Xiaozhi Gao

All Publications

• Clinical Utility of Protein Language Models in Resolution of Variants of Uncertain Significance inKCNQ1, KCNH2, andSCN5ACompared With Patch-Clamp Functional Characterization. Circulation. Genomic and precision medicine Ye, D., Garmany, R., Martinez-Barrios, E., Gao, X., Neves, R. A., Tester, D. J., Bains, S., Zhou, W., Giudicessi, J. R., Ackerman, M. J. 2024: e004584

  Abstract

  BACKGROUND: Genetic testing for cardiac channelopathies is the standard of care. However, many rare genetic variants remain classified as variants of uncertain significance (VUS) due to lack of epidemiological and functional data. Whether deep protein language models may aid in VUS resolution remains unknown. Here, we set out to compare how 2 deep protein language models perform at VUS resolution in the 3 most common long-QT syndrome-causative genes compared with the gold-standard patch clamp.METHODS: A total of 72 rare nonsynonymous VUS (9 KCNQ1, 19 KCNH2, and 50 SCN5A) were engineered by site-directed mutagenesis and expressed in either HEK293 cells or TSA201 cells. Whole-cell patch-clamp technique was used to functionally characterize these variants. The protein language models, ESM1b and AlphaMissense, were used to predict the variant effect of missense variants and compared with patch clamp.RESULTS: Considering variants in all 3 genes, the ESM1b model had a receiver operator curve-area under the curve of 0.75 (P=0.0003). It had a sensitivity of 88% and a specificity of 50%. AlphaMissense performed well compared with patch-clamp with an receiver operator curve-area under the curve of 0.85 (P<0.0001), sensitivity of 80%, and specificity of 76%.CONCLUSIONS: Deep protein language models aid in VUS resolution with high sensitivity but lower specificity. Thus, these tools cannot fully replace functional characterization but can aid in reducing the number of variants that may require functional analysis.

  View details for DOI 10.1161/CIRCGEN.124.004584

  View details for PubMedID 39119706

• Temporal Association Between Vaping and Risk of Cardiac Events. Mayo Clinic proceedings Bains, S., Garmany, R., Neves, R., Giudicessi, J. R., Gao, X., Tester, D. J., Bos, J. M., Ackerman, M. J. 2024; 99 (2): 241-248

  Abstract

  To describe our early observations with sudden cardiac arrest (SCA) and sudden death (SD) in patients using vape products.A retrospective analysis of Mayo Clinic's Windland Smith Rice Genetic Heart Rhythm Clinic and Sudden Death Genomics Laboratory was performed on all SCA survivors and decedents who presented between January 1, 2007, and December 31, 2021, to identify patients/decedents with a history of vaping. Data abstraction included patient demographics, clinical characteristics, and documented use of vape products.Among 144 SCA survivors and 360 SD victims, there were six individuals (1%; 3 females) with unexplained SCA (n=4) or SD (n=2) that was temporally associated with vaping use with a mean age at sentinel event of 23±5 years. The SCA survivors include a 19-year-old male who was resuscitated from documented ventricular fibrillation 40 minutes after vaping and a 19-year-old male who was resuscitated from ventricular fibrillation a few hours post vaping. The first SD victim was a 19-year-old female with exercise-induced asthma who died in her sleep after vaping that evening. Autopsy results showed eosinophilic infiltrates in the lung tissue and death was attributed to bronchial asthma. The second vaping-associated death involved a 26-year-old male whose autopsy attributed the death to acute respiratory distress syndrome.We have identified six young individuals with a history of vaping who experienced a near fatal episode or a tragic SD. Although larger cohort studies are needed to quantify the actual risk of SD, it seems prudent to sound an early warning about vaping's potential lethality.

  View details for DOI 10.1016/j.mayocp.2023.09.017

  View details for PubMedID 38309936

• Injectable contraceptive Depo-Provera induces erratic beating patterns in patient-specific induced pluripotent stem cell-derived cardiomyocytes with long QT syndrome type 2. Heart rhythm Pinsky, A. M., Gao, X., Bains, S., Kim, C. J., Louradour, J., Odening, K. E., Tester, D. J., Giudicessi, J. R., Ackerman, M. J. 2023; 20 (6): 910-917

  Abstract

  Long QT syndrome type 2 (LQT2) is caused by pathogenic variants in KCNH2. LQT2 may manifest as QT prolongation on an electrocardiogram and present with arrhythmic syncope/seizures and sudden cardiac arrest/death. Progestin-based oral contraceptives may increase the risk of LQT2-triggered cardiac events in women. We previously reported on a woman with LQT2 and recurrent cardiac events temporally related and attributed to the progestin-based contraceptive medroxyprogesterone acetate ("Depo-Provera" [Depo] MilliporeSigma, Catalog# 1378001, St. Louis, MO).The purpose of this study was to evaluate the arrhythmic risk of Depo in a patient-specific induced pluripotent stem cell-derived cardiomyocyte (iPSC-CM) model of LQT2.An iPSC-CM line was generated from a 40-year-old woman with p.G1006Afs∗49-KCNH2. A CRISPR/Cas9 gene-edited/variant-corrected isogenic control iPSC-CM line was generated. FluoVolt (Invitrogen, F10488, Waltham, MA) was used to measure the action potential duration after treatment with 10 μM Depo. Erratic beating patterns characterized as alternating spike amplitudes, alternans, or early afterdepolarization-like phenomena were assessed using multielectrode array (MEA) after 10 μM Depo, 1 μM isoproterenol (ISO), or combined Depo + ISO treatment.Depo treatment shortened the action potential duration at 90% repolarization of G1006Afs∗49 iPSC-CMs from 394 ± 10 to 303 ± 10 ms (P < .0001). Combined Depo + ISO treatment increased the percentage of electrodes displaying erratic beating in G1006Afs∗49 iPSC-CMs (baseline: 18% ± 5% vs Depo + ISO: 54% ± 5%; P < .0001) but not in isogenic control iPSC-CMs (baseline: 0% ± 0% vs Depo + ISO: 10% ± 3%; P = .9659).This cell study provides a potential mechanism for the patient's clinically documented Depo-associated episodes of recurrent ventricular fibrillation. This in vitro data should prompt a large-scale clinical assessment of Depo's potential proarrhythmic effect in women with LQT2.

  View details for DOI 10.1016/j.hrthm.2023.03.002

  View details for PubMedID 36889623

• Functional characterization and identification of a therapeutic for a novel SCN5A-F1760C variant causing type 3 long QT syndrome refractory to all guideline-directed therapies. Heart rhythm Stutzman, M. J., Gao, X., Kim, M., Ye, D., Zhou, W., Tester, D. J., Giudicessi, J. R., Shannon, K., Ackerman, M. J. 2023; 20 (5): 709-717

  Abstract

  Pathogenic variants in the SCN5A-encoded Nav1.5 sodium channel cause type 3 long QT syndrome (LQT3). We present the case of an infant with severe LQT3 who was refractory to multiple pharmacologic therapies as well as bilateral stellate ganglionectomy. The patient's novel variant, p.F1760C-SCN5A, involves a critical residue of the Nav1.5's local anesthetic binding domain.The purpose of this study was to characterize functionally the p.F1760C-SCN5A variant using TSA-201 and patient-specific induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs).Whole-cell patch clamp was used to assess p.F1760C-SCN5A associated sodium currents with/without lidocaine (Lido), flecainide, and phenytoin (PHT) in TSA-201 cells. p.F1760C-SCN5A and CRISPR-Cas9 variant-corrected isogenic control (IC) iPSC-CMs were generated. FluoVolt voltage dye was used to measure the action potential duration (APD) with/without mexiletine or PHT.V1/2 of inactivation was right-shifted significantly in F1760C cells (-72.2 ± 0.7 mV) compared to wild-type (WT) cells (-86.3 ± 0.9 mV; P <.0001) resulting in a marked increase in window current. F1760C increased sodium late current 2-fold from 0.18% ± 0.04% of peak in WT to 0.49% ± 0.07% of peak in F1760C (P = .0005). Baseline APD to 90% repolarization (APD90) was increased markedly in F1760C iPSC-CMs (601 ± 4 ms) compared to IC iPSC-CMs (423 ± 15 ms; P <.0001). However, 4-hour treatment with 10 μM mexiletine failed to shorten APD90, and treatment with 5μM PHT significantly decreased APD90 of F1760C iPSC-CMs (453 ± 6 ms; P <.0001).PHT rescued electrophysiological phenotype and APD of a novel p.F1760C-SCN5A variant. The antiepileptic drug PHT may be an effective alternative therapeutic for the treatment of LQT3, especially for variants that disrupt the Lido/mexiletine binding site.

  View details for DOI 10.1016/j.hrthm.2023.01.032

  View details for PubMedID 36731785

• SGK1 inhibition attenuated the action potential duration in patient- and genotype-specific re-engineered heart cells with congenital long QT syndrome. Heart rhythm O2 Kim, M., Das, S., Tester, D. J., Pradhananga, S., Hamrick, S. K., Gao, X., Srinivasan, D., Sager, P. T., Ackerman, M. J. 2023; 4 (4): 268-274

  Abstract

  Background: Long QT syndrome (LQTS) stems from pathogenic variants in KCNQ1 (LQT1), KCNH2 (LQT2), or SCN5A (LQT3) and is characterized by action potential duration (APD) prolongation. Inhibition of serum and glucocorticoid regulated kinase-1 (SGK1) is proposed as a novel therapeutic for LQTS.Objective: The study sought to test the efficacy of novel, selective SGK1 inhibitors in induced pluripotent stem cell-derived cardiomyocyte (iPSC-CM) models of LQTS.Methods: The mexiletine (MEX)-sensitive SCN5A-P1332L iPSC-CMs were tested initially compared with a CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 SCN5A-P1332L variant-corrected isogenic control (IC). The SGK1-I1 therapeutic efficacy, compared with MEX, was tested for APD at 90% repolarization (APD90) shortening in SCN5A-P1332L, SCN5A-R1623Q, KCNH2-G604S, and KCNQ1-V254M iPSC-CMs using FluoVolt.Results: The APD90 was prolonged in SCN5A-P1332L iPSC-CMs compared with its IC (646 ± 7 ms vs 482 ± 23 ms; P < .0001). MEX shortened the APD90 to 560 ± 7 ms (52% attenuation, P < .0001). SGK1-I1 shortened the APD90 to 518 ± 5 ms (78% attenuation, P < .0001) but did not shorten the APD90 in the IC. SGK1-I1 shortened the APD90 of the SCN5A-R1623Q iPSC-CMs (753 ± 8 ms to 475 ± 19 ms compared with 558 ± 19 ms with MEX), the KCNH2-G604S iPSC-CMs (666 ± 10 ms to 574 ± 18 ms vs 538 ± 15 ms after MEX), and the KCNQ1-V254M iPSC-CMs (544 ± 10 ms to 475 ± 11ms; P = .0004).Conclusions: Therapeutically inhibiting SGK1 effectively shortens the APD in human iPSC-CM models of the 3 major LQTS genotypes. These preclinical data support development of SGK1 inhibitors as novel, first-in-class therapy for patients with congenital LQTS.

  View details for DOI 10.1016/j.hroo.2023.02.003

  View details for PubMedID 37124559

• A novel functional variant residing outside the SCN5A-encoded Nav1.5 voltage-sensing domain causes multifocal ectopic Purkinje-related premature contractions. HeartRhythm case reports Gao, X., Ye, D., Zhou, W., Tester, D. J., Ackerman, M. J., Giudicessi, J. R. 2022; 8 (1): 54-59

  View details for DOI 10.1016/j.hrcr.2021.11.002

  View details for PubMedID 35070709

  View details for PubMedCentralID PMC8767173

• Negligible-Cost and Weekend-Free Chemically Defined Human iPSC Culture. Stem cell reports Kuo, H. H., Gao, X., DeKeyser, J. M., Fetterman, K. A., Pinheiro, E. A., Weddle, C. J., Fonoudi, H., Orman, M. V., Romero-Tejeda, M., Jouni, M., Blancard, M., Magdy, T., Epting, C. L., George, A. L., Burridge, P. W. 2020; 14 (2): 256-270

  Abstract

  Human induced pluripotent stem cell (hiPSC) culture has become routine, yet the cost of pluripotent cell media, frequent medium changes, and the reproducibility of differentiation have remained restrictive. Here, we describe the formulation of a hiPSC culture medium (B8) as a result of the exhaustive optimization of medium constituents and concentrations, establishing the necessity and relative contributions of each component to the pluripotent state and cell proliferation. The reagents in B8 represent only 3% of the costs of commercial media, made possible primarily by the in-lab generation of three E. coli-expressed, codon-optimized recombinant proteins: fibroblast growth factor 2, transforming growth factor β3, and neuregulin 1. We demonstrate the derivation and culture of 34 hiPSC lines in B8 as well as the maintenance of pluripotency long term (over 100 passages). This formula also allows a weekend-free feeding schedule without sacrificing capacity for differentiation.

  View details for DOI 10.1016/j.stemcr.2019.12.007

  View details for PubMedID 31928950

  View details for PubMedCentralID PMC7013200