General Trends in the Calnexin-Dependent Expression and Pharmacological Rescue of Clinical CFTR Variants

Reviewer #1 (Public review):

Summary:

This research investigates how the cellular protein quality control machinery influences the effectiveness of cystic fibrosis (CF) treatments across different genetic variants. CF is caused by mutations in the CFTR gene, with over 1,700 known disease-causing variants that primarily work through protein misfolding mechanisms. While corrector drugs like those in Trikafta therapy can stabilize some misfolded CFTR proteins, the reasons why certain variants respond to treatment while others don't remain unclear. The authors hypothesized that the cellular proteostasis network-the machinery that manages protein folding and quality control-plays a crucial role in determining drug responsiveness across different CFTR variants. The researchers focused on calnexin (CANX), a key chaperone protein that recognizes misfolded glycosylated proteins. Using CRISPR-Cas9 gene editing combined with deep mutational scanning, they systematically analyzed how CANX affects the expression and corrector drug response of 234 clinically relevant CF variants in HEK293 cells.

In terms of findings, this study revealed that CANX is generally required for robust plasma membrane expression of CFTR proteins, and CANX disproportionately affects variants with mutations in the C-terminal domains of CFTR and modulates later stages of protein assembly. Without CANX, many variants that would normally respond to corrector drugs lose their therapeutic responsiveness. Furthermore, loss of CANX caused broad changes in how CF variants interact with other cellular proteins, though these effects were largely separate from changes in CFTR channel activity.

This study has some limitations: the research was conducted in HEK293 cells rather than lung epithelial cells, which may not fully reflect the physiological context of CF. Additionally, the study only examined known disease-causing variants and used methodological approaches that could potentially introduce bias in the data analysis.

How cellular quality control mechanisms influence the therapeutic landscape of genetic diseases is an emerging field. Overall, this work provides important cellular context for understanding CF mutation severity and suggests that the proteostasis network significantly shapes how different CFTR variants respond to corrector therapies. The findings could pave the way for more personalized CF treatments tailored to patients' specific genetic variants and cellular contexts.

Strengths:

(1) This work makes an important contribution to the field of variant effect prediction by advancing our understanding of how genetic variants impact protein function.

(2) The study provides valuable cellular context for CFTR mutation severity, which may pave the way for improved CFTR therapies that are customized to patient-specific cellular contexts.

(3) The research provides further insight into the biological mechanisms underlying approved CFTR therapies, enhancing our understanding of how these treatments work.

(4) The authors conducted a comprehensive and quantitative analysis, and they made their raw and processed data as well as analysis scripts publicly available, enabling closer examination and validation by the broader scientific community.

Weaknesses:

(1) The study only considers known disease-causing variants, which limits the scope of findings and may miss important insights from variants of uncertain significance.

(2) The cellular context of HEK293 cells is quite removed from lung epithelia, the primary tissue affected in cystic fibrosis, potentially limiting the clinical relevance of the findings.

(3) Methodological choices, such as the expansion of sorted cell populations before genetic analysis, may introduce possible skew or bias in the data that could affect interpretation.

(4) While the impact on surface trafficking is convincingly demonstrated, how cellular proteostasis affects CFTR function requires further study, likely within a lung-specific cellular context to be more clinically relevant.

Reviewer #2 (Public review):

In this work, the authors use deep mutational scanning (DMS) to examine the effect of the endogenous chaperone calnexin (CANX) on the plasma membrane expression (PME) and potential pharmacological stabilization cystic fibrosis disease variants. This is important because there are over 1,700 loss-of-function mutations that can lead to the disease Cystic Fibrosis (CF), and some of these variants can be pharmacologically rescued by small-molecule "correctors," which stabilize the CFTR protein and prevent its degradation. This study expands on previous work to specifically identify which mutations affect sensitivity to CFTR modulators, and further develops the work by examining the effect of a known CFTR interactor-CANX-on PME and corrector response.

Overall, this approach provides a useful atlas of CF variants and their downstream effects, both at a basal level as well as in the context of a perturbed proteostasis. Knockout of CANX leads to an overall reduced plasma membrane expression of CFTR with CF variants located at the C-terminal domains of CFTR, which seem to be more affected than the others. This study then repeats their DMS approach, using PME as a readout, to probe the effect of either VX-445 or VX-455 + VX-661-which are two clinically relevant CFTR pharmacological modulators. I found this section particularly interesting for the community because the exact molecular features that confer drug resistance/sensitivity are not clear. When CANX is knocked out, cells that normally respond to VX-445 are no longer able to be rescued, and the DMS data show that these non-responders are CF variants that lie in the VX-445 binding site. Based on computational data, the authors speculate that NBD2 assembly is compromised, but that remains to be experimentally examined. Cells lacking CANX were also resistant to combinatorial treatment of VX-445 + VX-661, showing that these two correctors were unable to compensate for the lack of this critical chaperone.

One major strength of this manuscript is the mass spectrometry data, in which 4 CF variants were profiled in parental and CANX KO cells. This analysis provides some explanatory power to the observation that the delF508 variant is resistant to correctors in CANX KO cells, which is because correctors were found not to affect protein degradation interactions in this context. Findings such as this provide potential insights into intriguing new hypothesis, such as whether addition of an additional proteostasis regulators, such as a proteosome inhibitor, would facilitate a successful rescue. Taken together, the data provided can be generative to researchers in the field and may be useful in rationalizing some of the observed phenotypes conferred by the various CF variants, as well as the impact of CANX on those effects.

To complete their analysis of CF variants in CANX KO cells, the research also attempted to relate their data, primarily based on PME, to functional relevance. They observed that, although CANX KO results in a large reduction in PME (~30% reduction), changes in the actual activation of CFTR (and resultant quenching of their hYFP sensor) were "quite modest." This is an important experiment and caveat to the PME data presented above since changes in CFTR activity does not strictly require changes in PME. In addition, small molecule correctors also do not drastically alter CFTR function in the context of CANX KO. The authors reason that this difference is due to a sort of compensatory mechanism in which the functionally active CFTR molecules that are successfully assembled in an unbalanced proteostasis system (CANX KO) are more active than those that are assembled with the assistance of CANX. While I generally agree with this statement, it is not directly tested and would be challenging to actually test.

The selected model for all the above experiments was HEK293T cells. The authors then demonstrate some of their major findings in Fischer rat thyroid cell monolayers. Specifically, cells lacking CANX are less sensitive to rescue by CFTR modulators than the WT. This highlights the importance of CANX in supporting the maturation of CFTR and the dependence of chemical correctors on the chaperone. Although this is demonstrated specifically for CANX in this manuscript, I imagine a more general claim can be made that chemical correctors depend on a functional/balanced proteostasis system, which is supported by the manuscript data. I am surprised by the discordance between HEK293T PME levels compared to the CTFR activity. The authors offer a reasonable explanation about the increase in specific activity of the mature CFTR protein following CANX loss.

For the conclusions and claims relevant to CANX and CF variant surveying of PME/function, I find the manuscript to provide solid evidence to achieve this aim. The manuscript generates a rich portrait of the influence of CF mutations both in WT and CANX KO cells. While the focus of this study is a specific chaperone, CANX, this manuscript has the potential to impact many researchers in the broad field of proteostasis.