20.109(F13): Mod 2 Day 6 Transfection of SH2 Domains

Introduction

Laser light path for Odyssey Licor Scanner. Image from Odyssey handbook.

Since you were last in lab, the teaching staff blocked your nitrocellulose membranes with Odyssey Blocking Buffer (OBB) -- a non-mammalian serum based buffer that is proprietary to Licor, Inc -- and then incubated the membrane with primary antibody at 4C on a shaker for approximately 16 hours.

Recall that the membranes were cut into various pieces so that we can evaluate a few components of the EGFR signaling pathway. As a reminder, show below is a diagram of how the membrane was cut, and below is a list of the antibodies that were used and their dilutions.

• All groups: tyrosine 1068 pY1068-EGFR & EGFR

Depending on what inhibitor you have chosen to evaluate on M2D6/7, you will either detect the phosphorylation of:

• PI3K pathway: pS473-Akt, total Akt, & GAPDH
• STAT3 pathway: pY705-STAT3, total STAT3, & GAPDH
• Erk pathway: pT202/pY204-Erk & total Erk

Today we will use infrared (IR) secondary antibodies and scan the Western blots using a specially constructed microscope located in the Lauffenburger lab to determine the phosphorylation of EGFR in response to your experimental conditions last time.

The following antibodies were used for all blots:

• anti-GAPDH, raised in rabbit at 1:10,000
• anti-EGFR, raised in goat at 1:2000

Depending on your choice:

• anti-pY1068-EGFR, raised in rabbit at 1:1000
• anti-pY992-EGFR, raised in rabbit at 1:1000
• anti-pY1173-EGFR, raised in rabbit at 1:1000
  

Part 2.1: Day Two of Western Blot Analysis -- Secondary Antibody

Now we will wash off the primary antibody and then continue with the blot analysis:

1. Using a 500 mL glass bottle and the 10x TBS stock on the front bench, make a 500 mL 1x TBS stock using DI water from the lab sink.
2. Now add enough Tween 20 to make a 0.1% solution (TBS-T). Tween-20 is located on the front bench. Shake the bottle well to mix.
3. Obtain your blots from the front bench. Pour off the antibody solutions into the sink and add enough TBS-T to cover your membranes -- between 10-15 mL should work, but you don't need to measure this out. Keep in mind that the washing steps work by dilution, so it is a balance between adding enough to create a sink for the primary antibody, but not so much that you make a huge mess on the shaker!
4. Shake your container for 10 min.
5. Repeat for a total of 3 washes. Note: the time and number of washes was determined previously and can depend on your primary antibody!
6. During your washes, dilute the secondary antibodies in 10 mL of OBB. They are light sensitive so find them on the front bench and then wrap your 15 mL conical in aluminum foil.
   • For GAPDH (Rabbit) -- use the anti-Rabbit IR800 antibody at 1:15,000
   • For EGFR (Goat) / p-EGFR (Rabbit) -- use the anti-Goat IR680 at 1:10,000 and anti-Rabbit IR800 at 1:10,000
   • Why can we mix these antibodies?
7. After the last wash, add your secondary antibody and place it on the dark shaker for 45 min.
8. Pour off the secondary antibody and wash the membranes 3x, 7 min in TBS-T
9. After the last wash, rinse the membranes 1x with 25 mL PBS. Pour off the PBS and keep in another 25mL of PBS until you can scan the membrane.

Part 2.2: Imaging the Western Blot

Sample placement for Western blot on Odyssey scanner. Image from Odyssey handbook

The Licor Odyssey scanner is a solid-state laser scanning microscope that concurrently images two wavelengths (700 and 800 nm), allowing for simultaneous detection of two (or more -- how?) antibodies.

The Odyssey scanner is located in the Lauffenburger lab in room 56-378. In groups of two you will go with a member of the teaching staff to scan your blots. The scanner has a variety of settings that control the resolution of the final image and the amount of light that is collected by the microscope objective. You will learn about those settings at the microscope. Be sure to note them in your lab notebook so that you may include them in your Methods section.

Scanning your Western blot is only the first step! You just did a lot of work to obtain what appears to be observational data. However, we can use densitometry to quantify the change in EGFR phosphorylation. Therefore, once you obtain your Western blot images -- which will be .tif files -- use ImageJ (a freeware for biological imaging from the NIH) to perform a densitometric analysis on your bands. A tutorial from NAVBO is attached here for instructions on performing densitometry. You will use this analysis in the FNT assignment for next time and it will help you to limber up your mind for the BRET analysis on M2D7.

For Next Time

1. Perform a densiometric analysis using your Western blot data and determine the EC50 for your growth factor in regards to EGFR phosphorylation. Remember to control for potential loading differences between wells in your gel and any variation in total EGFR expression. Hint: See your lecture notes and remember to scale your data from 0 to 1.

Notes for Teaching Faculty

TA notes, mod 2