TGF-β signaling regulates neuronal C1q expression and developmental synaptic refinement
Authors: Beth Stevens
Allison R Bialas
Journal: Nature Neuroscience (2013)
Discipline: NEUROSCIENCE & BEHAVIOR
Keywords: Immune molecules; complement proteins; synaptic refinement; plasticity; C1q
Affiliations: 1] Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [2] Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, USA.

Abstract:  Immune molecules, including complement proteins C1q and C3, have emerged as critical mediators of synaptic refinement and plasticity. Complement localizes to synapses and refines the developing visual system through C3-dependent microglial phagocytosis of synapses. Retinal ganglion cells (RGCs) express C1q, the initiating protein of the classical complement cascade, during retinogeniculate refinement; however, the signals controlling C1q expression and function remain elusive. Previous work implicated an astrocyte-derived factor in regulating neuronal C1q expression. Here we identify retinal transforming growth factor (TGF)-β as a key regulator of neuronal C1q expression and synaptic pruning in the developing visual system. Mice lacking TGF-β receptor II (TGFβRII) in retinal neurons had reduced C1q expression in RGCs and reduced synaptic localization of complement, and phenocopied refinement defects observed in complement-deficient mice, including reduced eye-specific segregation and microglial engulfment of RGC inputs. These data implicate TGF-β in regulating neuronal C1q expression to initiate complement- and microglia-mediated synaptic pruning. 

Retracted: Yes

PubPeer comments:
 This paper contains a series of duplicated values in the raw data tables. Most include the repetition of several decimal numbers. Could authors check these concerns please? Related to Figure 7B: ![file] Figure 1B: The repetition of values is highly unexpected ![file] Figure 2E: ![file] Related to Figure 3C: Exp1 and Exp3 same values obtained ![file] Figure 4D: Pattern more similar than expected ![file] Figure 6D: mouse 1 and mouse 6 ![file] , 
 The more you look the more you find. Looks troubling. Figure 1A. The bar graph for the u201cMDu201d sample does not match the source data provided. Figure 1B. None of the time points match the source data provided. Additionally, the figure legend states N=4 but there are 6 replicates in the source data. Figure 1C. The source data used to generate these graphs is not provided. Figure 1D. The C1qA blot has a slight clockwise tilt while the controls do not. There is a small dot in the top left corner of the blot presented in the figure thatu2019s absent from the whole blot. In fact, this blot looks more like the TGFBRII blot. Figure 1F. The figure legend states n=3 but 5 experimental replicates are provided in the source data. Figure 2D. Number duplications in the source data. Figure 2E. Number duplications in the source data, mismatch between the decimal points between measurements, occasional whole numbers where all other measurements have 2-4 decimal places. Figure 2G. Number duplications in the source data. Figure 2i. The gel shown in the figure is not the one highlighted in the whole gels supplement. Rather it is the blot on the left side. Figure 2J. Number duplications in the source data. Occasional whole numbers where all other measurements have 2-4 decimal places. Figure 3C. Number duplications and odd whole numbers for controls. Figure 3E. This blot makes no sense. Looking at supplementary figure 6, there are one set of GAPDH controls (WT,KO) for 2 sets of TGFBRII samples. Moreover, it seems like the blot is probed with a single antibody. Figure 4B. Curious repetition of a whole u201c1u201d in three of the WT values. Figure 4D. Number duplications in the source data. Figure legend states N=4 but only 3 replicates are reported in the source data. Figure 4F. Figure legend states N=3 but only 4 data points are shown in the graph. Figure 5B. Number duplication in the source data. An unusual value of u201c1u201d repeated 3 times where all other values have many decimal places. Figure 5C. Same issue as above. Figure 5E. Figure legend states N=4 but data on only 3 mice provided in source data. Figure 6C. Likely number duplications in the source data. Values match to the third or fourth decimal place. Figure 6D. Number duplications in the source data. Figure 7B. Entire columns of data have been duplicated. Supplemental figure 1F. GAPDH blot is duplicated in Supplemental figure 2C. ![file] ![file] , 
 There seem to be more duplicated values in the data supporting the figures (please see images) and some inconsistencies in the text and the supporting data. Also in some figures, the numbers in the sheets don t seem to match the graphs in the figures. Could the authors please check these issues? Figure 1A. The bar graph for the u201cMDu201d sample does not match the source data provided. Figure 1B. The time points do not match the source data provided. Additionally, the figure legend states N=4 but there are 6 replicates in the source data. Figure 1C. The source data used to generate these graphs is not provided. Figure 1D. The C1qA blot has a slight clockwise tilt while the controls do not. There is a small dot in the top left corner of the blot presented in the figure thatu2019s absent from the whole blot. Figure 1F. The figure legend states n=3 but 5 experimental replicates are provided in the source data. Figure 2i. The gel shown in the figure is not the one highlighted in the whole gels supplement. Rather it is the blot on the left side. Figure 4D. Figure legend states N=4 but only 3 replicates are reported in the source data. Figure 4F. Figure legend states N=3 but only 4 data points are shown in the graph. Figure 5E. Figure legend states N=4 but data on only 3 mice provided in source data. Supplemental figure 1F. GAPDH blot is duplicated in Supplemental figure 2C. ![file] ![file] , 
 Thank you. We have been looking into these issues in depth and we have been in communication with the journal. We will follow up as soon as possible. , 
 Thank you. I admire the corresponding author for taking action so fast. Retraction Note: TGF-u03b2 signaling regulates neuronal C1q expression and developmental synaptic refinement Retraction of: Nature Neuroscience https: doi.org 10.1038 nn.3560, published online 27 October 2013. https: www.nature.com articles s41593-021-00877-7 The corresponding author contacted the journal with concerns regarding the integrity of the data related to this Article. In follow-up experiments, key aspects of the published results that showed evidence that retinal TGF-u03b2R2 signaling regulates neuronal C1q expression and developmental synaptic refinement could not be replicated. Most importantly, Figs. 6b and 7, from mice deficient in retinal TGF-u03b2 receptor 2 (Tgfbr2u2013 u2013), were found to contain errors and the results could not be replicated in recent independent follow-up analyses. Moreover, C1q mRNA or protein is not reproducibly upregulated following acute (6u201324 h) treatment of pure retinal ganglion cell (RGC) cultures with astrocyte-conditioned media (Fig 1b,e,f) or TGF-u03b2 (Fig 2e). Given these findings and other inaccuracies in the Article and Source Data we have since uncovered, the authors wish to retract it. We deeply regret these errors and apologize to our scientific colleagues. All the authors agree with the retraction. ,