Your idea is correct. There is a strong relation between autophagy and ER stress. See 

Salazar M, Carracedo A, Salanueva ÍJ, Hernández-Tiedra S, Lorente M, Egia A, Vázquez P, Blázquez C, Torres S, García S, Nowak J. Cannabinoid action induces autophagy-mediated cell death through stimulation of ER stress in human glioma cells. The Journal of clinical investigation. 2009 May 1;119(5):1359.

and

Qin L, Wang Z, Tao L, Wang Y. ER stress negatively regulates AKT/TSC/mTOR pathway to enhance autophagy. Autophagy. 2010 Feb 16;6(2):239-47.

I think that the issue has been already proved.

An interesting experiment would be to test the drug concomitantly blocking autophagy with cloroquine or hydroxycloroquine.

Best regards.

Hi, Tomas, thank you for providing these two papers. I read them briefly and found out they were talking about autophagy can contribute to the ERS-mediated apoptosis. However, in my situation, the autophagy was inhibited( or like I said in question, the related protein was decreased) while the ERS occured.

It seems that in your case, the drug you are using stimulates akt-mtor pathway instead of reducing its activity. This is unusual. Can you tell me the substance you are experimenting with?

Dear Zheng,

Have you done apoptosis?

-ER stress can activate apoptosis through UPR and CHOP, and this may result in autophagy inhibition. Apoptosis experiments can help you to prove that.

Best regards

Dear Utaipan,

Yes I've tried apoptosis assay. It did happen. Then there's another question, since the ER stress induce autophagy, but apoptosis suppress the autophagy, does it make sense they are happening at the same time?

You can see the following papers: 

Tyson, John J., et al. "Dynamic modeling of estrogen signaling and cell fate in breast cancer cells." Nature reviews. Cancer 11.7 (2011): 523.

Tavassoly, I., et al. "Dynamic modeling of the interaction between autophagy and apoptosis in mammalian cells." CPT: pharmacometrics & systems pharmacology 4.4 (2015): 263-272.

The interaction among ER stress , Autophagy and Apoptosis has a dynamics. If apoptosis is induced, it can reduce autophagy. 

See the paper

Parmar et al. "Modelling the effect of GRP78 on anti-oestrogen sensitivity and resistance in breast cancer" interface Focus. 2013 Aug 6; 3(4): 20130012.

We had a similar experimental conundrum to explain through a mathematical model. In the resistant breast cancer cells, the drug ICI, and also ICI+(GRP78 knockdown) induced UPR but not autophagy. The mdoel worked when we considered that the activated mTOR inhibits autophagy.

Did you look at mTOR activation?

Believe your own data. Open your mind, and use those existing theories of ER stress, autophagy and apoptosis as references to explore your own view. They are not final, and you could be the one to modify them to the truth. Natural products (NPs), if not purified compounds, could contain many different ingredients, which would provoke a gemisch of reactions, including ER stress and autophagy. Your NPs clearly inhibited synthesis of some autophagy-related proteins and processing of LC-I to LC-II. While you're examining the "ER stress," it is essential to be certain whether the stress was caused by protein or lipid factors. They are different, in particular one of the important components of LC-II, phosphotidylethanolamine, which was converted from phosphotidylserine in mitochondria. Traffiking of these molecules becomes fascinating, especially when cells were challenged with exogenous chemicals that would interrupt transport of important molecules to maintain routine cellular function, and they suggested that autophagy, from my own point of view, is a combined biological phenomenum of cell struggling to survival; it is not a mechnical switch to death.  

autophagy and apoptosis are so close in ER-stress context but there are several pathways for each of them, and it completely depends on the period of constant stimuli;

24-48 h; Grp78 and xbp1 upregulate (in this stage procedure is reversible)

72-168 h; atf4, chop up-regulate

BEst,