Collateral deletion of the mitochondrial AAA+ ATPase ATAD1 sensitizes cancer cells to proteasome dysfunction
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eLife assessment
The authors identify co-deletion of the mitochondrial AAA+ ATPase ATAD1 with the tumor suppressor PTEN as a factor modifying cancer prognosis, based on a new mechanism of increasing sensitivity to proteotoxic stress induced by proteasome inhibition. The authors also identify the mitochondrial E3 ubiquitin ligase MARCH5 as a gene whose deletion is synthetically lethal with ATAD1. These findings suggest that the use of proteasome-targeting agents may be useful in patients with tumors dually deleted for ATAD1 and PTEN. The study is based on convincing evidence, and makes an innovative contribution to the understanding of the biology of tumors with 10q23 deletions.
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Abstract
The tumor suppressor gene PTEN is the second most commonly deleted gene in cancer. Such deletions often include portions of the chromosome 10q23 locus beyond the bounds of PTEN itself, which frequently disrupts adjacent genes. Coincidental loss of PTEN -adjacent genes might impose vulnerabilities that could either affect patient outcome basally or be exploited therapeutically. Here, we describe how the loss of ATAD1 , which is adjacent to and frequently co-deleted with PTEN , predisposes cancer cells to apoptosis triggered by proteasome dysfunction and correlates with improved survival in cancer patients. ATAD1 directly and specifically extracts the pro-apoptotic protein BIM from mitochondria to inactivate it. Cultured cells and mouse xenografts lacking ATAD1 are hypersensitive to clinically used proteasome inhibitors, which activate BIM and trigger apoptosis. This work furthers our understanding of mitochondrial protein homeostasis and could lead to new therapeutic options for the hundreds of thousands of cancer patients who have tumors with chromosome 10q23 deletion.
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Author Response
Reviewer #1 (Public Review):
In this manuscript, Winter and colleagues define the sensitivity of cancer cells lacking the mitochondrial AAA+ ATAD1 to proteasome inhibition. They show that ATAD1 is often co-deleted with PTEN¬ in many different types of cancer. Using two complementary CRISPR screens in two distinct cell models, they identified the mitochondrial E3 ubiquitin ligase MARCH5 as a gene whose deletion is synthetically lethal with ATAD1. Since MARCH5 was previously reported to function to attenuate apoptotic signaling through mechanisms including promoting degradation of pro-apoptotic factors including BIM1, they sought to define the specific role of ATAD1 in regulating pro-apoptotic factor. They present evidence that ATAD1 extracts the pro-apoptotic protein BIMEL from mitochondria to facilitate its …
Author Response
Reviewer #1 (Public Review):
In this manuscript, Winter and colleagues define the sensitivity of cancer cells lacking the mitochondrial AAA+ ATAD1 to proteasome inhibition. They show that ATAD1 is often co-deleted with PTEN¬ in many different types of cancer. Using two complementary CRISPR screens in two distinct cell models, they identified the mitochondrial E3 ubiquitin ligase MARCH5 as a gene whose deletion is synthetically lethal with ATAD1. Since MARCH5 was previously reported to function to attenuate apoptotic signaling through mechanisms including promoting degradation of pro-apoptotic factors including BIM1, they sought to define the specific role of ATAD1 in regulating pro-apoptotic factor. They present evidence that ATAD1 extracts the pro-apoptotic protein BIMEL from mitochondria to facilitate its inactivation by mechanisms including degradation and inhibitory phosphorylation - a mechanism that appears enhanced during proteasome inhibition. This suggested that ATAD1-deficient cells could be preferentially sensitive to proteasome inhibitors. Consistent with this, expression of ATAD1 in ATAD1deficient cells decreases sensitivity to proteasome inhibition. Similarly, depletion of ATAD1 in PC3 cells increased sensitivity to proteasome inhibition in xenografts, although somewhat curiously a corresponding increase in BIM was not readily observed (NOXA levels did increase). Finally, the authors show that prostate cancer patients with combined PTEN1/ATAD1 deletion show improved survival as compared to tumors where PTEN1 was deleted alone. Ultimately, these results support a model whereby ATAD1 promotes tumor cell survival and highlights that ATAD1 deletion may represent a vulnerability that can be exploited to treat tumors through the use of proteasome inhibitors.
Overall, this is an interesting and generally well-performed study that defines the mechanistic and functional implications of a genetic 'hitchhiker' in the context of cancer cell survival. The synthetic lethality for ATAD1 and MARCH5 observed using two different genetic approaches (deletion/overexpression) in two different cell models underscores a strong link between these two genes. Further, the data showing an important role for ATAD1 in regulating BIM mitochondrial localization/cytosolic phosphorylation are interesting. The evidence demonstrating relationships between ATAD1 and proteasome sensitivity is also convincing. However, there are some weaknesses. For example, the direct relationship between ATAD1-dependent prosurvival activities and BIM is not clearly defined. This is evident as BIM1 depletion did not influence ATAD1-deficient PC3 cells' sensitivity to bortezomib and BIM was not significantly impacted in the xenograft models. BIM deletion did partially rescue synthetic lethality in Jurkat cells deficient in both MARCH5 and ATAD1, indicating a potential role in those cells. While the authors do address this, these results do create a disconnect within the studies that complicates the overall interpretation, as the specific importance of BIM regulation by ATAD1 in different models is not consistent or always clear. Regardless, this study does reveal new insights into the genetic relationship between ATAD1 deficiency and proteasome inhibition that could have direct therapeutic potential to improve the treatment of patients. Further, considering that the anti-apoptotic roles for ATAD1 appear to extend beyond BIM regulation, this will open new avenues for investigation of the underlying molecular mechanisms whereby ATAD1 contributes to regulating apoptotic signaling in cancer and other models. With that being said, tempering the writing to better highlight that BIM regulation does not explain the ATAD1 protection observed across cancer cell models (it is the case in some, but not all) would be helpful. While there is value in the new mechanistic insight provided into the potential mechanism of ATAD1-dependent apoptotic regulation, more focus on the specific relationship between ATAD1 deficiency and proteasome inhibitor sensitivity would better suit the current work.
Reviewer #2 (Public Review):
This manuscript by Winter et al represents an analysis of the function of the ATAD1 gene in cancer. At present, the manuscript makes a number of interesting observations, with strong experimental support. First, the authors show that tumors with PTEN deletions frequently have additional mutations in ATAD1, and that prostate tumors with both mutations are associated with a shorter period of survival. Second, tumors lacking ATAD1 are more sensitive to proteotoxic stress, based in part on an increased tendency to apoptosis. Third, the ATAD1 protein interacts with BIM, and interactions with BIM contribute in part to an increased tendency to apoptosis. Fourth, ATAD1 and MARCH5 have at least moderate synthetic sick/lethal interactions; together with other data, this suggests they control the release of BIM from the OMM, contributing to its degradation. Overall, the data suggest that tumors with ATAD1 deletions may be particularly vulnerable to drugs that induce proteotoxic stress, suggesting new potential therapeutic regimens, which would be a valuable contribution to the field. The level of data presented here is already substantial; however, some additional experiments to support the authors' contentions would strengthen the work. Some claims about the mechanism are overstated given the current body of data and should be qualified.
First, we thank the reviewers and editors for considering our work and providing insightful critiques. We are also grateful that our prior reviews from another journal were considered as part of a holistic review. Overall, we have rewritten key aspects of the manuscript to emphasize strengths pointed out by the reviewers (the relationship between the proteasome and ATAD1) while de-emphasizing the claims surrounding ATAD1 and BIM. Specifically, we added a new paragraph to the discussion section to help focus the reader on how loss of ATAD1 sensitizes cells to ubiquitin proteasome system (UPS) dysfunction and describe the implications thereof. We also removed a paragraph from the discussion that may have put undue emphasis on BIM. Lastly, we reconfigured our schematic figure (Fig 4F) to describe a model in which ATAD1 and the UPS represent two parallel pathways of dealing with proteins on the OMM, where loss of one pathway increases dependency on the other. We believe that BIM is an important piece of this story, and clearly demonstrate that ATAD1-dependent extraction of BIM partly explains the synthetic lethality of ATAD1 and MARCH5. However, we agree with the reviewers that to focus too much on BIM detracts from the more general thesis of the work, as described above. We added another paragraph to the discussion that describes limitations of the study, to explicitly outline what our manuscript does and does not demonstrate.
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eLife assessment
The authors identify co-deletion of the mitochondrial AAA+ ATPase ATAD1 with the tumor suppressor PTEN as a factor modifying cancer prognosis, based on a new mechanism of increasing sensitivity to proteotoxic stress induced by proteasome inhibition. The authors also identify the mitochondrial E3 ubiquitin ligase MARCH5 as a gene whose deletion is synthetically lethal with ATAD1. These findings suggest that the use of proteasome-targeting agents may be useful in patients with tumors dually deleted for ATAD1 and PTEN. The study is based on convincing evidence, and makes an innovative contribution to the understanding of the biology of tumors with 10q23 deletions.
-
Reviewer #1 (Public Review):
In this manuscript, Winter and colleagues define the sensitivity of cancer cells lacking the mitochondrial AAA+ ATAD1 to proteasome inhibition. They show that ATAD1 is often co-deleted with PTEN¬ in many different types of cancer. Using two complementary CRISPR screens in two distinct cell models, they identified the mitochondrial E3 ubiquitin ligase MARCH5 as a gene whose deletion is synthetically lethal with ATAD1. Since MARCH5 was previously reported to function to attenuate apoptotic signaling through mechanisms including promoting degradation of pro-apoptotic factors including BIM1, they sought to define the specific role of ATAD1 in regulating pro-apoptotic factor. They present evidence that ATAD1 extracts the pro-apoptotic protein BIMEL from mitochondria to facilitate its inactivation by mechanisms …
Reviewer #1 (Public Review):
In this manuscript, Winter and colleagues define the sensitivity of cancer cells lacking the mitochondrial AAA+ ATAD1 to proteasome inhibition. They show that ATAD1 is often co-deleted with PTEN¬ in many different types of cancer. Using two complementary CRISPR screens in two distinct cell models, they identified the mitochondrial E3 ubiquitin ligase MARCH5 as a gene whose deletion is synthetically lethal with ATAD1. Since MARCH5 was previously reported to function to attenuate apoptotic signaling through mechanisms including promoting degradation of pro-apoptotic factors including BIM1, they sought to define the specific role of ATAD1 in regulating pro-apoptotic factor. They present evidence that ATAD1 extracts the pro-apoptotic protein BIMEL from mitochondria to facilitate its inactivation by mechanisms including degradation and inhibitory phosphorylation - a mechanism that appears enhanced during proteasome inhibition. This suggested that ATAD1-deficient cells could be preferentially sensitive to proteasome inhibitors. Consistent with this, expression of ATAD1 in ATAD1-deficient cells decreases sensitivity to proteasome inhibition. Similarly, depletion of ATAD1 in PC3 cells increased sensitivity to proteasome inhibition in xenografts, although somewhat curiously a corresponding increase in BIM was not readily observed (NOXA levels did increase). Finally, the authors show that prostate cancer patients with combined PTEN1/ATAD1 deletion show improved survival as compared to tumors where PTEN1 was deleted alone. Ultimately, these results support a model whereby ATAD1 promotes tumor cell survival and highlights that ATAD1 deletion may represent a vulnerability that can be exploited to treat tumors through the use of proteasome inhibitors.
Overall, this is an interesting and generally well-performed study that defines the mechanistic and functional implications of a genetic 'hitchhiker' in the context of cancer cell survival. The synthetic lethality for ATAD1 and MARCH5 observed using two different genetic approaches (deletion/overexpression) in two different cell models underscores a strong link between these two genes. Further, the data showing an important role for ATAD1 in regulating BIM mitochondrial localization/cytosolic phosphorylation are interesting. The evidence demonstrating relationships between ATAD1 and proteasome sensitivity is also convincing. However, there are some weaknesses. For example, the direct relationship between ATAD1-dependent prosurvival activities and BIM is not clearly defined. This is evident as BIM1 depletion did not influence ATAD1-deficient PC3 cells' sensitivity to bortezomib and BIM was not significantly impacted in the xenograft models. BIM deletion did partially rescue synthetic lethality in Jurkat cells deficient in both MARCH5 and ATAD1, indicating a potential role in those cells. While the authors do address this, these results do create a disconnect within the studies that complicates the overall interpretation, as the specific importance of BIM regulation by ATAD1 in different models is not consistent or always clear. Regardless, this study does reveal new insights into the genetic relationship between ATAD1 deficiency and proteasome inhibition that could have direct therapeutic potential to improve the treatment of patients. Further, considering that the anti-apoptotic roles for ATAD1 appear to extend beyond BIM regulation, this will open new avenues for investigation of the underlying molecular mechanisms whereby ATAD1 contributes to regulating apoptotic signaling in cancer and other models. With that being said, tempering the writing to better highlight that BIM regulation does not explain the ATAD1 protection observed across cancer cell models (it is the case in some, but not all) would be helpful. While there is value in the new mechanistic insight provided into the potential mechanism of ATAD1-dependent apoptotic regulation, more focus on the specific relationship between ATAD1 deficiency and proteasome inhibitor sensitivity would better suit the current work.
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Reviewer #2 (Public Review):
This manuscript by Winter et al represents an analysis of the function of the ATAD1 gene in cancer. At present, the manuscript makes a number of interesting observations, with strong experimental support. First, the authors show that tumors with PTEN deletions frequently have additional mutations in ATAD1, and that prostate tumors with both mutations are associated with a shorter period of survival. Second, tumors lacking ATAD1 are more sensitive to proteotoxic stress, based in part on an increased tendency to apoptosis. Third, the ATAD1 protein interacts with BIM, and interactions with BIM contribute in part to an increased tendency to apoptosis. Fourth, ATAD1 and MARCH5 have at least moderate synthetic sick/lethal interactions; together with other data, this suggests they control the release of BIM from …
Reviewer #2 (Public Review):
This manuscript by Winter et al represents an analysis of the function of the ATAD1 gene in cancer. At present, the manuscript makes a number of interesting observations, with strong experimental support. First, the authors show that tumors with PTEN deletions frequently have additional mutations in ATAD1, and that prostate tumors with both mutations are associated with a shorter period of survival. Second, tumors lacking ATAD1 are more sensitive to proteotoxic stress, based in part on an increased tendency to apoptosis. Third, the ATAD1 protein interacts with BIM, and interactions with BIM contribute in part to an increased tendency to apoptosis. Fourth, ATAD1 and MARCH5 have at least moderate synthetic sick/lethal interactions; together with other data, this suggests they control the release of BIM from the OMM, contributing to its degradation. Overall, the data suggest that tumors with ATAD1 deletions may be particularly vulnerable to drugs that induce proteotoxic stress, suggesting new potential therapeutic regimens, which would be a valuable contribution to the field. The level of data presented here is already substantial; however, some additional experiments to support the authors' contentions would strengthen the work. Some claims about the mechanism are overstated given the current body of data and should be qualified.
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