Inducible degradation of lncRNA Sros1 promotes IFN-γ-mediated activation of innate immune responses by stabilizing Stat1 mRNA
Authors: Xiaoqing Xu
Zhongyang Shen
Yong Zhao
Yang Liu
Henan Xu
Bo Huang
Yan Jiang
Xuetao Cao
Xiaoping Su
Yuanwu Ma
Journal: Nature Immunology (2019)
Discipline: IMMUNOLOGY
Keywords: Interferon-γ; noncoding RNAs; RNA-binding proteins; macrophages; microRNA
Affiliations: Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China., National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai, China., Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China., Fuwai Central China Cardiovascular Hospital, Chinese Academy of Medical Sciences, Zhengzhou, China., Tianjin First Center Hospital, Tianjin, China., Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China. ., National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai, China. ., College of Life Sciences, Nankai University, Tianjin, China. .

Abstract:  Interferon-γ (IFN-γ) is essential for the innate immune response to intracellular bacteria. Noncoding RNAs and RNA-binding proteins (RBPs) need to be further considered in studies of regulation of the IFN-γ-activated signaling pathway in macrophages. In the present study, we found that the microRNA miR-1 promoted IFN-γ-mediated clearance of Listeria monocytogenes in macrophages by indirectly stabilizing the Stat1 messenger RNA through the degradation of the cytoplasmic long noncoding RNA Sros1. Inducible degradation or genetic loss of Sros1 led to enhanced IFN-γ-dependent activation of the innate immune response. Mechanistically, Sros1 blocked the binding of Stat1 mRNA to the RBP CAPRIN1, which stabilized the Stat1 mRNA and, consequently, promoted IFN-γ-STAT1-mediated innate immunity. These observations shed light on the complex RNA-RNA regulatory networks involved in cytokine-initiated innate responses in host-pathogen interactions. 

Retracted: No

PubPeer comments:
 Fig. 1: e and g, Fig. 6:e The same gel with different exposure time or different contrast. The phosphorylated protein runs faster? ![file] ![file] ![file] , 
 One more from Supplementary Figures: ![file] , 
 ![file] ![file] The area marked here appears to be more similar than expected...Supplementary Figure 2c,2a , 
 #1 Please note that the Supplementary Info provides larger uncropped blot images. They clearly disprove your claims for Figures 1e and 6e, because the background bands are obviously different in the JAK2 vs. p-JAK2 blots. For Fig 1g, the differences are less clear, but because JAK2 and p-JAK2 blots are expected to look similar, I see no objective reason to think they are anything other than what is claimed. It is clear the blots were cut into thin strips, so there is much opportunity for the appearance of features that might be unique to one of the two blots Clips from the Supplement are pasted below. **Fig 1e:** ![file] **Fig 1g (mis-labelled Fig 1f in the Supplement):** ![file] **Fig 6e:** ![file] **Adjusted-levels version of Fig 1g:** ![file] , 
 Fig 1g. Look at the background carefully. ![file] , 
 If they probe phosho-antibodies first, then stripping and adding the total antibody, it is still OK. But the flow and H E images are too similar for different treatment. , 
 #3 Fig 2C : ![file] , 
 #6 Anybody doing scientific research knows the exactly same results mean that the stripping did not work. The second time probe still shows the first time signal. Also, all phospho-forms run faster than corresponding plain proteinsu2014they lack basic science sense. , 
 ![file] changed as green and red, and then merge, you can see the most of yellow dot colocalized. , 
 #7 ![file] These two look different to me , 
 #10 As different similar as successive sections, perhaps? , 
 #10 They are probably adjacent sections from the same lung. , 
 #4 Looks like stripping and re-probing, especially for 1e 1g as the shape of membrane (and background) is highly similar. Although stripping would be a routine procedure but it should be assured the previous antibody is totally removed, other wise it will interfere with chemiluminescence in second blot. That may be the reason why blots of total protein and phoshoprotein have similar bands. Some protocols will suggest doing an exposure after stripping to make sure the previous antibody has been removed. , 
 #8 Actually you are wrong. It depends the antibody. Some antibodies are easily to be stripped off completely. I am not sure what the case of p-JAK2 is. , 
 #13 If you do an exposure after stripping it will only tell you whether the secondary antibody is removed. There is no way to tell whether the primary antibody was removed by stripping. Seriously, stripping fraught with dangers like this, and I do not recommend it. , 
 The journal has posted an editor s note regarding some of these questionable pics: https: www.nature.com articles s41590-019-0542-7  Change history 22 November 2019Editoru2019s Note: It has been reported that there are errors in Supplementary Figures 2a and c. In Supplementary Figure 2a, the F4 80 v CD11b plot from miR-1- - mice was inadvertently replaced with a duplicate of the corresponding miR-1+ + plot. In Supplementary Figure 2c, an image of PBS-treated miR-1- - mouse lung was inadvertently replaced with an image of the corresponding PBS-treated miR-1+ + mouse lung. These errors were reported by the authors shortly before publication of the Article. However, it was unfortunately not possible to correct the issue before publication. We are now working with the authors to check the remaining figures. ,