The lysosome-associated apoptosis-inducing protein containing the pleckstrin homology (PH) and FYVE domains (LAPF), representative of a novel family of PH and FYVE domain-containing proteins, induces caspase-independent apoptosis via the lysosomal-mitochondrial pathway
Authors: Yuzhen Wang
Wei Chen
Taoyong Chen
Lihuang Zhang
Weigang He
Nan Li
Changfei Li
Tao Wan
Yanmei Han
Xuetao Cao
Journal: Journal of Biological Chemistry (2005)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Lysosomes; LAPF; apoptosis; PH domain; FYVE domain
Affiliations: Institute of Immunology, Zhejiang University, 353 Yanan Road, Hangzhou 310031, Zhejiang, China.

Abstract:  Lysosomes have recently been identified as important apoptotic signal integrators in response to various stimuli. Here we report the functional characterization of LAPF, a novel lysosome-associated apoptosis-inducing protein containing PH and FYVE domains. LAPF is a representative of a new protein family, the Phafins (protein containing both PH and FYVE domains), which consists of 14 unidentified proteins from various species. Overexpression of LAPF in L929 cells induces apoptosis and also increases cell sensitivity to TNFalpha-induced apoptosis, concomitant with its translocation to lysosomes. Two mutants of LAPF, either lacking the PH or FYVE domain, failed to induce cell death and translocate to lysosomes, suggesting that both domains are required for its apoptosis-inducing activity and relocation. We demonstrate that LAPF may induce apoptosis via the following steps: LAPF translocation to lysosomes, lysosomal membrane permeabilization (LMP), release of cathepsin (cath) D and L, mitochondrial membrane permeabilization (MMP), release of apoptosis-inducing factor (AIF), and caspase-independent apoptosis. The cath D-specific inhibitor attenuates LAPF-induced apoptosis, indicating a pivotal role of lysosomes in LAPF-initiated apoptosis. We also demonstrate that the lysosomal pathway was employed in the typical apoptotic model in which high dose TNFalpha was used to stimulate L929 cells. Silencing of LAPF expression by small RNA interference protected L929 cells from hTNFalpha-induced apoptosis by impairing hTNFalpha-triggered LMP and MMP. Therefore, LAPF may launch caspase-independent apoptosis through the lysosomal-mitochondrial pathway. 

Retracted: No

PubPeer comments:
 Posting a finding by another reader in Figure 3G. Lanes 6 and 7 appear to share some similarities to lanes 8 and 9. Shown with boxes of the same color. The similarities are not in the bands of interest, but in the background above and below the bands. This is very unexpected. Could the authors please comment?  , 
 Dear BIK. I think those could be coincidence. If you check those areas closely enough, you would discover lots of different features. The details are shown in the below figure.  , 
 I also think it is a coincidence, there is a band between lane 7 and lane 8. And there are many other differences. , 
 #3 Dr. Biku2019s reader is correct. There are many artefacts that can be exactly co-superimposed. The probability that this happened by chance is not on the side of the figure creator. Given that the results presented in this paper are of contemporary interest, I may get around to indicating the use of what I take to be the brush tool in Fig. 3B to disguise the similarity between two pasted gel bands. For the moment, here is some contrast-enhanced background in three lanes of a Fig. 6G Shanghaied ImmunoBlot (aka SIB), repurposed for what are claimed to be two different experiments.  , 
 #4 Having now got around to indicating the use of what I take to be the brush tool in Fig. 3B to disguise the similarity between two pasted gel bands, I see that there is a bit more to these Shanghaied ImmunoBlots: Multiple pasting are evident in the backgrounds of both these SIBs too.  , 
 #3 Noise is what gives the game away, as it does here. Definitely deliberate manipulation of the data, given the care taken, but noise is very, very difficult to cheat. , 
 #3 The differences can be clarified by way of superimposition... here, black white-reversing lanes 7-8, and superimposing them on lanes 9-10 so that similar areas cancel out as gray, with comparatively lighter areas within 7-8 becoming darker.  Spoiler alert: There aren t many differences. , 
 #5 My own version of Fig 3A, contrastified with Powerpoint:  I think we can all agree that it is not normal for the background above the mock and hLAPF blobs in the actin band to include a row of stitches.  , 
 2020 Expression of Concern. https: www.jbc.org content 295 26 8877 The publisher of the Journal of Biological Chemistry is issuing an Expression of Concern to inform readers that credible concerns have been raised regarding some of the data and conclusions in the article listed above. The Journal of Biological Chemistry will provide additional information as it becomes available. , 
 Retraction on Jan 1, 2021, published online May 22, 2021 https: www.jbc.org article S0021-9258(21)00557-3 fulltext Withdrawal: The lysosome-associated apoptosis-inducing protein containing the pleckstrin homology (PH) and FYVE domains (LAPF), representative of a novel family of PH and FYVE domain-containing proteins, induces caspase-independent apoptosis via the lysosomal-mitochondrial pathway This article has been withdrawn by the authors. The Journal states there is inappropriate image manipulation of a repeating pattern in the background of the LAPF and actin immunoblots in Fig. 3B. There are also multiple inappropriate image manipulations of duplicated regions in background of the gel in Fig. 3G. There are also signs of background manipulation in bottom panels of Fig. 6B. Additionally, a region of the AIF immunoblots in Fig. 6G is duplicated. The authors state that they disagree with the Journalu2019s findings. The authors state that this study was conducted nearly 20 years ago. The age of the work and the lack of availability of data storage makes it difficult for the authors to retrieve the requested raw data. The authorsu2019 offer to replace the images in question with those from another experiment with the same conditions was declined by the Journal. The authors state that the above issues do not affect the interpretation of the data nor conclusions of this research study. This article describes the discovery of a novel molecule, LAPF, and the characterization of its lysosome-associated apoptosis-inducing function. The withdrawing authors state that its function and mechanism have been confirmed in breast cancer and other types of cancer by other independent studies. The authors have indicated that they plan to resubmit the findings elsewhere for publication. ,