GBE 308 | Course Introduction and Application Information - Department of Genetics and Bioengineering

Course Name

Cancer Biology and Genetics

Code	Semester	Theory (hour/week)	Application/Lab (hour/week)	Local Credits	ECTS
GBE 308	Spring	2	2	3	5

Prerequisites

GBE 100 To succeed (To get a grade of at least DD)

Course Language

English

Course Type

Required

Course Level

First Cycle

Mode of Delivery

face to face

Teaching Methods and Techniques of the Course

Discussion
Group Work
Problem Solving
Case Study
Q&A
Application: Experiment / Laboratory / Workshop
Lecture / Presentation

National Occupation Classification

-

Course Coordinator

Dr. Öğr. Üyesi Cihangir Yandım

Course Lecturer(s)

Dr. Öğr. Üyesi Cihangir Yandım

Assistant(s)

-

Course Objectives

The main purpose of this course is to explain the molecular behavior of the cell in the context of different real scenarios, to teach the basic mechanisms that lead to cancer and the logic of treatment strategies targeting them. After evaluating the multi-step formation process of cancer within the scope of different cellular mechanisms and their complex relationships, it is aimed to investigate and solve cancer-related problems with experimental designs, accompanied by literature review, and to interpret the results within possible cases.

Learning Outcomes

#	Content	PC Sub	* Contribution Level
#	Content	PC Sub	1	2	3	4	5
1	Will be able to describe the stages of cancer formation,
2	Will be able to detect disorders related to the complex relationships between cell cycle, DNA damage, cell death, autophagy, cellular aging and signal pathway mechanisms,
3	Will be able to design basic experiments to solve cancer related problems,
4	Will be able to interpret the results of molecular cancer findings,
5	Will be able to discuss the treatment methods in the field of cancer from different perspectives by explaining them from a molecular perspective,
6	Will be able to design a project involving molecular Genetics and Bioengineering methods in the field of cancer.

Course Description

This course explains the relationship of cellular mechanisms learned in other Genetics and Bioengineering courses with cancer and presents complex problems related to cancer. It reveals the general formation process of cancer, changes in tumor suppressor and oncogenes, their effects on the cell cycle, and the relationship between cell death, autophagy and cellular senescence. It also covers DNA damage and its molecular repair, its importance in therapeutic approaches, complex relationships between signaling pathways, tumor evolution and genomic perturbations, cancer metabolism, angiogenesis, metastasis, cancer stem cells and epigenetics, and basic cancer immunology.

Course Category	Core Courses	X
	Major Area Courses
	Supportive Courses
	Media and Management Skills Courses
	Transferable Skill Courses

Week	Subjects	Related Preparation	Learning Outcome
1	Introduction to cancer	Chapter 2. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199. Hanahan, Douglas, and Robert A. Weinberg. "The hallmarks of cancer." Cell 100.1 (2000): 57-70. Hanahan, Douglas, and Robert A. Weinberg. "Hallmarks of cancer: the next generation." Cell 144.5 (2011): 646-674.
2	Cell cycle mechanisms	Chapter 11. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199
3	Cell cycle mechanisms	Chapter 8. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199.
4	Cellular Oncogenes	Chapter 8. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199.
5	Cell death and autophagy	Chapter 9. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199. Elmore, Susan. "Apoptosis: a review of programmed cell death." Toxicologic pathology 35.4 (2007): 495-516. Glick, Danielle, Sandra Barth, and Kay F. Macleod. "Autophagy: cellular and molecular mechanisms." The Journal of pathology 221.1 (2010): 3-12. Nikoletopoulou, Vassiliki, et al. "Crosstalk between apoptosis, necrosis and autophagy." Biochimica et Biophysica Acta (BBA)-Molecular Cell Research 1833.12 (2013): 3448-3459. Ichim, Gabriel, and Stephen WG Tait. "A fate worse than death: apoptosis as an oncogenic process." Nature Reviews Cancer 16.8 (2016): 539-548.
6	Cell death and autophagy	Chapter 9. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199. Elmore, Susan. "Apoptosis: a review of programmed cell death." Toxicologic pathology 35.4 (2007): 495-516. Glick, Danielle, Sandra Barth, and Kay F. Macleod. "Autophagy: cellular and molecular mechanisms." The Journal of pathology 221.1 (2010): 3-12. Nikoletopoulou, Vassiliki, et al. "Crosstalk between apoptosis, necrosis and autophagy." Biochimica et Biophysica Acta (BBA)-Molecular Cell Research 1833.12 (2013): 3448-3459. Ichim, Gabriel, and Stephen WG Tait. "A fate worse than death: apoptosis as an oncogenic process." Nature Reviews Cancer 16.8 (2016): 539-548.
7	DNA damage repeair and chemotherapy	Chapter 12 & Chapter 16. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199. Basu, Ashis K. "DNA damage, mutagenesis and cancer." International journal of molecular sciences 19.4 (2018): 970. Curtin, Nicola J. "DNA repair dysregulation from cancer driver to therapeutic target." Nature Reviews Cancer 12.12 (2012): 801-817. Roos, Wynand P., Adam D. Thomas, and Bernd Kaina. "DNA damage and the balance between survival and death in cancer biology." Nature Reviews Cancer 16.1 (2016): 20-33. Helleday, Thomas, et al. "DNA repair pathways as targets for cancer therapy." Nature Reviews Cancer 8.3 (2008): 193-204.
8	Midterm	-
9	Cellular senescence and cancer	Chapter 10. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199. Campisi, Judith. "Aging, cellular senescence, and cancer." Annual review of physiology 75 (2013): 685-705. Herranz, Nicolás, and Jesús Gil. "Mechanisms and functions of cellular senescence." The Journal of clinical investigation 128.4 (2018): 1238-1246.
10	Signal transduction and cancer research design	Chapter 5 & 6. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199. Lemmon, Mark A., and Joseph Schlessinger. "Cell signaling by receptor tyrosine kinases." Cell 141.7 (2010): 1117-1134. Manning, Brendan D., and Alex Toker. "AKT/PKB signaling: navigating the network." Cell 169.3 (2017): 381-405. Han, Fei, et al. "The critical role of AMPK in driving Akt activation under stress, tumorigenesis and drug resistance." Nature communications 9.1 (2018): 1-16.
11	Genomic instability and resistance in cancer	Negrini, Simona, Vassilis G. Gorgoulis, and Thanos D. Halazonetis. "Genomic instability—an evolving hallmark of cancer." Nature reviews Molecular cell biology 11.3 (2010): 220-228. Holohan, Caitriona, et al. "Cancer drug resistance: an evolving paradigm." Nature Reviews Cancer 13.10 (2013): 714-726.
12	Cancer metabolism, hypoxia and angiogenesis	Chapter 13. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199. Vazquez, Alexei, et al. "Cancer metabolism at a glance." Journal of cell science 129.18 (2016): 3367-3373. Muz, Barbara, et al. "The role of hypoxia in cancer progression, angiogenesis, metastasis, and resistance to therapy." Hypoxia 3 (2015): 83. Weis, Sara M., and David A. Cheresh. "Tumor angiogenesis: molecular pathways and therapeutic targets." Nature medicine 17.11 (2011): 1359-1370.
13	Tumour evolution and epigenetics	Chapter 11. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199. Dawson, Mark A., and Tony Kouzarides. "Cancer epigenetics: from mechanism to therapy." cell 150.1 (2012): 12-27. Nassar, Dany, and Cédric Blanpain. "Cancer stem cells: basic concepts and therapeutic implications." Annual Review of Pathology: Mechanisms of Disease 11 (2016): 47-76. McGranahan, Nicholas, and Charles Swanton. "Clonal heterogeneity and tumor evolution: past, present, and the future." Cell 168.4 (2017): 613-628. Ciriello, Giovanni, et al. "Emerging landscape of oncogenic signatures across human cancers." Nature genetics 45.10 (2013): 1127-1133.
14	Metastasis, immune response and immunotherapy of cancer	Chapter 14. Weinberg, R.A. The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199. Riggi, Nicolo, Michel Aguet, and Ivan Stamenkovic. "Cancer metastasis: a reappraisal of its underlying mechanisms and their relevance to treatment." Annual Review of Pathology: Mechanisms of Disease 13 (2018): 117-140. Galluzzi, Lorenzo, et al. "Immunogenic cell death in cancer and infectious disease." Nature Reviews Immunology 17.2 (2017): 97-111.
15	Semester Review
16	Final exam

Course Notes/Textbooks

The Biology of Cancer (2nd ed.). W.W. Norton & Company (2013) ISBN: 9780815342199.

Suggested Readings/Materials

Hanahan, Douglas, and Robert A. Weinberg. "The hallmarks of cancer." cell 100.1 (2000): 57-70.
Hanahan, Douglas, and Robert A. Weinberg. "Hallmarks of cancer: the next generation." cell 144.5 (2011): 646-674.
Elmore, Susan. "Apoptosis: a review of programmed cell death." Toxicologic pathology 35.4 (2007): 495-516.
Glick, Danielle, Sandra Barth, and Kay F. Macleod. "Autophagy: cellular and molecular mechanisms." The Journal of pathology 221.1 (2010): 3-12.
Nikoletopoulou, Vassiliki, et al. "Crosstalk between apoptosis, necrosis and autophagy." Biochimica et Biophysica Acta (BBA)-Molecular Cell Research 1833.12 (2013): 3448-3459.
Ichim, Gabriel, and Stephen WG Tait. "A fate worse than death: apoptosis as an oncogenic process." Nature Reviews Cancer 16.8 (2016): 539-548.
Elmore, Susan. "Apoptosis: a review of programmed cell death." Toxicologic pathology 35.4 (2007): 495-516.
Glick, Danielle, Sandra Barth, and Kay F. Macleod. "Autophagy: cellular and molecular mechanisms." The Journal of pathology 221.1 (2010): 3-12.
Nikoletopoulou, Vassiliki, et al. "Crosstalk between apoptosis, necrosis and autophagy." Biochimica et Biophysica Acta (BBA)-Molecular Cell Research 1833.12 (2013): 3448-3459.
Ichim, Gabriel, and Stephen WG Tait. "A fate worse than death: apoptosis as an oncogenic process." Nature Reviews Cancer 16.8 (2016): 539-548.
Basu, Ashis K. "DNA damage, mutagenesis and cancer." International journal of molecular sciences 19.4 (2018): 970.
Curtin, Nicola J. "DNA repair dysregulation from cancer driver to therapeutic target." Nature Reviews Cancer 12.12 (2012): 801-817.
Roos, Wynand P., Adam D. Thomas, and Bernd Kaina. "DNA damage and the balance between survival and death in cancer biology." Nature Reviews Cancer 16.1 (2016): 20-33.
Helleday, Thomas, et al. "DNA repair pathways as targets for cancer therapy." Nature Reviews Cancer 8.3 (2008): 193-204.
Campisi, Judith. "Aging, cellular senescence, and cancer." Annual review of physiology 75 (2013): 685-705.
Herranz, Nicolás, and Jesús Gil. "Mechanisms and functions of cellular senescence." The Journal of clinical investigation 128.4 (2018): 1238-1246.
Lemmon, Mark A., and Joseph Schlessinger. "Cell signaling by receptor tyrosine kinases." Cell 141.7 (2010): 1117-1134.
Manning, Brendan D., and Alex Toker. "AKT/PKB signaling: navigating the network." Cell 169.3 (2017): 381-405.
Han, Fei, et al. "The critical role of AMPK in driving Akt activation under stress, tumorigenesis and drug resistance." Nature communications 9.1 (2018): 1-16.
Negrini, Simona, Vassilis G. Gorgoulis, and Thanos D. Halazonetis. "Genomic instability—an evolving hallmark of cancer." Nature reviews Molecular cell biology 11.3 (2010): 220-228.
Holohan, Caitriona, et al. "Cancer drug resistance: an evolving paradigm." Nature Reviews Cancer 13.10 (2013): 714-726.
Vazquez, Alexei, et al. "Cancer metabolism at a glance." Journal of cell science 129.18 (2016): 3367-3373.
Muz, Barbara, et al. "The role of hypoxia in cancer progression, angiogenesis, metastasis, and resistance to therapy." Hypoxia 3 (2015): 83.
Weis, Sara M., and David A. Cheresh. "Tumor angiogenesis: molecular pathways and therapeutic targets." Nature medicine 17.11 (2011): 1359-1370.
Dawson, Mark A., and Tony Kouzarides. "Cancer epigenetics: from mechanism to therapy." cell 150.1 (2012): 12-27.
Nassar, Dany, and Cédric Blanpain. "Cancer stem cells: basic concepts and therapeutic implications." Annual Review of Pathology: Mechanisms of Disease 11 (2016): 47-76.
McGranahan, Nicholas, and Charles Swanton. "Clonal heterogeneity and tumor evolution: past, present, and the future." Cell 168.4 (2017): 613-628.
Ciriello, Giovanni, et al. "Emerging landscape of oncogenic signatures across human cancers." Nature genetics 45.10 (2013): 1127-1133.
Riggi, Nicolo, Michel Aguet, and Ivan Stamenkovic. "Cancer metastasis: a reappraisal of its underlying mechanisms and their relevance to treatment." Annual Review of Pathology: Mechanisms of Disease 13 (2018): 117-140.
Galluzzi, Lorenzo, et al. "Immunogenic cell death in cancer and infectious disease." Nature Reviews Imm

Semester Activities	Number	Weighting	LO 1	LO 2	LO 3	LO 4	LO 5	LO 6
Participation
Laboratory / Application
Field Work
Quizzes / Studio Critiques
Portfolio
Homework / Assignments
Presentation / Jury
Project	1	35
Seminar / Workshop
Oral Exams
Midterm	1	30
Final Exam	1	35
Total

Weighting of Semester Activities on the Final Grade	2	65
Weighting of End-of-Semester Activities on the Final Grade	1	35
Total

Semester Activities	Number	Duration (Hours)	Workload
Theoretical Course Hours (Including exam week: 16 x total hours)	16	2	32
Laboratory / Application Hours (Including exam week: '.16.' x total hours)	16	2	32
Study Hours Out of Class	14	1	14
Field Work			0
Quizzes / Studio Critiques			0
Portfolio			0
Homework / Assignments			0
Presentation / Jury			0
Project	1	37	37
Seminar / Workshop			0
Oral Exam			0
Midterms	1	15	15
Final Exam	1	20	20
		Total	150

#	PC Sub	Program Competencies/Outcomes	* Contribution Level
#	PC Sub	Program Competencies/Outcomes	1	2	3	4	5
1	To have adequate knowledge in Mathematics, Science and Genetics and Bioengineering; to be able to use theoretical and applied information in these areas on complex engineering problems.		-	-	-	-	-
2	To be able to identify, define, formulate, and solve complex Genetics and Bioengineering problems; to be able to select and apply proper analysis and modeling methods for this purpose.		-	X	-	-	-
3	To be able to design a complex system, process, device or product under realistic constraints and conditions, in such a way as to meet the requirements; to be able to apply modern design methods for this purpose.		-	-	-	-	-
4	To be able to devise, select, and use modern techniques and tools needed for analysis and solution of complex problems in Genetics and Bioengineering applications; to be able to use information technologies effectively.		-	-	-	-	-
5	To be able to design and conduct experiments, gather data, analyze and interpret results for investigating complex engineering problems or Genetics and Bioengineering research topics.		-	-	-	X	-
6	To be able to work efficiently in Genetics and Bioengineering disciplinary and multi-disciplinary teams; to be able to work individually.		-	-	-	X	-
7	To be able to communicate effectively in Turkish, both orally and in writing; to be able to author and comprehend written reports, to be able to prepare design and implementation reports, to present effectively, to be able to give and receive clear and comprehensible instructions.		-	-	-	-	-
8	To have knowledge about global and social impact of Genetics and Bioengineering practices on health, environment, and safety; to have knowledge about contemporary issues as they pertain to engineering; to be aware of the legal ramifications of Genetics and Bioengineering solutions.		-	-	-	-	-
9	To be aware of ethical behavior, professional and ethical responsibility; to have knowledge about standards utilized in Genetics and Bioengineering applications.		-	-	-	-	-
10	To have knowledge about industrial practices such as project management, risk management, and change management; to have awareness of entrepreneurship and innovation; to have knowledge about sustainable development.		-	-	-	-	-
11	To be able to collect data in the area of Genetics and Bioengineering, and to be able to communicate with colleagues in a foreign language.		-	-	-	-	-
12	To be able to speak a second foreign language at a medium level of fluency efficiently.		-	-	-	-	-
13	To recognize the need for lifelong learning; to be able to access information, to be able to stay current with developments in science and technology; to be able to relate the knowledge accumulated throughout the human history to Genetics and Bioengineering.		-	-	-	-	-