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ttna ttnb Cronos

With regard to the primary area of contention, we recognize that we have done an inadequate job drawing a path between our observations in the zebrafish model and human cardiac disease. In the revised manuscript we have sought to make a clearer, more compelling case with the following changes:

A) Comparison of zebrafish and human titin:

The following text is included verbatim in the revised manuscript and we have included a new Figure ( Largest Supplier attantou European trendy black white patent high heel party Cheapest Outlet Discount Sale Yi0NInRD
) to graphically illustrate the domain organization of human TTN and zebrafish and , as suggested. Our primary objectives in this section are to 1) highlight the similarities between the human and zebrafish Titin proteins, and 2) emphasize that the paralogous ttna and ttnb proteins are both essential for skeletal muscle sarcomere development, creating a scenario where, at least in skeletal muscle, studying a homozygote knockout of one of these genes bears resemblance to studying a heterozygote in mammals.

We have also rephrased the text accordingly. Please see: “As a result of an ancestral genome duplication event, zebrafish include two titin genes: and […] severe disruption of skeletal muscle sarcomeric architecture, highlighting the mutual contribution of the two genes (14).”

B) Tissue-specific quantitative and developmental survey of expression:

In the revised manuscript, we have added 3 new figure panels that characterize expression in zebrafish and mouse by whole mount in situ hybridization (with one probe specific to ) and by quantitative real-time PCR ( Outlet Fast Delivery Classic Ladies Designer Dance Shoes Factory Clearance Shop New Arrival Cheap Price nJNdjg
). Our primary observation is that expression is at high levels in zebrafish skeletal muscle during development (∼2:1 ratio of to full-length ), but drops off dramatically during adulthood (∼1:70 ratio). Although the expression in zebrafish heart also appears to be developmentally regulated, it is much lower than in skeletal muscle, with a ∼1:5 ratio at 72 hr and 1:30 ratio in adulthood.

In contrast, the relative levels of in mouse heart are much higher than in skeletal muscle, with nearly a 1:1 ratio of to full-length Titin in E12.5 heart. Thereafter mouse cardiac expression of decreases to ∼20–30% of full-length Titin. Skeletal muscle expression varies widely across development and in different muscle beds with a 1:5 ratio in mouse hindlimb at P2, and between 1:16 and ∼1:1000 ratios in adult extensor digitorum longus (fast-twitch) and soleus (slow-twitch) muscle, respectively.

We indicate that the poor expression of in zebrafish heart can be a possible explanation for the indistinguishable cardiac phenotypes of N- and C-terminal truncation mutants, though the fact that plays a minimal role in cardiac development is probably also contributing to the severity of the mutants.

In addition to the additional Figure 6 , we have included two paragraphs summarizing the tissue-specific and developmental stage results: “We next surveyed the expression levels of in cardiac and skeletal muscle […] expression varies across development and in different muscle beds with a 1:5 ratio in mouse hindlimb at P2, and between 1:16 and ∼1:1000 ratios in adult extensor digitorum longus (fast-twitch) and soleus (slow-twitch) muscle, respectively.”

C) Interpretation of lack of variation in truncation mutation severity in heart:

We attribute the stark differences between skeletal muscle phenotypes in N- and C-terminal truncation mutants to 1) the prominent expression of in developing skeletal muscle and 2) the presence of an important functional paralog, , which can substitute for function. Unfortunately, in cardiac muscle the contribution of both of these factors is severely diminished, including low expression of , and a more minimal role for in cardiac sarcomerogenesis.

We are reassured that there is prominent expression of in developing mouse heart, which is in keeping with playing an important role in mammalian heart development and therefore consistent with the lack of intensifying DCM phenotypic severity. Interestingly, others have described a prominent band on protein gels of developing mouse and rat heart tissue at the expected molecular weight of , which is substantially diminished in adulthood. This band has been dismissed as a degradation product – but we speculate that in some cases this is very likely to be .

We touch on the limited cardiac expression of in zebrafish as well as the limited contribution of in heart development as explanation for our zebrafish cardiac results. We also include an additional paragraph in the Discussion: “Our work also proposes an alternative explanation for the consistently observed ‘T2’ band on protein gels, which migrates at the expected molecular weight of . This has invariably been labeled a C-terminal degradation product, as it reacts with A-band antibodies (25). However, in keeping with expression patterns in development, the T2 band was prominently seen in developing mouse (25) and rat hearts (26), but was markedly reduced in adulthood. It is possible that, at least in some situations, T2 and represent the same isoform.”

D) Perturbation induced discrimination of N- and C-terminal heterozygotes:

We agree that perturbation experiments in heterozygotes (such as was done with mice, Gramlich et al, 2009) would have been more consistent with the human disease scenario, although the presence of paralogs complicates this situation in zebrafish. Although we tried isoproterenol (and angiotensin II) at several doses and at several developmental time points and used natriuretic peptide levels as readout, we were not able to consistently distinguish WT fish from heterozygotes (N- or C). Given the low cardiac expression of , we suspect that even with an optimized assay, the distinction of N- and C-terminal truncation mutants from one another would be very challenging. Cronos

This is an excellent point. Our prior approach to NMD estimate was inadequate and involved normalizing total to levels in homozygote null mutants. In the revised manuscript we have performed targeted RNA-Seq of the mutant exons in heterozygote embryos to estimate NMD by looking at allelic imbalance ( Figure 2D ). Comparing raw counts of mutant and WT alleles, we see ∼80% of the mutant transcript degraded, in keeping with established NMD efficacy. Interestingly, we see very little variation across the length of the transcript. We have also performed qPCR to estimate the ratio of to full-length in N-terminal and C-terminal mutants and find the expected result ( Figure 5B ): a high ratio of to full-length for all N-terminal mutants and a much lower rate, more comparable to WT, for the C-terminal mutants. We suspect that some variation in promoter activity for the full-length and transcripts could account for some of the variation in these ratios within the N- and C-terminal mutant groups.

We have modified the text and figures to include this data, which we believe strengthens our story. For example, we now state: “Given that NMD substantially reduces the levels of transcripts with premature termination codons ( Figure 2D ), we reasoned that we should be able to distinguish N- and C-terminal truncation mutants by the ratio of to full-length transcript. In mutants, which would degrade full-length but not , we would anticipate a higher :full-length ratio than in mutants mutants, which should degrade both transcripts approximately equally. As expected, we see a much higher ratio of :full-length transcript levels in mutants than in mutants ( Figure 5B ).”

We have now performed qPCR to demonstrate ∼78% knockdown efficiency using our morpholino. Either exon skipping or intron retention arising from morpholino injection should result in an N-terminal truncation on top of the C-terminal mutation. In conjunction with NMD, this intervention should result in residual C-terminal truncated protein being at ∼5% of the level of . Given that we see no amelioration in skeletal muscle function (fish remain immobile) or architecture, it is difficult to reconcile this observation with a dominant negative mechanism. Similarly, for dosage to be responsible for the difference between N- and C-terminal truncations, we would not expect to have seen similar levels of NMD for N- and C-terminal truncations nor see persistence of skeletal muscle pathology with such a low level of mutant C-terminal protein present.

In the manuscript, we have made the following changes: “Knockdown by morpholino was effective (∼78% knockdown efficiency, data not shown) and the combined action of NMD and morpholino knockdown would be expected to reduce mutant ttna protein to only ∼5% of the level of ttnb protein. Nonetheless we were unable to rescue skeletal muscle architecture in mutants ( Figure 3B ). We thus concluded that mutants do not act as dominant negatives and that an alternative explanation was needed.”

Cronos

We have updated this gel to include morpholino knockdown controls as well as loading controls. We have found this gel technically challenging to execute, potentially because of the long running time ∼6 required, but we believe the results are now convincing.

We have modified this section and included 2 new figure panels: 1) one that depicts the position of mutations in DCM patients and control populations or from the senior athletes onto a schematic of the TTN meta-transcript 2) a ratio of mutations found in regions C-terminal to the promoter to those in the N-terminus in different populations. We have eliminated the figure panel that emphasizes the location of senior athlete mutations to the terminal exon of the Novex-3 isoform. In fact, when we referred to the Novex-3 isoform we meant only those mutations mapping to the terminal exon, which is unique to this isoform.

The following text is now included in the revised manuscript: “We compared the frequency and distribution of TTN truncation mutations to those found in unselected controls and healthy volunteers from a recent sequencing study (CTLlit) (7) […] As expected, in end-stage DCM we observed a much higher rate of mutants C-terminal to than N-terminal (30:1), followed by unselected DCM (37:11), literature controls (6:11, 2:2, 10:7 for FHS, healthy volunteers and JHS) and senior athletes (0:3).”

We apologize for creating the impression that our work has resulted in newfound certainty in genotype-phenotype correlations. From our experience taking care of many dozens of families with inherited cardiomyopathies, such determinism is never the case. We have moderated language that makes any such suggestion in the revision. We would like to address some of the above comments and concerns:

1) The presence of ‘controls’ with C-terminal truncations does not eliminate the possibility that these mutations do in fact have cardiac consequences that fall short of overt heart failure, which was the motivation for studying a hyper-normal senior athlete population. Finding C-terminal truncations in the senior athlete population would have cast greater doubt on whether such mutations are sufficient to compromise cardiovascular fitness.

2) We are encouraged by this report of subclinical skeletal manifestations in DCM TTN patients though we cannot find any published studies that have rigorously documented this.

3) We have eliminated mention of the HCM association with TTN.

4) Our work actually does not address if N-terminal truncations – especially in constitutive exons – are deleterious. We analyzed the senior athletes with the hope that we might find N-terminal truncations though small sample size precludes robust conclusions. We do note that in Supplementary Table 12 of Herman et al, the dozen or so families with evidence of segregation in 2 or more members all had C-terminal truncations.

Please see the following passage in the manuscript: “Our results have two clinical implications for titinopathy patients […] although it is unclear whether there is a restricted developmental window where this might be possible.”

[Editors' note: further revisions were requested prior to acceptance, as described below.]

eLifeReviewer #2: Reviewer #3: ttnb Cronos ttna ttna

In the revised manuscript we have added two paragraphs (shown below) at the beginning of the Discussion to summarize our findings and highlight the strengths and limitations of the system we have used. Although we firmly believe that our findings represent a substantial advance in this field, with strong biological and clinical implications, we recognize the challenges of studying adult onset autosomal dominant diseases with incomplete penetrance in any sort of animal model. Even if one can bring about phenotypic distinctions with artificial perturbations or genetic modifiers or use increasingly sensitive phenotyping methods to capture differences, one cannot be sure such stresses or distinctions are in fact relevant to the human disease process. Furthermore, TTN brings about an even greater challenge because of the technical challenge of performing rescue experiments with a 110 kilobase transgene.

With regard to Reviewer 3’s final comment, we do not understand the statement of how a knockdown of a mutant allele in the setting of a WT alternative () is of no value in assessing a dominant negative mode of action and instead “emphasize(s) the failure of the zebrafish experiments as described to capture the biology of either human skeletal or cardiac titin disease”. If one accepts that is rescuing the null, this is analogous to performing allele specific knockdown of a mutant protein in a heterozygote and looking at phenotypic impact. In the manuscript, we stress: “Loss of function experiments across a number of systems have demonstrated Titin’s importance in diverse aspects of sarcomere development and function, including the ordered assembly of sarcomeric constituents […] Nonetheless, taking all of our results together, we find it a highly plausible explanation that a superimposed deficiency in expression of the protein product would result in the more severe forms of human cardiac disease seen in DCM patients with C-terminal TTN truncations.”

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Jun Zou

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Erron W Titus

Christiana Yuan

Chenxu Shi

Shruthi Patchava

Elizabeth Halper

Jasmine Garg

Irina Movsesyan

Chaoying Yin

Roland Wu

Lisa D Wilsbacher

Jiandong Liu

Ronald L Hager

Shaun R Coughlin

Martin Jinek

Clive R Pullinger

John P Kane

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Pui-Yan Kwok

Rahul C Deo

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