Ornithine-A urea cycle metabolite enhances autophagy and controls Mycobacterium tuberculosis infection
Authors: Padmaja Paidipally
Abul K Azad
Ramakrishna Vankayalapati
Buka Samten
Rajesh Kumar Radhakrishnan
Sachin Mulik
Larry S Schlesinger
Ramya Sivangala Thandi
Deepak Tripathi
Journal: Nature Communications (2020)
Discipline: Multidisciplinary
Keywords: Macrophages; Mycobacterium tuberculosis; infection; disease progression; alveolar macrophages
Affiliations: Department of Pulmonary Immunology, Center for Biomedical Research, University of Texas Health Center, Tyler, TX, 75708, USA., Texas Biomedical Research Institute, San Antonio, TX, 78227, USA., Department of Pulmonary Immunology, Center for Biomedical Research, University of Texas Health Center, Tyler, TX, 75708, USA. .

Abstract:  Macrophages are professional phagocytes known to play a vital role in controlling Mycobacterium tuberculosis (Mtb) infection and disease progression. Here we compare Mtb growth in mouse alveolar (AMs), peritoneal (PMs), and liver (Kupffer cells; KCs) macrophages and in bone marrow-derived monocytes (BDMs). KCs restrict Mtb growth more efficiently than all other macrophages and monocytes despite equivalent infections through enhanced autophagy. A metabolomics comparison of Mtb-infected macrophages indicates that ornithine and imidazole are two top-scoring metabolites in Mtb-infected KCs and that acetylcholine is the top-scoring in Mtb-infected AMs. Ornithine, imidazole and atropine (acetylcholine inhibitor) inhibit Mtb growth in AMs. Ornithine enhances AMPK mediated autophagy whereas imidazole directly kills Mtb by reducing cytochrome P450 activity. Intranasal delivery of ornithine or imidazole or the two together restricts Mtb growth. Our study demonstrates that the metabolic differences between Mtb-infected AMs and KCs lead to differences in the restriction of Mtb growth. 

Retracted: No

PubPeer comments:
 Brought to my attention by a reader. Figure 3C. * Red boxes: GAPDH panels of lanes 1-2 appear identical to those of lanes 5-6. ![file] , 
 Figure 5F and 7E. * Green arrows: Lanes 9-10 of the GAPDH panel in Figure 5F look very similar to lanes 4-5 of the GAPDH panel in Figure 7E, if one of the two panels is rotated 180 degrees and stretched differently. Looking at the legends, they appear to be showing different experiments. ![file] Here is a close up, with applied rotation to show the similarities between the two panels. ![file] , 
 Figure 7D. * The 10x enlargement panels do not appear to match the 4x panels, and definitely not with the indicated box. * Blue boxes: The 10x Mtb H37Rv+Ornithine panel appears to overlap with the 10x Mtb H37Rv+Imidazole panel. ![file] , 
 * Pink boxes: Figure 6C and Figure 7G appear to be showing the same panel. ![file] Legend Figure 6C:  *The number of LC-3B puncta relative to the cell area (10 cells per condition) was quantified using ImageJ. p 0.0012.* Legend Figure 7G:  *The immunofluorescence intensity (A.U.) of LC-3B are shown. Data are representative of three independent experiments. Five mice per group were used for each independent experiment. p 0.0013. Statistical analysis was performed using paired two-tailed t test and data are represented as the mean u00b1 SD.* , 
 Might as well bring up the similarities between the AM and PM controls in Figure 2J, marked here in orange and aqua: ![file] , 
 Moving on to the supplemental, Figure S1. * Purple boxes: The 2nd panel in A (95% pure AMs) looks very similar to the first panel in D (94% pure BDMs), albeit rotated AND mirrored. Purple arrows show the orientation. * Orange and aqua boxes show similarities to panels in Figure 2J, but these might represent the same experiments. * Green box: the 3rd panel in C (90% pure KCs) appears to look similar to the KC + Mtb H37Rv panel in Figure 2J (shown above in comment #5). These do not appear to represent the same experiments. ![file] Here is a close up of panels A and D, rotated and mirrored, with some specific areas highlighted with boxes of the same color for comparison. Some dots appear disappear between panels A and D. This is not a simple duplication. ![file] , 
 I just noticed an additional problem in Figure 5F, so reposting the Figure 5F 7E comparison. * Lime green arrows: Lanes 9-10 of the GAPDH panel in Figure 5F look very similar to lanes 4-5 of the GAPDH panel in Figure 7E, if one of the two panels is rotated 180 degrees and stretched differently. Looking at the legends, they appear to be showing different experiments. * Moss boxes: In Figure 5F, LC-3A LC-3B panel: Lanes 1 2 look very similar to lanes 3 4. ![file] , 
 Supplementary Figure S5. * Some sets of measurements look very similar between different panels. Marked with brown and teal boxes. ![file] , 
 Supplementary Figure S10. Many sets of measurements look very similar across different panels. I invite you to compare the red, orange, moss green, purple, blue, pink, and dark red datapoints. Basically all of them. ![file] , 
 Spot the similarities in Figure S11A. ![file] , 
 Supplementary Figure S16 is supposed to show us the  uncropped gels . These are not uncropped gels. ![file] , 
 Thank you so much for letting me know. I will look at all data to proceed further. Thanks again. , 
 Dear dr. Vankayalapati - it has been a year without any update. Would you have something to share here, please? Did you contact the journal? ,