (2 cancer and three normal controls).

Results

 Using NGS we identified 3845/44886 (9%), 3575/43186 (8.3%) novel variants among tumor samples in compared to 1795/43832(4%), 1759/44241 (4%), 1813/44967 (4%) in control sample (p=0.0001). Among the novel variants, variant with significant score in (SIFT and PolyPhen) tools were (317/1759 (18%), 353/1795 (20%) in tumor samples and 217/1795 (12%), 202/1759 (11%) and 52/1813(3%) in control samples (p=0.0001). Pathway analysis of the significant score genes reported The Chromobox family gene (Cbx), DNA-repair proteins (XRCC) genes families. Intriguingly, APOBEC family (APOBEC4, APOBEC3H and APOBEC3A) were predicted to be mutated. Results of PCR and in situ hyperdization of (EBV) virus showed faint signal. Interestingly, quantitative PCR (qRT-PCR) analysis of APOBEC3B show 6 fold increases in the CRC tissue in compare with matched normal controls.

Conclusions

In conclusion, we proposed that APOBEC family may affect the detected somatic novel mutation and lead to cancer.  Knowledge of APOBECs mutagenesis in cancer may yield significant diagnostic, prognostic value and new therapeutic opportunities. 

 

 Name

Omnia Elfatih yousif

Title

PhD, molecular biology

Affiliations of presenter

Researcher, federal ministry of health

 

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FGFR2 Gene

ABSTRACT

AN ASSOCIATION OF FGFR2 RS2981582 WITH BREAST CANCER AMONG SUDANESE PATEINTS: A POTENTIAL BIOMARKER FOR BREAST CANCER PREDICTION

 

Sajda Mustafa Satti Abd Elgader1,2, Mai Abdul Rahman Masri2

1 Department of Biology and Biotechnology, Faculty of Science and Technology, Al-Neelain University, Khartoum, Sudan sajdascience@gmail.com.

2Genetics and Molecular biology lab, Center of cell and molecular biology research, Department of Zoology, Faculty of Science, University of Khartoum, Khartoum, Sudan. Mai_masri@hotmail.com.

 

Aim: The current study targeted the role of the C/T SNP (rs2981582) of the FGFR2 gene and some non-genetic risk factors on the risk of breast cancer among Sudanese females. The interaction between that SNP and other known risk factors was also evaluated.

Background: The rs2981582 single nucleotide polymorphism in the Fibroblast Growth Factor Receptor 2 gene has been constantly associated with an increased risk of susceptibility to breast cancer across several human populations.

Methods: DNA was extracted and PCR-RFLP data from 81 cases and 81 controls was analyzed.

Results: The risk allele (T allele) of the rs2981582 polymorphism was associated with an increased risk of breast cancer (P-value= 0.0017) (OR =2.2, CI95%=1.34 to 3.53). Breast cancer risk, significantly, increased with TT genotype (P-value =0.0023) (OR=1.711 CI95%=1.16 to 4.04) when compared to the other two genotypes (CC and CT). Significant association was also encountered between history of benign tumors (P-value = 0.0001), and breast cancer in first degree relatives (P-value=0.045) (OR=7.22 CI95%=1.047 to 81.2) in cases carrying this polymorphism.

Conclusions: Our findings suggest that FGFR2 rs2981582 is significantly associated with breast cancer susceptibility in Sudanese women and present a potential biomarker for breast cancer prediction.

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HL & ALCL

GENE EXPRESSION PROFILES OF HODGKIN LYMPHOMA (HL) And ANAPLASTIC LARGE CELL LYMPHOMA (ALCL) CELL LINES

Nihad Hassan1 , Kamal H. Mohamed 2 , Diponkar Banerjee 3, Faisal M. Fadlelmola 1

1 Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Sudan               

2 Radiation and Isotope Centre of Khartoum (RICK) 

3 Division of Anatomical Pathology, Eastern Ontario Regional Laboratory Association and The Ottawa Hospital  

Background: Hodgkin’s lymphoma (HL) and Anaplastic large cell lymphoma (ALCL) are subtypes of human malignant lymphomas. The borderline is not well characterised in the context of morphologic, immunophenotypic, and clinical characteristics between the two diseases, as well as they both express CD30. The use of gene expression microarray in diseases is a genomic technology that improves and provides more accurate diagnosis. Aim and Method: Here TM4 suits software was used to analyse gene expression microarray data for four haematopoietic cell lines comprised KMH2 and L428 of human HL derived cell lines, and DEL and SR786 of ALCL-derived ones. Results: An overall of hundred and twenty-one genes were showed to have a significant differential expressed patterns in all cell lines, among which five of them were considered to be a diagnostic biomarker candidate. Furthermore, the candidate differentially expressed genes were subjected to pathway and protein-protein interactions analysis. The study showed that three of them were found to be involved in different 83 pathways and the majority were shown to have interactions with many other proteins. Conclusion: Significant findings have showed a resemblance to other symmetrical studies in the literature. In contrast some genes have exhibited different levels of expression than has been reported. On the other hand, part of the findings has not been previously reported in Lymphoma literature but it has been involved in other types of cancer. Further downstream analysis with tissue microarray and protein array is needed for the validation and confirmation of these results. 

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TELOMERE VARIATION & BREAST CANCER AND HCC

THE ROLE OF TELOMERE COPY NUMBER VARIATION IN PROGNOSIS OF BREAST CANCER AND HEPATOCELLULAR CARCINOMA IN SUDANESE PATIENTS, A CASE-CONTROL STUDY.

Maram A. Suliman1,2, Muntasir E. Ibrahim2

1 Department of Human Biology, Ibn Sina University, Khartoum, Sudan.

2 Department of molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.

1 maram.a.suliman@gmail.com

2 mibrahim@iend.org

ABSTRACT

Aim: To assess the role of Telomere Length (TL) variance in Breast Cancer (BC) and Hepatocellular Carcinoma (HCC) pathology in Sudan and to verify if TL can be a reliable early detection marker for both cancers using Real Time PCR.

Background: Previously, telomere length was recommended as clinical outcome predictor in different cancers.

Methods: In this study, genomic DNA was extracted from 58 tumor and paired non-tumorous tissues samples plus blood samples from BC patients and their age matched healthy controls, also 42 blood samples were used from HCC patients and their age matched healthy controls. A real-time PCR assay was used to estimate genomic telomeres copy numbers and thus their length.

Results: Using the 2 ∆∆Ct method, our results showed that there was an increase in the average of copies in tumor tissues of BC cases (71.4 copies) in compare to cases’ normal tissues (19.3 copies), and (10.9 copies) in cases blood in compare to (14.8 copies) the blood of their matched healthy controls. Consistently TL was long in (63%) of BC patients, unlike in HCC patients where only (9.5%) had long telomeres where HCC samples exhibited very few telomeric DNA copies (0.47 copies) in cases and (0.2 copies) in their matched healthy controls. TL was found to be greatly affected by a female pregnancy status in BC patients (P = 0.02). Also the age at which a female get pregnant for the first time showed a strong effect on TL (P = 0.02). In HCC patients, TL showed a very strong positive correlation with age (P =0.01), although not statistically significant in BC patients, possibly due to the low number of this population. Another strong cofounder that found to affect the TL was Ethnicity were it showed significant difference in BC (P = 0.012) and HCC (P = 0.035).

Conclusion: In light of the above results, Telomeric copy number can be an early predictor for Breast Cancer and Hepatocellular Carcinoma as well.

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MICRO-RNA 153 EXPRESSIONS IN BREAST CANCER IN SUDAN

 

      MICRO-RNA 153 EXPRESSIONS IN BREAST CANCER IN SUDAN

 A POTENTIAL BIOMARKER?

 

   Duaa Ali Ahmed1, 2; Mohammed.O.Elseideg 2;  Tamador Elhadi 2; Hiba Salah 2; Mohamed.A.wadatallah3

   Muntaser E Ibrahim 2

 

 1 Department of Internal Medicine, Sudan Medical Specialization Board.

 2 Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum,                        

   Sudan

 3 Ibrahem Malik teaching hospital, University of Khartoum.

 

BACKGROUND: Breast cancer is the most common cancer in women worldwide constituting 24.2% of newly diagnosed cancer in women. In Sudan it’s a major health problem with incidence rate 25.1/100,000. Major challenge in breast cancer management is searching for sensitive, specific and minimally invasive biomarkers for early detection of breast cancer. Micro-RNA(miR) are a class of small noncoding RNA that regulate gene expression at post-transcriptional level. MiR plays important roles in tumor initiation, metastasis and drug resistance. Wide genome Methylome analysis of breast cancer in Sudanese revealed differential methylation of miRNA 153-2 in breast cancer with high specificity.

AIM: The primary aim of this study is to investigate whether miR153 expression is altered in breast cancer tissue compared with healthy control in Sudanese patients.

Methodology: This is an observational, pilot, case control study. Seven confirmed breast cancer patients were included. Cancerous breast tissues (cases) were taken during surgery and a (control) samples were taken from healthy margins from the same patients. Easy blue was used for RNA extraction and expression was measured by Real time PCR, the 2nd most sensitive and specific approach for RNA detection after next generation sequencing.

Results:  miRNA-153 is found to be differentially overexpressed by 39.4 fold more -on average- in breast cancer tissues compared to normal controls.  This outcome, in case of further validation in a larger sample, may have an important diagnostic and prognostic role.

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ASSESSMENT OF CYTOCHROME P450

ASSESSMENT OF CYTOCHROME P450 2E1 (G-1293C, RS3813867) GENE POLYMORPHISM IN SUDANESE PATIENTS WITH ACUTE MYELOID LEUKAEMIA & controls

 

Alaa. M. Hamad1*, Hanan. B. Eltahir2, Faisal M. Fadlelmola3,4

 

1*Department of Biotechnology, School of pharmacy, Ahfad university for women, Sudan.

2Department of Biochemistry, Faculty of Medicine, University of El Imam El Mahdi, Sudan.

3Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, Sudan.

4H3ABioNet University of Khartoum Node as members of the H3Africa Consortium.

Corresponding author Email: alaahamad607@gmail.com*

 

Background Acute myeloid leukemia (AML) is a complicated, heterogeneous disease involving the presence of a clonal expansion of neoplastic myeloid cells with variable degrees of differentiation and varying clinical, morphologic, immunologic, molecular characteristics and cytogenetic abnormalities. The exact cause of leukemia is unknown. A combination of genetic factors and environmental factors are believed to play a role, an exposure to xenobiotic like cigarette smoking and other chemicals was found to be associated with polymorphism of cytochrome 2E1 in Eastern countries like Chinese and Japanese patients with AML, but in Africa was found to be markedly different. The CYP2E1 gene activates nitrosamine chemicals into more toxic or carcinogenic forms, therefore it receives a great deal of attention in terms of occupational cancers.

 The aim of this study was to investigate the role of polymorphism in cytochrome 2E1 G-1293C (rs3813867) in developing AML in Khartoum state. After taken then informed consent, 25 AML patients and 38 healthy controls were included in the study.

Methods DNA was isolated from whole blood. Genotyping of 2E1 G-1293C (rs3813867) was performed by PCR-RFLP analysis followed by DNA sequencing for the flanking region of the gene.  

Results The frequency of the c1 allele of CYP2E1 gene was found to be the predominant one in both patients and healthy controls 100% (p=0.02) with c1/c1 genotype.

Conclusion Our results suggest that CYP2E1*5B variant rs3813867 plays no role in development of AML in Sudanese samples. 

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Shaza Fadlalah poster

ANALYSIS OF SOMATIC MUTATION IN SOUTH AFRICAN BREAST CANCER       PATIENTS USING GENE EXPRESSION

 

Shaza Fadlalla¹

1Centre for Bioinformatics and Computational Biology, Genomics Research Institute and Department of Biochemistry

 

 

Background

Breast cancer has a high prevalence in South Africa, being the second most common form of cancer in women. Screening and early diagnosis of breast cancer is critically important for the successful treatment of this disease. Two high penetrance breast cancer susceptibility genes, BRCA1 and BRCA2 are clinically the most important genes associated with hereditary breast cancer.

International studies investigating the BRCA and other markers for breast cancer in African populations is limited. Effective markers are urgently needed for screening and management, and also for further molecular understanding of breast cancer in southern African population.

Aim

Identification of driver genes in a patient’s tumour may assist in the understanding of cancer progression and the selection of suitable treatment protocols.

Methods

FFPE tuomer samples were analyzed in the study, gene Expression analysis was done on somatic samples using the NanoString PanCancer Pathway Panel (NanoString, USA).Expression data was normalized and differentiated using nanostringdiff, Pathway analysis for differentially-expressed genes in somatic samples was performed using reactomePA.

Results

NanoString counts in the FFPE-based somatic samples were generally much lower than in the normal breast tissue controls. Counts from samples up to 48% of counts from the 770 cancer-related nCounter genes were discarded as they approached background levels. For the remaining genes, differentially expressed genes were identified using nanostringdiff. Annotation was done for Reactome Pathways using reactomePA .Predominant pathways included cell-cycle pathways and signalling pathways.

Conclusion

Gene expression data showed possible driver mutations in POLR2B, LRPB1, SMAD1 and MAP3K4. Gene expression analysis showed a significant disruption of signal transduction and G1 phase effects.

 

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Rutto

DETECTING NOVEL BIOMARKERS FOR OVARIAN CANCER: ROLE OF RAD51AP1

Authors: Vincent Ruttoh1,2, Emmanouil Karteris2, Dimple Chudasama2

Affiliations

  1. Kenya Medical Research Institute (KEMRI)
  2. Brunel University, London

Ovarian carcinoma is the most lethal gynecologic malignancy in developed countries with a five-year survival rate of less than 40%. This is due to the asymptomatic nature of ovarian cancer and lack of reliable assay that can be used in early diagnosis hence 80% of the cases are detected in stages III or IV when the chances of a 5-year survival has diminished. Despite advances in treatment options, the treatment outcomes for patients have remained largely unchanged over the past few decades. There is no single molecular profile that has been that has been able to overcome the limitations of CA125.

Using microarray data of multiple cancer studies and a combination of in silico networks, we first derived a unique-network for ovarian cancer and then identified the genes that are uniquely involved in this mechanism.  RAD51AP1 was one of the genes identified.  Ovarian tissue microarrays were then analyzed immunohistochemically for protein expression of RAD51AP1. Patient serum was then analyzed using quantitative RT-PCR to measure gene expression RAD51AP1.

RAD51AP1 was expressed constitutively in all serous papillary carcinoma tissues Immunohistochemical analysis of ovarian and lung cancer tissues and unaffected controls demonstrated that significant quantitative and qualitative change in RAD51AP1 protein expression between normal and cancerous tissues. Significant expression was also observed between tumour grade and RAD51AP1 protein expression. qRT-PCR results showed that RAD51AP1 was overexpressed in blood samples of ovarian cancer patients compared to healthy controls.

RAD51AP1 is a promising prognostic and/or predictive biomarker candidate. Its role in ovarian cancer oncogenesis should be studied further before being validated for clinical use.

 

Presenter: Mr. Vincent Ruttoh

Affiliation: Kenya Medical Research Institute

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Okunola

IN VIVO AND IN VITRO TOXICOLOGICAL STUDIES OF CO-EXPOSURE TO SUPERPARAMAGNETIC IRON OXIDE NANOPARTICLES AND SOLID LIPID NANOPARTICLES

 

 

1ALABI A. OKUNOLA*, 2SILVA H. ADNY, 3BAKARE A. ADEKUNLE, 2CRECZYNSKI-PASA B. TÂNIA

1Department of Biology, Federal University of Technology, Akure, Ondo State, Nigeria.

Email: 1alabiokunola@yahoo.com, oalabi@futa.edu.ng

2Departamento de Ciências Farmacêuticas, Universidade Federal de Santa Catarina, P O Box 476, Florianópolis, SC 88040-900, Brazil.

3Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria

*Paper Presenter

Abstract

Aim: To evaluate the possible cytogenotoxicity of co-exposure to Solid lipid nanoparticles (SLNs) and Superparamagnetic iron oxide nanoparticles (SPIONs), and the mechanism of action.

Background: Data on the toxicity of SLNs and SPIONs is insufficient, and no data exist on the toxicity of co-exposure to the two nanoparticles. In nature, human, animal and environment are co-exposed to different NPs at the same time from different sources.

Methods: In vitro cytotoxicity of SPIONs, SLNs and their 1:1 mixture using Alamar blue assay in NIH/3T3 (murine embryo fibroblast cells) cell line; and in vivo genotoxicity using murine bone marrow micronucleus assay were investigated. The molecular mechanisms underlining the induced cytogenotoxicity were studied through cell cycle analysis, detection of reactive oxygen species and alterations in mitochondrial membrane potential.

Results: The results showed that SPIONs has low cytotoxicity compared to SLNs. However, the mixture of SPIONs and SLNs showed synergistic effect in NIH/3T3. In mice, there was a significant increase (p<0.05) in micronucleated polychromatic erythrocytes (MNPCE) and nuclear abnormalities (NA) in SPIONs, SLNs and their mixture treated mice. The mixture induced the highest frequency of MNPCE and NA. Apoptosis triggered by reactive oxygen species increase and disturbances in mitochondrial membrane potential were the probable mechanisms of action.

Conclusion: Co-exposure to SLNs and SPIONs nanoparticles is more cytogenotoxic than the individual nanoparticle,hence, care should be taken in human exposure to multiple nanoparticles from different consumer products.

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