Associate Professor of Medicine (Cardiovascular Medicine)


  • Lac-Phe mediates the anti-obesity effect of metformin. bioRxiv : the preprint server for biology Xiao, S., Li, V. L., Lyu, X., Chen, X., Wei, W., Abbasi, F., Knowles, J. W., Deng, S., Tiwari, G., Shi, X., Zheng, S., Farrell, L., Chen, Z. Z., Taylor, K. D., Guo, X., Goodarzi, M. O., Wood, A. C., Ida Chen, Y. D., Lange, L. A., Rich, S. S., Rotter, J. I., Clish, C. B., Tahir, U. A., Gerszten, R. E., Benson, M. D., Long, J. Z. 2023


    Metformin is a widely prescribed anti-diabetic medicine that also reduces body weight. The mechanisms that mediate metformin's effects on energy balance remain incompletely defined. Here we show that metformin is a powerful pharmacological inducer of the anorexigenic metabolite Lac-Phe in mice as well as in two independent human cohorts. In cell culture, metformin drives Lac-Phe biosynthesis via inhibition of complex I, increased glycolytic flux, and intracellular lactate mass action. Other biguanides and structurally distinct inhibitors of oxidative phosphorylation also increase Lac-Phe levels in vitro. Genetic ablation of CNDP2, the principal biosynthetic enzyme for Lac-Phe, in mice renders animals resistant to metformin's anorexigenic and anti-obesity effects. Mediation analyses also support a role for Lac-Phe in metformin's effect on body mass index in humans. These data establish the CNDP2/Lac-Phe pathway as a critical mediator of the effects of metformin on energy balance.

    View details for DOI 10.1101/2023.11.02.565321

    View details for PubMedID 37961394

    View details for PubMedCentralID PMC10635077

  • Principles for Health Information Collection, Sharing, and Use: A Policy Statement From the American Heart Association CIRCULATION Spector-Bagdady, K., Armoundas, A. A., Arnaout, R., Hall, J. L., McSwain, B., Knowles, J. W., Price, W., Rawat, D. B., Riegel, B., Wang, T. Y., Wiley, K., Chung, M. K., Amer Heart Assoc Advocacy Coor 2023; 148 (13): 1061-1069


    The evolution of the electronic health record, combined with advances in data curation and analytic technologies, increasingly enables data sharing and harmonization. Advances in the analysis of health-related and health-proxy information have already accelerated research discoveries and improved patient care. This American Heart Association policy statement discusses how broad data sharing can be an enabling driver of progress by providing data to develop, test, and benchmark innovative methods, scalable insights, and potential new paradigms for data storage and workflow. Along with these advances come concerns about the sensitive nature of some health data, equity considerations about the involvement of historically excluded communities, and the complex intersection of laws attempting to govern behavior. Data-sharing principles are therefore necessary across a wide swath of entities, including parties who collect health information, funders, researchers, patients, legislatures, commercial companies, and regulatory departments and agencies. This policy statement outlines some of the key equity and legal background relevant to health data sharing and responsible management. It then articulates principles that will guide the American Heart Association's engagement in public policy related to data collection, sharing, and use to continue to inform its work across the research enterprise, as well as specific examples of how these principles might be applied in the policy landscape. The goal of these principles is to improve policy to support the use or reuse of health information in ways that are respectful of patients and research participants, equitable in impact in terms of both risks and potential benefits, and beneficial across broad and demographically diverse communities in the United States.

    View details for DOI 10.1161/CIR.0000000000001173

    View details for Web of Science ID 001072138200013

    View details for PubMedID 37646159

  • RNA interference targeting ANGPTL3 for triglyceride and cholesterol lowering: phase 1 basket trial cohorts. Nature medicine Watts, G. F., Schwabe, C., Scott, R., Gladding, P. A., Sullivan, D., Baker, J., Clifton, P., Hamilton, J., Given, B., Melquist, S., Zhou, R., Chang, T., San Martin, J., Gaudet, D., Goldberg, I. J., Knowles, J. W., Hegele, R. A., Ballantyne, C. M. 2023


    Elevated triglycerides and non-high-density lipoprotein cholesterol (HDL-C) are risk factors for atherosclerotic cardiovascular disease (ASCVD). ARO-ANG3 is an RNA interference therapy that targets angiopoietin-like protein 3 (ANGPTL3), a regulator of lipoprotein metabolism. This first-in-human, phase 1, randomized, placebo-controlled, open-label trial investigated single and repeat ARO-ANG3 doses in four cohorts of fifty-two healthy participants and one cohort of nine participants with hepatic steatosis, part of a basket trial. Safety (primary objective) and pharmacokinetics (in healthy participants) and pharmacodynamics (secondary objectives) of ARO-ANG3 were evaluated. ARO-ANG3 was generally well tolerated, with similar frequencies of treatment-emergent adverse events in active and placebo groups. Systemic absorption of ARO-ANG3 in healthy participants was rapid and sustained, with a mean Tmax of 6.0-10.5h and clearance from plasma within 24-48h after dosing with a mean t of 3.9-6.6h. In healthy participants, ARO-ANG3 treatment reduced ANGPTL3 (mean -45% to -78%) 85days after dose. Reductions in triglyceride (median -34% to -54%) and non-HDL-C (mean -18% to -29%) (exploratory endpoints) concentrations occurred with the three highest doses. These early-phase data support ANGPTL3 as a potential therapeutic target for ASCVD treatment. identifier: NCT03747224.

    View details for DOI 10.1038/s41591-023-02494-2

    View details for PubMedID 37626170

  • A single-cell CRISPRi platform for characterizing candidate genes relevant to metabolic disorders in human adipocytes. American journal of physiology. Cell physiology Bielczyk-Maczynska, E., Sharma, D., Blencowe, M., Saliba Gustafsson, P., Gloudemans, M. J., Yang, X., Carcamo-Orive, I., Wabitsch, M., Svensson, K. J., Park, C. Y., Quertermous, T., Knowles, J. W., Li, J. 2023


    CROP-Seq combines gene silencing using CRISPR interference with single-cell RNA sequencing. Here, we applied CROP-Seq to study adipogenesis and adipocyte biology. Human preadipocyte SGBS cell line expressing KRAB-dCas9 was transduced with a sgRNA library. Following selection, individual cells were captured using microfluidics at different timepoints during adipogenesis. Bioinformatic analysis of transcriptomic data was used to determine the knock-down effects, the dysregulated pathways, and to predict cellular phenotypes. Single-cell transcriptomes recapitulated adipogenesis states. For all targets, over 400 differentially expressed genes were identified at least at one timepoint. As a validation of our approach, the knock-down of PPARG and CEBPB (which encode key proadipogenic transcription factors) resulted in the inhibition of adipogenesis. Gene set enrichment analysis generated hypotheses regarding the molecular function of novel genes. MAFF knock-down led to downregulation of transcriptional response to proinflammatory cytokine TNF-α in preadipocytes and to decreased CXCL-16 and IL-6 secretion. TIPARP knock-down resulted in increased expression of adipogenesis markers. In summary, this powerful, hypothesis-free tool can identify novel regulators of adipogenesis, preadipocyte and adipocyte function associated with metabolic disease.

    View details for DOI 10.1152/ajpcell.00148.2023

    View details for PubMedID 37486064

  • Plasma proteomic signatures of a direct measure of insulin sensitivity in two population cohorts. Diabetologia Zanetti, D., Stell, L., Gustafsson, S., Abbasi, F., Tsao, P. S., Knowles, J. W., Zethelius, B., Ärnlöv, J., Balkau, B., Walker, M., Lazzeroni, L. C., Lind, L., Petrie, J. R., Assimes, T. L. 2023


    The euglycaemic-hyperinsulinaemic clamp (EIC) is the reference standard for the measurement of whole-body insulin sensitivity but is laborious and expensive to perform. We aimed to assess the incremental value of high-throughput plasma proteomic profiling in developing signatures correlating with the M value derived from the EIC.We measured 828 proteins in the fasting plasma of 966 participants from the Relationship between Insulin Sensitivity and Cardiovascular disease (RISC) study and 745 participants from the Uppsala Longitudinal Study of Adult Men (ULSAM) using a high-throughput proximity extension assay. We used the least absolute shrinkage and selection operator (LASSO) approach using clinical variables and protein measures as features. Models were tested within and across cohorts. Our primary model performance metric was the proportion of the M value variance explained (R2).A standard LASSO model incorporating 53 proteins in addition to routinely available clinical variables increased the M value R2 from 0.237 (95% CI 0.178, 0.303) to 0.456 (0.372, 0.536) in RISC. A similar pattern was observed in ULSAM, in which the M value R2 increased from 0.443 (0.360, 0.530) to 0.632 (0.569, 0.698) with the addition of 61 proteins. Models trained in one cohort and tested in the other also demonstrated significant improvements in R2 despite differences in baseline cohort characteristics and clamp methodology (RISC to ULSAM: 0.491 [0.433, 0.539] for 51 proteins; ULSAM to RISC: 0.369 [0.331, 0.416] for 67 proteins). A randomised LASSO and stability selection algorithm selected only two proteins per cohort (three unique proteins), which improved R2 but to a lesser degree than in standard LASSO models: 0.352 (0.266, 0.439) in RISC and 0.495 (0.404, 0.585) in ULSAM. Reductions in improvements of R2 with randomised LASSO and stability selection were less marked in cross-cohort analyses (RISC to ULSAM R2 0.444 [0.391, 0.497]; ULSAM to RISC R2 0.348 [0.300, 0.396]). Models of proteins alone were as effective as models that included both clinical variables and proteins using either standard or randomised LASSO. The single most consistently selected protein across all analyses and models was IGF-binding protein 2.A plasma proteomic signature identified using a standard LASSO approach improves the cross-sectional estimation of the M value over routine clinical variables. However, a small subset of these proteins identified using a stability selection algorithm affords much of this improvement, especially when considering cross-cohort analyses. Our approach provides opportunities to improve the identification of insulin-resistant individuals at risk of insulin resistance-related adverse health consequences.

    View details for DOI 10.1007/s00125-023-05946-z

    View details for PubMedID 37329449

    View details for PubMedCentralID 5866840

  • Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models. Scientific data Li, J., Jin, C., Gustafsson, S., Rao, A., Wabitsch, M., Park, C. Y., Quertermous, T., Knowles, J. W., Bielczyk-Maczynska, E. 2023; 10 (1): 387


    Adipogenesis is a process in which fat-specific progenitor cells (preadipocytes) differentiate into adipocytes that carry out the key metabolic functions of the adipose tissue, including glucose uptake, energy storage, and adipokine secretion. Several cell lines are routinely used to study the molecular regulation of adipogenesis, in particular the immortalized mouse 3T3-L1 line and the primary human Simpson-Golabi-Behmel syndrome (SGBS) line. However, the cell-to-cell variability of transcriptional changes prior to and during adipogenesis in these models is not well understood. Here, we present a single-cell RNA-Sequencing (scRNA-Seq) dataset collected before and during adipogenic differentiation of 3T3-L1 and SGBS cells. To minimize the effects of experimental variation, we mixed 3T3-L1 and SGBS cells and used computational analysis to demultiplex transcriptomes of mouse and human cells. In both models, adipogenesis results in the appearance of three cell clusters, corresponding to preadipocytes, early and mature adipocytes. These data provide a groundwork for comparative studies on these widely used in vitro models of human and mouse adipogenesis, and on cell-to-cell variability during this process.

    View details for DOI 10.1038/s41597-023-02293-x

    View details for PubMedID 37328521

    View details for PubMedCentralID 2597101

  • Contemporary Homozygous Familial Hypercholesterolemia in the United States: Insights From the CASCADE FH Registry. Journal of the American Heart Association Cuchel, M., Lee, P. C., Hudgins, L. C., Duell, P. B., Ahmad, Z., Baum, S. J., Linton, M. F., de Ferranti, S. D., Ballantyne, C. M., Larry, J. A., Hemphill, L. C., Kindt, I., Gidding, S. S., Martin, S. S., Moriarty, P. M., Thompson, P. P., Underberg, J. A., Guyton, J. R., Andersen, R. L., Whellan, D. J., Benuck, I., Kane, J. P., Myers, K., Howard, W., Staszak, D., Jamison, A., Card, M. C., Bourbon, M., Chora, J. R., Rader, D. J., Knowles, J. W., Wilemon, K., McGowan, M. P. 2023: e029175


    Background Homozygous familial hypercholesterolemia (HoFH) is a rare, treatment-resistant disorder characterized by early-onset atherosclerotic and aortic valvular cardiovascular disease if left untreated. Contemporary information on HoFH in the United States is lacking, and the extent of underdiagnosis and undertreatment is uncertain. Methods and Results Data were analyzed from 67 children and adults with clinically diagnosed HoFH from the CASCADE (Cascade Screening for Awareness and Detection) FH Registry. Genetic diagnosis was confirmed in 43 patients. We used the clinical characteristics of genetically confirmed patients with HoFH to query the Family Heart Database, a US anonymized payer health database, to estimate the number of patients with similar lipid profiles in a "real-world" setting. Untreated low-density lipoprotein cholesterol levels were lower in adults than children (533 versus 776mg/dL; P=0.001). At enrollment, atherosclerotic cardiovascular disease and supravalvular and aortic valve stenosis were present in 78.4% and 43.8% and 25.5% and 18.8% of adults and children, respectively. At most recent follow-up, despite multiple lipid-lowering treatment, low-density lipoprotein cholesterol goals were achieved in only a minority of adults and children. Query of the Family Heart Database identified 277 individuals with profiles similar to patients with genetically confirmed HoFH. Advanced lipid-lowering treatments were prescribed for 18%; 40% were on no lipid-lowering treatment; atherosclerotic cardiovascular disease was reported in 20%; familial hypercholesterolemia diagnosis was uncommon. Conclusions Only patients with the most severe HoFH phenotypes are diagnosed early. HoFH remains challenging to treat. Results from the Family Heart Database indicate HoFH is systemically underdiagnosed and undertreated. Earlier screening, aggressive lipid-lowering treatments, and guideline implementation are required to reduce disease burden in HoFH.

    View details for DOI 10.1161/JAHA.122.029175

    View details for PubMedID 37119068

  • Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models. bioRxiv : the preprint server for biology Li, J., Jin, C., Gustafsson, S., Rao, A., Wabitsch, M., Park, C. Y., Quertermous, T., Bielczyk-Maczynska, E., Knowles, J. W. 2023


    Adipogenesis is a process in which fat-specific progenitor cells (preadipocytes) differentiate into adipocytes that carry out the key metabolic functions of the adipose tissue, including glucose uptake, energy storage, and adipokine secretion. Several cell lines are routinely used to study the molecular regulation of adipogenesis, in particular the immortalized mouse 3T3-L1 line and the primary human Simpson-Golabi-Behmel syndrome (SGBS) line. However, the cell-to-cell variability of transcriptional changes prior to and during adipogenesis in these models is not well understood. Here, we present a single-cell RNA-Sequencing (scRNA-Seq) dataset collected before and during adipogenic differentiation of 3T3-L1 and SGBS cells. To minimize the effects of experimental variation, we mixed 3T3-L1 and SGBS cells and used computational analysis to demultiplex transcriptomes of mouse and human cells. In both models, adipogenesis results in the appearance of three cell clusters, corresponding to preadipocytes, early and mature adipocytes. These data provide a groundwork for comparative studies on human and mouse adipogenesis, as well as on cell-to-cell variability in gene expression during this process.

    View details for DOI 10.1101/2023.03.27.534456

    View details for PubMedID 37034809

    View details for PubMedCentralID PMC10081256

  • The relationship between insulin resistance and ion mobility lipoprotein fractions. American journal of preventive cardiology Rowland, C. M., Abbasi, F., Shiffman, D., Knowles, J. W., McPhaul, M. J. 2023; 13: 100457


    Objective: Insulin resistance (IR) increases risk of type 2 diabetes and atherosclerotic cardiovascular disease and is associated with lipid and lipoprotein abnormalities including high triglycerides (TG) and low high-density lipoprotein cholesterol (HDL-C). Lipoprotein size and lipoprotein subfractions (LS) have also been used to assist in identifying persons with IR. Associations of LS and IR have not been validated using both direct measures of IR and direct measures of LS. We assessed the usefulness of fasting lipoprotein subfractions (LS) by ion mobility to identify individuals with IR.Methods: Lipid panel, LS by ion mobility (LS-IM), and IR by steady-state plasma glucose (SSPG) concentration were assessed in 526 adult volunteers without diabetes. IR was defined as being in the highest tertile of SSPG concentration. LS-IM score was calculated by linear combination of regression coefficients from a stepwise regression analysis with SSPG concentration as the dependent variable. Improvement in prediction of IR was evaluated after combining LS-IM score with TG/HDL-C, TG/HDL-C and BMI as well as with TG/HDL-C, BMI, sex, race and ethnicity. IR prediction was evaluated by area under the receiver operating characteristic curve (AUC) and positive predictive value (PPV) considering the highest 5% of scores as positive test.Results: Prediction of IR was similar by LS-IM score and TG/HDL-C (AUC=0.68; PPV=0.59 and AUC=0.70; PPV=0.59, respectively) and prediction was improved when LS-IM was combined with TG/HDL-C (AUC=0.73; PPV=0.70), TG/HDL-C and BMI (AUC=0.82; PPV=0.81) and with TG/HDL-C, BMI, sex, race and ethnicity (AUC=0.84; PPV=0.89).Conclusion: For identifying individuals with IR, LS-IM score and TG/HDL-C are comparable and their combination further improves IR prediction by TG/HDL-C alone. Among patients who have undergone IM testing, the LS-IM score may assist prioritization of subjects for further evaluation and interventions to reduce IR.

    View details for DOI 10.1016/j.ajpc.2022.100457

    View details for PubMedID 36619297

  • G protein-coupled receptor 151 regulates glucose metabolism and hepatic gluconeogenesis. Nature communications Bielczyk-Maczynska, E., Zhao, M., Zushin, P. H., Schnurr, T. M., Kim, H. J., Li, J., Nallagatla, P., Sangwung, P., Park, C. Y., Cornn, C., Stahl, A., Svensson, K. J., Knowles, J. W. 2022; 13 (1): 7408


    Human genetics has been instrumental in identification of genetic variants linked to type 2 diabetes. Recently a rare, putative loss-of-function mutation in the orphan G-protein coupled receptor 151 (GPR151) was found to be associated with lower odds ratio for type 2 diabetes, but the mechanism behind this association has remained elusive. Here we show that Gpr151 is a fasting- and glucagon-responsive hepatic gene which regulates hepatic gluconeogenesis. Gpr151 ablation in mice leads to suppression of hepatic gluconeogenesis genes and reduced hepatic glucose production in response to pyruvate. Importantly, the restoration of hepatic Gpr151 levels in the Gpr151 knockout mice reverses the reduced hepatic glucose production. In this work, we establish a previously unknown role of Gpr151 in the liver that provides an explanation to the lowered type 2 diabetes risk in individuals with nonsynonymous mutations in GPR151.

    View details for DOI 10.1038/s41467-022-35069-9

    View details for PubMedID 36456565

    View details for PubMedCentralID 508922

  • Chronic liver disease-related mortality in diabetes before and during the COVID-19 in the United States. Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver Kim, D., Alshuwaykh, O., Dennis, B. B., Cholankeril, G., Knowles, J. W., Ahmed, A. 2022


    BACKGROUND: Global pandemic of COVID-19 represents an unprecedented challenge. COVID-19 has predominantly targeted vulnerable populations with pre-existing chronic medical diseases, such as diabetes and chronic liver disease.AIMS: We estimated chronic liver disease-related mortality trends among individuals with diabetes before and during the COVID-19 pandemic.METHODS: Utilizing the US national mortality database and Census, we determined the quarterly age-standardized chronic liver disease-related mortality and quarterly percentage change (QPC) among individuals with diabetes.RESULTS: The quarterly age-standardized mortality for chronic liver disease and/or cirrhosis among individuals with diabetes remained stable before the COVID-19 pandemic and sharply increased during the COIVD-19 pandemic at a QPC of 8.5%. The quarterly mortality from nonalcoholic fatty liver disease (NAFLD) and alcohol-related liver disease (ALD) increased markedly during the COVID-19 pandemic. Mortality for hepatitis C virus (HCV) infection declined with a quarterly rate of -3.3% before the COVID-19 pandemic and remained stable during the COVID-19 pandemic. While ALD- and HCV-related mortality was higher in men than in women, NAFLD-related mortality in women was higher than in men.CONCLUSIONS: The sharp increase in mortality for chronic liver disease and/or cirrhosis among individuals with diabetes during the COVID-19 pandemic was associated with increased mortality from NAFLD and ALD.

    View details for DOI 10.1016/j.dld.2022.09.006

    View details for PubMedID 36182570

  • Analysis of Insulin Resistance Among Children and Adolescents in Slovenia With Hypercholesterolemia After Treatment With Statins. JAMA network open Groselj, U., Sikonja, J., Mlinaric, M., Kotnik, P., Battelino, T., Knowles, J. W. 2022; 5 (9): e2231097

    View details for DOI 10.1001/jamanetworkopen.2022.31097

    View details for PubMedID 36094507

  • Creation of the American Heart Association Journals' Equity, Diversity, and Inclusion Editorial Board: The Next Step to Achieving the 2024 Impact Goal. Circulation Lewis, E. F., Beaty, C., Boltze, J., Breathett, K., Clair, W. K., de Las Fuentes, L., Essien, U. R., Goodell, H., Hinson, H. E., Kershaw, K. N., Knowles, J. W., Mazimba, S., Mujahid, M., Okafor, H. E., Woo Park, K., Schultz, J. 2022: 101161CIRCULATIONAHA122061450

    View details for DOI 10.1161/CIRCULATIONAHA.122.061450

    View details for PubMedID 35862071

  • Apolipoprotein B, Residual Cardiovascular Risk After Acute Coronary Syndrome, and Effects of Alirocumab. Circulation Hagström, E., Steg, P. G., Szarek, M., Bhatt, D. L., Bittner, V. A., Danchin, N., Diaz, R., Goodman, S. G., Harrington, R. A., Jukema, J. W., Liberopoulos, E., Marx, N., McGinniss, J., Manvelian, G., Pordy, R., Scemama, M., White, H. D., Zeiher, A. M., Schwartz, G. G. 2022: 101161CIRCULATIONAHA121057807


    Apolipoprotein B (apoB) provides an integrated measure of atherogenic risk. Whether apoB levels and apoB lowering hold incremental predictive information on residual risk after acute coronary syndrome beyond that provided by low-density lipoprotein cholesterol is uncertain.The ODYSSEY OUTCOMES trial (Evaluation of Cardiovascular Outcomes After an Acute Coronary Syndrome During Treatment With Alirocumab) compared the proprotein convertase subtilisin/kexin type 9 inhibitor alirocumab with placebo in 18 924 patients with recent acute coronary syndrome and elevated atherogenic lipoproteins despite optimized statin therapy. Primary outcome was major adverse cardiovascular events (MACEs; coronary heart disease death, nonfatal myocardial infarction, fatal/nonfatal ischemic stroke, hospitalization for unstable angina). Associations between baseline apoB or apoB at 4 months and MACEs were assessed in adjusted Cox proportional hazards and propensity score-matched models.Median follow-up was 2.8 years. In proportional hazards analysis in the placebo group, MACE incidence increased across increasing baseline apoB strata (3.2 [95% CI, 2.9-3.6], 4.0 [95% CI, 3.6-4.5], and 5.5 [95% CI, 5.0-6.1] events per 100 patient-years in strata <75, 75-<90, ≥90 mg/dL, respectively; Ptrend<0.0001) and after adjustment for low-density lipoprotein cholesterol (Ptrend=0.035). Higher baseline apoB stratum was associated with greater relative (Ptrend<0.0001) and absolute reduction in MACEs with alirocumab versus placebo. In the alirocumab group, the incidence of MACEs after month 4 decreased monotonically across decreasing achieved apoB strata (4.26 [95% CI, 3.78-4.79], 3.09 [95% CI, 2.69-3.54], and 2.41 [95% CI, 2.11-2.76] events per 100 patient-years in strata ≥50, >35-<50, and ≤35 mg/dL, respectively). Compared with propensity score-matched patients from the placebo group, treatment hazard ratios for alirocumab also decreased monotonically across achieved apoB strata. Achieved apoB was predictive of MACEs after adjustment for achieved low-density lipoprotein cholesterol or non-high-density lipoprotein cholesterol but not vice versa.In patients with recent acute coronary syndrome and elevated atherogenic lipoproteins, MACEs increased across baseline apoB strata. Alirocumab reduced MACEs across all strata of baseline apoB, with larger absolute reductions in patients with higher baseline levels. Lower achieved apoB was associated with lower risk of MACEs, even after accounting for achieved low-density lipoprotein cholesterol or non-high-density lipoprotein cholesterol, indicating that apoB provides incremental information. Achievement of an apoB level ≤35 mg/dL may reduce lipoprotein-attributable residual risk after acute coronary syndrome.URL: Unique identifier: NCT01663402.

    View details for DOI 10.1161/CIRCULATIONAHA.121.057807

    View details for PubMedID 35770629

  • Generation of two iPSC lines from hypertrophic cardiomyopathy patients carrying MYBPC3 and PRKAG2 variants. Stem cell research Manhas, A., Jahng, J. W., Vera, C. D., Shenoy, S. P., Knowles, J. W., Wu, J. C. 2022; 61: 102774


    Hypertrophic cardiomyopathy (HCM) is an inherited cardiac disorder characterized by a thick left ventricular wall and an increased risk of arrhythmias, heart failure, and sudden cardiac death. The MYBPC3 and PRAKG2 are known causal genes for HCM. Here we generated two human-induced pluripotent stem cell lines from two HCM patients carrying two heterozygous mutations in MYBPC3 (c.459delC) and PRKAG2 (c.1703C > T). Both iPSC lines expressed pluripotent markers, had a normal karyotype, and were able to differentiate into three germ layers, making them potentially valuable tools for modeling HCM in vitro and investigating the pathological mechanisms related to these two variants.

    View details for DOI 10.1016/j.scr.2022.102774

    View details for PubMedID 35413566

  • Integration of genetic colocalizations with physiological and pharmacological perturbations identifies cardiometabolic disease genes. Genome medicine Gloudemans, M. J., Balliu, B., Nachun, D., Schnurr, T. M., Durrant, M. G., Ingelsson, E., Wabitsch, M., Quertermous, T., Montgomery, S. B., Knowles, J. W., Carcamo-Orive, I. 2022; 14 (1): 31


    BACKGROUND: Identification of causal genes for polygenic human diseases has been extremely challenging, and our understanding of how physiological and pharmacological stimuli modulate genetic risk at disease-associated loci is limited. Specifically, insulin resistance (IR), a common feature of cardiometabolic disease, including type 2 diabetes, obesity, and dyslipidemia, lacks well-powered genome-wide association studies (GWAS), and therefore, few associated loci and causal genes have been identified.METHODS: Here, we perform and integrate linkage disequilibrium (LD)-adjusted colocalization analyses across nine cardiometabolic traits (fasting insulin, fasting glucose, insulin sensitivity, insulin sensitivity index, type 2 diabetes, triglycerides, high-density lipoprotein, body mass index, and waist-hip ratio) combined with expression and splicing quantitative trait loci (eQTLs and sQTLs) from five metabolically relevant human tissues (subcutaneous and visceral adipose, skeletal muscle, liver, and pancreas). To elucidate the upstream regulators and functional mechanisms for these genes, we integrate their transcriptional responses to 21 relevant physiological and pharmacological perturbations in human adipocytes, hepatocytes, and skeletal muscle cells and map their protein-protein interactions.RESULTS: We identify 470 colocalized loci and prioritize 207 loci with a single colocalized gene. Patterns of shared colocalizations across traits and tissues highlight different potential roles for colocalized genes in cardiometabolic disease and distinguish several genes involved in pancreatic beta-cell function from others with a more direct role in skeletal muscle, liver, and adipose tissues. At the loci with a single colocalized gene, 42 of these genes were regulated by insulin and 35 by glucose in perturbation experiments, including 17 regulated by both. Other metabolic perturbations regulated the expression of 30 more genes not regulated by glucose or insulin, pointing to other potential upstream regulators of candidate causal genes.CONCLUSIONS: Our use of transcriptional responses under metabolic perturbations to contextualize genetic associations from our custom colocalization approach provides a list of likely causal genes and their upstream regulators in the context of IR-associated cardiometabolic risk.

    View details for DOI 10.1186/s13073-022-01036-8

    View details for PubMedID 35292083

  • Integration of genetic colocalizations with physiological and pharmacological perturbations identifies cardiometabolic disease genes Gloudemans, M. J., Balliu, B., Nachun, D., Durrant, M. G., Ingelsson, E., Wabitsch, M., Quertermous, T., Montgomery, S. B., Knowles, J., Carcamo-Orive, I. W B SAUNDERS CO-ELSEVIER INC. 2022: S24-S25
  • A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome medicine Marwaha, S., Knowles, J. W., Ashley, E. A. 2022; 14 (1): 23


    Rare diseases affect 30 million people in the USA and more than 300-400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25-35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.

    View details for DOI 10.1186/s13073-022-01026-w

    View details for PubMedID 35220969

  • Online Patient Education Materials Related to Lipoprotein(a): Readability Assessment. Journal of medical Internet research Pearson, K., Ngo, S., Ekpo, E., Sarraju, A., Baird, G., Knowles, J., Rodriguez, F. 1800; 24 (1): e31284


    BACKGROUND: Lipoprotein(a) (Lp(a)) is a highly proatherogenic lipid fraction that is a clinically significant risk modifier. Patients wanting to learn more about Lp(a) are likely to use online patient educational materials (OPEMs). However, the readability of OPEMs may exceed the health literacy of the public.OBJECTIVE: This study aims to assess the readability of OPEMs related to Lp(a). We hypothesized that the readability of these online materials would exceed the sixth grade level recommended by the American Medical Association.METHODS: Using an online search engine, we queried the top 20 search results from 10 commonly used Lp(a)-related search terms to identify a total of 200 websites. We excluded duplicate websites, advertised results, research journal articles, or non-patient-directed materials, such as those intended only for health professionals or researchers. Grade level readability was calculated using 5 standard readability metrics (automated readability index, SMOG index, Coleman-Liau index, Gunning Fog score, Flesch-Kincaid score) to produce robust point (mean) and interval (CI) estimates of readability. Generalized estimating equations were used to model grade level readability by each search term, with the 5 readability scores nested within each OPEM.RESULTS: A total of 27 unique websites were identified for analysis. The average readability score for the aggregated results was a 12.2 (95% CI 10.9798-13.3978) grade level. OPEMs were grouped into 6 categories by primary source: industry, lay press, research foundation and nonprofit organizations, university or government, clinic, and other. The most readable category was OPEMs published by universities or government agencies (9.0, 95% CI 6.8-11.3). The least readable OPEMs on average were the ones published by the lay press (13.0, 95% CI 11.2-14.8). All categories exceeded the sixth grade reading level recommended by the American Medical Association.CONCLUSIONS: Lack of access to readable OPEMs may disproportionately affect patients with low health literacy. Ensuring that online content is understandable by broad audiences is a necessary component of increasing the impact of novel therapeutics and recommendations regarding Lp(a).

    View details for DOI 10.2196/31284

    View details for PubMedID 35014955

  • G protein-coupled receptor 151 regulates glucose metabolism and hepatic gluconeogenesis Nature Communications Bielczyk-Maczynska, E., Zhao, M., Zushin, P. H., Schnurr, T. M., Kim, H., Li, J., Sangwung, P., Nallagatla, P., Park, C., Cornn, C., Stahl, A., Svensson, K. J., Knowles, J. W. 2022
  • Interactions of physical activity, muscular fitness, adiposity, and genetic risk for NAFLD. Hepatology communications Schnurr, T. M., Katz, S. F., Justesen, J. M., O'Sullivan, J. W., Saliba-Gustafsson, P., Assimes, T. L., Carcamo-Orive, I., Ahmed, A., Ashley, E. A., Hansen, T., Knowles, J. W. 2022


    Genetic predisposition and unhealthy lifestyle are risk factors for nonalcoholic fatty liver disease (NAFLD). We investigated whether the genetic risk of NAFLD is modified by physical activity, muscular fitness, and/or adiposity. In up to 242,524 UK Biobank participants without excessive alcohol intake or known liver disease, we examined cross-sectional interactions and joint associations of physical activity, muscular fitness, body mass index (BMI), and a genetic risk score (GRS) with alanine aminotransferase (ALT) levels and the proxy definition for suspected NAFLD of ALT levels > 30 U/L in women and >40 U/L in men. Genetic predisposition to NAFLD was quantified using a GRS consisting of 68 loci known to be associated with chronically elevated ALT. Physical activity was assessed using accelerometry, and muscular fitness was estimated by measuring handgrip strength. We found that increased physical activity and grip strength modestly attenuate genetic predisposition to elevation in ALT levels, whereas higher BMI markedly amplifies it (all p values < 0.001). Among those with normal weight and high level of physical activity, the odds of suspected NAFLD were 1.6-fold higher in those with high versus low genetic risk (reference group). In those with high genetic risk, the odds of suspected NAFLD were 12-fold higher in obese participants with low physical activity versus those with normal weight and high physical activity (odds ratio for NAFLD = 19.2 and 1.6, respectively, vs. reference group). Conclusion: In individuals with high genetic predisposition for NAFLD, maintaining a normal body weight and increased physical activity may reduce the risk of NAFLD.

    View details for DOI 10.1002/hep4.1932

    View details for PubMedID 35293152

  • Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. The New England journal of medicine Gorzynski, J. E., Goenka, S. D., Shafin, K., Jensen, T. D., Fisk, D. G., Grove, M. E., Spiteri, E., Pesout, T., Monlong, J., Baid, G., Bernstein, J. A., Ceresnak, S., Chang, P. C., Christle, J. W., Chubb, H., Dalton, K. P., Dunn, K., Garalde, D. R., Guillory, J., Knowles, J. W., Kolesnikov, A., Ma, M., Moscarello, T., Nattestad, M., Perez, M., Ruzhnikov, M. R., Samadi, M., Setia, A., Wright, C., Wusthoff, C. J., Xiong, K., Zhu, T., Jain, M., Sedlazeck, F. J., Carroll, A., Paten, B., Ashley, E. A. 2022

    View details for DOI 10.1056/NEJMc2112090

    View details for PubMedID 35020984

  • Coronary Artery Disease Risk of Familial Hypercholesterolemia Genetic Variants Independent of Clinically Observed Longitudinal Cholesterol Exposure. Circulation. Genomic and precision medicine Clarke, S. L., Tcheandjieu, C., Hilliard, A. T., Lee, M., Lynch, J., Chang, K. M., Miller, D., Knowles, J. W., O'Donnell, C., Tsao, P., Rader, D. J., Wilson, P. W., Sun, Y. V., Gaziano, M., Assimes, T. L. 2022: CIRCGEN121003501


    Familial hypercholesterolemia (FH) genetic variants confer risk for coronary artery disease independent of LDL-C (low-density lipoprotein cholesterol) when considering a single measurement. In real clinical settings, longitudinal LDL-C data are often available through the electronic health record. It is unknown whether genetic testing for FH variants provides additional risk-stratifying information once longitudinal LDL-C is considered.We used the extensive electronic health record data available through the Million Veteran Program to conduct a nested case-control study. The primary outcome was coronary artery disease, derived from electronic health record codes for acute myocardial infarction and coronary revascularization. Incidence density sampling was used to match case/control exposure windows, defined by the date of the first LDL-C measurement to the date of the first coronary artery disease code of the index case. Adjustments for the first, maximum, or mean LDL-C were analyzed. FH variants in LDLR, APOB, and PCSK9 were assessed by custom genotype array.In a cohort of 23 091 predominantly prevalent cases at enrollment and 230 910 matched controls, FH variant carriers had an increased risk for coronary artery disease (odds ratio [OR], 1.53 [95% CI, 1.24-1.89]). Adjusting for mean LDL-C led to the greatest attenuation of the risk estimate, but significant risk remained (odds ratio, 1.33 [95% CI, 1.08-1.64]). The degree of attenuation was not affected by the number and the spread of LDL-C measures available.The risk associated with carrying an FH variant cannot be fully captured by the LDL-C data available in the electronic health record, even when considering multiple LDL-C measurements spanning more than a decade.

    View details for DOI 10.1161/CIRCGEN.121.003501

    View details for PubMedID 35143253

  • The Clinical Genome Resource (ClinGen) Familial Hypercholesterolemia Variant Curation Expert Panel consensus guidelines for LDLR variant classification. Genetics in medicine : official journal of the American College of Medical Genetics Chora, J. R., Iacocca, M. A., Tichy, L., Wand, H., Kurtz, C. L., Zimmermann, H., Leon, A., Williams, M., Humphries, S. E., Hooper, A. J., Trinder, M., Brunham, L. R., Costa Pereira, A., Jannes, C. E., Chen, M., Chonis, J., Wang, J., Kim, S., Johnston, T., Soucek, P., Kramarek, M., Leigh, S. E., Carrie, A., Sijbrands, E. J., Hegele, R. A., Freiberger, T., Knowles, J. W., Bourbon, M., ClinGen Familial Hypercholesterolemia Expert Panel 1800


    PURPOSE: In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published consensus standardized guidelines for sequence-level variant classification in Mendelian disorders. To increase accuracy and consistency, the Clinical Genome Resource Familial Hypercholesterolemia (FH) Variant Curation Expert Panel was tasked with optimizing the existing ACMG/AMP framework for disease-specific classification in FH. In this study, we provide consensus recommendations for the most common FH-associated gene, LDLR, where >2300 unique FH-associated variants have been identified.METHODS: The multidisciplinary FH Variant Curation Expert Panel met in person and through frequent emails and conference calls to develop LDLR-specific modifications of ACMG/AMP guidelines. Through iteration, pilot testing, debate, and commentary, consensus among experts was reached.RESULTS: The consensus LDLR variant modifications to existing ACMG/AMP guidelines include (1) alteration of population frequency thresholds, (2) delineation of loss-of-function variant types, (3) functional study criteria specifications, (4) cosegregation criteria specifications, and (5) specific use and thresholds for in silico prediction tools, among others.CONCLUSION: Establishment of these guidelines as the new standard in the clinical laboratory setting will result in a more evidence-based, harmonized method for LDLR variant classification worldwide, thereby improving the care of patients with FH.

    View details for DOI 10.1016/j.gim.2021.09.012

    View details for PubMedID 34906454

  • Signaling defects associated with insulin resistance in non-diabetic and diabetic individuals and modification by sex. The Journal of clinical investigation Haider, N., Lebastchi, J., Jayavelu, A. K., Batista, T. M., Pan, H., Dreyfuss, J. M., Carcamo-Orive, I., Knowles, J. W., Mann, M., Kahn, C. R. 2021


    Insulin resistance is present in one-quarter of the general population, predisposing to a wide-range of diseases. Our aim was to identify cell-intrinsic determinants of insulin resistance in this population using IPS cell-derived myoblasts (iMyos). We found that these cells exhibited a large network of altered protein phosphorylation in vitro. Integrating these data with data from type-2-diabetic iMyos revealed critical sites of conserved altered phosphorylation in IRS-1, AKT, mTOR and TBC1D1, in addition to changes in protein phosphorylation involved in Rho/Rac signaling, chromatin organization and RNA processing. There were also striking differences in the phosphoproteome in cells from males versus females. These sex-specific and insulin resistance defects were linked to functional differences in downstream actions. Thus, there are cell-autonomous signaling alterations associated with insulin resistance within the general population and important differences in males and females, many of which are shared with diabetes, and contribute to differences in physiology and disease.

    View details for DOI 10.1172/JCI151818

    View details for PubMedID 34506305

  • Statins Are Associated With Increased Insulin Resistance and Secretion. Arteriosclerosis, thrombosis, and vascular biology Abbasi, F., Lamendola, C., Harris, C. S., Harris, V., Tsai, M., Tripathi, P., Abbas, F., Reaven, G., Reaven, P., Snyder, M. P., Kim, S. H., Knowles, J. W. 2021: ATVBAHA121316159


    OBJECTIVE: Statin treatment reduces the risk of atherosclerotic cardiovascular disease but is associated with a modest increased risk of type 2 diabetes, especially in those with insulin resistance or prediabetes. Our objective was to determine the physiological mechanism for the increased type 2 diabetes risk. Approach and Results: We conducted an open-label clinical trial of atorvastatin 40 mg daily in adults without known atherosclerotic cardiovascular disease or type 2 diabetes at baseline. The co-primary outcomes were changes at 10 weeks versus baseline in insulin resistance as assessed by steady-state plasma glucose during the insulin suppression test and insulin secretion as assessed by insulin secretion rate area under the curve (ISRAUC) during the graded-glucose infusion test. Secondary outcomes included glucose and insulin, both fasting and during oral glucose tolerance test. Of 75 participants who enrolled, 71 completed the study (median age 61 years, 37% women, 65% non-Hispanic White, median body mass index, 27.8 kg/m2). Atorvastatin reduced LDL (low-density lipoprotein)-cholesterol (median decrease 53%, P<0.001) but did not change body weight. Compared with baseline, atorvastatin increased insulin resistance (steady-state plasma glucose) by a median of 8% (P=0.01) and insulin secretion (ISRAUC) by a median of 9% (P<0.001). There were small increases in oral glucose tolerance test glucoseAUC (median increase, 0.05%; P=0.03) and fasting insulin (median increase, 7%; P=0.01).CONCLUSIONS: In individuals without type 2 diabetes, high-intensity atorvastatin for 10 weeks increases insulin resistance and insulin secretion. Over time, the risk of new-onset diabetes with statin use may increase in individuals who become more insulin resistant but are unable to maintain compensatory increases in insulin secretion.REGISTRATION: URL:; Unique identifier: NCT02437084.

    View details for DOI 10.1161/ATVBAHA.121.316159

    View details for PubMedID 34433298

  • Genetics of Type 2 Diabetes: Opportunities for Precision Medicine: JACC Focus Seminar. Journal of the American College of Cardiology Kim, D. S., Gloyn, A. L., Knowles, J. W. 2021; 78 (5): 496-512


    Type 2 diabetes (T2D) is highly prevalent and is a strong contributor for cardiovascular disease. However, there is significant heterogeneity in disease pathogenesis and the risk of complications. Enormous progress has been made in our ability to catalog genetic variation associated with T2D risk and variation in disease-relevant quantitative traits. These discoveries hold the potential to shed light on tractable targets and pathways for safe and effective therapeutic development, but the promise of precision medicine has been slow to be realized. Recent studies have identified subgroups of individuals with differential risk for intermediate phenotypes (eg, lipid levels, fasting insulin, body mass index) that contribute to T2D risk, helping to account for the observed clinical heterogeneity. These "partitioned genetic risk scores" not only have the potential to identify patients at greatest risk of cardiovascular disease and rapid disease progression, but also could aid patient stratification bridging the gap toward precision medicine for T2D.

    View details for DOI 10.1016/j.jacc.2021.03.346

    View details for PubMedID 34325839

  • Diverse Racial/Ethnic Group Underreporting and Underrepresentation in High-Impact Cholesterol Treatment Trials. Circulation Sarraju, A., Valencia, A., Knowles, J. W., Maron, D. J., Rodriguez, F. 2021; 143 (24): 2409-2411

    View details for DOI 10.1161/CIRCULATIONAHA.120.050034

    View details for PubMedID 34125567

  • Health disparities in cardiometabolic risk among Black and Hispanic youth in the United States. American journal of preventive cardiology Katz, S. F., Rodriguez, F., Knowles, J. W. 2021; 6: 100175


    Cardiometabolic risk factors in children and adolescents track into adulthood and are associated with increased risk of atherosclerotic cardiovascular disease. The purpose of this review is to examine the pervasive race and ethnic disparities in cardiometabolic risk factors among Black and Hispanic youth in the United States. We focus on three traditional cardiometabolic risk factors (obesity, type 2 diabetes mellitus, and dyslipidemia) as well as on the emerging cardiometabolic risk factor of non-alcoholic fatty liver disease. Additionally, we highlight interventions aimed at improving cardiometabolic health among these minority pediatric populations. Finally, we advocate for continued research on effective prevention strategies to reduce cardiometabolic risk and avert further disparities in cardiovascular morbidity and mortality.

    View details for DOI 10.1016/j.ajpc.2021.100175

    View details for PubMedID 34327498

  • Generation of two heterozygous MYBPC3 mutation-carrying human iPSC lines, SCVIi001-A and SCVIi002-A, for modeling hypertrophic cardiomyopathy. Stem cell research Liu, L., Shenoy, S. P., Jahng, J. W., Liu, Y., Knowles, J. W., Zhuge, Y., Wu, J. C. 2021; 53: 102279


    Hypertrophic cardiomyopathy (HCM) is an inherited heart disease that can cause sudden cardiac death and heart failure. HCM often arises from mutations in sarcomeric genes, among which the MYBPC3 is the most frequently mutated. Here we generated two human induced pluripotent stem cell (iPSC) lines from a HCM patient who has a familial history of HCM and his daughter who carries the pathogenic non-coding mutation. All lines show the typical morphology of pluripotent cells, a high expression of pluripotency markers, normal karyotype, and in vitro capacity to differentiate into all three germ layers. These lines provide a valuable resource for studying the molecular basis of HCM and drug screening for HCM.

    View details for DOI 10.1016/j.scr.2021.102279

    View details for PubMedID 33743363

  • Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nature genetics Bonder, M. J., Smail, C., Gloudemans, M. J., Fresard, L., Jakubosky, D., D'Antonio, M., Li, X., Ferraro, N. M., Carcamo-Orive, I., Mirauta, B., Seaton, D. D., Cai, N., Vakili, D., Horta, D., Zhao, C., Zastrow, D. B., Bonner, D. E., HipSci Consortium, iPSCORE consortium, Undiagnosed Diseases Network, PhLiPS consortium, Wheeler, M. T., Kilpinen, H., Knowles, J. W., Smith, E. N., Frazer, K. A., Montgomery, S. B., Stegle, O., Jan Bonder, M., Seaton, D., Jakubosky, D. A., Brown, C. D., Park, Y. 2021


    Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.

    View details for DOI 10.1038/s41588-021-00800-7

    View details for PubMedID 33664507

  • Validation of an Integrated Risk Tool, Including Polygenic Risk Score, for Atherosclerotic Cardiovascular Disease in Multiple Ethnicities and Ancestries. The American journal of cardiology Weale, M. E., Riveros-Mckay, F., Selzam, S., Seth, P., Moore, R., Tarran, W. A., Gradovich, E., Giner-Delgado, C., Palmer, D., Wells, D., Saffari, A., Sivley, R. M., Lachapelle, A. S., Wand, H., Clarke, S. L., Knowles, J. W., O'Sullivan, J. W., Ashley, E. A., McVean, G., Plagnol, V., Donnelly, P. 2021


    The American College of Cardiology / American Heart Association pooled cohort equations tool (ASCVD-PCE) is currently recommended to assess 10-year risk for atherosclerotic cardiovascular disease (ASCVD). ASCVD-PCE does not currently include genetic risk factors. Polygenic risk scores (PRSs) have been shown to offer a powerful new approach to measuring genetic risk for common diseases, including ASCVD, and to enhance risk prediction when combined with ASCVD-PCE. Most work to date, including the assessment of tools, has focused on performance in individuals of European ancestries. Here we present evidence for the clinical validation of a new integrated risk tool (IRT), ASCVD-IRT, which combines ASCVD-PCE with PRS to predict 10-year risk of ASCVD across diverse ethnicity and ancestry groups. We demonstrate improved predictive performance of ASCVD-IRT over ASCVD-PCE, not only in individuals of self-reported White ethnicities (net reclassification improvement (NRI) (with 95% confidence interval) = 2.7% (1.1 - 4.2)) but also Black / African American / Black Caribbean / Black African (NRI = 2.5% (0.6 - 4.3)) and South Asian (Indian, Bangladeshi or Pakistani) ethnicities (NRI = 8.7% (3.1 - 14.4)). NRI confidence intervals were wider and included zero for ethnicities with smaller sample sizes, including Hispanic (NRI = 7.5% (-1.4 - 16.5)), but PRS effect sizes in these ethnicities were significant and of comparable size to those seen in individuals of White ethnicities. Comparable results were obtained when individuals were analysed by genetically inferred ancestry. Together, these results validate the performance of ASCVD-IRT in multiple ethnicities and ancestries, and favour their generalisation to all ethnicities and ancestries.

    View details for DOI 10.1016/j.amjcard.2021.02.032

    View details for PubMedID 33675770

  • RECOMMENDATIONS FOR LDLR VARIANT INTERPRETATION BY THE CLINGEN'S FAMILIAL HYPERCHOLESTEROLEMIA EXPERT PANEL Chora, J., Iacocca, M., Tichy, L., Wand, H., Kurtz, L. C., Zimmermann, H., Meredith, A., Williams, M., Humphries, S. E., Hooper, A. J., Brunham, L., Pereira, A., Chen, M., Wang, J., Trinder, M., Jannes, C., Chonis, J., Kim, S., Pesaran, T., Johnston, T., Carrie, A., Leigh, S., Hegele, R. A., Sijbrands, E., Freiberger, T., Knowles, J. W., Bourbon, M. LIPPINCOTT WILLIAMS & WILKINS. 2021
  • The need for polygenic score reporting standards in evidence-based practice: lipid genetics use case. Current opinion in lipidology Wand, H. n., Knowles, J. W., Clarke, S. L. 2021


    Polygenic scores (PGS) are used to quantify the genetic predisposition for heritable traits, with hypothesized utility for personalized risk assessments. Lipid PGS are primed for clinical translation, but evidence-based practice changes will require rigorous PGS standards to ensure reproducibility and generalizability. Here we review applicable reporting and technical standards for dyslipidemia PGS translation along phases of the ACCE (Analytical validity, Clinical validity, Clinical utility, Ethical considerations) framework for evaluating genetic tests.New guidance suggests existing standards for study designs incorporating the ACCE framework are applicable to PGS and should be adopted. One recent example is the Clinical Genomics Resource (ClinGen) and Polygenic Score Catalog's PRS reporting standards, which define minimal requirements for describing rationale for score development, study population definitions and data parameters, risk model development and application, risk model evaluation, and translational considerations, such as generalizability beyond the target population studied.Lipid PGS are likely to be integrated into clinical practice in the future. Clinicians will need to be prepared to determine if and when lipid PGS is useful and valid. This decision-making will depend on the quality of evidence for the clinical use of PGS. Establishing reporting standards for PGS will help facilitate data sharing and transparency for critical evaluation, ultimately benefiting the efficiency of evidence-based practice.

    View details for DOI 10.1097/MOL.0000000000000733

    View details for PubMedID 33538426

  • An integrated approach to identify environmental modulators of genetic risk factors for complex traits. American journal of human genetics Balliu, B., Carcamo-Orive, I., Gloudemans, M. J., Nachun, D. C., Durrant, M. G., Gazal, S., Park, C. Y., Knowles, D. A., Wabitsch, M., Quertermous, T., Knowles, J. W., Montgomery, S. B. 2021


    Complex traits and diseases can be influenced by both genetics and environment. However, given the large number of environmental stimuli and power challenges for gene-by-environment testing, it remains a critical challenge to identify and prioritize specific disease-relevant environmental exposures. We propose a framework for leveraging signals from transcriptional responses to environmental perturbations to identify disease-relevant perturbations that can modulate genetic risk for complex traits and inform the functions of genetic variants associated with complex traits. We perturbed human skeletal-muscle-, fat-, and liver-relevant cell lines with 21 perturbations affecting insulin resistance, glucose homeostasis, and metabolic regulation in humans and identified thousands of environmentally responsive genes. By combining these data with GWASs from 31 distinct polygenic traits, we show that the heritability of multiple traits is enriched in regions surrounding genes responsive to specific perturbations and, further, that environmentally responsive genes are enriched for associations with specific diseases and phenotypes from the GWAS Catalog. Overall, we demonstrate the advantages of large-scale characterization of transcriptional changes in diversely stimulated and pathologically relevant cells to identify disease-relevant perturbations.

    View details for DOI 10.1016/j.ajhg.2021.08.014

    View details for PubMedID 34582792

  • Isthmin-1 is an adipokine that promotes glucose uptake and improves glucose tolerance and hepatic steatosis. Cell metabolism Jiang, Z., Zhao, M., Voilquin, L., Jung, Y., Aikio, M. A., Sahai, T., Dou, F. Y., Roche, A. M., Carcamo-Orive, I., Knowles, J. W., Wabitsch, M., Appel, E. A., Maikawa, C. L., Camporez, J. P., Shulman, G. I., Tsai, L., Rosen, E. D., Gardner, C. D., Spiegelman, B. M., Svensson, K. J. 2021


    With the increasing prevalence of type 2 diabetes and fatty liver disease, there is still an unmet need to better treat hyperglycemia and hyperlipidemia. Here, we identify isthmin-1 (Ism1) as an adipokine and one that has a dual role in increasing adipose glucose uptake while suppressing hepatic lipid synthesis. Ism1 ablation results in impaired glucose tolerance, reduced adipose glucose uptake, and reduced insulin sensitivity, demonstrating an endogenous function for Ism1 in glucose regulation. Mechanistically, Ism1 activates a PI3K-AKT signaling pathway independently of the insulin and insulin-like growth factor receptors. Notably, while the glucoregulatory function is shared with insulin, Ism1 counteracts lipid accumulation in the liver by switching hepatocytes from a lipogenic to a protein synthesis state. Furthermore, therapeutic dosing of recombinant Ism1 improves diabetes in diet-induced obese mice and ameliorates hepatic steatosis in a diet-induced fatty liver mouse model. These findings uncover an unexpected, bioactive protein hormone that might have simultaneous therapeutic potential for diabetes and fatty liver disease.

    View details for DOI 10.1016/j.cmet.2021.07.010

    View details for PubMedID 34348115

  • Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness. PLoS computational biology Carcamo-Orive, I., Henrion, M. Y., Zhu, K., Beckmann, N. D., Cundiff, P., Moein, S., Zhang, Z., Alamprese, M., D'Souza, S. L., Wabitsch, M., Schadt, E. E., Quertermous, T., Knowles, J. W., Chang, R. 2020; 16 (12): e1008491


    Insulin resistance (IR) precedes the development of type 2 diabetes (T2D) and increases cardiovascular disease risk. Although genome wide association studies (GWAS) have uncovered new loci associated with T2D, their contribution to explain the mechanisms leading to decreased insulin sensitivity has been very limited. Thus, new approaches are necessary to explore the genetic architecture of insulin resistance. To that end, we generated an iPSC library across the spectrum of insulin sensitivity in humans. RNA-seq based analysis of 310 induced pluripotent stem cell (iPSC) clones derived from 100 individuals allowed us to identify differentially expressed genes between insulin resistant and sensitive iPSC lines. Analysis of the co-expression architecture uncovered several insulin sensitivity-relevant gene sub-networks, and predictive network modeling identified a set of key driver genes that regulate these co-expression modules. Functional validation in human adipocytes and skeletal muscle cells (SKMCs) confirmed the relevance of the key driver candidate genes for insulin responsiveness.

    View details for DOI 10.1371/journal.pcbi.1008491

    View details for PubMedID 33362275

  • SPECIFICATION OF ACMG/AMP GUIDELINES FOR STANDARDIZED VARIANT INTERPRETATION IN FAMILIAL HYPERCHOLESTEROLEMIA: ON BEHALF OF THE CLINGEN FH VARIANT CURATION EXPERT PANEL Iacocca, M. A., Chora, J. R., Freiberger, T., Carrie, A., Sijbrands, E. J., Wand, H., Williams, M., Zimmermann, H., Leon, A., Kurtz, C. L., Tichy, L., Alves, A. C., Wang, J., Cuchel, M., Humphries, S. E., Defesche, J. C., Mata, P., Santos, R. D., Kullo, I. J., Brunham, L. R., Hegele, R. A., Knowles, J. W., Bourbon, M. ELSEVIER IRELAND LTD. 2020: E5
  • RNAi inhibition of angiopoietin-like protein 3 (ANGPTL3) with ARO-ANG3 mimics the lipid and lipoprotein profile of familial combined hypolipidemia Watts, G. F., Schwabe, C., Scott, R., Gladding, P., Sullivan, D., Baker, J., Clifton, P., Hamilton, J., Given, B., San Martin, J., Melquist, S., Knowles, J. W., Goldberg, Hegele, R., Ballantyne, C. OXFORD UNIV PRESS. 2020: 3331
  • RNA interference targeting apolipoprotein C-III with ARO-APOC3 in healthy volunteers mimics lipid and lipoprotein findings seen in subjects with inherited apolipoprotein C-III deficiency Schwabe, C., Scott, R., Sullivan, D., Baker, J., Clifton, P., Hamilton, J., Given, B., San Martin, J., Melquist, S., Watts, G. F., Goldberg, Knowles, J. W., Hegele, R., Ballantyne, C. OXFORD UNIV PRESS. 2020: 3330
  • Children with Heterozygous Familial Hypercholesterolemia in the United States: Data from the CASCADE FH Registry. The Journal of pediatrics de Ferranti, S. D., Shrader, P., Linton, M. F., Knowles, J. W., Hudgins, L. C., Benuck, I., Kindt, I., O'Brien, E. C., Peterson, A. L., Ahmad, Z. S., Clauss, S., Duell, P. B., Shapiro, M. D., Wilemon, K., Gidding, S. S., Neal, W. 2020


    OBJECTIVE: To describe enrollment characteristics of youth in the CAscade SCreening for Awareness and DEtection (CASCADE) Familial Hypercholesterolemia Registry.STUDY DESIGN: Cross-sectional analysis of 493 participants <18 years old with heterozygous FH recruited from US lipid clinics (n=20), between April 1, 2014 and January 12, 2018. At enrollment, some were new patients and some were in care. Clinical characteristics are described, including lipid levels and lipid lowering treatments (LLTs).RESULTS: Mean age at diagnosis was 9.4 (4.0) years; 47% female, 68% white and 12% Hispanic. Average (SD) highest LDL-C was 238 (61) mg/dL prior to treatment. Lipid lowering therapy (LLT) was used by 64% of participants; 56% were treated with statin. LDL-C declined 84 mg/dL (33%) among those treated with LLT; statins produced the greatest decline, 100 mg/dL (39% reduction). At enrollment, 39% had reached an LDL-C goal, either <130 mg/dL or ≥50% decrease from pre-treatment; 20% of those on LLT reached both goals.CONCLUSIONS: Among youth enrolled in CASCADE FH, diagnosis occurred relatively late, only 77% of children eligible for LLT were on treatment and 39% of those treated met LDL-C goals. Opportunities exist for earlier diagnosis, broader use of LLT, and greater LDL-C lowering.

    View details for DOI 10.1016/j.jpeds.2020.09.042

    View details for PubMedID 32976895

  • Expression of Glycolytic Enzymes in Induced Pluripotent Stem Cells, Derived Megakaryocytes, and Endothelial Cells Chandra, A., Vaidya, D., Chang, R., Knowles, J., Carcamo-Oribe, I., Kammers, K., Martin, J., Taub, M., Hoyle, D., Gao, Y., Yanek, L., Kral, B., Faraday, N., Becker, D., Mathias, R., Cheng, L., Leek, J., Wang, Z., Becker, L. LIPPINCOTT WILLIAMS & WILKINS. 2020
  • Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats. Nature communications Jakubosky, D., Smith, E. N., D'Antonio, M., Jan Bonder, M., Young Greenwald, W. W., D'Antonio-Chronowska, A., Matsui, H., i2QTL Consortium, Stegle, O., Montgomery, S. B., DeBoever, C., Frazer, K. A., Bonder, M. J., Cai, N., Carcamo-Orive, I., D'Antonio, M., Frazer, K. A., Young Greenwald, W. W., Jakubosky, D., Knowles, J. W., Matsui, H., McCarthy, D. J., Mirauta, B. A., Montgomery, S. B., Quertermous, T., Seaton, D. D., Smail, C., Smith, E. N., Stegle, O. 2020; 11 (1): 2928


    Structural variants (SVs) and short tandem repeats (STRs) are important sources of genetic diversity but are not routinely analyzed in genetic studies because they are difficult to accurately identify and genotype. Because SVs and STRs range in size and type, it is necessary to apply multiple algorithms that incorporate different types of evidence from sequencing data and employ complex filtering strategies to discover a comprehensive set of high-quality and reproducible variants. Here we assemble a set of 719 deep whole genome sequencing (WGS) samples (mean 42*) from 477 distinct individuals which we use to discover and genotype a wide spectrum of SV and STR variants using five algorithms. We use 177 unique pairs of genetic replicates to identify factors that affect variant call reproducibility and develop a systematic filtering strategy to create of one of the most complete and well characterized maps of SVs and STRs to date.

    View details for DOI 10.1038/s41467-020-16481-5

    View details for PubMedID 32522985

  • Properties of structural variants and short tandem repeats associated with gene expression and complex traits. Nature communications Jakubosky, D., D'Antonio, M., Bonder, M. J., Smail, C., Donovan, M. K., Young Greenwald, W. W., Matsui, H., i2QTL Consortium, D'Antonio-Chronowska, A., Stegle, O., Smith, E. N., Montgomery, S. B., DeBoever, C., Frazer, K. A., Bonder, M. J., Cai, N., Carcamo-Orive, I., D'Antonio, M., Frazer, K. A., Young Greenwald, W. W., Jakubosky, D., Knowles, J. W., Matsui, H., McCarthy, D. J., Mirauta, B. A., Montgomery, S. B., Quertermous, T., Seaton, D. D., Smail, C., Smith, E. N., Stegle, O. 2020; 11 (1): 2927


    Structural variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants which vastly differ in their sizes and distributions across the genome. Here, we identify genomic features of SV classes and STRs that are associated with gene expression and complex traits, including their locations relative to eGenes, likelihood of being associated with multiple eGenes, associated eGene types (e.g., coding, noncoding, level of evolutionary constraint), effect sizes, linkage disequilibrium with tagging single nucleotide variants used in GWAS, and likelihood of being associated with GWAS traits. We identify a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and show that they are highly enriched for being associated with GWAS traits. Our study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits.

    View details for DOI 10.1038/s41467-020-16482-4

    View details for PubMedID 32522982

  • Insulin Resistance and Mitochondrial Dysfunction Mediated by Nat1 Deficiency Sangwung, P., Fathzadeh, M., Knowles, J. AMER DIABETES ASSOC. 2020
  • Gaps in Dyslipidemia Care Among Working-Aged Individuals With Employer-Sponsored Health Care. Journal of the American Heart Association Shiffman, D., Louie, J. Z., Devlin, J. J., Knowles, J. W., McPhaul, M. J. 2020: e015807


    Background The American Heart Association and American College of Cardiology guidelines defined patient-management groups that would benefit from lowering of low-density lipoprotein cholesterol (LDL-C). We assessed gaps in dyslipidemia care among employees and spouses with health benefits. Methods and Results We studied 17889 employees and spouses who were covered by an employer-sponsored health plan and participated in an annual health assessment. Using medical claims, laboratory tests, and risk assessment questionnaires, we found that 43% of participants were in one of 4 patient-management groups: secondary prevention, severe hypercholesterolemia (LDL-C ≥190mg/dL at least once in the preceding 5years), diabetes mellitus, or elevated 10-year risk of cardiovascular disease. To assess gaps in dyslipidemia care, we used LDL-C ≤70mg/dL as the goal for both the secondary prevention group and those in the elevated 10-year risk group with >20% risk; LDL-C ≤100mg/dL was used for the other groups. Among those in patient-management groups, 27.3% were in the secondary prevention group, 7.4% were in the severe hypercholesterolemia group, 29.9% were in the diabetes mellitus group, and 35.4% were in the elevated 10-year risk group. About 74% of those in patient-management groups had above-goal LDL-C levels, whereas only 31% had evidence of a lipid-lowering therapy in the past 6months: 45% in the secondary prevention group, 31% in the severe hypercholesterolemia group, 36% in the diabetes mellitus group, and 17% in the elevated 10-year risk group. Conclusions The substantial gaps in LDL-C treatment and goal attainment among members of an employer-sponsored medical plan who were mostly aware of their LDL-C levels indicate the need for gap-closure initiatives.

    View details for DOI 10.1161/JAHA.119.015807

    View details for PubMedID 32319337

  • Delisting STAP1: The Rise and Fall of a Putative Hypercholesterolemia Gene. Arteriosclerosis, thrombosis, and vascular biology Hegele, R. A., Knowles, J. W., Horton, J. D. 2020; 40 (4): 847–49

    View details for DOI 10.1161/ATVBAHA.120.314006

    View details for PubMedID 32208993

  • Association of insulin resistance, from mid-life to late-life, with aortic stiffness in late-life: the Atherosclerosis Risk in Communities Study. Cardiovascular diabetology Poon, A. K., Meyer, M. L., Tanaka, H., Selvin, E., Pankow, J., Zeng, D., Loehr, L., Knowles, J. W., Rosamond, W., Heiss, G. 2020; 19 (1): 11


    BACKGROUND: Insulin resistance may contribute to aortic stiffening that leads to end-organ damage. We examined the cross-sectional association and prospective association of insulin resistance and aortic stiffness in older adults without diabetes.METHODS: We analyzed 2571 men and women at Visit 5 (in 2011-2013), and 2350 men and women at repeat examinations from baseline at Visit 1 (in 1987-1989) to Visit 5 (in 2011-2013). Linear regression was used to estimate the difference in aortic stiffness per standard unit of HOMA-IR, TG/HDL-C, and TyG at Visit 5. Linear mixed effects were used to assess if high, as opposed to non-high, aortic stiffness (>75th percentile) was preceded by a faster annual rate of change in log-HOMA-IR, log-TG/HDL-C, and log-TyG from Visit 1 to Visit 5.RESULTS: The mean age of participants was 75years, 37% (n=957) were men, and 17% (n=433) were African American. At Visit 5, higher HOMA-IR, higher TG/HDL-C, and higher TyG were associated with higher aortic stiffness (16cm/s per SD (95% CI 6, 27), 29cm/s per SD (95% CI 18, 40), and 32cm/s per SD (95% CI 22, 42), respectively). From Visit 1 to Visit 5, high aortic stiffness, compared to non-high aortic stiffness, was not preceded by a faster annual rate of change in log-HOMA-IR from baseline to 9years (0.030 (95% CI 0.024, 0.035) vs. 0.025 (95% CI 0.021, 0.028); p=0.15) or 9years onward (0.011 (95% CI 0.007, 0.015) vs. 0.011 (95% CI 0.009, 0.013); p=0.31); in log-TG/HDL-C from baseline to 9years (0.019 (95% CI 0.015, 0.024) vs. 0.024 (95% CI 0.022, 0.026); p=0.06) or 9years onward (-0.007 (95% CI -0.010, -0.005) vs. -0.009 (95% CI -0.010, -0.007); p=0.08); or in log-TyG from baseline to 9years (0.002 (95% CI 0.002, 0.003) vs. 0.003 (95% CI 0.003, 0.003); p=0.03) or 9years onward (0 (95% CI 0, 0) vs. 0 (95% CI 0, 0); p=0.08).CONCLUSIONS: Among older adults without diabetes, insulin resistance was associated with aortic stiffness, but the putative role of insulin resistance in aortic stiffness over the life course requires further study.

    View details for DOI 10.1186/s12933-020-0986-y

    View details for PubMedID 31992297

Knowles Lab publications and collaborations