1. How to present a scientific paper Dr. Rebecca B. Riggins Department of Oncology, Georgetown University rbr7@georgetown.edu

2. Outline Preliminary thoughts on the assigned reading Typical structure of a scientific paper –Differences dictated by journal in which it is published Discussion of Zhao et al., with comparisons to Schafer et al. Final thoughts on the assigned reading

3. Today’s readings

4. ‘A scientific paper is like an hourglass’ Introduction (Materials and Methods) Results Discussion Abstract = mini hourglass

5. ‘The width of the hourglass is inversely proportional to importance’ RESULTS and the HYPOTHESIS/RATI ONALE are key when it comes to presenting a scientific paper The Introduction is useful for background The Discussion is a useful summary Introduction (Materials and Methods) Results Discussion

6. Zhao et al.: ErbB2, glycolysis, and breast cancer growth Key words in the title will be better described in the Introduction section This should guide you in preparing 3 or 4 slides to introduce the paper and why the study is important…

7. Cancer cell metabolism Normal cells and cancer cells differ in how they derive energy from glucose Normal: aerobic Cancer: anaerobic Cancer cell glycolysis dependence = Warburg effect Explain this graphically using simple images O 2 +glucose  glycolysis  oxidative phosphorylation  38 ATP glucose  glycolysis only  2 ATP

8. Please DON’T do this

9. A simple diagram of glycolysis vs. oxidative phosphorylation http://www.nutritionaloncology.org/images/aerobicGlycolysis.jpg Multiple molecules and pathways can regulate glycolysis Some of these include: Ras, PI3K, mTOR, Src These are all targets of the receptor tyrosine kinase ErbB2  Please cite your source!

10. The full ErbB family signaling pathway ErbB1ErbB1 ErbB1ErbB1 c-Fos El k1 c-Jun mTOR PDK1 HBEGF PLC-  PKC Nck Ras Raf MEK 1/2 ERKs p38 JNK PI3K p70S6K Akt/ PKB PAK CDC42 Anti-Apoptosis ErbB1ErbB1 ErbB2ErbB2 ErbB3ErbB3 ErbB4ErbB4 TGF  EGF Areg Btc Ereg Nrg 1,2 MKK 3/6 GRB2 SOS SHC Nrg 3,4 Translation Gene Expression ErbB3ErbB3 ErbB3ErbB3 GSK3  FKHR ErbB4ErbB4 ErbB4ErbB4 ErbB4ErbB4 ErbB4ErbB4 ErbB1ErbB1 ErbB4ErbB4 ErbB3ErbB3 ErbB2ErbB2 2009 ProteinLounge.com 2009 ProteinLounge.com C

11. Relevant ErbB family signaling ErbB1ErbB1 ErbB1ErbB1 c-Fos Elk1 c-Jun mTOR PDK1 HBEGF Ras Raf MEK 1/2 ERKs p38 JNK PI3K p70S6K Akt/ PKB PAK CDC42 Anti-Apoptosis ErbB1ErbB1 ErbB2ErbB2 TGF  EGF Areg Btc Ereg Nrg 1,2 MKK 3/6 GRB2 SOS SHC Translation Gene Expression GSK3  FKHR ErbB3ErbB3 ErbB2ErbB2 2009 ProteinLounge.com 2009 ProteinLounge.com C Ligands Receptors Intracellular signaling Translation

12. How might ErbB2 regulate glycolysis? Lactate dehydrogenase A (LDH-A) is a key glycolytic enzyme, and its expression is increased in mouse mammary epithelial cells that overexpress a form of ErbB2 Heat shock factor 1 (HSF1) is a transcription factor that regulates glucose metabolism which is itself regulated by Ras (a target of ErbB2) Does ErbB2 regulate glycolysis through these molecules?

13. Experimental results Select key figures that illustrate the important points –These are often positive, but if there is room for criticism please provide it Do NOT attempt to describe every panel of every figure

14. Overexpression of Erb2 promotes glycolysis in breast cancer cells  O2 consumption http://www.nutritionaloncology.org/images/aerobicGlycolysis.jpg

15. Overexpression of ErbB2 increases LDH-A and HSF1 …and knockdown of ErbB2 reduces LDH-A expression and glycolysis

16. Downregulation of HSF1 = reduced LDH-A and glycolysis  Use of Hsf1 -/- cells is a way to confirm siRNA results

17. Glycolysis inhibitors, ErbB2, and cancer http://www.nutritionaloncology.org/images/aerobicGlycolysis.jpg 2DG = glucose analog that cannot undergo glycolysis Oxamate = inhibitor of LDH, which converts pyruvate to lactate Oligomycin = inhibitor of oxidative phosphorylation Are ErbB2 overexpressing cells more sensitive to glycolysis inhibitors (and less sensitive to oxidative phosphorylation inhibitor)?

18. Overexpression of ErbB2 =  sensitivity to glycolysis inhibitors, and  sensitivity to oxidative phosphorylation inhibitors Glycolysis inhibitorOxidative phosphorylation inhibitor Similar results with 2DG in another cell line overexpressing ErbB2

19. Downregulation HSF1 inhibits ErbB2 effects on glycolysis and sensitivity to inhibitors  Again, use of Hsf1 -/- cells is a way to confirm siRNA results

20. Summary of Results ErbB1ErbB1 ErbB2ErbB2 Upregulation of HSF1 protein Increased LDH-A expression, enzyme activity ErbB1ErbB1 ErbB2ErbB2 ErbB1ErbB1 ErbB2ErbB2 Increased glycolysis Increased cell growth Glycolysis inhibitors ErBB2 siRNA HSF1 siRNA

21. Discussion section This is a summary of the major findings, and their importance for the field of study The first paragraph is the summary Subsequent paragraphs elaborate on the key findings and place them in context

22. Schafer et al.: metabolic defects due to cellular detachment Nature papers are ‘different’

23. Thank you for your attention! Questions? If you would like an electronic copy of this presentation, you can download it here: http://openwetware.org/wiki/Riggins_Lab Under Resources, click ‘Lectures’ Click ‘How to present a scientific paper’