Tester, David J.

Abstract Background Long-QT syndrome type 1 (LQT1) is a genetic channelopathy characterized by loss-of-function variants in the repolarizing potassium channel KCNQ1/IKs which lead to QT-prolongation and predisposes patients to adverse events such as cardiac arrhythmias. Clincally, during catecholamine infusion or exercise stress test, patients with LQT1 present a paradoxical QT prolongation. Purpose To investigate whether a gene-therapy approach targeting the defective K+-channel, through a KCNQ1 suppression-and-replacement (SupRep) strategy, can restore the healthy phenotype at baseline and under catecholamine infusion in LQT1 transgenic rabbits. Methods Our proprietary dual component suppression-and-replacement (SupRep) gene therapy was created by combining a custom-designed KCNQ1 shRNA and a shRNA-immune (shIMM) KCNQ1 cDNA into AAV9. In vivo KCNQ1-SupRep gene therapy was performed by targeted intra-aortic root injection during balloon occlusion. Two or three weeks post gene therapy, 12-lead ECGs were assessed in adult transgenic LQT1 (KCNQ1-Y315S, loss-of IKs) and wild-type (WT) rabbits to determine the effect of SupRep gene therapy on QT-duration at baseline and under catecholamine infusion (10nM isoproterenol, 5mL/h). Ventricular cardiomyocytes (VCMs) were isolated to investigate the effect of SupRep gene therapy on action potential duration (APD) and calcium transients (Ca2+T) at baseline and under isoproterenol infusion. Results At the cellular level, VCMs isolated from SupRep treated LQT1 rabbits showed a significant shortening of the APD90 as compared to UT-LQT1 (p<0.0001). At the whole animal level, at baseline, the QTi (%) of the UT-LQT1 transgenic rabbits (122±3) was significantly longer compared to the WT rabbits (105±2, p<0.0001). Treatment with AAV9-KCNQ1-SupRep shortened significantly the QTi of the transgenic LQT1 rabbits as compared to the UT-LQT1 rabbits (111±2, p=0.0115). To further investigate the effect of SupRep gene therapy, 12-lead ECGs were obtained in UT-LQT1, sham-treated LQT1, SupRep-treated LQT1, and WT rabbits under ISO infusion. While reaching a 20% increase in heart rate during ISO stimulation, the UT-LQT1 and the sham treated LQT1 rabbits showed a marked QT prolongation, with ΔQTi of 31.4% and 24.5%, respectively, as compared to baseline. In contrast, the SupRep-treated LQT1 rabbit behaved nearly identical to the WT rabbit during ISO infusion, showing a ΔQTi of 16.9% as compared to 16.5% in the WT rabbit. Similarly, in contrast to the UT-LQT1, VCMs isolated from SupRep-treated LQT1 rabbits demonstrated a normalization of the APD and Ca2+T under ISO stimulation, showing a significantly shortened APD90 (p<0.0001) and Ca2+T90 (p=0.0025) which was similar to what was observed in WT VCMs. Conclusion In vivo KCNQ1 suppression-and-replacement gene therapy normalizes the pathologically prolonged APD/QT interval and restores a physiological response to catecholamine infusion in treated LQT1 transgenic rabbits.

Introduction: Most of long QT syndrome (LQTS) is explained by pathogenic variants in KCNQ1 , KCNH2 , or SCN5A . However, ~10-20% of LQTS index cases remain genetically elusive following commercial genetic testing. Here, we identified and functionally characterized a novel LQTS genetic substrate in a multi-generational, “genotype negative” LQTS pedigree. Methods: The index case was a 40-year-old female with a history of syncope, seizures, ventricular fibrillation, and a family history of LQTS and sudden death. Although anticipated to have KCNH2- mediated LQT2, commercial genetic testing of all LQTS-causative genes was negative. Genome sequencing and variant analysis was performed on 6 affected family members. Patient-specific and CRISPR/Cas9 “gene-corrected” isogenic control induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) were generated. RT-PCR was used to determine the effects of the identified variant on splicing. Action potential duration (APD) and field potential duration (FPD) were measured using voltage-sensing dye (Fluovolt) and microelectrode array, respectively. Results: No ultra-rare, nonsynonymous heterozygous variants co-segregated among the 6 LQTS phenotype-positive individuals. Instead, a deep intronic KCNH2 variant (c.3331-316 G>T) was present in all affected individuals. RT-PCR analysis of patient-specific iPSC-CM-derived RNA revealed that c.3331-316 G>T creates a novel 89 base-pair exon residing between canonical exons 14 and 15 of KCNH2 that results in a frame-shift variant annotated as p.S1112Pfs*171. The APD 90 was significantly longer in p.S1112Pfs*171-iPSC-CMs (647 ± 12 ms, n=50) compared to isogenic control iPSC-CMs (412 ± 10 ms, n=50, p < 0.0001). Further, the FPD was significantly longer in p.S1112Pfs*171-iPSC-CMs (349 ± 8 ms, n=48) compared to isogenic control iPSC-CMs (209 ± 10 ms, n=20, p < 0.0001). Conclusions: A novel deep intronic KCNH2 variant was identified in a multi-generational genetically elusive LQTS pedigree. The patient-derived and isogenic control iPSC-CMs establish that the p.S1112Pfs*171-KCNH2 variant is the monogenetic cause for this family’s LQTS. As suggested by the phenotype, this family indeed has KCNH2 -mediated LQT2 albeit stemming from a deep intronic variant .

Introduction: Type 2 long QT syndrome (LQT2) is caused by loss-of-function variants in the KCNH2 -encoded K v 11.1 potassium channel which is essential for the rapid delayed rectifier channel (I Kr ) that governs phase 3 of cardiac action potential (AP). No current therapies target the molecular cause of LQT2. Methods: A dual-component “suppression-and-replacement” (SupRep) KCNH2 gene therapy was created by cloning into a single construct a custom-designed KCNH2 shRNA that produces ~80% knockdown (suppression) and a “shRNA-immune” (shIMM) KCNH2 cDNA modified by the introduction of synonymous single nucleotide substitutions within the shRNA target site (replacement). The ability of KCNH2-SupRep gene therapy to suppress and replace LQT2-causative variants in KCNH2 was evaluated via heterologous expression in TSA201 cells. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) were generated from two patients with LQT2 (KCNH2-G604S and -N633S). CRISPR-Cas9 corrected isogenic control iPSC-CMs were made. Both lines were treated with KCNH2-SupRep or non-targeting control shRNA (shCT). FluoVolt voltage dye was used to measure the APD. Results: KCNH2-SupRep achieved mutation-independent suppression of wild-type KCNH2 and both LQT2-causative variants with simultaneous replacement of KCNH2-shIMM as measured by allele-specific qRT-PCR. Treatment with KCNH2-SupRep resulted in shortening of the pathologically prolonged APD at 90% repolarization (APD 90 ) to near isogenic control APD 90 levels (G604S: isogenic controls, 424 + 39 ms and N633S: isogenic controls, 433 + 16 ms) compared to treatment with non-targeting shCT (G604S: SupRep treated, 399±105 ms vs. shCT treated, 577±39 ms, p<0.0001; N633S: SupRep treated, 432±85 ms vs. shCT treated, 483±65 ms, p<0.005). Conclusions: We provide the first proof-of-principle gene therapy for correction of LQT2. Like our sentinel discovery of SupRep gene therapy for LQT1, KCNH2-SupRep successfully suppressed and replaced KCNH2 to normal wild-type levels. In TSA201 cells, co-transfection of LQT2 variants and KCNH2-SupRep caused mutation-independent suppression-and-replacement of KCNH2 . In LQT2 iPSC-CMs, KCNH2-SupRep shortened the APD, thereby eliminating the pathognomonic feature of LQT2.

Introduction: Loss-of-function (LOF) and gain-of-function (GOF) pathogenic variants in the KCNH2 -encoded Kv11.1 potassium channel cause type 2 long QT syndrome(LQT2) and type 1 short QT syndrome (SQT1), respectively. Given the prevalence of KCNH2- mediated heart disease (1 in 8000 for LQT2,1 in 100,000 for SQT1) and the reduced penetrance/variable expressivity seen in LQTS and SQTS, large databases such as the Genome Aggregation Database (gnomAD, n=141,352 individuals) might harbor subjects with unidentified LQT2/SQT1-causative mutations. Objective: To determine which “ultra-rare” KCNH2 missense variants (MVs) in gnomAD are most likely to be LQT2- or SQT1-causative. Methods: A list of gnomAD-derived MVs in KCNH2 was compiled. The frequency of each MV in gnomAD was assessed. Each MV was analyzed by 8 in silico pathogenicity prediction tools. MVs that were seen once in gnomAD and predicted damaging by all 8 tools were considered possible LQT2/SQT1-causative MVs worthy of functional validation via whole-cell patch clamp. Results: Overall, 233/474 (49%) of gnomAD KCNH2 MVs were seen in just 1 of >140,000 subjects. Of these, 2 (0.4%) MVs (S320W, S379Y) were predicted damaging by 8 in silico tools. Both S320W and S379Y localize to the N-terminus of the Kv11.1 potassium channel. There was no significant change in peak or tail current density between heterozygously expressed KCNH2-S320W (n=13, p=NS) and KCNH2-WT (n=13). However, heterozygous KCNH2-S379Y (n=12) produced a marked increase in peak current density across the range -30 mV to +20 mV and shifted the V 1/2 of activation by -17 mV (p < 0.001). Also, tail current density of S379Y channels significantly increased across the range -20 mV to +20 mV and the V 1/2 of deactivation shifted by -26 mV (p < 0.001). Conclusion: With this stringent requirement of ultra-rarity, universal prediction of damaging impact, and functionally abnormal electrophysiological properties, one SQT1-causative pathogenic variant in gnomAD was identified consistent with the predicted frequency of SQTS. The search continues among the remaining 32 ultra-rare MVs in KCNH2 where at least 75% of the in silico tools predicted deleterious impact of the MV to find the 15-20 subjects in gnomAD’s population who ought to have an LQT2-causative MV.

Introduction: Loss-of-function (LOF) variants in the KCNH2 -encoded Kv11.1 potassium channel cause type 2 long QT syndrome (LQT2). To date, hundreds of KCNH2 missense variants (MVs) have been published as “disease-causative”. However, it has been suggested that 10% of rare LQTS variants in the literature may be "false positives”. Objective: To determine previously published KCNH2 variants that are likely false positives and warrant demotion to at least likely benign status. Methods: A list of all case-derived LQT2-associated MVs from six large published compendia was compiled. The frequency of each MV within the Genome Aggregation Database (gnomAD, n = 141,352 individuals) was recorded. Eight in silico variant assessment tools were used to grade each MV. Variants (n=8) absent in gnomAD but predicted “benign” by all 8 tools were considered potential false positives, despite being ultra-rare, and were characterized functionally using whole-cell patch clamp. Results: Overall, 339 KCNH2 MVs were identified among LQTS cases. Of these, 13 (4%) were seen at a minor allele frequency (MAF) > 0.0004 in gnomAD. This MAF cut-off is derived from the frequency of R176W-KCNH2, a well-established albeit weakly penetrant (i.e. < 20%) LQT2-causative MV. Variants seen at MAF > R176W-KCNH2 are unlikely to be LQT2-contributing. However, 253 MVs (75%) were absent in gnomAD. Of these, 8 (4%) MVs (I96V, G187S, A203T, P241L, H254Q, G314S, P935S, and P963T) were predicted by all 8 in silico tools to be benign and had never been characterized functionally. Patch clamp studies did not demonstrate any LOF perturbation for these 8 MVs. Conclusion: This study offers compelling evidence for the demotion from LQT2-causative status to likely benign status for 21 (6%) of the 339 previously published LQT2 MVs based either on i) gnomAD MAF unacceptably high for a 1:8000 disorder (LQT2) for 13 MVs or ii) ultra-rarity (never seen in gnomAD) but in silico variant assessment tools predicting benign impact of the amino acid substitution and in vitro functional validation studies devoid of LOF for 8 additional MVs. This meticulous “pruning” exercise must be conducted for all published variants previously implicated as the monogenic cause for LQTS in particular and all genetic heart diseases in general.

KCNQ1 encodes the voltage-gated α-subunit of the I Ks channel complex (Kv7.1), and KCNQ1 mutations are associated with multiple arrhythmia syndromes. Over the past 12 years, hundreds of different KCNQ1 mutations have been linked to congenital long QT syndrome but only three KCNQ1 variants, each identified in only one family, are linked to familial early-onset AF (<50 years of age). The scant genetic linkage between KCNQ1 and early-onset AF raises the question as to whether these KCNQ1 variants actually cause familial early-onset AF or simply unmask a latent genetic predisposition. We now report that a single KCNQ1 variant, pArg231His or R231H, is identified in five unrelated families with a high penetrance of familial early-onset AF. Whole-cell patch clamp of cells heterologously expressing the obligatory I Ks β-subunit KCNE1 with wild-type KCNQ1 (WT) or WT and R231H (to mimic the patients’ genotypes) showed that cells co-expressing R231H increased current at negative and resting membrane potentials. Additionally, currents recorded from cells using a human atrial action potential (AP) waveform at physiological temperature showed that WT is minimally activated during the atrial AP and co-expression of R231H increases current measured during the atrial AP waveform by greater than 20-fold (WT, n = 10; WT & R231H, n = 12, p<0.0001). Simulations using a computational model of a human atrial AP also predicted that I Ks is normally minimally activated in the atria and R231H would dramatically increase I Ks and shorten the atrial AP. We conclude that KCNQ1 mutations are capable of causing familial early-onset AF by increasing I Ks during the atrial AP and shortening atrial refractoriness.

Background: Potentially lethal syndromes such as long QT syndrome (LQTS) and catecholaminergic polymorphic ventricular tachycardia (CPVT) may account for a significant number of autopsy-negative sudden unexplained deaths (SUD). Here, the spectrum and prevalence of putative LQTS-/CPVT-causative mutations in autopsy- negative SUD was determined following a cardiac channel molecular autopsy. Methods: From September 1998 to October 2010, 173 cases of SUD (106 males, 18 ± 13 years, 89% white) were referred by Medical Examiners/Coroners for a cardiac channel molecular autopsy. Using PCR, DHPLC, and DNA sequencing, a comprehensive mutational analysis of the LQTS-susceptibility genes ( KCNQ1 , KCNH2 , SCN5A, KCNE1, and KCNE2 ) and a targeted analysis of the CPVT1-associated gene ( RYR2 ) was conducted. Results: Overall, 45 putative pathogenic mutations (20 RYR2 , 11 KCNQ1 , 6 KCNH2 , 6 SCN5A , and 2 KCNE2 , absent in 400 - 700 controls, were identified in 45 (26%) autopsy negative SUD cases. The yield was greatest for those with an exercise-induced death (16/46, 35%) or a positive personal/family history of a syncope (13/25, 52%), or sudden death (9/20, 45%). Females had a higher yield (26/67, 39%) than males (19/106, 18%, p < 0.005) especially if the SUD was during adolescence (12/25, 48% females vs. 9/50, 18% males). Females were more likely to have LQTS-associated mutations (65%) while males were more likely to have CPVT1-associated mutations (58%). Among SUD victims with exercise-induced death, the yield was much higher among the 1 - 10 year olds compared to the 11 -20 year olds (females, 71% vs 14%, p<0.05; males, 60% vs 15%, p = 0.07). However for those with death during a period of sleep, the 11 - 20 year olds had a much higher yield than the 1-10 year old group (females, 75% vs 0%, p<0.01; males 18% vs 6%). Conclusions: Over one-fourth of autopsy-negative SUD may stem from LQTS and CPVT. A cardiac channel molecular autopsy should be considered as a standard part of the evaluation of autopsy-negative SUD especially among children with exercise-induced SUD, adolescent females, and those with a positive personal/family history of cardiac events. A two-tiered approach starting with the LQTS-susceptibility genes in females and the CPVT-susceptibility genes in males may be prudent.

Introduction: Recently, we demonstrated transcriptional down-regulation of hypertrophy pathways in myectomy tissue derived from patients with obstructive hypertrophic cardiomyopathy (HCM) despite translational activation of associated hypertrophy pathways. Previous studies of other forms of cardiac hypertrophy demonstrate hypertrophy pathways are activated via histone acetylation and histone deacetylase (HDAC) inhibitors prevented development of hypertrophy. Whether histone modifications regulate hypertrophy pathways in HCM remains unexplored. Methods: Chromatin immunoprecipitation sequencing (ChIP-seq) was performed on myectomy tissues from 40 patients with HCM and 23 controls to characterize differential histone marks for H3K4me3 (active promoter), H3K9ac (active promoter), H3K9me3 (heterochromatin), H3K27ac (active enhancer), H3K27me3 (repression) across the genome. The differential histone marks were integrated with RNA-sequencing (RNA-seq) data derived from the same patients. Results: Overall, we identified 2,912 (7%) differential H3K4me3 peaks impacting 5 pathways, 23,339 (21%) differential H3K9ac peaks impacting 87 pathways, 33 (0.05%) differential H3K9me3 peaks, and 58,837 (42%) differential H3K27ac peaks impacting 50 pathways. There was increased H3K27ac (q-value = 0.002) and H3K9ac (q-value = 0.009) at RAS-MAPK loci. Univariate analysis of concordance between H3K9ac with RNA-seq data showed activation of cardiac hypertrophy signaling (z-score=4.5; -log [BH p-value] = 3.1), while H3K27me showed down-regulation of cardiac hypertrophy signaling (z-score=-2.4; -log [BH p-value] = 2.4). Multivariate integration of the ChIP-seq data with RNA-seq data identified 3,189 transcripts concordant with all five histone marks impacting 254 pathways, 18 (7%) of which are involved in cardiac hypertrophy. Conclusions: Myectomy tissue from patients with obstructive HCM shows enrichment of histone modifications at cardiac hypertrophy loci with activation via H3K27 and H3K9 acetylation and repression via H3K27 methylation. Further studies are needed to understand the balance and temporal relationship between these competing regulators in HCM pathobiology and the potential for epigenetic therapies.

Abstract Background/Introduction Arrhythmogenic mitral valve prolapse syndrome (AMVPS) is a female-predominant sudden cardiac death (SCD)-predisposing disorder characterized clinically by myxomatous mitral valve prolapse (MVP), inferolateral T-wave inversions and complex ventricular ectopy. However, insights into the pathogenesis and potential genetic basis of AMVPS are currently lacking. Purpose Considering recent case reports that suggest a potential role for genetic cardiomyopathies in the pathogenesis of AMVPS, we sought to determine the yield of pathogenic/likely pathogenic (P/LP) genetic variants in strong evidence cardiomyopathy-susceptibility genes amongst AMVPS patients who underwent clinical genetic testing. Methods In this retrospective study, the medical records of 4,907 patients referred to our cardiovascular genetics clinic was used to identify those patients with a clinical phenotype consistent with AMVPS. After exclusion of individuals with severe mitral valve regurgitation, pertinent clinical, electrocardiographic, imaging and genetic testing data was extracted from the electronic record. For those AMVPS that underwent a form of genetic testing that encompassed 23 Clinical Genome Resource-defined strong/definitive evidence cardiomyopathy-susceptibility genes, ultra-rare (minor allele frequency ≤ 0.00005 in the Genome Aggregation Database [n=141,456 individuals]) non-synonymous variants identified within these genes were adjudicated independently as P, LP or variant of uncertain significance with the assistance of Varsome. The frequency of P/LP variants was then compared to a previously published cohort of 973 ostensibly healthy control exomes. Results Overall, 56 unrelated patients with suspected AMVPS were identified (82% female; average age at presentation of 31 ± 13 years; 32% with a family history of MVP and/or SCD). Of these, 24/56 (43%) underwent a form of clinical genetic testing that encompassed the pre-defined panel of cardiomyopathy-susceptibility genes. In comparison to control exomes (n=973), P/LP variants in strong/definitive evidence cardiomyopathy-susceptibility genes were over-represented in AMVPS patients [4/24 (16.7%) vs 20/973 (2.1%); p=0.002]. Interestingly, this enrichment was driven in large part by an excess number of A-band-localizing P/LP truncating variants in TTN-encoded titin in AMVPS cases [3/24 (12.5%) versus 4/973 (0.4%); p=0.0004]. Conclusion This study provides further evidence that a subset of AMVPS may arise secondary to a "two-hit" model whereby an underlying cardiomyopathic genetic substrate is exacerbated by the mechanical force generated by genetically unrelated myxomatous MVP resulting in maladaptive and ventricular arrhythmia-predisposing fibrosis within the inferobasal left ventricle and posteromedial papillary muscles. Larger studies are needed to better understand the potential role of genetic testing in the diagnosis, risk-stratification and management of patients with suspected AMVPS.

Introduction: Calmodulin (CaM)-mediated long QT syndrome (CaM-LQTS) is a genetic arrhythmia disorder characterized by a high prevalence of life-threatening ventricular arrhythmias occurring very early in life, frequent T-wave alternans, markedly prolonged QT intervals (QTc > 600 ms), and intermittent 2:1 AV block. Three distinct genes ( CALM1 , CALM2 , and CALM3 ) all encode for the identical CaM protein. Conventional LQTS pharmacotherapies fail to adequately protect against potentially lethal cardiac events in patients with CaM-LQTS. Here, we developed a CALM1 “ suppression-replacement (SupRep)” gene therapy with the goal of rescuing the prolonged cardiac action potential duration (APD) and increased Ca 2+ amplitude (ΔF/F0) in patient-derived induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) from a patient with CALM1 -mediated LQTS. Methods: Custom designed CALM1 -targeting shRNAs were tested for knockdown efficiency using TSA201 cells and RT-qPCR. A dual-component SupRep CALM1 gene therapy was created by cloning into a single construct a custom-designed CALM1 shRNA that produces knockdown (suppression) and a “shRNA-immune” (shIMM) CALM1 cDNA (replacement). Patient-specific CALM1-F142L iPSC-CMs were generated from a patient with severe LQTS (QTc = 515 ms). FluoVolt voltage-sensing dye was used to measure the APD at 90% repolarization (APD 90 ). Calcium transient amplitude was measured using Fluo-4 indicator. Results: Overall, 6 unique candidate CALM1 -targeting shRNAs were tested for knockdown efficiency in a transient transfection CALM1 over-expression TSA201 cell system. One candidate shRNA had an 80% knockdown efficiency of CALM1. Following transfection with CALM1 -SupRep gene therapy, the APD 90 was significantly decreased in F142L iPSC-CMs compared to untreated cells (F142L: 665 ± 9 ms [n=40] vs F142L + SupRep: 353 ± 9 ms [n=20], p<0.0001). Ca 2+ amplitude was significantly decreased following SupRep transfection when compared to untreated cells (0.99 ± 0.04 vs 0.8 ± 0.06, p=0.02). Conclusions: Here, we provide the first proof-of-principle SupRep gene therapy for CALM1-mediated LQTS. CALM1 -SupRep gene therapy shortened significantly the pathologically prolonged APD 90 in CALM1 -F142L patient-derived iPSC-CMs.