COBRA1 is a co-factor of BRCA1 that was identified to be the β-subunit of the NELF complex (Negative elongation factor) which stalls RNA polymerase II and prevents elongation of the message. The reported levels of expression of COBRA1 (NELF-B) in different types of cancers varied; COBRA1 is down-regulated in breast cancer, whereas in the upper gastrointestinal carcinomas it is up-regulated. The exact role of COBRA1 being a tumor suppressor gene or an oncogene remains unclear. To date, the levels of expression of COBRA1 in Hepatocellular Carcinomas (HCCs) are not yet tested. In an attempt to understand part of the complicated molecular events involved in the development of HCC, we collected 16 primary HCC tissues and their corresponding non-neoplastic specimens from patients undergoing either liver resection or liver transplantation. Samples were divided into two categories; those which undergone treatment prior to surgical procedure, TACE (Transarterial Chemoembolization) or radiofrequency ablation, and others that were not treated. All samples were examined at the RNA and protein levels using RT-PCR and western blotting respectively. All the results were quantified and normalized to the endogenous housekeeping gene using ImageJ software. The levels of expression were calculated relative to the expression of the corresponding non-neoplastic tissue. COBRA1 expression was tested and correlated to other molecules that were reported to be deregulated in HCC and were thought to be linked to COBRA1. These molecules were NANOG which is a marker for cell stemness; β-CATENIN a key player in the Wnt signaling pathway. We found that the transcript levels of COBRA1 were elevated in the entire cohort of the untreated cancer specimens when compared to the corresponding non-neoplastic tissues. The protein level of COBRA1 on the other hand, was elevated in only 6 untreated HCC specimens. The protein expressed by the NANOG and β-CATENIN was found to be up-regulated simultaneously with the COBRA1 in four samples. Unlike the untreated samples, treated cancer specimens displayed a decreased expression of COBRA1, NANOG and β-CATENIN. Our results propose COBRA1 as a novel oncogene in HCCs that may be used as a prognostic marker.


Biotechnology Program

Degree Name

MS in Biotechnology

Graduation Date

Fall 1-10-2013

Submission Date


First Advisor

Amleh, Asma

Committee Member 1

Zada, Suher

Committee Member 2

Moustafa, Mona


72 p.

Document Type

Master's Thesis

Library of Congress Subject Heading 1

Liver -- Cancer -- Egypt.


The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. The author has granted the American University in Cairo or its agents a non-exclusive license to archive this thesis, dissertation, paper, or record of study, and to make it accessible, in whole or in part, in all forms of media, now or hereafter known.

Institutional Review Board (IRB) Approval

Approval has been obtained for this item


AUC for funding, Al-Alfi foundation for sponsoring my studies. Dr. Asma Amleh for her continuous guidance, help, and support and for her time and effort throughout the whole thesis. My extended regards and appreciation to Dr. Mahmoud el Meteini for providing the samples, bearing my presence in the O.R and his willingness to explain things during the operation. I would like to sincerely thank all his surgical team especially Dr. Mohammed Radi, Dr. Hany Saeed, Dr. Mohammed Bahaa, and Dr. Mostafa Shereif for their extreme help in providing the operations' schedule, the patients' data and explaining patients' conditions when possible. This work would have never been done without your help. I am extremely thanking Dr. Mohamed Fathy for providing one of the examined samples, Dr. Alaa Fayez for getting me in contact with Dr. el Meteini. I deeply recognize Mona Allouba for working on the project and her help with the results as well as Alaa Ahmed for her work on the project. I would also like to thank all our research team for brain storming, trouble shooting, new ideas and encouragements; I learnt a lot because of you. The biotechnology program directors Dr. Rania Siam and Dr. Ahmed Mostafa. My Appreciation to Alyaa Mahmoud for helping with the data analysis. Eman Rabie and Aya Youssef for critically reviewing the manuscript. My deep greetings and acknowledgments to my dear friends, colleagues and company who made the 3 years of the masters a very good experience to live; Mai Yosry, Laila Ziko, Nourhan Mofeed, Nahla Hussien and all my class and lab mates. Words are never enough to thank you. Finally, my life time company Nada Rashad and Dina Osama for helping in reviewing the manuscript and for the emotional support.

Available for download on Tuesday, February 02, 9999